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Getahun Strobel A, Prasad P, Lane CR, Naidu R, Autar S, Young-Sharma T, Richards M, Suka A, Cameron D, James R, Prasad R, Buising K, Howden BP, Prasad V. The changing epidemiology of antimicrobial resistance in Fiji: a descriptive analysis of antimicrobial susceptibility and trends of endemic and emerging pathogens, 2019-2022. Lancet Reg Health West Pac 2024; 45:101036. [PMID: 38516290 PMCID: PMC10955629 DOI: 10.1016/j.lanwpc.2024.101036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/04/2024] [Accepted: 02/19/2024] [Indexed: 03/23/2024]
Abstract
Background There is a paucity of data on antimicrobial resistance in Fiji. The aim of this study was to determine the antimicrobial susceptibility profile of bacterial isolates from clinical samples at Colonial War Memorial Hospital in Fiji. Methods This retrospective study reviewed four-year of data from January 1, 2019, through December 31, 2022. Laboratory testing was carried out using locally approved protocols. Selective antimicrobial susceptibility testing was performed whereby only isolates resistant to first line antimicrobials were tested against second line antimicrobials. Only the first isolate of a given species per patient in a single year were included in the analysis. WHONET software and Microsoft Excel were used for analysis. Findings A total of 29,222 bacterial isolates were included, 62% (n = 18,084) were Gram-negative bacteria. K. pneumoniae was the most common (n = 5363), followed by E. coli (n = 4321). Extended spectrum beta lactamase (ESBL) production increased from 30% in 2019 to 43% in 2022 amongst K. pneumoniae, and 10%-23% in E coli. There were 733 carbapenem-resistant isolates identified from clinical samples, 61% (n = 445) were A. baumannii, 15% (n = 110) E. coli and 14% (n = 101) P. aeruginosa. Amongst the E. coli isolates tested, susceptibility to meropenem declined from 99% (272/274) in 2019 to 79% (255/325) in 2022. The rate of methicillin resistance amongst Staphylococcus aureus was steady, remaining between 11% and 13%. Interpretation This study demonstrated a high rate of MDR amongst Gram-negative bacteria, especially ESBL producing K. pneumoniae and E. coli and carbapenem-resistant A. baumannii. The emergence and rapid spread of carbapenemase producing E. coli in Fiji's largest hospital is of particular concern. There is an urgent need to allocate resources to improve existing capacity and to develop effective multimodal strategies to detect, manage and control the spread of MDR organisms. Funding This study was supported by the Medical Research Future Fund through the Australian government (grant number APP 1200970).
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Affiliation(s)
- Aneley Getahun Strobel
- Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Prinika Prasad
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Courtney R. Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ravi Naidu
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Sanjeshni Autar
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Tracey Young-Sharma
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Matthew Richards
- Infection Prevention and Surveillance Service, The Royal Melbourne Hospital, Melbourne, Australia
| | - Ana Suka
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Donna Cameron
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Rodney James
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ravendra Prasad
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Kirsty Buising
- Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- The Royal Melbourne Hospital, Melbourne, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vinita Prasad
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
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Getahun Strobel A, Prasad P, Prasad V, Naidu R, Young-Sharma T, Suka A, Richards M, Cameron D, Lane CR, Buising K, Howden BP, Autar S. The epidemiology of enterococci in a tertiary hospital and primary healthcare facilities in Fiji (2019-2022). J Glob Antimicrob Resist 2024; 37:102-107. [PMID: 38565419 DOI: 10.1016/j.jgar.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES We analysed 4 y of laboratory data to characterise the species and determine the antimicrobial susceptibility profiles of enterococci as human pathogens in Fiji. The study also investigated the molecular epidemiology amongst the subset of vancomycin-resistant enterococci (VRE). METHODS This retrospective study reviewed bacteriological data from Colonial War Memorial Hospital (CWMH) and other healthcare facilities in the Central and Eastern divisions of Fiji. Phenotypic, antimicrobial susceptibility and vanA and vanB PCR testing were performed using locally approved protocols. The first clinical isolates per patient with antimicrobial susceptibility testing results in a single year were included in the analysis. Data was analysed using WHONET software and Microsoft Excel. RESULTS A total of 1817 enterococcal isolates were reported, 1415 from CWMH and 402 from other healthcare facilities. The majority of isolates, 75% (n = 1362) were reported as undifferentiated Enterococcus spp., 17.8% (n = 324) were specifically identified as Enterococcus faecalis and 6.7% (n = 122) as E. faecium. Overall, 10% of the enterococci isolates were from blood cultures. Among isolates from CWMH, <15% of E. faecium were susceptible to ampicillin, and 17.2% were vancomycin resistant. Overall, 874 enterococcal isolates (including the undifferentiated species) were tested against vancomycin, of which 4.8% (n = 42) were resistance. All of the VRE isolates tested (n = 15) expressed vanA genes. CONCLUSIONS This study demonstrates the clinical importance of VRE, particularly van A E. faecium in the national referral hospital in Fiji. Enhanced phenotypic and molecular surveillance data are needed to better understand enterococci epidemiology and help guide specific infection prevention and control measures and antibiotic prescribing guidelines.
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Affiliation(s)
- Aneley Getahun Strobel
- Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
| | - Prinika Prasad
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Vinita Prasad
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Ravi Naidu
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Tracey Young-Sharma
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Ana Suka
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Matthew Richards
- Infection Prevention and Surveillance Service, The Royal Melbourne Hospital, Melbourne, Australia
| | - Donna Cameron
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for infection and Immunity, Melbourne, Australia
| | - Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for infection and Immunity, Melbourne, Australia
| | - Kirsty Buising
- Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; The Royal Melbourne Hospital, Melbourne, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for infection and Immunity, Melbourne, Australia.
| | - Sanjeshni Autar
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
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3
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Nang SC, Lu J, Yu HH, Wickremasinghe H, Azad MAK, Han M, Zhao J, Rao G, Bergen PJ, Velkov T, Sherry N, McCarthy DT, Aslam S, Schooley RT, Howden BP, Barr JJ, Zhu Y, Li J. Phage resistance in Klebsiella pneumoniae and bidirectional effects impacting antibiotic susceptibility. Clin Microbiol Infect 2024:S1198-743X(24)00145-9. [PMID: 38522841 DOI: 10.1016/j.cmi.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
OBJECTIVES Bacteriophage (phage) therapy is a promising anti-infective option to combat antimicrobial resistance. However, the clinical utilization of phage therapy has been severely compromised by the potential emergence of phage resistance. Although certain phage resistance mechanisms can restore bacterial susceptibility to certain antibiotics, a lack of knowledge of phage resistance mechanisms hinders optimal use of phages and their combination with antibiotics. METHODS Genome-wide transposon screening was performed with a mutant library of Klebsiella pneumoniae MKP103 to identify phage pKMKP103_1-resistant mutants. Phage-resistant phenotypes were evaluated by time-kill kinetics and efficiency of plating assays. Phage resistance mechanisms were investigated with adsorption, one-step growth, and mutation frequency assays. Antibiotic susceptibility was determined with broth microdilution and population analysis profiles. RESULTS We observed a repertoire of phage resistance mechanisms in K pneumoniae, such as disruption of phage binding (fhuA::Tn and tonB::Tn), extension of the phage latent period (mnmE::Tn and rpoN::Tn), and increased mutation frequency (mutS::Tn and mutL::Tn). Notably, in contrast to the prevailing view that phage resistance re-sensitizes antibiotic-resistant bacteria, we observed a bidirectional steering effect on bacterial antibiotic susceptibility. Specifically, rpoN::Tn increased susceptibility to colistin while mutS::Tn and mutL::Tn increased resistance to rifampicin and colistin. DISCUSSION Our findings demonstrate that K pneumoniae employs multiple strategies to overcome phage infection, which may result in enhanced or reduced antibiotic susceptibility. Mechanism-guided phage steering should be incorporated into phage therapy to better inform clinical decisions on phage-antibiotic combinations.
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Affiliation(s)
- Sue C Nang
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jing Lu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Heidi H Yu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hasini Wickremasinghe
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Mohammad A K Azad
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Meiling Han
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jinxin Zhao
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Gauri Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Phillip J Bergen
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Tony Velkov
- Biomedicine Discovery Institute, Department of Pharmacology, Monash University, Clayton, Victoria, Australia
| | - Norelle Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David T McCarthy
- Department of Civil Engineering, Monash University, Clayton, Victoria, Australia
| | - Saima Aslam
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Robert T Schooley
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Yan Zhu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jian Li
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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Nong Y, Steinig E, Pollock GL, Taiaroa G, Carter GP, Monk IR, Pang S, Daley DA, Coombs GW, Forde BM, Harris PNA, Sherry NL, Howden BP, Pasricha S, Baines SL, Williamson DA. Emergence and clonal expansion of a qacA-harbouring sequence type 45 lineage of methicillin-resistant Staphylococcus aureus. Commun Biol 2024; 7:349. [PMID: 38514781 PMCID: PMC10957945 DOI: 10.1038/s42003-024-06012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
The past decade has seen an increase in the prevalence of sequence type (ST) 45 methicillin-resistant Staphylococcus aureus (MRSA), yet the underlying drivers for its emergence and spread remain unclear. To better understand the worldwide dissemination of ST45 S. aureus, we performed phylogenetic analyses of Australian isolates, supplemented with a global population of ST45 S. aureus genomes. Our analyses revealed a distinct lineage of multidrug-resistant ST45 MRSA harbouring qacA, predominantly found in Australia and Singapore. Bayesian inference predicted that the acquisition of qacA occurred in the late 1990s. qacA was integrated into a structurally variable region of the chromosome containing Tn552 (carrying blaZ) and Tn4001 (carrying aac(6')-aph(2")) transposable elements. Using mutagenesis and in vitro assays, we provide phenotypic evidence that qacA confers tolerance to chlorhexidine. These findings collectively suggest both antimicrobial resistance and the carriage of qacA may play a role in the successful establishment of ST45 MRSA.
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Affiliation(s)
- Yi Nong
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Eike Steinig
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Georgina L Pollock
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Doherty Applied Microbial Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stanley Pang
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Denise A Daley
- Australian Group on Antimicrobial Resistance, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Brian M Forde
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
| | - Patrick N A Harris
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Norelle L Sherry
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Shivani Pasricha
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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5
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Buultjens AH, Vandelannoote K, Mercoulia K, Ballard S, Sloggett C, Howden BP, Seemann T, Stinear TP. High performance Legionella pneumophila source attribution using genomics-based machine learning classification. Appl Environ Microbiol 2024; 90:e0129223. [PMID: 38289130 PMCID: PMC10952463 DOI: 10.1128/aem.01292-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 02/08/2024] Open
Abstract
Fundamental to effective Legionnaires' disease outbreak control is the ability to rapidly identify the environmental source(s) of the causative agent, Legionella pneumophila. Genomics has revolutionized pathogen surveillance, but L. pneumophila has a complex ecology and population structure that can limit source inference based on standard core genome phylogenetics. Here, we present a powerful machine learning approach that assigns the geographical source of Legionnaires' disease outbreaks more accurately than current core genome comparisons. Models were developed upon 534 L. pneumophila genome sequences, including 149 genomes linked to 20 previously reported Legionnaires' disease outbreaks through detailed case investigations. Our classification models were developed in a cross-validation framework using only environmental L. pneumophila genomes. Assignments of clinical isolate geographic origins demonstrated high predictive sensitivity and specificity of the models, with no false positives or false negatives for 13 out of 20 outbreak groups, despite the presence of within-outbreak polyclonal population structure. Analysis of the same 534-genome panel with a conventional phylogenomic tree and a core genome multi-locus sequence type allelic distance-based classification approach revealed that our machine learning method had the highest overall classification performance-agreement with epidemiological information. Our multivariate statistical learning approach maximizes the use of genomic variation data and is thus well-suited for supporting Legionnaires' disease outbreak investigations.IMPORTANCEIdentifying the sources of Legionnaires' disease outbreaks is crucial for effective control. Current genomic methods, while useful, often fall short due to the complex ecology and population structure of Legionella pneumophila, the causative agent. Our study introduces a high-performing machine learning approach for more accurate geographical source attribution of Legionnaires' disease outbreaks. Developed using cross-validation on environmental L. pneumophila genomes, our models demonstrate excellent predictive sensitivity and specificity. Importantly, this new approach outperforms traditional methods like phylogenomic trees and core genome multi-locus sequence typing, proving more efficient at leveraging genomic variation data to infer outbreak sources. Our machine learning algorithms, harnessing both core and accessory genomic variation, offer significant promise in public health settings. By enabling rapid and precise source identification in Legionnaires' disease outbreaks, such approaches have the potential to expedite intervention efforts and curtail disease transmission.
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Affiliation(s)
- Andrew H. Buultjens
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Center for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Koen Vandelannoote
- Bacterial Phylogenomics Group, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Karolina Mercoulia
- Department of Microbiology and Immunology, Microbiology Diagnostic Unit, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Susan Ballard
- Department of Microbiology and Immunology, Microbiology Diagnostic Unit, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Clare Sloggett
- Department of Microbiology and Immunology, Microbiology Diagnostic Unit, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Center for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Microbiology Diagnostic Unit, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Microbiology Diagnostic Unit, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Center for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
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6
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Eales O, Plank MJ, Cowling BJ, Howden BP, Kucharski AJ, Sullivan SG, Vandemaele K, Viboud C, Riley S, McCaw JM, Shearer FM. Key Challenges for Respiratory Virus Surveillance while Transitioning out of Acute Phase of COVID-19 Pandemic. Emerg Infect Dis 2024; 30:e230768. [PMID: 38190760 PMCID: PMC10826770 DOI: 10.3201/eid3002.230768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
To support the ongoing management of viral respiratory diseases while transitioning out of the acute phase of the COVID-19 pandemic, many countries are moving toward an integrated model of surveillance for SARS-CoV-2, influenza virus, and other respiratory pathogens. Although many surveillance approaches catalyzed by the COVID-19 pandemic provide novel epidemiologic insight, continuing them as implemented during the pandemic is unlikely to be feasible for nonemergency surveillance, and many have already been scaled back. Furthermore, given anticipated cocirculation of SARS-CoV-2 and influenza virus, surveillance activities in place before the pandemic require review and adjustment to ensure their ongoing value for public health. In this report, we highlight key challenges for the development of integrated models of surveillance. We discuss the relative strengths and limitations of different surveillance practices and studies as well as their contribution to epidemiologic assessment, forecasting, and public health decision-making.
