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McGuire E, Collin SM, Brown CS, Saito M. Community-Acquired Staphylococcus aureus Bacteremia Among People Who Inject Drugs: A National Cohort Study in England, 2017-2020. Clin Infect Dis 2024; 78:1443-1450. [PMID: 38315893 PMCID: PMC11175704 DOI: 10.1093/cid/ciae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/03/2024] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND People who inject drugs (PWID) are at increased risk of community-acquired Staphylococcus aureus bacteremia (CA-SAB), but little is known about clinical outcomes of CA-SAB in PWID compared with the wider population of patients with CA-SAB. METHODS Three national datasets were linked to provide clinical and mortality data on patients hospitalized with CA-SAB in England between 1 January 2017 and 31 December 2020. PWID were identified using the International Classification of Diseases, Tenth Revision code for "mental health and behavioral disorder due to opioid use" (F11). Multivariable logistic regression was used to estimate adjusted odds ratios (aORs) for associations of PWID with 30-day all-cause mortality and 90-day hospital readmission. RESULTS In 10 045 cases of CA-SAB, 1612 (16.0%) were PWID. Overall, 796 (7.9%) patients died within 30 days of CA-SAB admission and 1189 (11.8%) patients were readmitted to hospital within 90 days of CA-SAB. In those without infective endocarditis, there was strong evidence of lower odds of mortality among PWID compared with non-PWID (aOR, 0.47 [95% confidence interval {CI}: .33-.68]; P < .001), whereas there was no association in CA-SAB case fatality with endocarditis (aOR, 1.40 [95% CI: .87-2.25]; P = .163). PWID were less likely to be readmitted within 90 days of CA-SAB (aOR, 0.79 [95% CI: .65-.95]; P = .011). CONCLUSIONS In this large cohort study of patients with CA-SAB in England, PWID had lower odds of death in the absence of endocarditis and lower odds of readmission within 90 days compared to non-PWID patients. This study highlights the overrepresentation of PWID among patients with CA-SAB nationally.
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Affiliation(s)
- Emma McGuire
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU), and Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
- Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Simon M Collin
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Colin S Brown
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU), and Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
- National Institute for Health and Care Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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2
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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] [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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3
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Legg A, Roberts JA, Roberts MA, Cass A, Davies J, Tong SYC, Davis JS. Avoiding misclassification of acute kidney injury: Timing is everything. Nephrology (Carlton) 2024; 29:100-104. [PMID: 37820650 PMCID: PMC10952645 DOI: 10.1111/nep.14246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
Accurate detection of acute kidney injury (AKI) in clinical trials is important. Using a 'baseline' creatinine from trial enrolment may not be ideal for understanding a participant's true baseline kidney function. We aimed to determine if a 'pre-trial baseline creatinine' resulted in comparable creatinine concentrations to a 'trial baseline creatinine', and how the timing of baseline creatinine affected the incidence of AKI in the Combination Antibiotic therapy for MEthicillin Resistant Staphylococcus aureus (CAMERA2) randomised trial. Study sites retrospectively collected a pre-trial baseline creatinine from up to 1 year before CAMERA2 trial enrolment ideally when the patient was medically stable. Baseline creatinine from CAMERA2 (the 'trial baseline creatinine'), was the highest creatinine measurement in the 24 h preceding trial randomisation. We used Wilcoxon sign rank test to compare pre-trial and trial baseline creatinine concentrations. We included 217 patients. The median pre-trial baseline creatinine was significantly lower than the median trial baseline creatinine (82 μmol/L [IQR 65-104 μmol/L] versus 86 μmol/L [IQR 66-152 μmol/L] p = <0.001). Using pre-trial baseline creatinine, 48 of 217 patients (22%) met criteria for an AKI at CAMERA2 enrolment and only 5 of these patients met criteria for an AKI using the CAMERA2 study protocol (using baseline creatinine from trial entry). Using a baseline creatinine from the time of trial enrolment failed to detect many patients with AKI. Trial protocols should consider the optimal timing of baseline creatinine and the limitations of using a baseline creatinine during an acute illness.
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Affiliation(s)
- Amy Legg
- Menzies School of Health ResearchCharles Darwin UniversityDarwinNorthern TerritoryAustralia
- Herston Infectious Diseases Institute, Metro North HealthBrisbaneQueenslandAustralia
| | - Jason A. Roberts
- Herston Infectious Diseases Institute, Metro North HealthBrisbaneQueenslandAustralia
- Faculty of MedicineUniversity of Queensland Centre for Clinical Research (UQCCR)BrisbaneQueenslandAustralia
- Departments of Intensive Care Medicine and PharmacyRoyal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
- Nîmes University Hospital, Division of Anaesthesiology Critical Care Emergency and Pain MedicineUniversity of MontpellierNîmesFrance
| | - Matthew A. Roberts
- Eastern Health Clinical SchoolMonash UniversityBox HillVictoriaAustralia
| | - Alan Cass
- Menzies School of Health ResearchCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Jane Davies
- Menzies School of Health ResearchCharles Darwin UniversityDarwinNorthern TerritoryAustralia
- Department of Infectious DiseasesRoyal Darwin HospitalDarwinNorthern TerritoryAustralia
| | - Steven Y. C. Tong
- Victorian Infectious Diseases Service, The Royal Melbourne HospitalPeter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Joshua S. Davis
- Menzies School of Health ResearchCharles Darwin UniversityDarwinNorthern TerritoryAustralia
- School of Medicine and Public HealthThe University of NewcastleNewcastleNew South WalesAustralia
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4
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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] [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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5
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Wu B, Peng M, Tong Y, Wang X, Ding Y, Cheng X. Distribution of bacteria and risk factors in patients with multidrug-resistant pneumonia in a single center rehabilitation ward. Medicine (Baltimore) 2023; 102:e35023. [PMID: 37682183 PMCID: PMC10489429 DOI: 10.1097/md.0000000000035023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023] Open
Abstract
Stroke patients may have dysphagia and frequent aspiration increasing exposure to antibiotics and the chance of multidrug-resistant (MDR) bacteria infection. This study investigated clinical risk factors and related antibiotic use of MDR bacteria infection in stroke patients in the rehabilitation ward, hoping that it can help prevent and reduce the condition of MDR bacteria. A retrospective cohort study was conducted using the database of stroke patients with pneumonia admitted to the rehabilitation ward from January 1, 2020, to June 30, 2022. The selected stroke patients were divided into the MDR and non-MDR groups. Analyze the infection bacteria of the 2 groups. Forward logistic regression was applied to identify possible independent MDR bacteria infection risk factors. A total of 323 patients were included. The top 3 common MDR pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii. Almost all Pseudomonas aeruginosa and Acinetobacter baumannii are resistant to ertapenem. National Institute of Health stroke scale at admission was associated with MDR bacteria infection pneumonia (OR [odds ratio] = 1.078, 95%CI [1.017, 1.142]). Long-term tracheotomy (OR = 2.695, 95%CI [1.232, 5.897]), hypoalbuminemia (OR = 473, 95%CI [1.318, 4.642]), and bilateral cerebral hemisphere stroke (OR = 4.021, 95%CI [2.009, 8.048]) were significant clinical risk factors of MDR pneumonia after stroke. The detection rate of MDR bacteria has increased. Understanding the distribution and drug resistance of MDR bacteria in stroke patients with pneumonia in the neurological rehabilitation ward and the related susceptibility of MDR bacteria infection is necessary. This way, the treatment plan can be adjusted more timely, avoiding the abuse of antibiotics.