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7
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Djordjevic SP, Jarocki VM, Seemann T, Cummins ML, Watt AE, Drigo B, Wyrsch ER, Reid CJ, Donner E, Howden BP. Genomic surveillance for antimicrobial resistance - a One Health perspective. Nat Rev Genet 2024; 25:142-157. [PMID: 37749210 DOI: 10.1038/s41576-023-00649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.
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Affiliation(s)
- Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia.
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia.
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, South Australia, Australia
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Cameron J Reid
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia
| | - Benjamin P Howden
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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8
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Ferdinand AS, McEwan C, Lin C, Betham K, Kandan K, Tamolsaian G, Pugeva B, McKenzie J, Browning G, Gilkerson J, Coppo M, James R, Peel T, Levy S, Townell N, Jenney A, Stewardson A, Cameron D, Macintyre A, Buising K, Howden BP. Development of a cross-sectoral antimicrobial resistance capability assessment framework. BMJ Glob Health 2024; 9:e013280. [PMID: 38232993 PMCID: PMC10806917 DOI: 10.1136/bmjgh-2023-013280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024] Open
Abstract
Antimicrobial resistance (AMR) is an urgent and growing global health concern, and a clear understanding of existing capacities to address AMR, particularly in low-income and middle-income countries (LMICs), is needed to inform national priorities, investment targets and development activities. Across LMICs, there are limited data regarding existing mechanisms to address AMR, including national AMR policies, current infection prevention and antimicrobial prescribing practices, antimicrobial use in animals, and microbiological testing capacity for AMR. Despite the development of numerous individual tools designed to inform policy formulation and implementation or surveillance interventions to address AMR, there is an unmet need for easy-to-use instruments that together provide a detailed overview of AMR policy, practice and capacity. This paper describes the development of a framework comprising five assessment tools which provide a detailed assessment of country capacity to address AMR within both the human and animal health sectors. The framework is flexible to meet the needs of implementers, as tools can be used separately to assess the capacity of individual institutions or as a whole to align priority-setting and capacity-building with AMR National Action Plans (NAPs) or national policies. Development of the tools was conducted by a multidisciplinary team across three phases: (1) review of existing tools; (2) adaptation of existing tools; and (3) piloting, refinement and finalisation. The framework may be best used by projects which aim to build capacity and foster cross-sectoral collaborations towards the surveillance of AMR, and by LMICs wishing to conduct their own assessments to better understand capacity and capabilities to inform future investments or the implementation of NAPs for AMR.
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Affiliation(s)
- Angeline S Ferdinand
- WHO Collaborating Centre for Antimicrobial Resistance, Doherty Institute, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity at the University of Melbourne, Melbourne, Victoria, Australia
| | - Callum McEwan
- WHO Collaborating Centre for Antimicrobial Resistance, Doherty Institute, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity at the University of Melbourne, Melbourne, Victoria, Australia
| | - Chantel Lin
- WHO Collaborating Centre for Antimicrobial Resistance, Doherty Institute, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity at the University of Melbourne, Melbourne, Victoria, Australia
| | - Kassandra Betham
- WHO Collaborating Centre for Antimicrobial Resistance, Doherty Institute, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity at the University of Melbourne, Melbourne, Victoria, Australia
| | - Karishma Kandan
- WHO Collaborating Centre for Antimicrobial Resistance, Doherty Institute, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity at the University of Melbourne, Melbourne, Victoria, Australia
| | | | - Barry Pugeva
- Burnet Institute, Melbourne, Victoria, Australia
| | - Joanna McKenzie
- Molecular Epidemiology Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Glenn Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | - James Gilkerson
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mauricio Coppo
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
- Escuela de Medicina Veterinaria, Universidad Andrés Bello, Santiago, Chile
| | - Rodney James
- Doherty Institute, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute, Melbourne, Victoria, Australia
| | - Trisha Peel
- Department of Infectious Diseases, Monash University and Alfred Health, Melbourne, Victoria, Australia
| | - Steph Levy
- Burnet Institute, Melbourne, Victoria, Australia
| | - Nicola Townell
- Infectious Disease Department, Sunshine Coast University Hospital, Sunshine Coast, Queensland, Australia
| | - Adam Jenney
- Department of Infectious Diseases, Monash University, Clayton, Victoria, Australia
| | - Andrew Stewardson
- Department of Infectious Diseases, Alfred Health, Melbourne, Victoria, Australia
| | - Donna Cameron
- WHO Collaborating Centre for Antimicrobial Resistance, Doherty Institute, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity at the University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Macintyre
- Nossal Institute for Global Health, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kirsty Buising
- WHO Collaborating Centre for Antimicrobial Resistance, Doherty Institute, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- WHO Collaborating Centre for Antimicrobial Resistance, Doherty Institute, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity at the University of Melbourne, Melbourne, Victoria, Australia
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9
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Zufan SE, Mercoulia K, Kwong JC, Judd LM, Howden BP, Seemann T, Stinear TP. High-performance enrichment-based genome sequencing to support the investigation of hepatitis A virus outbreaks. Microbiol Spectr 2024; 12:e0283423. [PMID: 38018979 PMCID: PMC10783085 DOI: 10.1128/spectrum.02834-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/14/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE This proof-of-concept study introduces a hybrid capture oligo panel for whole-genome sequencing of all six human pathogenic hepatitis A virus (HAV) subgenotypes, exhibiting a higher sensitivity than some conventional genotyping assays. The ability of hybrid capture to enrich multiple targets allows for a single, streamlined workflow, thus facilitating the potential harmonization of molecular surveillance of HAV with other enteric viruses. Even challenging sample matrices can be accommodated, making them suitable for broad implementation in clinical and public health laboratories. This innovative approach has significant implications for enhancing multijurisdictional outbreak investigations as well as our understanding of the global diversity and transmission dynamics of HAV.
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Affiliation(s)
- Sara E. Zufan
- The Center for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Karolina Mercoulia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jason C. Kwong
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Louise M. Judd
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- The Center for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Torsten Seemann
- The Center for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- The Center for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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10
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Dorji T, Horan K, Sherry NL, Tay EL, Globan M, Viberg L, Bond K, Denholm JT, Howden BP, Andersson P. Whole genome sequencing of drug-resistant Mycobacterium tuberculosis isolates in Victoria, Australia. Int J Infect Dis 2024; 138:46-53. [PMID: 37967715 DOI: 10.1016/j.ijid.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
OBJECTIVES Whole genome sequencing (WGS) can identify clusters, transmission patterns, and drug resistance mutations. This is important in low-burden settings such as Australia, as it can assist in efficient contact tracing and surveillance. METHODS We conducted a retrospective cohort study using WGS from 155 genomically defined drug-resistant Mycobacterium tuberculosis (DR-TB) isolates collected between 2018-2021 in Victoria, Australia. Bioinformatic analysis was performed to identify resistance-conferring mutations, lineages, clusters and understand how local sequences compared with international context. RESULTS Of the 155 sequences, 42% were identified as lineage 2 and 35% as lineage 1; 65.8% (102/155) were isoniazid mono-resistant, 8.4% were multi-drug resistant TB and 5.8% were pre-extensively drug-resistant / extensively drug-resistant TB. The most common mutations were observed in katG and fabG1 genes, especially at Ser315Thr and fabG1 -15 C>T for first-line drugs. Ser450Leu was the most frequent mutation in rpoB gene. Phylogenetic analysis confirmed that Victorian DR-TB were associated with importation events. There was little evidence of local transmission with only five isolate pairs. CONCLUSION Isoniazid-resistant TB is the commonest DR-TB in Victoria, and the mutation profile is similar to global circulating DR-TB. Most cases are diagnosed among migrants with limited transmission. This study highlights the value of WGS in identification of clusters and resistance-conferring mutations. This information is crucial in supporting disease mitigation and treatment strategies.
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Affiliation(s)
- Thinley Dorji
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Norelle L Sherry
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Ee Laine Tay
- Communicable Disease Epidemiology and Surveillance, Health Protection Branch, Public Health Division, Department of Health, Melbourne, Australia
| | - Maria Globan
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Linda Viberg
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Katherine Bond
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Royal Melbourne Hospital, Melbourne, Australia
| | - Justin T Denholm
- Royal Melbourne Hospital, Melbourne, Australia; Victorian Tuberculosis Program. Melbourne Health at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Department of Infectious Diseases at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Centre for Pathogen Genomics, University of Melbourne, Australia.
| | - Patiyan Andersson
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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11
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Baines SL, Guérillot R, Ballard S, Johnson PDR, Stinear TP, Roberts S, Howden BP. Genomic investigation of the emergence of vanD vancomycin-resistant Enterococcus faecium. Access Microbiol 2023; 5:000712.v3. [PMID: 38188239 PMCID: PMC10765050 DOI: 10.1099/acmi.0.000712.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024] Open
Abstract
Vancomycin-resistant Enterococcus (VRE) is an increasingly identified cause of human disease, with most infections resulting from the vanA and vanB genotypes; less is known about other clinically relevant genotypes. Here we report a genomic exploration of a vanD VRE faecium (VREfm), which arose de novo during a single infectious episode. The genomes of the vancomycin-susceptible E. faecium (VSEfm) recipient and resulting VREfm were subjected to long-read sequencing and closed, with whole-genome alignments, cross-mapping and orthologue clustering used to identify genomic variation. Three key differences were identified. (i) The VREfm chromosome gained a 142.6 kb integrative conjugative element (ICE) harbouring the vanD locus. (ii) The native ligase (ddl) was disrupted by an ISEfm1 insertion. (iii) A large 1.74 Mb chromosomal inversion of unknown consequence occurred. Alignment and phylogenetic-based comparisons of the VREfm with a global collection of vanD-harbouring genomes identified strong similarities in the 120-160 kb genomic region surrounding vanD, suggestive of a common mobile element and integration site, irrespective of the diverse taxonomic, geographical and host origins of the isolates. This isolate diversity revealed that this putative ICE (and its source) is globally disseminated and is capable of being acquired by different genera. Although the incidence of vanD VREfm is low, understanding its emergence and potential for spread is crucial for the ongoing efforts to reduce antimicrobial resistance.
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Affiliation(s)
- Sarah L. Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Paul D. R. Johnson
- Department of Infectious Diseases, Austin Health, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sally Roberts
- Department of Microbiology, LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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12
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Baker KS, Jauneikaite E, Hopkins KL, Lo SW, Sánchez-Busó L, Getino M, Howden BP, Holt KE, Musila LA, Hendriksen RS, Amoako DG, Aanensen DM, Okeke IN, Egyir B, Nunn JG, Midega JT, Feasey NA, Peacock SJ. Genomics for public health and international surveillance of antimicrobial resistance. Lancet Microbe 2023; 4:e1047-e1055. [PMID: 37977162 DOI: 10.1016/s2666-5247(23)00283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission, and is already beginning to revolutionise how public health surveillance networks monitor and tackle bacterial AMR. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome. In 2022, a workshop series and online consultation brought together international experts in AMR and pathogen genomics to assess the status of genomic applications for AMR surveillance in a range of settings. Here we focus on discussions around the use of genomics for public health and international AMR surveillance, noting the potential advantages of, and barriers to, implementation, and proposing recommendations from the working group to help to drive the adoption of genomics in public health AMR surveillance. These recommendations include the need to build capacity for genome sequencing and analysis, harmonising and standardising surveillance systems, developing equitable data sharing and governance frameworks, and strengthening interactions and relationships among stakeholders at multiple levels.
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Affiliation(s)
- Kate S Baker
- Department for Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Katie L Hopkins
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain; CIBERESP, ISCIII, Madrid, Spain
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Benjamin P Howden
- The Centre for Pathogen Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Lillian A Musila
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate - Africa, Nairobi, Kenya; Kenya Medical Research Institute, Nairobi, Kenya
| | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Daniel G Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa; School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Oxford, UK
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana, West Africa
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Malawi
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13
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Baker KS, Jauneikaite E, Nunn JG, Midega JT, Atun R, Holt KE, Walia K, Howden BP, Tate H, Okeke IN, Carattoli A, Hsu LY, Hopkins KL, Muloi DM, Wheeler NE, Aanensen DM, Mason LCE, Rodgus J, Hendriksen RS, Essack SY, Egyir B, Halpin AL, MacCannell DR, Campos J, Srikantiah P, Feasey NA, Peacock SJ. Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group. Lancet Microbe 2023; 4:e1035-e1039. [PMID: 37977164 DOI: 10.1016/s2666-5247(23)00281-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 11/19/2023]
Abstract
Nearly a century after the beginning of the antibiotic era, which has been associated with unparalleled improvements in human health and reductions in mortality associated with infection, the dwindling pipeline for new antibiotic classes coupled with the inevitable spread of antimicrobial resistance (AMR) poses a major global challenge. Historically, surveillance of bacteria with AMR typically relied on phenotypic analysis of isolates taken from infected individuals, which provides only a low-resolution view of the epidemiology behind an individual infection or wider outbreak. Recent years have seen increasing adoption of powerful new genomic technologies with the potential to revolutionise AMR surveillance by providing a high-resolution picture of the AMR profile of the bacteria causing infections and providing real-time actionable information for treating and preventing infection. However, many barriers remain to be overcome before genomic technologies can be adopted as a standard part of routine AMR surveillance around the world. Accordingly, the Surveillance and Epidemiology of Drug-resistant Infections Consortium convened an expert working group to assess the benefits and challenges of using genomics for AMR surveillance. In this Series, we detail these discussions and provide recommendations from the working group that can help to realise the massive potential benefits for genomics in surveillance of AMR.
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Affiliation(s)
- Kate S Baker
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Rifat Atun
- Harvard T H Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kamini Walia
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, Ansarinagar, New Delhi, India
| | - Benjamin P Howden
- The Centre for Pathogen Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Heather Tate
- Office of Research, US Food and Drug Administration Center for Veterinary Medicine, Laurel, MD, USA
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Li Yang Hsu
- Saw Swee Hock School of Public Health and Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Katie L Hopkins
- HCAI, Fungal, AMR, AMU, and Sepsis Division and Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Dishon M Muloi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| | - Nicole E Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, Edgbaston, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Oxford, UK
| | - Lewis C E Mason
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Department of Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Jonah Rodgus
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sabiha Y Essack
- Antimicrobial Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana
| | - Alison L Halpin
- Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Duncan R MacCannell
- Office of Advanced Molecular Detection, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Josefina Campos
- National Center of Genomics and Bioinformatics, ANLIS Malbran, Buenos Aires, Argentina
| | - Padmini Srikantiah
- Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
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14
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Higgs C, Kumar LS, Stevens K, Strachan J, Korman T, Horan K, Daniel D, Russell M, McDevitt CA, Sherry NL, Stinear TP, Howden BP, Gorrie CL. Comparison of contemporary invasive and non-invasive Streptococcus pneumoniae isolates reveals new insights into circulating anti-microbial resistance determinants. Antimicrob Agents Chemother 2023; 67:e0078523. [PMID: 37823632 PMCID: PMC10649040 DOI: 10.1128/aac.00785-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/23/2023] [Indexed: 10/13/2023] Open
Abstract
Streptococcus pneumoniae is a major human pathogen with a high burden of disease. Non-invasive isolates (those found in non-sterile sites) are thought to be a key source of invasive isolates (those found in sterile sites) and a reservoir of anti-microbial resistance (AMR) determinants. Despite this, pneumococcal surveillance has almost exclusively focused on invasive isolates. We aimed to compare contemporaneous invasive and non-invasive isolate populations to understand how they interact and identify differences in AMR gene distribution. We used a combination of whole-genome sequencing and phenotypic anti-microbial susceptibility testing and a data set of invasive (n = 1,288) and non-invasive (n = 186) pneumococcal isolates, collected in Victoria, Australia, between 2018 and 2022. The non-invasive population had increased levels of antibiotic resistance to multiple classes of antibiotics including beta-lactam antibiotics penicillin and ceftriaxone. We identified genomic intersections between the invasive and non-invasive populations and no distinct phylogenetic clustering of the two populations. However, this analysis revealed sub-populations overrepresented in each population. The sub-populations that had high levels of AMR were overrepresented in the non-invasive population. We determined that WamR-Pneumo was the most accurate in silico tool for predicting resistance to the antibiotics tested. This tool was then used to assess the allelic diversity of the penicillin-binding protein genes, which acquire mutations leading to beta-lactam antibiotic resistance, and found that they were highly conserved (≥80% shared) between the two populations. These findings show the potential of non-invasive isolates to serve as reservoirs of AMR determinants.
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Affiliation(s)
- Charlie Higgs
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lamali Sadeesh Kumar
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Janet Strachan
- Communicable Diseases Branch, Department of Health, Victoria, Australia
| | - Tony Korman
- Department of Microbiology, Monash Health, Clayton, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Diane Daniel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Madeline Russell
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Norelle L. Sherry
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire L. Gorrie
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
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15
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Zufan SE, Lau KA, Donald A, Hoang T, Foster CSP, Sikazwe C, Theis T, Rawlinson WD, Ballard SA, Stinear TP, Howden BP, Jennison AV, Seemann T. Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance. Microb Genom 2023; 9. [PMID: 38019123 DOI: 10.1099/mgen.0.001146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
The COVID-19 pandemic has necessitated the rapid development and implementation of whole-genome sequencing (WGS) and bioinformatic methods for managing the pandemic. However, variability in methods and capabilities between laboratories has posed challenges in ensuring data accuracy. A national working group comprising 18 laboratory scientists and bioinformaticians from Australia and New Zealand was formed to improve data concordance across public health laboratories (PHLs). One effort, presented in this study, sought to understand the impact of the methodology on consensus genome concordance and interpretation. SARS-CoV-2 WGS proficiency testing programme (PTP) data were retrospectively obtained from the 2021 Royal College of Pathologists of Australasia Quality Assurance Programmes (RCPAQAP), which included 11 participating Australian laboratories. The submitted consensus genomes and reads from eight contrived specimens were investigated, focusing on discordant sequence data and findings were presented to the working group to inform best practices. Despite using a variety of laboratory and bioinformatic methods for SARS-CoV-2 WGS, participants largely produced concordant genomes. Two participants returned five discordant sites in a high-Cτ replicate, which could be resolved with reasonable bioinformatic quality thresholds. We noted ten discrepancies in genome assessment that arose from nucleotide heterogeneity at three different sites in three cell-culture-derived control specimens. While these sites were ultimately accurate after considering the participants' bioinformatic parameters, it presented an interesting challenge for developing standards to account for intrahost single nucleotide variation (iSNV). Observed differences had little to no impact on key surveillance metrics, lineage assignment and phylogenetic clustering, while genome coverage <90 % affected both. We recommend PHLs bioinformatically generate two consensus genomes with and without ambiguity thresholds for quality control and downstream analysis, respectively, and adhere to a minimum 90 % genome coverage threshold for inclusion in surveillance interpretations. We also suggest additional PTP assessment criteria, including primer efficiency, detection of iSNVs and minimum genome coverage of 90 %. This study underscores the importance of multidisciplinary national working groups in informing guidelines in real time for bioinformatic quality acceptance criteria. It demonstrates the potential for enhancing public health responses through improved data concordance and quality control in SARS-CoV-2 genomic analysis during pandemic surveillance.
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Affiliation(s)
- Sara E Zufan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Angela Donald
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tuyet Hoang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Charles S P Foster
- Serology and Virology Division (SAViD) SEALS Microbiology, NSW Health Pathology, Sydney, NSW, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Chisha Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine Western Australia, Nedlands, WA, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | | | - William D Rawlinson
- RCPAQAP Biosecurity, St. Leonards, NSW, Australia
- Serology and Virology Division (SAViD) SEALS Microbiology, NSW Health Pathology, Sydney, NSW, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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16
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Mellergaard M, Skovbakke SL, Jepsen SD, Panagiotopoulou N, Hansen ABR, Tian W, Lund A, Høgh RI, Møller SH, Guérillot R, Hayes AS, Erikstrup LT, Andresen L, Peleg AY, Larsen AR, Stinear TP, Handberg A, Erikstrup C, Howden BP, Goletz S, Frees D, Skov S. Clinical Staphylococcus aureus inhibits human T-cell activity through interaction with the PD-1 receptor. mBio 2023; 14:e0134923. [PMID: 37796131 PMCID: PMC10653905 DOI: 10.1128/mbio.01349-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/08/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Therapies that target and aid the host immune defense to repel cancer cells or invading pathogens are rapidly emerging. Antibiotic resistance is among the largest threats to human health globally. Staphylococcus aureus (S. aureus) is the most common bacterial infection, and it poses a challenge to the healthcare system due to its significant ability to develop resistance toward current available therapies. In long-term infections, S. aureus further adapt to avoid clearance by the host immune defense. In this study, we discover a new interaction that allows S. aureus to avoid elimination by the immune system, which likely supports its persistence in the host. Moreover, we find that blocking the specific receptor (PD-1) using antibodies significantly relieves the S. aureus-imposed inhibition. Our findings suggest that therapeutically targeting PD-1 is a possible future strategy for treating certain antibiotic-resistant staphylococcal infections.
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Affiliation(s)
- Maiken Mellergaard
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Line Skovbakke
- Biotherapeutic Glycoengineering and Immunology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Stine Dam Jepsen
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nafsika Panagiotopoulou
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Amalie Bøge Rud Hansen
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Weihua Tian
- Biotherapeutic Glycoengineering and Immunology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Astrid Lund
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Illum Høgh
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sofie Hedlund Møller
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Romain Guérillot
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ashleigh S. Hayes
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Lars Andresen
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anton Y. Peleg
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Melbourne, Victoria, Australia
| | - Anders Rhod Larsen
- Statens Serum Institute, Microbiology and Infection Control, Copenhagen, Denmark
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Aase Handberg
- Department of Clinical Biochemistry, Aalborg University Hospital, North Denmark Region, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Steffen Goletz
- Biotherapeutic Glycoengineering and Immunology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Dorte Frees
- Food Safety and Zoonosis, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Skov
- Department of Veterinary and Animal Sciences, Laboratory of immunology, Section for Preclinical Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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17
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Sharkey LKR, Guerillot R, Walsh CJ, Turner AM, Lee JYH, Neville SL, Klatt S, Baines SL, Pidot SJ, Rossello FJ, Seemann T, McWilliam HEG, Cho E, Carter GP, Howden BP, McDevitt CA, Hachani A, Stinear TP, Monk IR. The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in Staphylococcus aureus. mBio 2023; 14:e0226223. [PMID: 37850732 PMCID: PMC10746227 DOI: 10.1128/mbio.02262-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
Among the 16 two-component systems in the opportunistic human pathogen Staphylococcus aureus, only WalKR is essential. Like the orthologous systems in other Bacillota, S. aureus WalKR controls autolysins involved in peptidoglycan remodeling and is therefore intimately involved in cell division. However, despite the importance of WalKR in S. aureus, the basis for its essentiality is not understood and the regulon is poorly defined. Here, we defined a consensus WalR DNA-binding motif and the direct WalKR regulon by using functional genomics, including chromatin immunoprecipitation sequencing, with a panel of isogenic walKR mutants that had a spectrum of altered activities. Consistent with prior findings, the direct regulon includes multiple autolysin genes. However, this work also revealed that WalR directly regulates at least five essential genes involved in lipoteichoic acid synthesis (ltaS): translation (rplK), DNA compaction (hup), initiation of DNA replication (dnaA, hup) and purine nucleotide metabolism (prs). Thus, WalKR in S. aureus serves as a polyfunctional regulator that contributes to fundamental control over critical cell processes by coordinately linking cell wall homeostasis with purine biosynthesis, protein biosynthesis, and DNA replication. Our findings further address the essentiality of this locus and highlight the importance of WalKR as a bona fide target for novel anti-staphylococcal therapeutics. IMPORTANCE The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. This sensory network is key to S. aureus versatility and success as a pathogen. Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental S. aureus cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication.
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Affiliation(s)
- Liam K. R. Sharkey
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Calum J. Walsh
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Adrianna M. Turner
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jean Y. H. Lee
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarah L. Baines
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando J. Rossello
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Hamish E. G. McWilliam
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Victoria, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
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18
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Ba X, Raisen CL, Restif O, Cavaco LM, Vingsbo Lundberg C, Lee JYH, Howden BP, Bartels MD, Strommenger B, Harrison EM, Larsen AR, Holmes MA, Larsen J. Cryptic susceptibility to penicillin/β-lactamase inhibitor combinations in emerging multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages. Nat Commun 2023; 14:6479. [PMID: 37838722 PMCID: PMC10576800 DOI: 10.1038/s41467-023-42245-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023] Open
Abstract
Global spread of multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages underscores the need for new therapeutic strategies. Here we show that many S. epidermidis isolates belonging to these lineages display cryptic susceptibility to penicillin/β-lactamase inhibitor combinations under in vitro conditions, despite carrying the methicillin resistance gene mecA. Using a mouse thigh model of S. epidermidis infection, we demonstrate that single-dose treatment with amoxicillin/clavulanic acid significantly reduces methicillin-resistant S. epidermidis loads without leading to detectable resistance development. On the other hand, we also show that methicillin-resistant S. epidermidis is capable of developing increased resistance to amoxicillin/clavulanic acid during long-term in vitro exposure to these drugs. These findings suggest that penicillin/β-lactamase inhibitor combinations could be a promising therapeutic candidate for treatment of a high proportion of methicillin-resistant S. epidermidis infections, although the in vivo risk of resistance development needs to be further addressed before they can be incorporated into clinical trials.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Claire L Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lina Maria Cavaco
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Jean Y H Lee
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mette D Bartels
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Birgit Strommenger
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark.
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19
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Giulieri SG, Guérillot R, Holmes NE, Baines SL, Hachani A, Hayes AS, Daniel DS, Seemann T, Davis JS, Van Hal S, Tong SYC, Stinear TP, Howden BP. A statistical genomics framework to trace bacterial genomic predictors of clinical outcomes in Staphylococcus aureus bacteremia. Cell Rep 2023; 42:113069. [PMID: 37703880 DOI: 10.1016/j.celrep.2023.113069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 06/29/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023] Open
Abstract
Outcomes of severe bacterial infections are determined by the interplay between host, pathogen, and treatments. While human genomics has provided insights into host factors impacting Staphylococcus aureus infections, comparatively little is known about S. aureus genotypes and disease severity. Building on the hypothesis that bacterial pathoadaptation is a key outcome driver, we developed a genome-wide association study (GWAS) framework to identify adaptive mutations associated with treatment failure and mortality in S. aureus bacteremia (1,358 episodes). Our research highlights the potential of vancomycin-selected mutations and vancomycin minimum inhibitory concentration (MIC) as key explanatory variables to predict infection severity. The contribution of bacterial variation was much lower for clinical outcomes (heritability <5%); however, GWASs allowed us to identify additional, MIC-independent candidate pathogenesis loci. Using supervised machine learning, we were able to quantify the predictive potential of these adaptive signatures. Our statistical genomics framework provides a powerful means to capture adaptive mutations impacting severe bacterial infections.