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Affiliation(s)
- Bangqi Wu
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Maohan Peng
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Department of Respiratory and Critical Care Medicine, Pengzhou People’s Hospital, Pengzhou, China
| | - Yuanyuan Tong
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xuhui Wang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yi Ding
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xinyue Cheng
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
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6
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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] [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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7
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Buis D, van Werkhoven CH, van Agtmael MA, Bax HI, Berrevoets M, de Boer M, Bonten M, Bosmans JE, Branger J, Douiyeb S, Gelinck L, Jong E, Lammers A, Van der Meer J, Oosterheert JJ, Sieswerda E, Soetekouw R, Stalenhoef JE, Van der Vaart TW, Bij de Vaate EA, Verkaik NJ, Van Vonderen M, De Vries PJ, Prins JM, Sigaloff K. Safe shortening of antibiotic treatment duration for complicated Staphylococcus aureus bacteraemia (SAFE trial): protocol for a randomised, controlled, open-label, non-inferiority trial comparing 4 and 6 weeks of antibiotic treatment. BMJ Open 2023; 13:e068295. [PMID: 37085305 PMCID: PMC10124302 DOI: 10.1136/bmjopen-2022-068295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
INTRODUCTION A major knowledge gap in the treatment of complicated Staphylococcus aureus bacteraemia (SAB) is the optimal duration of antibiotic therapy. Safe shortening of antibiotic therapy has the potential to reduce adverse drug events, length of hospital stay and costs. The objective of the SAFE trial is to evaluate whether 4 weeks of antibiotic therapy is non-inferior to 6 weeks in patients with complicated SAB. METHODS AND ANALYSIS The SAFE-trial is a multicentre, non-inferiority, open-label, parallel group, randomised controlled trial evaluating 4 versus 6 weeks of antibiotic therapy for complicated SAB. The study is performed in 15 university hospitals and general hospitals in the Netherlands. Eligible patients are adults with methicillin-susceptible SAB with evidence of deep-seated or metastatic infection and/or predictors of complicated SAB. Only patients with a satisfactory clinical response to initial antibiotic treatment are included. Patients with infected prosthetic material or an undrained abscess of 5 cm or more at day 14 of adequate antibiotic treatment are excluded. Primary outcome is success of therapy after 180 days, a combined endpoint of survival without evidence of microbiologically confirmed disease relapse. Assuming a primary endpoint occurrence of 90% in the 6 weeks group, a non-inferiority margin of 7.5% is used. Enrolment of 396 patients in total is required to demonstrate non-inferiority of shorter antibiotic therapy with a power of 80%. Currently, 152 patients are enrolled in the study. ETHICS AND DISSEMINATION This is the first randomised controlled trial evaluating duration of antibiotic therapy for complicated SAB. Non-inferiority of 4 weeks of treatment would allow shortening of treatment duration in selected patients with complicated SAB. This study is approved by the Medical Ethics Committee VUmc (Amsterdam, the Netherlands) and registered under NL8347 (the Netherlands Trial Register). Results of the study will be published in a peer-reviewed journal. TRIAL REGISTRATION NUMBER NL8347 (the Netherlands Trial Register).