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Affiliation(s)
- Stefano G Giulieri
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia.
| | - Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Natasha E Holmes
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Ashleigh S Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Diane S Daniel
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Joshua S Davis
- Department of Infectious Diseases, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia; Menzies School of Health Research, Charles Darwin University, Casuarina, NT 0810, Australia
| | - Sebastiaan Van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia
| | - Steven Y C Tong
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
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20
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Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde S, Webb HE, Afolayan AO, Alexander AP, Anandan S, Andrews JR, Ashton PM, Basnyat B, Bavdekar A, Bogoch II, Clemens JD, da Silva KE, De A, de Ligt J, Diaz Guevara PL, Dolecek C, Dutta S, Ehlers MM, Francois Watkins L, Garrett DO, Godbole G, Gordon MA, Greenhill AR, Griffin C, Gupta M, Hendriksen RS, Heyderman RS, Hooda Y, Hormazabal JC, Ikhimiukor OO, Iqbal J, Jacob JJ, Jenkins C, Jinka DR, John J, Kang G, Kanteh A, Kapil A, Karkey A, Kariuki S, Kingsley RA, Koshy RM, Lauer AC, Levine MM, Lingegowda RK, Luby SP, Mackenzie GA, Mashe T, Msefula C, Mutreja A, Nagaraj G, Nagaraj S, Nair S, Naseri TK, Nimarota-Brown S, Njamkepo E, Okeke IN, Perumal SPB, Pollard AJ, Pragasam AK, Qadri F, Qamar FN, Rahman SIA, Rambocus SD, Rasko DA, Ray P, Robins-Browne R, Rongsen-Chandola T, Rutanga JP, Saha SK, Saha S, Saigal K, Sajib MSI, Seidman JC, Shakya J, Shamanna V, Shastri J, Shrestha R, Sia S, Sikorski MJ, Singh A, Smith AM, Tagg KA, Tamrakar D, Tanmoy AM, Thomas M, Thomas MS, Thomsen R, Thomson NR, Tupua S, Vaidya K, Valcanis M, Veeraraghavan B, Weill FX, Wright J, Dougan G, Argimón S, Keane JA, Aanensen DM, Baker S, Holt KE. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 2023; 12:e85867. [PMID: 37697804 PMCID: PMC10506625 DOI: 10.7554/elife.85867] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
Background The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Danielle J Ingle
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
| | | | - Mabel K Aworh
- Nigeria Field Epidemiology and Laboratory Training ProgrammeAbujaNigeria
- College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | | | - Ka Lip Chew
- National University HospitalSingaporeSingapore
| | - John A Crump
- Centre for International Health, University of OtagoDunedinNew Zealand
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
- Malawi-Liverpool Wellcome Programme, Kamuzu University of Health SciencesBlantyreMalawi
| | - Benjamin P Howden
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Christopher M Parry
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- University of AntwerpAntwerpBelgium
| | - Hattie E Webb
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Ayorinde Oluwatobiloba Afolayan
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Philip M Ashton
- Malawi-Liverpool Wellcome ProgrammeBlantyreMalawi
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Buddha Basnyat
- Oxford University Clinical Research Unit NepalKathmanduNepal
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of TorontoTorontoCanada
| | - John D Clemens
- International Vaccine InstituteSeoulRepublic of Korea
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
- UCLA Fielding School of Public HealthLos AngelesUnited States
- Korea UniversitySeoulRepublic of Korea
| | - Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Anuradha De
- Topiwala National Medical CollegeMumbaiIndia
| | - Joep de Ligt
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | | | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Shanta Dutta
- ICMR - National Institute of Cholera & Enteric DiseasesKolkataIndia
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoriaSouth Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory ServicePretoriaSouth Africa
| | | | | | - Gauri Godbole
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew R Greenhill
- Federation University AustraliaChurchillAustralia
- Papua New Guinea Institute of Medical ResearchGorokaPapua New Guinea
| | - Chelsey Griffin
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Madhu Gupta
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | | | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Juan Carlos Hormazabal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP)SantiagoChile
| | - Odion O Ikhimiukor
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Claire Jenkins
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | - Jacob John
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Gagandeep Kang
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Arti Kapil
- All India Institute of Medical SciencesDelhiIndia
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research InstituteNairobiKenya
| | | | | | - AC Lauer
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Myron M Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
| | | | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Grant Austin Mackenzie
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Tapfumanei Mashe
- National Microbiology Reference LaboratoryHarareZimbabwe
- World Health OrganizationHarareZimbabwe
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | | | - Satheesh Nair
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | | | | | - Iruka N Okeke
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of OxfordOxfordUnited Kingdom
- The NIHR Oxford Biomedical Research CentreOxfordUnited Kingdom
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
| | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | | | - Savitra Devi Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | - Pallab Ray
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Roy Robins-Browne
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
- Murdoch Children’s Research Institute, Royal Children’s HospitalParkvilleAustralia
| | | | | | | | | | | | - Mohammad Saiful Islam Sajib
- Child Health Research FoundationDhakaBangladesh
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgowUnited Kingdom
| | | | - Jivan Shakya
- Dhulikhel HospitalDhulikhelNepal
- Institute for Research in Science and TechnologyKathmanduNepal
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | - Jayanthi Shastri
- Topiwala National Medical CollegeMumbaiIndia
- Kasturba Hospital for Infectious DiseasesMumbaiIndia
| | - Rajeev Shrestha
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | - Sonia Sia
- Research Institute for Tropical Medicine, Department of HealthMuntinlupa CityPhilippines
| | - Michael J Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | | | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable DiseasesJohannesburgSouth Africa
| | - Kaitlin A Tagg
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Dipesh Tamrakar
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | | | - Maria Thomas
- Christian Medical College, LudhianaLudhianaIndia
| | | | | | | | - Siaosi Tupua
- Ministry of Health, Government of SamoaApiaSamoa
| | | | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | | | - Jackie Wright
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
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21
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Soley JK, Jago M, Walsh CJ, Khomarbaghi Z, Howden BP, Lagator M. Pervasive genotype-by-environment interactions shape the fitness effects of antibiotic resistance mutations. Proc Biol Sci 2023; 290:20231030. [PMID: 37583318 PMCID: PMC10427823 DOI: 10.1098/rspb.2023.1030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/21/2023] [Indexed: 08/17/2023] Open
Abstract
The fitness effects of antibiotic resistance mutations are a major driver of resistance evolution. While the nutrient environment affects bacterial fitness, experimental studies of resistance typically measure fitness of mutants in a single environment only. We explored how the nutrient environment affected the fitness effects of rifampicin-resistant rpoB mutations in Escherichia coli under several conditions critical for the emergence and spread of resistance-the presence of primary or secondary antibiotic, or the absence of any antibiotic. Pervasive genotype-by-environment (GxE) interactions determined fitness in all experimental conditions, with rank order of fitness in the presence and absence of antibiotics being strongly dependent on the nutrient environment. GxE interactions also affected the magnitude and direction of collateral effects of secondary antibiotics, in some cases so drastically that a mutant that was highly sensitive in one nutrient environment exhibited cross-resistance to the same antibiotic in another. It is likely that the mutant-specific impact of rpoB mutations on the global transcriptome underpins the observed GxE interactions. The pervasive, mutant-specific GxE interactions highlight the importance of doing what is rarely done when studying the evolution and spread of resistance in experimental and clinical work: assessing fitness of antibiotic-resistant mutants across a range of relevant environments.
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Affiliation(s)
- Jake K. Soley
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Matthew Jago
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Calum J. Walsh
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Zahra Khomarbaghi
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Mato Lagator
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
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22
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Herisse M, Ishida K, Staiger-Creed J, Judd L, Williams SJ, Howden BP, Stinear TP, Dahse HM, Voigt K, Hertweck C, Pidot SJ. Discovery and Biosynthesis of the Cytotoxic Polyene Terpenomycin in Human Pathogenic Nocardia. ACS Chem Biol 2023; 18:1872-1879. [PMID: 37498707 DOI: 10.1021/acschembio.3c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nocardia are opportunistic human pathogens that can cause a range of debilitating and difficult to treat infections of the lungs, brain, skin, and soft tissues. Despite their close relationship to the well-known secondary metabolite-producing genus, Streptomyces, comparatively few natural products are known from the Nocardia, and even less is known about their involvement in the pathogenesis. Here, we combine chemistry, genomics, and molecular microbiology to reveal the production of terpenomycin, a new cytotoxic and antifungal polyene from a human pathogenic Nocardia terpenica isolate. We unveil the polyketide synthase (PKS) responsible for terpenomycin biosynthesis and show that it combines several unusual features, including "split", skipped, and iteratively used modules, and the use of the unusual extender unit methoxymalonate as a starter unit. To link genes to molecules, we constructed a transposon mutant library in N. terpenica, identifying a terpenomycin-null mutant with an inactivated terpenomycin PKS. Our findings show that the neglected actinomycetes have an unappreciated capacity for the production of bioactive molecules with unique biosynthetic pathways waiting to be uncovered and highlights these organisms as producers of diverse natural products.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Jordan Staiger-Creed
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Louise Judd
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Spencer J Williams
- School of Chemistry, University of Melbourne, Melbourne, Victoria 3000, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
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23
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Stockdale JE, Susvitasari K, Tupper P, Sobkowiak B, Mulberry N, Gonçalves da Silva A, Watt AE, Sherry NL, Minko C, Howden BP, Lane CR, Colijn C. Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19. Nat Commun 2023; 14:4830. [PMID: 37563113 PMCID: PMC10415581 DOI: 10.1038/s41467-023-40544-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Serial intervals - the time between symptom onset in infector and infectee - are a fundamental quantity in infectious disease control. However, their estimation requires knowledge of individuals' exposures, typically obtained through resource-intensive contact tracing efforts. We introduce an alternate framework using virus sequences to inform who infected whom and thereby estimate serial intervals. We apply our technique to SARS-CoV-2 sequences from case clusters in the first two COVID-19 waves in Victoria, Australia. We find that our approach offers high resolution, cluster-specific serial interval estimates that are comparable with those obtained from contact data, despite requiring no knowledge of who infected whom and relying on incompletely-sampled data. Compared to a published serial interval, cluster-specific serial intervals can vary estimates of the effective reproduction number by a factor of 2-3. We find that serial interval estimates in settings such as schools and meat processing/packing plants are shorter than those in healthcare facilities.
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Affiliation(s)
| | | | - Paul Tupper
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | | | - Nicola Mulberry
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Norelle L Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Corinna Minko
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
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24
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Ballard SA, Sherry NL, Howden BP. Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards. Microb Genom 2023; 9:mgen001097. [PMID: 37590046 PMCID: PMC10483410 DOI: 10.1099/mgen.0.001097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/04/2023] [Indexed: 08/18/2023] Open
Abstract
Pathogen genomics has transitioned rapidly from the research setting into a powerful tool now routinely used in public health microbiology, for surveillance, outbreak investigations and disease control. As these investigations can have significant public health, treatment and legal impacts, we must ensure the accuracy of these results through validation of testing processes. For laboratories working in this space, it is important to approach this work with a quality and accreditation framework in mind, working towards implementation of quality systems and test validation that meet international regulatory standards. Here we outline the key international standards and processes that lead toward accreditation for pathogen genomics.
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Affiliation(s)
- Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St Melbourne, 3000, Australia
| | - Norelle L. Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St Melbourne, 3000, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, Austin Hospital, 145 Studley Rd., Heidelberg, Victoria 3084, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St Melbourne, 3000, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, Austin Hospital, 145 Studley Rd., Heidelberg, Victoria 3084, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Australia
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25
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Porter AF, Featherstone L, Lane CR, Sherry NL, Nolan ML, Lister D, Seemann T, Duchene S, Howden BP. The importance of utilizing travel history metadata for informative phylogeographical inferences: a case study of early SARS-CoV-2 introductions into Australia. Microb Genom 2023; 9:mgen001099. [PMID: 37650865 PMCID: PMC10483412 DOI: 10.1099/mgen.0.001099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023] Open
Abstract
Inferring the spatiotemporal spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via Bayesian phylogeography has been complicated by the overwhelming sampling bias present in the global genomic dataset. Previous work has demonstrated the utility of metadata in addressing this bias. Specifically, the inclusion of recent travel history of SARS-CoV-2-positive individuals into extended phylogeographical models has demonstrated increased accuracy of estimates, along with proposing alternative hypotheses that were not apparent using only genomic and geographical data. However, as the availability of comprehensive epidemiological metadata is limited, many of the current estimates rely on sequence data and basic metadata (i.e. sample date and location). As the bias within the SARS-CoV-2 sequence dataset is extensive, the degree to which we can rely on results drawn from standard phylogeographical models (i.e. discrete trait analysis) that lack integrated metadata is of great concern. This is particularly important when estimates influence and inform public health policy. We compared results generated from the same dataset, using two discrete phylogeographical models: one including travel history metadata and one without. We utilized sequences from Victoria, Australia, in this case study for two unique properties. Firstly, the high proportion of cases sequenced throughout 2020 within Victoria and the rest of Australia. Secondly, individual travel history was collected from returning travellers in Victoria during the first wave (January to May) of the coronavirus disease 2019 (COVID-19) pandemic. We found that the implementation of individual travel history was essential for the estimation of SARS-CoV-2 movement via discrete phylogeography models. Without the additional information provided by the travel history metadata, the discrete trait analysis could not be fit to the data due to numerical instability. We also suggest that during the first wave of the COVID-19 pandemic in Australia, the primary driving force behind the spread of SARS-CoV-2 was viral importation from international locations. This case study demonstrates the necessity of robust genomic datasets supplemented with epidemiological metadata for generating accurate estimates from phylogeographical models in datasets that have significant sampling bias. For future work, we recommend the collection of metadata in conjunction with genomic data. Furthermore, we highlight the risk of applying phylogeographical models to biased datasets without incorporating appropriate metadata, especially when estimates influence public health policy decision making.
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Affiliation(s)
- Ashleigh F. Porter
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leo Featherstone
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Courtney R. Lane
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Norelle L. Sherry
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia
| | | | | | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC, Australia
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26
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Higgs C, Kumar LS, Stevens K, Strachan J, Sherry NL, Horan K, Zhang J, Stinear TP, Howden BP, Gorrie CL. Population structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in Victoria, Australia. Microb Genom 2023; 9:mgen001070. [PMID: 37471116 PMCID: PMC10438814 DOI: 10.1099/mgen.0.001070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Streptococcus pneumoniae is a major human pathogen and can cause a range of conditions from asymptomatic colonization to invasive pneumococcal disease (IPD). The epidemiology and distribution of IPD-causing serotypes in Australia has undergone large changes following the introduction of the 7-valent pneumococcal conjugate vaccine (PCV) in 2005 and the 13-valent PCV in 2011. In this study, to provide a contemporary understanding of the IPD causing population in Victoria, Australia, we aimed to examine the population structure and prevalence of antimicrobial resistance using whole-genome sequencing and comprehensive antimicrobial susceptibility data of 1288 isolates collected between 2018 and 2022. We observed high diversity among the isolates with 52 serotypes, 203 sequence types (STs) and 70 Global Pneumococcal Sequencing Project Clusters (GPSCs) identified. Serotypes contained in the 13v-PCV represented 35.3 % (n=405) of isolates. Antimicrobial resistance (AMR) to at least one antibiotic was identified in 23.8 % (n=358) of isolates with penicillin resistance the most prevalent (20.3 %, n=261 using meningitis breakpoints and 5.1 % n=65 using oral breakpoints). Of the AMR isolates, 28 % (n=101) were multidrug resistant (MDR) (resistant to three or more drug classes). Vaccination status of cases was determined for a subset of isolates with 34 cases classified as vaccine failure events (fully vaccinated IPD cases of vaccine serotype). However, no phylogenetic association with failure events was observed. Within the highly diverse IPD population, we identified six high-risk sub-populations of public health concern characterized by high prevalence, high rates of AMR and MDR, or serotype inclusion in vaccines. High-risk serotypes included serotypes 3, 19F, 19A, 14, 11A, 15A and serofamily 23. In addition, we present our data validating seroBA for in silico serotyping to facilitate ISO-accreditation of this test in routine use in a public health reference laboratory and have made this data set available. This study provides insights into the population dynamics, highlights non-vaccine serotypes of concern that are highly resistant, and provides a genomic framework for the ongoing surveillance of IPD in Australia which can inform next-generation IPD prevention strategies.
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Affiliation(s)
- Charlie Higgs
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lamali Sadeesh Kumar
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Norelle L. Sherry
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Josh Zhang
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire L. Gorrie
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
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27
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Xu L, Henriksen C, Mebus V, Guérillot R, Petersen A, Jacques N, Jiang JH, Derks RJE, Sánchez-López E, Giera M, Leeten K, Stinear TP, Oury C, Howden BP, Peleg AY, Frees D. A Clinically Selected Staphylococcus aureus clpP Mutant Survives Daptomycin Treatment by Reducing Binding of the Antibiotic and Adapting a Rod-Shaped Morphology. Antimicrob Agents Chemother 2023; 67:e0032823. [PMID: 37184389 PMCID: PMC10269151 DOI: 10.1128/aac.00328-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Daptomycin is a last-resort antibiotic used for the treatment of infections caused by Gram-positive antibiotic-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA). Treatment failure is commonly linked to accumulation of point mutations; however, the contribution of single mutations to resistance and the mechanisms underlying resistance remain incompletely understood. Here, we show that a single nucleotide polymorphism (SNP) selected during daptomycin therapy inactivates the highly conserved ClpP protease and is causing reduced susceptibility of MRSA to daptomycin, vancomycin, and β-lactam antibiotics as well as decreased expression of virulence factors. Super-resolution microscopy demonstrated that inactivation of ClpP reduced binding of daptomycin to the septal site and diminished membrane damage. In both the parental strain and the clpP strain, daptomycin inhibited the inward progression of septum synthesis, eventually leading to lysis and death of the parental strain while surviving clpP cells were able to continue synthesis of the peripheral cell wall in the presence of 10× MIC daptomycin, resulting in a rod-shaped morphology. To our knowledge, this is the first demonstration that synthesis of the outer cell wall continues in the presence of daptomycin. Collectively, our data provide novel insight into the mechanisms behind bacterial killing and resistance to this important antibiotic. Also, the study emphasizes that treatment with last-line antibiotics is selective for mutations that, like the SNP in clpP, favor antibiotic resistance over virulence gene expression.
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Affiliation(s)
- Lijuan Xu
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Henriksen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Viktor Mebus
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Romain Guérillot
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Nicolas Jacques
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Jhih-Hang Jiang
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Rico J. E. Derks
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| | - Elena Sánchez-López
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| | - Kirsten Leeten
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Cécile Oury
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Anton Y. Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Dorte Frees
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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28
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Hachani A, Giulieri SG, Guérillot R, Walsh CJ, Herisse M, Soe YM, Baines SL, Thomas DR, Cheung SD, Hayes AS, Cho E, Newton HJ, Pidot S, Massey RC, Howden BP, Stinear TP. A high-throughput cytotoxicity screening platform reveals agr-independent mutations in bacteraemia-associated Staphylococcus aureus that promote intracellular persistence. eLife 2023; 12:84778. [PMID: 37289634 DOI: 10.7554/elife.84778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Staphylococcus aureus infections are associated with high mortality rates. Often considered an extracellular pathogen, S. aureus can persist and replicate within host cells, evading immune responses, and causing host cell death. Classical methods for assessing S. aureus cytotoxicity are limited by testing culture supernatants and endpoint measurements that do not capture the phenotypic diversity of intracellular bacteria. Using a well-established epithelial cell line model, we have developed a platform called InToxSa (intracellular toxicity of S. aureus) to quantify intracellular cytotoxic S. aureus phenotypes. Studying a panel of 387 S. aureus bacteraemia isolates, and combined with comparative, statistical, and functional genomics, our platform identified mutations in S. aureus clinical isolates that reduced bacterial cytotoxicity and promoted intracellular persistence. In addition to numerous convergent mutations in the Agr quorum sensing system, our approach detected mutations in other loci that also impacted cytotoxicity and intracellular persistence. We discovered that clinical mutations in ausA, encoding the aureusimine non-ribosomal peptide synthetase, reduced S. aureus cytotoxicity, and increased intracellular persistence. InToxSa is a versatile, high-throughput cell-based phenomics platform and we showcase its utility by identifying clinically relevant S. aureus pathoadaptive mutations that promote intracellular residency.
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Affiliation(s)
- Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Stefano G Giulieri
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Calum J Walsh
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ye Mon Soe
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - David R Thomas
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Infection and Immunity Program, Department of Microbiology and Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Shane Doris Cheung
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Australia
| | - Ashleigh S Hayes
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Australia
| | - Hayley J Newton
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Infection and Immunity Program, Department of Microbiology and Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Sacha Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ruth C Massey
- School of Microbiology, University College Cork, Cork, Ireland
- School of Medicine, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
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29
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Henderson A, Cheng MP, Chew KL, Coombs GW, Davis JS, Grant JM, Gregson D, Giulieri SG, Howden BP, Lee TC, Nguyen V, Mora JM, Morpeth SC, Robinson JO, Tong SYC, Van Hal SJ. A multi-site, international laboratory study to assess the performance of penicillin susceptibility testing of Staphylococcus aureus. J Antimicrob Chemother 2023; 78:1499-1504. [PMID: 37071589 PMCID: PMC10232234 DOI: 10.1093/jac/dkad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 03/29/2023] [Indexed: 04/19/2023] Open
Abstract
OBJECTIVES There is clinical uncertainty over the optimal treatment for penicillin-susceptible Staphylococcus aureus (PSSA) infections. Furthermore, there is concern that phenotypic penicillin susceptibility testing methods are not reliably able to detect some blaZ-positive S. aureus. METHODS Nine S. aureus isolates, including six genetically diverse strains harbouring blaZ, were sent in triplicate to 34 participating laboratories from Australia (n = 14), New Zealand (n = 6), Canada (n = 12), Singapore (n = 1) and Israel (n = 1). We used blaZ PCR as the gold standard to assess susceptibility testing performance of CLSI (P10 disc) and EUCAST (P1 disc) methods. Very major errors (VMEs), major error (MEs) and categorical agreement were calculated. RESULTS Twenty-two laboratories reported 593 results according to CLSI methodology (P10 disc). Nineteen laboratories reported 513 results according to the EUCAST (P1 disc) method. For CLSI laboratories, the categorical agreement and calculated VME and ME rates were 85% (508/593), 21% (84/396) and 1.5% (3/198), respectively. For EUCAST laboratories, the categorical agreement and calculated VME and ME rates were 93% (475/513), 11% (84/396) and 1% (3/198), respectively. Seven laboratories reported results for both methods, with VME rates of 24% for CLSI and 12% for EUCAST. CONCLUSIONS The EUCAST method with a P1 disc resulted in a lower VME rate compared with the CLSI methods with a P10 disc. These results should be considered in the context that among collections of PSSA isolates, as determined by automated MIC testing, less than 10% harbour blaZ. Furthermore, the clinical relevance of phenotypically susceptible, but blaZ-positive S. aureus, remains unclear.
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Affiliation(s)
- Andrew Henderson
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | - Matthew P Cheng
- Department of Medicine, and Laboratory Medicine, McGill University Health Centre, Montreal, Canada
| | - Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Geoffrey W Coombs
- Department of Antimicrobial Resistance, and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, Australia
| | - Joshua S Davis
- Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia
- Department of Infectious Diseases, John Hunter Hospital, Newcastle, Australia
| | - Jennifer M Grant
- Department of Medicine, Vancouver Coastal Health, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Dan Gregson
- Department of Pathology, Laboratory Medicine, and Medicine, Cummings School of Medicine at The University of Calgary, Calgary, Canada
| | - Stefano G Giulieri
- Department of Microbiology, and Immunology, The University of Melbourne, Melbourne, Australia
- Victorian Infectious Diseases Services, The Royal Melbourne Hospital, Melbourne, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, Austin Hospital, Heidelberg, Australia
| | - Todd C Lee
- Department of Medicine, McGill University, Montreal, Canada
| | - Vi Nguyen
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jocelyn M Mora
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Susan C Morpeth
- Microbiology Laboratory, Middlemore Hospital (Counties Manukau Te Whatu Ora), Otahuhu, New Zealand
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - James O Robinson
- Department of Infectious Diseases, Royal Perth Hospital, Perth, Australia
- Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Services, The Royal Melbourne Hospital, Melbourne, Australia
| | - Sebastiaan J Van Hal
- Department of Microbiology, and Infectious Diseases, Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Sydney, Australia
- School of Medicine, The University of Sydney, Sydney, Australia
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30
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Wagner TM, Janice J, Schulz M, Ballard SA, da Silva AG, Coombs GW, Daley DA, Pang S, Mowlaboccus S, Stinear T, Hegstad K, Howden BP, Sundsfjord A. Reversible vancomycin susceptibility within emerging ST1421 Enterococcus faecium strains is associated with rearranged vanA-gene clusters and increased vanA plasmid copy number. Int J Antimicrob Agents 2023:106849. [PMID: 37187337 DOI: 10.1016/j.ijantimicag.2023.106849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 05/17/2023]
Abstract
Vancomycin variable enterococci (VVE) are van-positive enterococci with a vancomycin susceptible phenotype (VVE-S) that can convert to a resistant phenotype (VVE-R) and be selected for during vancomycin exposure. VVE-R outbreaks have been reported in Canada and Scandinavian countries. This study aimed to examine the presence of VVE in whole genome sequenced (WGS) Australian bacteremia Enterococcus faecium (Efm) isolates collected through the Australian Group on Antimicrobial resistance (AGAR) network. Eight potential VVEAus isolates, all identified as Efm ST1421, were selected based on the presence of vanA and a vancomycin susceptible phenotype. During vancomycin selection two potential VVE-S harboring intact vanHAX genes, but lacking the prototypic vanRS and vanZ genes, reverted to a resistant phenotype (VVEAus-R). Spontaneous VVEAus-R reversion occurred at a frequency of 4-6 × 10-8 resistant colonies per parent cell in vitro after 48 h and led to high-level vancomycin and teicoplanin resistance. The S to R reversion was associated with a 44-bp deletion in the vanHAX promoter region and an increased vanA plasmid copy number. The deletion in the vanHAX promoter region enables an alternative constitutive promoter for the expression of vanHAX. Acquisition of vancomycin resistance was associated with a low fitness cost compared to the corresponding VVEAus-S isolate. The relative proportion of VVEAus-R versus VVEAus-S decreased over time in serial passages without vancomycin selection. Efm ST1421 is one of the predominant VanA-Efm multilocus sequence types found across most regions of Australia and has also been associated with a major prolonged VVE outbreak in Danish hospitals.
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Affiliation(s)
- Theresa Maria Wagner
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jessin Janice
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Mark Schulz
- The Microbiological Diagnostic Unit Public Health Laboratory and Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria, 3000, Australia
| | - Susan A Ballard
- The Microbiological Diagnostic Unit Public Health Laboratory and Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria, 3000, Australia
| | - Anders Goncalves da Silva
- The Microbiological Diagnostic Unit Public Health Laboratory and Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria, 3000, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Disease (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia; Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Denise A Daley
- Australian Group on Antimicrobial Resistance, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Stanley Pang
- Antimicrobial Resistance and Infectious Disease (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia; Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Disease (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia; Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Tim Stinear
- The Microbiological Diagnostic Unit Public Health Laboratory and Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria, 3000, Australia
| | - Kristin Hegstad
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory and Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria, 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia.
| | - Arnfinn Sundsfjord
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; The Microbiological Diagnostic Unit Public Health Laboratory and Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria, 3000, Australia.
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31
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Kiss C, Kotsanas D, Francis MJ, Sait M, Valcanis M, Lacey J, Connelly K, Rogers B, Ballard SA, Howden BP, Graham M. Molecular epidemiology, clinical features and significance of Shiga toxin detection from routine testing of gastroenteritis specimens. Pathology 2023:S0031-3025(23)00119-8. [PMID: 37271611 DOI: 10.1016/j.pathol.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 06/06/2023]
Abstract
After introduction of faecal multiplex PCR that includes targets for stx1 and stx2 genes, we found stx genes were detected in 120 specimens from 111 patients over a 31-month period from 2018-2020 from a total of 14,179 separate tests performed. The proportion of stx1 only vs stx2 only vs stx1 and stx2 was 35%, 22% and 42%, respectively. There were 54 specimens which were culture positive, with 33 different serotypes identified, the predominant serotype being O157:H7 (19%). Eighty-two patients had clinical data available; we found a high rate of fever (35%), bloody diarrhoea (34%), acute kidney injury (27%), hospital admission (80%) and detection of faecal co-pathogens (23%). Only one patient developed haemolytic uraemic syndrome. We found no significant association with stx genotype and any particular symptom or complication. We found a significant association of serotypes O157:H7 and O26:H11 with bloody stool, but no significant association with any other symptom or complication.