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Affiliation(s)
- Dtp Buis
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam Institute for Infection and Immunity, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - C H van Werkhoven
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - M A van Agtmael
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam Institute for Infection and Immunity, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - H I Bax
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - M Berrevoets
- Department of Internal Medicine, Elisabeth twee-steden Hospital, Tilburg, The Netherlands
| | - Mgj de Boer
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Mjm Bonten
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - J E Bosmans
- Department of Health Sciences, Faculty of Science, Amsterdam Public Health research institute, VU University Amsterdam, Amsterdam, The Netherlands
| | - J Branger
- Department of Internal Medicine, Flevohospital, Almere, The Netherlands
| | - S Douiyeb
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam Institute for Infection and Immunity, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Lbs Gelinck
- Department of Internal Medicine, Haaglanden Medisch Centrum, Den Haag, The Netherlands
| | - E Jong
- Department of Internal Medicine, Meander Medisch Centrum, Amersfoort, The Netherlands
| | - Ajj Lammers
- Department of Internal medicine & Infectious Diseases, Isala Zwolle, Zwolle, The Netherlands
| | - Jtm Van der Meer
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - J J Oosterheert
- Department of Internal Medicine, Infectious Diseases, UMC Utrecht, Utrecht, The Netherlands
| | - E Sieswerda
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - R Soetekouw
- Department of Internal Medicine, Spaarne Gasthuis, Haarlem/Hoofddorp, The Netherlands
| | - J E Stalenhoef
- Department of Internal Medicine, OLVG, Amsterdam, The Netherlands
| | - T W Van der Vaart
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - E A Bij de Vaate
- Department of Internal Medicine, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - N J Verkaik
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | | | - P J De Vries
- Department of Internal Medicine, Tergooi Hospital, Hilversum, The Netherlands
| | - J M Prins
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam Institute for Infection and Immunity, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Kce Sigaloff
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam Institute for Infection and Immunity, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
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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] [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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9
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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] [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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10
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Westgeest AC, Schippers EF, Delfos NM, Visser LG, de Fijter JW, de Boer MGJ, Lambregts MMC. Acute kidney injury in Staphylococcus aureus bacteremia. Eur J Clin Microbiol Infect Dis 2022; 41:431-437. [PMID: 34993670 DOI: 10.1007/s10096-021-04391-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/30/2021] [Indexed: 11/30/2022]
Abstract
Acute kidney injury (AKI) is a frequent complication in patients with Staphylococcus aureus bacteremia (SAB), with a significant impact on patient management and outcome. This study aimed to provide insight in the proportion of patients with SAB that develop AKI, the risk factors for developing AKI in this population, and its reversibility. In this retrospective, multicenter cohort study, adult patients with SAB were eligible for inclusion. Patient characteristics, clinical variables, and laboratory results were retrieved from the electronic patient files. Primary outcome was development of AKI, defined as 1.5 times baseline creatinine. Secondary outcomes were reversibility of AKI and risk factors for AKI. A total of 315 patients with SAB were included, of whom 115/315 (37%) developed acute kidney injury. In 68/115 (59%), the AKI was reversible. If kidney function recovered, this occurred within 7 days in 56/68 (82%) of patients. In multivariable logistic regression analyses, independent risk factors for AKI were as follows: complicated SAB, use of diuretics, and hemodynamic instability. Development of AKI was associated with 30-day mortality (OR 3.9; CI 2.2-6.9; p < 0.01). Acute kidney injury is a frequent complication in patients with Staphylococcus aureus bacteremia. Considering the irreversibility in a relevant proportion of patients, future research into the underlying pathophysiology and potential interventions is warranted.
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Affiliation(s)
- Annette C Westgeest
- Department of Infectious Diseases, Leiden University Medical Center (LUMC), C5-P, P.O. box 9600, 2300 RC, Leiden, The Netherlands. .,Department of Internal Medicine, Haga Teaching Hospital, The Hague, The Netherlands.
| | - Emile F Schippers
- Department of Infectious Diseases, Leiden University Medical Center (LUMC), C5-P, P.O. box 9600, 2300 RC, Leiden, The Netherlands.,Department of Internal Medicine, Haga Teaching Hospital, The Hague, The Netherlands