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Affiliation(s)
- Christopher Kiss
- Department of Microbiology, Monash Health, Clayton, Vic, Australia.
| | - Despina Kotsanas
- Monash Infectious Diseases, Monash Health, Clayton, Vic, Australia
| | | | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Jake Lacey
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Kathryn Connelly
- Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, Vic, Australia; Monash University School of Clinical Sciences, Monash Health, Clayton, Vic, Australia
| | - Benjamin Rogers
- Monash Infectious Diseases, Monash Health, Clayton, Vic, Australia; Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, Vic, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Maryza Graham
- Department of Microbiology, Monash Health, Clayton, Vic, Australia; Monash Infectious Diseases, Monash Health, Clayton, Vic, Australia; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, Vic, Australia
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32
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Mason LCE, Greig DR, Cowley LA, Partridge SR, Martinez E, Blackwell GA, Chong CE, De Silva PM, Bengtsson RJ, Draper JL, Ginn AN, Sandaradura I, Sim EM, Iredell JR, Sintchenko V, Ingle DJ, Howden BP, Lefèvre S, Njamkepo E, Weill FX, Ceyssens PJ, Jenkins C, Baker KS. Author Correction: The evolution and international spread of extensively drug resistant Shigella sonnei. Nat Commun 2023; 14:2302. [PMID: 37085572 PMCID: PMC10121638 DOI: 10.1038/s41467-023-38041-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Affiliation(s)
- Lewis C E Mason
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - David R Greig
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, UK
| | | | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Elena Martinez
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Grace A Blackwell
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Charlotte E Chong
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - P Malaka De Silva
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Rebecca J Bengtsson
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Jenny L Draper
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Andrew N Ginn
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
- Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia
| | - Indy Sandaradura
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Eby M Sim
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Microbiology Research, Westmead Hospital, Westmead, NSW, Australia
| | - Danielle J Ingle
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sophie Lefèvre
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | | | - Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, UK
| | - Kate S Baker
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK.
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK.
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Mason LCE, Greig DR, Cowley LA, Partridge SR, Martinez E, Blackwell GA, Chong CE, De Silva PM, Bengtsson RJ, Draper JL, Ginn AN, Sandaradura I, Sim EM, Iredell JR, Sintchenko V, Ingle DJ, Howden BP, Lefèvre S, Njampeko E, Weill FX, Ceyssens PJ, Jenkins C, Baker KS. The evolution and international spread of extensively drug resistant Shigella sonnei. Nat Commun 2023; 14:1983. [PMID: 37031199 PMCID: PMC10082799 DOI: 10.1038/s41467-023-37672-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant S. sonnei was reported in the United Kingdom. Here, we aimed to identify the genetic basis, evolutionary history, and international dissemination of the outbreak strain. Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a most recent common ancestor in 2018 carrying a low-fitness cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri. Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data.
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Affiliation(s)
- Lewis C E Mason
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - David R Greig
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, UK
| | | | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Elena Martinez
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Grace A Blackwell
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Charlotte E Chong
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - P Malaka De Silva
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Rebecca J Bengtsson
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Jenny L Draper
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Andrew N Ginn
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
- Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia
| | - Indy Sandaradura
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Eby M Sim
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Microbiology Research, Westmead Hospital, Westmead, NSW, Australia
| | - Danielle J Ingle
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sophie Lefèvre
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Elisabeth Njampeko
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | | | - Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, UK
| | - Kate S Baker
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK.
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK.
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Werner G, Couto N, Feil EJ, Novais A, Hegstad K, Howden BP, Friedrich AW, Reuter S. Taking hospital pathogen surveillance to the next level. Microb Genom 2023; 9. [PMID: 37099616 DOI: 10.1099/mgen.0.001008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
High-throughput bacterial genomic sequencing and subsequent analyses can produce large volumes of high-quality data rapidly. Advances in sequencing technology, with commensurate developments in bioinformatics, have increased the speed and efficiency with which it is possible to apply genomics to outbreak analysis and broader public health surveillance. This approach has been focused on targeted pathogenic taxa, such as Mycobacteria, and diseases corresponding to different modes of transmission, including food-and-water-borne diseases (FWDs) and sexually transmitted infections (STIs). In addition, major healthcare-associated pathogens such as methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and carbapenemase-producing Klebsiella pneumoniae are the focus of research projects and initiatives to understand transmission dynamics and temporal trends on both local and global scales. Here, we discuss current and future public health priorities relating to genome-based surveillance of major healthcare-associated pathogens. We highlight the specific challenges for the surveillance of healthcare-associated infections (HAIs), and how recent technical advances might be deployed most effectively to mitigate the increasing public health burden they cause.
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Affiliation(s)
- Guido Werner
- Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | - Natacha Couto
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Angela Novais
- UCIBIO-Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Kristin Hegstad
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Alexander W Friedrich
- Medical Faculty, University Hospital, Westphalia-Wilhelms-University Muenster, Germany
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Hygiene, University Hospital Freiburg, Germany
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Mu A, Klare WP, Baines SL, Ignatius Pang CN, Guérillot R, Harbison-Price N, Keller N, Wilksch J, Nhu NTK, Phan MD, Keller B, Nijagal B, Tull D, Dayalan S, Chua HHC, Skoneczny D, Koval J, Hachani A, Shah AD, Neha N, Jadhav S, Partridge SR, Cork AJ, Peters K, Bertolla O, Brouwer S, Hancock SJ, Álvarez-Fraga L, De Oliveira DMP, Forde B, Dale A, Mujchariyakul W, Walsh CJ, Monk I, Fitzgerald A, Lum M, Correa-Ospina C, Roy Chowdhury P, Parton RG, De Voss J, Beckett J, Monty F, McKinnon J, Song X, Stephen JR, Everest M, Bellgard MI, Tinning M, Leeming M, Hocking D, Jebeli L, Wang N, Ben Zakour N, Yasar SA, Vecchiarelli S, Russell T, Zaw T, Chen T, Teng D, Kassir Z, Lithgow T, Jenney A, Cole JN, Nizet V, Sorrell TC, Peleg AY, Paterson DL, Beatson SA, Wu J, Molloy MP, Syme AE, Goode RJA, Hunter AA, Bowland G, West NP, Wilkins MR, Djordjevic SP, Davies MR, Seemann T, Howden BP, Pascovici D, Tyagi S, Schittenhelm RB, De Souza DP, McConville MJ, Iredell JR, Cordwell SJ, Strugnell RA, Stinear TP, Schembri MA, Walker MJ. Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria. Nat Commun 2023; 14:1530. [PMID: 36934086 PMCID: PMC10024524 DOI: 10.1038/s41467-023-37200-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/06/2023] [Indexed: 03/20/2023] Open
Abstract
Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20-40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discovery and translational research.
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Affiliation(s)
- Andre Mu
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Wellcome Sanger Institute, Hinxton, UK
| | - William P Klare
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - C N Ignatius Pang
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- Bioinformatics Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nichaela Harbison-Price
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nadia Keller
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan Wilksch
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nguyen Thi Khanh Nhu
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Minh-Duy Phan
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Bernhard Keller
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Brunda Nijagal
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Hwa Huat Charlie Chua
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Dominik Skoneczny
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Jason Koval
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anup D Shah
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Nitika Neha
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Snehal Jadhav
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Amanda J Cork
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Kate Peters
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Olivia Bertolla
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Stephan Brouwer
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Steven J Hancock
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Laura Álvarez-Fraga
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - David M P De Oliveira
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Brian Forde
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Ashleigh Dale
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Warasinee Mujchariyakul
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Calum J Walsh
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ian Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Mabel Lum
- Bioplatforms Australia Ltd., Sydney, NSW, Australia
| | - Carolina Correa-Ospina
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Piklu Roy Chowdhury
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD, Australia
| | - James De Voss
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - James Beckett
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Francois Monty
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Jessica McKinnon
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Xiaomin Song
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - John R Stephen
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Marie Everest
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Matt I Bellgard
- Office of eResearch, Queensland University of Technology, Brisbane, QLD, Australia
- Center for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Matthew Tinning
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Michael Leeming
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Dianna Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nouri Ben Zakour
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Serhat A Yasar
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Stefano Vecchiarelli
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Tonia Russell
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Thiri Zaw
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Tyrone Chen
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Don Teng
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Zena Kassir
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Trevor Lithgow
- Centre to Impact AMR and Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Adam Jenney
- Centre to Impact AMR and Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Jason N Cole
- Department of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Victor Nizet
- Department of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Tania C Sorrell
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Anton Y Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
- Centre to Impact AMR and Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - David L Paterson
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jemma Wu
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Mark P Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Anna E Syme
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Robert J A Goode
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - Adam A Hunter
- Center for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Grahame Bowland
- Center for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Nicholas P West
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Marc R Wilkins
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Sonika Tyagi
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - David P De Souza
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Stuart J Cordwell
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mark A Schembri
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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36
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Dusadeepong R, Delvallez G, Cheng S, Meng S, Sreng N, Letchford J, Choun K, Teav S, Hardy L, Jacobs J, Hoang T, Seemann T, Howden BP, Glaser P, Stinear TP, Vandelannoote K. Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica subsp. enterica serovar Paratyphi A in Phnom Penh, Cambodia. Microb Genom 2023; 9. [PMID: 36961484 PMCID: PMC10132074 DOI: 10.1099/mgen.0.000972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023] Open
Abstract
In early 2020, the Medical Biology Laboratory of the Pasteur Institute of Cambodia isolated an unusually high number of fluoroquinolone-resistant Salmonella enterica subspecies enterica serovar Paratyphi A strains during its routine bacteriological surveillance activities in Phnom Penh, Cambodia. A public-health investigation was supported by genome sequencing of these Paratyphi A strains to gain insights into the genetic diversity and population structure of a potential outbreak of fluoroquinolone-resistant paratyphoid fever. Comparative genomic and phylodynamic analyses revealed the 2020 strains were descended from a previously described 2013-2015 outbreak of Paratyphi A infections. Our analysis showed sub-lineage 2.3.1 had remained largely susceptible to fluoroquinolone drugs until 2015, but acquired chromosomal resistance to these drugs during six separate events between late 2012 and 2015. The emergence of fluoroquinolone resistance was rapidly followed by the replacement of the original susceptible Paratyphi A population, which led to a dramatic increase of fluoroquinolone-resistant blood-culture-confirmed cases in subsequent years (2016-2020). The rapid acquisition of resistance-conferring mutations in the Paratyphi A population over a 3 year period is suggestive of a strong selective pressure on that population, likely linked with fluoroquinolone use. In turn, emergence of fluoroquinolone resistance has led to increased use of extended-spectrum cephalosporins like ceftriaxone that are becoming the drug of choice for empirical treatment of paratyphoid fever in Cambodia.
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Affiliation(s)
- Rutaiwan Dusadeepong
- Bacterial Phylogenomics Group, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
- Medical Biology Laboratory, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
| | - Gauthier Delvallez
- Medical Biology Laboratory, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
| | - Sokleaph Cheng
- Medical Biology Laboratory, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
- LMI Drug Resistance in South East Asia, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
| | - Soda Meng
- Medical Biology Laboratory, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
| | - Navin Sreng
- Laboratory of Environment and Food Safety, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
| | - Joanne Letchford
- Diagnostic Microbiology Development Program, Phnom Penh, Cambodia
| | - Kimcheng Choun
- Infectious Disease Department, Sihanouk Hospital Center of HOPE, Phnom Penh, Cambodia
| | - Syna Teav
- Laboratory Unit, Sihanouk Hospital Center of HOPE, Phnom Penh, Cambodia
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Tuyet Hoang
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Philippe Glaser
- Evolution and Ecology of Antibiotic Resistance Unit, APHP-CNRS-UMR6047, Institut Pasteur-University Paris-Saclay-Université Paris Cité, Paris, France
| | - Timothy P Stinear
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Koen Vandelannoote
- Bacterial Phylogenomics Group, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
- Medical Biology Laboratory, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
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37
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Davies MR, Keller N, Brouwer S, Jespersen MG, Cork AJ, Hayes AJ, Pitt ME, De Oliveira DMP, Harbison-Price N, Bertolla OM, Mediati DG, Curren BF, Taiaroa G, Lacey JA, Smith HV, Fang NX, Coin LJM, Stevens K, Tong SYC, Sanderson-Smith M, Tree JJ, Irwin AD, Grimwood K, Howden BP, Jennison AV, Walker MJ. Detection of Streptococcus pyogenes M1 UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA. Nat Commun 2023; 14:1051. [PMID: 36828918 PMCID: PMC9951164 DOI: 10.1038/s41467-023-36717-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
A new variant of Streptococcus pyogenes serotype M1 (designated 'M1UK') has been reported in the United Kingdom, linked with seasonal scarlet fever surges, marked increase in invasive infections, and exhibiting enhanced expression of the superantigen SpeA. The progenitor S. pyogenes 'M1global' and M1UK clones can be differentiated by 27 SNPs and 4 indels, yet the mechanism for speA upregulation is unknown. Here we investigate the previously unappreciated expansion of M1UK in Australia, now isolated from the majority of serious infections caused by serotype M1 S. pyogenes. M1UK sub-lineages circulating in Australia also contain a novel toxin repertoire associated with epidemic scarlet fever causing S. pyogenes in Asia. A single SNP in the 5' transcriptional leader sequence of the transfer-messenger RNA gene ssrA drives enhanced SpeA superantigen expression as a result of ssrA terminator read-through in the M1UK lineage. This represents a previously unappreciated mechanism of toxin expression and urges enhanced international surveillance.
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Affiliation(s)
- Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Nadia Keller
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Stephan Brouwer
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Amanda J Cork
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Miranda E Pitt
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - David M P De Oliveira
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nichaela Harbison-Price
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Olivia M Bertolla
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Bodie F Curren
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jake A Lacey
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Helen V Smith
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Ning-Xia Fang
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Martina Sanderson-Smith
- Illawarra Health and Medical Research Institute and Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Adam D Irwin
- University of Queensland Centre for Clinical Research, Brisbane, QLD, Australia.,Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Keith Grimwood
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia.,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, QLD, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Amy V Jennison
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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38
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Morris JM, Mercoulia K, Valcanis M, Gorrie CL, Sherry NL, Howden BP. Hidden Resistances: How Routine Whole-Genome Sequencing Uncovered an Otherwise Undetected blaNDM-1 Gene in Vibrio alginolyticus from Imported Seafood. Microbiol Spectr 2023; 11:e0417622. [PMID: 36602387 PMCID: PMC9927303 DOI: 10.1128/spectrum.04176-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/06/2022] [Indexed: 01/06/2023] Open
Abstract
Vibrio alginolyticus causes vibriosis of marine vertebrates, invertebrates, and humans, and while there have been several reports of multidrug resistance in V. alginolyticus, carbapenem resistance is rare. V. alginolyticus strain AUSMDU00064140 was isolated in Melbourne, Australia, from imported prawns. Routine genomic surveillance detected the presence of a full-length blaNDM-1 gene, subsequently shown to be collocated with additional acquired antimicrobial resistance genes on a resistance cassette on the largest chromosome, flanked by mobilization gene annotations. Comparisons to a previously described V. alginolyticus plasmid, pC1349, revealed differing gene content and arrangements between the resistance cassettes. Phylogenetic analysis was performed against a local and global data set (n = 109), demonstrating that AUSMDU00064140 was distinct and did not cluster with any other strains. Despite the presence of the complete blaNDM-1 gene and positive phenotypic assays for carbapenemase production, carbapenem MICs were low (meropenem MIC ≤0.5 mg/liter). However, it is still possible that this gene may be transferred to another species in the environment or a host, causing phenotypic carbapenem resistance and presenting a risk of great public health concern. IMPORTANCE Carbapenems are last-line antimicrobials, vital for use in human medicine. Antimicrobial resistance determinants such as blaNDM (New Delhi metallo-β-lactamase producing) genes conferring resistance to the carbapenem class of antimicrobials, are typically found in Enterobacterales (first described in 2009 from a Klebsiella pneumoniae isolate). Our study shows that Vibrio alginolyticus isolated from cooked prawn is able to harbor antimicrobial resistance (AMR) genes of public health concern, specifically a chromosomally located blaNDM-1 gene, and there is the potential for transmission of resistance genes. This may be linked with antimicrobial use in low- and middle-income settings, which has typically been high, unregulated, or not reported. Many countries, including Thailand, have implemented national strategic plans to incorporate the World Health Organization (WHO)'s Global Action Plan (2015) recommendations of a global One Health approach, including increased resources for surveillance of antimicrobial usage and AMR; however, efficient antimicrobial surveillance systems incorporating genomic and phenotypic testing of isolates are still lacking in many jurisdictions.
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Affiliation(s)
- Jacqueline M. Morris
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Karolina Mercoulia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Claire L. Gorrie
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Norelle L. Sherry
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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39
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Bastien S, Meyers S, Salgado-Pabón W, Giulieri SG, Rasigade JP, Liesenborghs L, Kinney KJ, Couzon F, Martins-Simoes P, Moing VL, Duval X, Holmes NE, Bruun NE, Skov R, Howden BP, Fowler VG, Verhamme P, Andersen PS, Bouchiat C, Moreau K, Vandenesch F. All Staphylococcus aureus bacteraemia-inducing strains can cause infective endocarditis: Results of GWAS and experimental animal studies. J Infect 2023; 86:123-133. [PMID: 36603774 PMCID: PMC10399548 DOI: 10.1016/j.jinf.2022.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/21/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023]
Abstract
OBJECTIVES We aimed at determining whether specific S. aureus strains cause infective endocarditis (IE) in the course of Staphylococcus aureus bacteraemia (SAB). METHODS A genome-wide association study (GWAS) including 924 S. aureus genomes from IE (274) and non-IE (650) SAB patients from international cohorts was conducted, and a subset of strains was tested with two experimental animal models of IE, one investigating the early step of bacterial adhesion to inflamed mice valves, the second evaluating the local and systemic developmental process of IE on mechanically-damaged rabbit valves. RESULTS The genetic profile of S. aureus IE and non-IE SAB strains did not differ when considering single nucleotide polymorphisms, coding sequences, and k-mers analysed in GWAS. In the murine inflammation-induced IE model, no difference was observed between IE and non-IE SAB strains both in terms of adhesion to the cardiac valves and in the propensity to cause IE; in the mechanical IE-induced rabbit model, there was no difference between IE and non-IE SAB strains regarding the vegetation size and CFU. CONCLUSION All strains of S. aureus isolated from SAB patients must be considered as capable of causing this common and lethal infection once they have accessed the bloodstream.
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Affiliation(s)
- Sylvère Bastien
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Severien Meyers
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Wilmara Salgado-Pabón
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, USA
| | - Stefano G Giulieri
- Department of Microbiology and Immunology and Department of Infectious Diseases, The University of Melbourne at the Doherty Institute for Infection and Immunity; Victorian Infectious Disease Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Australia
| | - Jean-Phillipe Rasigade
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Laurens Liesenborghs
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Kyle J Kinney
- Department of Microbiology and Immunology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Florence Couzon
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Patricia Martins-Simoes
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | | | - Xavier Duval
- Hôpital Bichat Claude Bernard, AP-HP, Paris, France; Inserm CIC 1425, Inserm UMR-1137 IAME, Cité Paris University, UFR de Médecine-Bichat, Paris, France
| | - Natasha E Holmes
- Department of Infectious Diseases, Austin Health, Heidelberg, Australia
| | - Niels Eske Bruun
- Clinical Institute, Copenhagen and Aalborg University, Aalborg, Denmark; Department of Cardiology, Zealand University Hospital Roskilde, Roskilde, Zealand, Denmark
| | - Robert Skov
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Benjamin P Howden
- Department of Microbiology and Immunology and Department of Infectious Diseases, The University of Melbourne at the Doherty Institute for Infection and Immunity; Victorian Infectious Disease Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Australia
| | - Vance G Fowler
- Duke University Medical Center, Durham, NC USA; Duke Clinical Research Institute, Durham, NC USA
| | - Peter Verhamme
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Paal Skytt Andersen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Coralie Bouchiat
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France.
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40
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Howden BP, Giulieri SG, Wong Fok Lung T, Baines SL, Sharkey LK, Lee JYH, Hachani A, Monk IR, Stinear TP. Staphylococcus aureus host interactions and adaptation. Nat Rev Microbiol 2023; 21:380-395. [PMID: 36707725 PMCID: PMC9882747 DOI: 10.1038/s41579-023-00852-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 01/28/2023]
Abstract
Invasive Staphylococcus aureus infections are common, causing high mortality, compounded by the propensity of the bacterium to develop drug resistance. S. aureus is an excellent case study of the potential for a bacterium to be commensal, colonizing, latent or disease-causing; these states defined by the interplay between S. aureus and host. This interplay is multidimensional and evolving, exemplified by the spread of S. aureus between humans and other animal reservoirs and the lack of success in vaccine development. In this Review, we examine recent advances in understanding the S. aureus-host interactions that lead to infections. We revisit the primary role of neutrophils in controlling infection, summarizing the discovery of new immune evasion molecules and the discovery of new functions ascribed to well-known virulence factors. We explore the intriguing intersection of bacterial and host metabolism, where crosstalk in both directions can influence immune responses and infection outcomes. This Review also assesses the surprising genomic plasticity of S. aureus, its dualism as a multi-mammalian species commensal and opportunistic pathogen and our developing understanding of the roles of other bacteria in shaping S. aureus colonization.
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Affiliation(s)
- Benjamin P. Howden
- grid.1008.90000 0001 2179 088XCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.410678.c0000 0000 9374 3516Department of Infectious Diseases, Austin Health, Heidelberg, Victoria Australia ,grid.416153.40000 0004 0624 1200Microbiology Department, Royal Melbourne Hospital, Melbourne, Victoria Australia
| | - Stefano G. Giulieri
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.416153.40000 0004 0624 1200Victorian Infectious Diseases Service, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Tania Wong Fok Lung
- grid.21729.3f0000000419368729Department of Paediatrics, Columbia University, New York, NY USA
| | - Sarah L. Baines
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Liam K. Sharkey
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Jean Y. H. Lee
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.419789.a0000 0000 9295 3933Department of Infectious Diseases, Monash Health, Clayton, Victoria Australia
| | - Abderrahman Hachani
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Ian R. Monk
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Timothy P. Stinear
- grid.1008.90000 0001 2179 088XCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
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41
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Niha MA, Draper AD, Viegas ODS, de Araujo RM, Joao JC, da Silva E, Barreto I, Sarmento N, Oakley T, Machado FDN, Fancourt NS, Marr I, Dos Santos Fernandes LN, Martins N, Arkell P, Tilman AJ, Dingle B, Freitas CC, Bhowmick PS, Sheridan S, Howden BP, Yan J, Francis JR, Martins N. The epidemiology of the COVID-19 pandemic in the small, low-resource country of Timor-Leste, January 2020 - June 2022. Commun Dis Intell (2018) 2023; 47. [PMID: 36654501 DOI: 10.33321/cdi.2023.47.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract Timor-Leste, a small, mountainous half-island nation which shares a land border with Indonesia and which is 550 km from Australia, has a population of 1.3 million and achieved independence for the second time in 2002. It is one of the poorest nations in Asia. In response to the global coronavirus disease 2019 (COVID-19) pandemic, the Timor-Leste Ministry of Health undertook surveillance and contact tracing activities on all notified COVID-19 cases. Between 1 January 2020 and 30 June 2022, there were 22,957 cases of COVID-19 notified which occurred in three waves, the first which was delayed until April 2021 (community transmission of B.1.466.2 variant following major flooding), followed by waves in August 2021 (B.1.617.2 Delta variant transmission) and February 2022 (B.1.1.529 Omicron variant transmission). There were 753 people hospitalised due to COVID-19 and 133 deaths. Of the 133 deaths, 122 (92%) were considered not fully vaccinated (< 2 COVID-19 vaccines) and none had received boosters. Timor-Leste implemented measures to control COVID-19, including: rapid closure of international borders; isolation of cases; quarantining of international arrivals and close contacts; restrictions on internal travel; social and physical distancing; and, finally, a country-wide vaccination program. The health system's capacity was never exceeded.
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Affiliation(s)
- Maria Av Niha
- Ministry of Health, Caicoli, Timor-Leste.,2. World Health Organization, Timor-Leste Office, Caicoli, Timor-Leste
| | - Anthony Dk Draper
- Centre for Disease Control, Public Health Unit, Top End Health Service, Northern Territory Government Department of Health, Darwin, Northern Territory, Australia.,Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.,National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
| | | | - Rui M de Araujo
- Centro Integrado de Gestão de Crise, Timor-Leste Government, Dili, Timor-Leste
| | | | | | - Ismail Barreto
- World Health Organization, Timor-Leste Office, Caicoli, Timor-Leste
| | - Nevio Sarmento
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Tessa Oakley
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Nicholas Ss Fancourt
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Ian Marr
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | | | - Paul Arkell
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Benjamin Dingle
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | | | - Sarah Sheridan
- National Centre for Immunisation Research and Surveillance, The Children's Hospital at Westmead, Westmead, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, University of Melbourne, Victoria, Australia
| | - Jennifer Yan
- Ministry of Health, Caicoli, Timor-Leste.,Paediatric Department, Royal Darwin Hospital, Northern Territory Department of Health, Darwin, Australia
| | - Joshua R Francis
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.,Paediatric Department, Royal Darwin Hospital, Northern Territory Department of Health, Darwin, Australia
| | - Nelson Martins
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
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42
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Porter AF, Purcell DFJ, Howden BP, Duchene S. Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink. Virus Evol 2023; 9:vead002. [PMID: 36751428 PMCID: PMC9896948 DOI: 10.1093/ve/vead002] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/11/2022] [Accepted: 01/08/2023] [Indexed: 01/12/2023] Open
Abstract
To investigate genetic signatures of adaptation to the mink host, we characterised the evolutionary rate heterogeneity in mink-associated severe acute respiratory syndrome coronaviruses (SARS-CoV-2). In 2020, the first detected anthropozoonotic spillover event of SARS-CoV-2 occurred in mink farms throughout Europe and North America. Both spill-back of mink-associated lineages into the human population and the spread into the surrounding wildlife were reported, highlighting the potential formation of a zoonotic reservoir. Our findings suggest that the evolutionary rate of SARS-CoV-2 underwent an episodic increase upon introduction into the mink host before returning to the normal range observed in humans. Furthermore, SARS-CoV-2 lineages could have circulated in the mink population for a month before detection, and during this period, evolutionary rate estimates were between 3 × 10-3 and 1.05 × 10-2 (95 per cent HPD, with a mean rate of 6.59 × 10-3) a four- to thirteen-fold increase compared to that in humans. As there is evidence for unique mutational patterns within mink-associated lineages, we explored the emergence of four mink-specific Spike protein amino acid substitutions Y453F, S1147L, F486L, and Q314K. We found that mutation Y453F emerged early in multiple mink outbreaks and that mutations F486L and Q314K may co-occur. We suggest that SARS-CoV-2 undergoes a brief, but considerable, increase in evolutionary rate in response to greater selective pressures during species jumps, which may lead to the occurrence of mink-specific mutations. These findings emphasise the necessity of ongoing surveillance of zoonotic SARS-CoV-2 infections in the future.
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Affiliation(s)
| | | | | | - Sebastian Duchene
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC 3010, Australia
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43
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Sherry NL, Horan KA, Ballard SA, Gonҫalves da Silva A, Gorrie CL, Schultz MB, Stevens K, Valcanis M, Sait ML, Stinear TP, Howden BP, Seemann T. An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance. Nat Commun 2023; 14:60. [PMID: 36599823 DOI: 10.1038/s41467-022-35713-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
Realising the promise of genomics to revolutionise identification and surveillance of antimicrobial resistance (AMR) has been a long-standing challenge in clinical and public health microbiology. Here, we report the creation and validation of abritAMR, an ISO-certified bioinformatics platform for genomics-based bacterial AMR gene detection. The abritAMR platform utilises NCBI's AMRFinderPlus, as well as additional features that classify AMR determinants into antibiotic classes and provide customised reports. We validate abritAMR by comparing with PCR or reference genomes, representing 1500 different bacteria and 415 resistance alleles. In these analyses, abritAMR displays 99.9% accuracy, 97.9% sensitivity and 100% specificity. We also compared genomic predictions of phenotype for 864 Salmonella spp. against agar dilution results, showing 98.9% accuracy. The implementation of abritAMR in our institution has resulted in streamlined bioinformatics and reporting pathways, and has been readily updated and re-verified. The abritAMR tool and validation datasets are publicly available to assist laboratories everywhere harness the power of AMR genomics in professional practice.