| | - Nathalie M Delfos
- Department of Internal Medicine, Alrijne Hospital, Leiderdorp, The Netherlands
| | - Leo G Visser
- Department of Infectious Diseases, Leiden University Medical Center (LUMC), C5-P, P.O. box 9600, 2300 RC, Leiden, The Netherlands
| | - Johan W de Fijter
- Department of Nephrology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Mark G J de Boer
- Department of Infectious Diseases, Leiden University Medical Center (LUMC), C5-P, P.O. box 9600, 2300 RC, Leiden, The Netherlands
| | - Merel M C Lambregts
- Department of Infectious Diseases, Leiden University Medical Center (LUMC), C5-P, P.O. box 9600, 2300 RC, Leiden, The Netherlands
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11
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Wiedermann CJ. Hypoalbuminemia as Surrogate and Culprit of Infections. Int J Mol Sci 2021; 22:4496. [PMID: 33925831 PMCID: PMC8123513 DOI: 10.3390/ijms22094496] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 02/07/2023] Open
Abstract
Hypoalbuminemia is associated with the acquisition and severity of infectious diseases, and intact innate and adaptive immune responses depend on albumin. Albumin oxidation and breakdown affect interactions with bioactive lipid mediators that play important roles in antimicrobial defense and repair. There is bio-mechanistic plausibility for a causal link between hypoalbuminemia and increased risks of primary and secondary infections. Serum albumin levels have prognostic value for complications in viral, bacterial and fungal infections, and for infectious complications of non-infective chronic conditions. Hypoalbuminemia predicts the development of healthcare-associated infections, particularly with Clostridium difficile. In coronavirus disease 2019, hypoalbuminemia correlates with viral load and degree of acute lung injury and organ dysfunction. Non-oncotic properties of albumin affect the pharmacokinetics and pharmacodynamics of antimicrobials. Low serum albumin is associated with inadequate antimicrobial treatment. Infusion of human albumin solution (HAS) supplements endogenous albumin in patients with cirrhosis of the liver and effectively supported antimicrobial therapy in randomized controlled trials (RCTs). Evidence of the beneficial effects of HAS on infections in hypoalbuminemic patients without cirrhosis is largely observational. Prospective RCTs are underway and, if hypotheses are confirmed, could lead to changes in clinical practice for the management of hypoalbuminemic patients with infections or at risk of infectious complications.
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Affiliation(s)
- Christian J. Wiedermann
- Institute of General Practice, Claudiana–College of Health Professions, 39100 Bolzano, Italy;
- Department of Public Health, Medical Decision Making and HTA, University of Health Sciences, Medical Informatics and Technology, 6060 Hall in Tyrol, Austria
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12
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Bitto NJ, Cheng L, Johnston EL, Pathirana R, Phan TK, Poon IKH, O'Brien-Simpson NM, Hill AF, Stinear TP, Kaparakis-Liaskos M. Staphylococcus aureus membrane vesicles contain immunostimulatory DNA, RNA and peptidoglycan that activate innate immune receptors and induce autophagy. J Extracell Vesicles 2021; 10:e12080. [PMID: 33815695 PMCID: PMC8015888 DOI: 10.1002/jev2.12080] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/12/2021] [Accepted: 03/04/2021] [Indexed: 12/14/2022] Open
Abstract
Gram‐positive bacteria ubiquitously produce membrane vesicles (MVs), and although they contribute to biological functions, our knowledge regarding their composition and immunogenicity remains limited. Here we examine the morphology, contents and immunostimulatory functions of MVs produced by three Staphylococcus aureus strains; a methicillin resistant clinical isolate, a methicillin sensitive clinical isolate and a laboratory‐adapted strain. We observed differences in the number and morphology of MVs produced by each strain and showed that they contain microbe‐associated molecular patterns (MAMPs) including protein, nucleic acids and peptidoglycan. Analysis of MV‐derived RNA indicated the presence of small RNA (sRNA). Furthermore, we detected variability in the amount and composition of protein, nucleic acid and peptidoglycan cargo carried by MVs from each S. aureus strain. S. aureus MVs activated Toll‐like receptor (TLR) 2, 7, 8, 9 and nucleotide‐binding oligomerization domain containing protein 2 (NOD2) signalling and promoted cytokine and chemokine release by epithelial cells, thus identifying that MV‐associated MAMPs including DNA, RNA and peptidoglycan are detected by pattern recognition receptors (PRRs). Moreover, S. aureus MVs induced the formation of and colocalized with autophagosomes in epithelial cells, while inhibition of lysosomal acidification using bafilomycin A1 resulted in accumulation of autophagosomal puncta that colocalized with MVs, revealing the ability of the host to degrade MVs via autophagy. This study reveals the ability of DNA, RNA and peptidoglycan associated with MVs to activate PRRs in host epithelial cells, and their intracellular degradation via autophagy. These findings advance our understanding of the immunostimulatory roles of Gram‐positive bacterial MVs in mediating pathogenesis, and their intracellular fate within the host.