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Affiliation(s)
- Norelle L Sherry
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia.,Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Kristy A Horan
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Anders Gonҫalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Claire L Gorrie
- Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Mark B Schultz
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Michelle L Sait
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia. .,Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia. .,Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia.
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia.,Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
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44
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Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. Nat Commun 2022; 13:7003. [PMID: 36385137 PMCID: PMC9667854 DOI: 10.1038/s41467-022-33713-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.
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Affiliation(s)
- Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Instituto Todos pela Saúde, São Paulo, SP, Brazil.
| | | | - Gytis Dudas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gabriel W Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Lucy E Matkin
- Department of Biology, University of Oxford, Oxford, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Neta S Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Fernando R Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, RS, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S D Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Ben Branda
- GISAID Global Data Science Initiative, Munich, Germany
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C Sabino
- Instituto Todos pela Saúde, São Paulo, SP, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Royal Veterinary College, Hawkshead, UK
| | | | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Marc A Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, UK.
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
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45
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Dale K, Globan M, Horan K, Sherry N, Ballard S, Tay EL, Bittmann S, Meagher N, Price DJ, Howden BP, Williamson DA, Denholm J. Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020. Lancet Reg Health West Pac 2022; 28:100556. [PMID: 36034164 PMCID: PMC9405109 DOI: 10.1016/j.lanwpc.2022.100556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Whole genome sequencing (WGS) is increasingly used by tuberculosis (TB) programs to monitor Mycobacterium tuberculosis (Mtb) transmission. We aimed to characterise the molecular epidemiology of TB and Mtb transmission in the low-incidence setting of Victoria, Australia, and assess the utility of WGS. METHODS WGS was performed on all first Mtb isolates from TB cases from 2017 to 2020. Potential clusters (≤12 single nucleotide polymorphisms [SNPs]) were investigated for epidemiological links. Transmission events in highly-related (≤5 SNPs) clusters were classified as likely or possible, based on the presence or absence of an epidemiological link, respectively. Case characteristics and transmission settings (as defined by case relationship) were summarised. Poisson regression was used to examine associations with secondary case number. FINDINGS Of 1844 TB cases, 1276 (69.2%) had sequenced isolates, with 182 (14.2%) in 54 highly-related clusters, 2-40 cases in size. Following investigation, 140 cases (11.0% of sequenced) were classified as resulting from likely/possible local-transmission, including 82 (6.4%) for which transmission was likely. Common identified transmission settings were social/religious (26.4%), household (22.9%) and family living in different households (7.1%), but many were uncertain (41.4%). While household transmission featured in many clusters (n = 24), clusters were generally smaller (median = 3 cases) than the fewer that included transmission in social/religious settings (n = 12, median = 7.5 cases). Sputum-smear-positivity was associated with higher secondary case numbers. INTERPRETATION WGS results suggest Mtb transmission commonly occurs outside the household in our low-incidence setting. Further work is required to optimise the use of WGS in public health management of TB. FUNDING The Victorian Tuberculosis Program receives block funding for activities including case management and contact tracing from the Victorian Department of Health. No specific funding for this report was received by manuscript authors or the Victorian Tuberculosis Program, and the funders had no role in the study design, data collection, data analysis, interpretation or report writing.
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Affiliation(s)
- Katie Dale
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Maria Globan
- Victorian Infectious Diseases Reference Laboratory (VIDRL), at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Norelle Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ee Laine Tay
- Communicable Disease Epidemiology and Surveillance, Health Protection Branch, Public Health Division, Department of Health, Victoria, Australia
| | - Simone Bittmann
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Niamh Meagher
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - David J. Price
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Deborah A. Williamson
- Victorian Infectious Diseases Reference Laboratory (VIDRL), at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Justin Denholm
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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46
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Sikorski MJ, Ma J, Hazen TH, Desai SN, Tupua S, Nimarota-Brown S, Sialeipata M, Rambocus S, Ballard SA, Valcanis M, Thomsen RE, Robins-Browne RM, Howden BP, Naseri TK, Levine MM, Rasko DA. Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa. PLoS Negl Trop Dis 2022; 16:e0010348. [PMID: 36251704 PMCID: PMC9612817 DOI: 10.1371/journal.pntd.0010348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/27/2022] [Accepted: 09/15/2022] [Indexed: 11/05/2022] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is either widely distributed or proximally transmitted via fecally-contaminated food or water to cause typhoid fever. In Samoa, where endemic typhoid fever has persisted over decades despite water quality and sanitation improvements, the local patterns of S. Typhi circulation remain unclear. From April 2018-June 2020, epidemiologic data and GPS coordinates were collected during household investigations of 260 acute cases of typhoid fever, and 27 asymptomatic shedders of S. Typhi were detected among household contacts. Spatial and temporal distributions of cases were examined using Average Nearest Neighbor and space-time hotspot analyses. In rural regions, infections occurred in sporadic, focal clusters contrasting with persistent, less clustered cases in the Apia Urban Area. Restrictions to population movement during nationwide lockdowns in 2019-2020 were associated with marked reductions of cases. Phylogenetic analyses of isolates with whole genome sequences (n = 186) revealed one dominant genotype 3.5.4 (n = 181/186) that contains three Samoa-exclusive sub-lineages: 3.5.4.1, 3.5.4.2, and 3.5.4.3. Variables of patient sex, age, and geographic region were examined by phylogenetic groupings, and significant differences (p<0.05) associated genetically-similar isolates in urban areas with working ages (20-49 year olds), and in rural areas with age groups typically at home (<5, 50+). Isolates from asymptomatic shedders were among all three sub-lineages. Whole genome sequencing provided evidence of bacterial genetic similarity, which corroborated 10/12 putative epidemiologic linkages among cases and asymptomatic shedders, as well as 3/3 repeat positives (presumed relapses), with a median of one single nucleotide polymorphism difference. These findings highlight various patterns of typhoid transmission in Samoa that differ between urban and rural regions as well as genomic subtypes. Asymptomatic shedders, detectable only through household investigations, are likely an important reservoir and mobile agent of infection. This study advances a "Samoan S. Typhi framework" that supports current and future typhoid surveillance and control efforts in Samoa.
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Affiliation(s)
- Michael J. Sikorski
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jianguo Ma
- Department of Geographical Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Tracy H. Hazen
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Sachin N. Desai
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Siaosi Tupua
- Ministry of Health, Government of Samoa, Apia, Samoa
| | | | | | - Savitra Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Roy M. Robins-Browne
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia,Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Myron M. Levine
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David A. Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,* E-mail:
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47
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Porter AF, Sherry N, Andersson P, Johnson SA, Duchene S, Howden BP. New rules for genomics-informed COVID-19 responses-Lessons learned from the first waves of the Omicron variant in Australia. PLoS Genet 2022; 18:e1010415. [PMID: 36227810 PMCID: PMC9560517 DOI: 10.1371/journal.pgen.1010415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Ashleigh F. Porter
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Norelle Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sandra A. Johnson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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48
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Mediati DG, Wong JL, Gao W, McKellar S, Pang CNI, Wu S, Wu W, Sy B, Monk IR, Biazik JM, Wilkins MR, Howden BP, Stinear TP, Granneman S, Tree JJ. Publisher Correction: RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3'UTR required for intermediate vancomycin resistance. Nat Commun 2022; 13:5683. [PMID: 36167839 PMCID: PMC9515158 DOI: 10.1038/s41467-022-33167-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Julia L Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Wei Gao
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Stuart McKellar
- Centre for Systems and Synthetic Biology, University of Edinburgh, Edinburgh, UK
| | - Chi Nam Ignatius Pang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sylvania Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Winton Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Brandon Sy
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Joanna M Biazik
- Electron Microscopy Unit, University of New South Wales, Kensington, NSW, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Sander Granneman
- Centre for Systems and Synthetic Biology, University of Edinburgh, Edinburgh, UK
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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49
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Watt AE, Sherry NL, Andersson P, Lane CR, Johnson S, Wilmot M, Horan K, Sait M, Ballard SA, Crachi C, Beck DJ, Marshall C, Kainer MA, Stuart R, McGrath C, Kwong JC, Bass P, Kelley PG, Crowe A, Guy S, Macesic N, Smith K, Williamson DA, Seemann T, Howden BP. State-wide genomic epidemiology investigations of COVID-19 in healthcare workers in 2020 Victoria, Australia: Qualitative thematic analysis to provide insights for future pandemic preparedness. The Lancet Regional Health - Western Pacific 2022; 25:100487. [PMID: 35677391 PMCID: PMC9168175 DOI: 10.1016/j.lanwpc.2022.100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background COVID-19 has affected many healthcare workers (HCWs) globally. We performed state-wide SARS-CoV-2 genomic epidemiological investigations to identify HCW transmission dynamics and provide recommendations to optimise healthcare system preparedness for future outbreaks. Methods Genome sequencing was attempted on all COVID-19 cases in Victoria, Australia. We combined genomic and epidemiologic data to investigate the source of HCW infections across multiple healthcare facilities (HCFs) in the state. Phylogenetic analysis and fine-scale hierarchical clustering were performed for the entire dataset including community and healthcare cases. Facilities provided standardised epidemiological data and putative transmission links. Findings Between March-October 2020, approximately 1,240 HCW COVID-19 infection cases were identified; 765 are included here, requested for hospital investigations. Genomic sequencing was successful for 612 (80%) cases. Thirty-six investigations were undertaken across 12 HCFs. Genomic analysis revealed that multiple introductions of COVID-19 into facilities (31/36) were more common than single introductions (5/36). Major contributors to HCW acquisitions included mobility of staff and patients between wards and facilities, and characteristics and behaviours of patients that generated numerous secondary infections. Key limitations at the HCF level were identified. Interpretation Genomic epidemiological analyses enhanced understanding of HCW infections, revealing unsuspected clusters and transmission networks. Combined analysis of all HCWs and patients in a HCF should be conducted, supported by high rates of sequencing coverage for all cases in the population. Established systems for integrated genomic epidemiological investigations in healthcare settings will improve HCW safety in future pandemics. Funding The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.
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Affiliation(s)
- Anne E. Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Norelle L. Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Courtney R. Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Sandra Johnson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Mathilda Wilmot
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Christina Crachi
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Dianne J. Beck
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Caroline Marshall
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Infectious Diseases, The University of Melbourne at the Doherty Institute, Melbourne, Victoria, Australia
| | - Marion A. Kainer
- Department of Infectious Diseases, Western Health, Footscray, Victoria, Australia
| | - Rhonda Stuart
- Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia
- South East Public Health Unit, Monash Health, Clayton, Victoria, Australia
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Christian McGrath
- Department of Infectious Diseases, The Northern Hospital, Epping, Victoria, Australia
| | - Jason C. Kwong
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Pauline Bass
- Infection Prevention and Healthcare Epidemiology Department, Alfred Health, Prahran, Victoria, Australia
| | - Peter G. Kelley
- Department of Infectious Diseases, Peninsula Health, Frankston, Victoria, Australia
| | - Amy Crowe
- Department of Microbiology, St Vincent's Hospital Melbourne, Fitzroy, Victoria, Australia
| | - Stephen Guy
- Department of Infectious Diseases, Eastern Health, Box Hill, Victoria, Australia
- Eastern Health Clinical School, Monash University, Victoria, Australia
| | - Nenad Macesic
- Department of Infectious Diseases, Epworth Hospital, Richmond, Victoria, Australia
| | - Karen Smith
- Centre for Research and Evaluation, Ambulance Victoria, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Victoria, Australia
| | - Deborah A. Williamson
- Department of Infectious Diseases, The University of Melbourne at the Doherty Institute, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Corresponding author at: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, 792 Elizabeth St, Melbourne, Victoria 3000, Australia.
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Dhital S, Deo P, Bharathwaj M, Horan K, Nickson J, Azad M, Stuart I, Chow SH, Gunasinghe SD, Bamert R, Li J, Lithgow T, Howden BP, Naderer T. Neisseria gonorrhoeae-derived outer membrane vesicles package β-lactamases to promote antibiotic resistance. Microlife 2022; 3:uqac013. [PMID: 37223348 PMCID: PMC10117772 DOI: 10.1093/femsml/uqac013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 05/25/2023]
Abstract
Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhoea. The treatment of gonorrhoea is becoming increasingly challenging, as N. gonorrhoeae has developed resistance to antimicrobial agents routinely used in the clinic. Resistance to penicillin is wide-spread partly due to the acquisition of β-lactamase genes. How N. gonorrhoeae survives an initial exposure to β-lactams before acquiring resistance genes remains to be understood. Here, using a panel of clinical isolates of N. gonorrhoeae we show that the β-lactamase enzyme is packaged into outer membrane vesicles (OMVs) by strains expressing blaTEM-1B or blaTEM-106, which protects otherwise susceptible clinical isolates from the β-lactam drug amoxycillin. We characterized the phenotypes of these clinical isolates of N. gonorrhoeae and the time courses over which the cross-protection of the strains is effective. Imaging and biochemical assays suggest that OMVs promote the transfer of proteins and lipids between bacteria. Thus, N. gonorrhoeae strains secret antibiotic degrading enzymes via OMVs enabling survival of otherwise susceptible bacteria.
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Affiliation(s)
| | | | - Manasa Bharathwaj
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Joshua Nickson
- Infection Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Mohammad Azad
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Isabella Stuart
- Infection Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Seong H Chow
- Infection Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Sachith D Gunasinghe
- Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
- European Molecular Biology Laboratory (EMBL) Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Rebecca Bamert
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Jian Li
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Thomas Naderer
- Corresponding author: Monash Biomedicine Discovery Institute, Dept of Biochemistry and Molecular Biology, Monash University, 19 Innovation Walk, Clayton, Victoria, 3800, Australia; E-mail:
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