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Affiliation(s)
- Natalie J Bitto
- Department of Physiology Anatomy and Microbiology La Trobe University Melbourne Victoria 3086 Australia.,Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia
| | - Lesley Cheng
- Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Melbourne Victoria 3086 Australia
| | - Ella L Johnston
- Department of Physiology Anatomy and Microbiology La Trobe University Melbourne Victoria 3086 Australia.,Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia
| | - Rishi Pathirana
- Department of Physiology Anatomy and Microbiology La Trobe University Melbourne Victoria 3086 Australia.,Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia
| | - Thanh Kha Phan
- Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Melbourne Victoria 3086 Australia
| | - Ivan K H Poon
- Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Melbourne Victoria 3086 Australia
| | - Neil M O'Brien-Simpson
- Centre for Oral Health Research Melbourne Dental School Bio21 Institute The University of Melbourne Parkville Victoria 3010 Australia
| | - Andrew F Hill
- Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Melbourne Victoria 3086 Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology Doherty Institute University of Melbourne Parkville Victoria 3010 Australia
| | - Maria Kaparakis-Liaskos
- Department of Physiology Anatomy and Microbiology La Trobe University Melbourne Victoria 3086 Australia.,Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia
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13
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Botheras CL, Bowe SJ, Cowan R, Athan E. C-reactive protein predicts complications in community-associated S. aureus bacteraemia: a cohort study. BMC Infect Dis 2021; 21:312. [PMID: 33794783 PMCID: PMC8015062 DOI: 10.1186/s12879-021-05962-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/07/2021] [Indexed: 12/12/2022] Open
Abstract
Background Staphylococcus aureus (S. aureus) bacteraemia is increasingly acquired from community settings and is associated with a mortality rate of up to 40% following complications. Identifying risk factors for complicated S. aureus bacteraemia would aid clinicians in targeting patients that benefit from expedited investigations and escalated care. Methods In this prospective observational cohort study, we aimed to identify risk factors associated with a complicated infection in community-onset S. aureus bacteraemia. Potential risk factors were collected from electronic medical records and included: - patient demographics, symptomology, portal of entry, and laboratory results. Results We identified several potential risk factors using univariate analysis. In a multiple logistic regression model, age, haemodialysis, and entry point from a diabetic foot ulcer were all significantly protective against complications. Conversely, an unknown entry point of infection, an entry point from an indwelling medical device, and a C-reactive protein concentration of over 161 mg/L on the day of admission were all significantly associated with complications. Conclusions We conclude that several factors are associated with complications including already conducted laboratory investigations and portal of entry of infection. These factors could aid the triage of at-risk patients for complications of S. aureus bacteraemia.
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Affiliation(s)
- Carly L Botheras
- School of Medicine, IMPACT, the Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia. .,School of Medicine, Faculty of Health, Deakin University, Geelong, Australia.
| | - Steven J Bowe
- Deakin Biostatistics Unit Faculty of Health, Deakin University, Geelong, Australia
| | - Raquel Cowan
- Department of Infectious Diseases, Barwon Health, Geelong, Australia
| | - Eugene Athan
- School of Medicine, IMPACT, the Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia.,School of Medicine, Faculty of Health, Deakin University, Geelong, Australia.,Department of Infectious Diseases, Barwon Health, Geelong, Australia
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14
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Copaescu A, James F, Mouhtouris E, Vogrin S, Smibert OC, Gordon CL, Drewett G, Holmes NE, Trubiano JA. The Role of Immunological and Clinical Biomarkers to Predict Clinical COVID-19 Severity and Response to Therapy-A Prospective Longitudinal Study. Front Immunol 2021; 12:646095. [PMID: 33815405 PMCID: PMC8009986 DOI: 10.3389/fimmu.2021.646095] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
Background The association of pro-inflammatory markers such as interleukin-6 (IL-6) and other biomarkers with severe coronavirus disease 2019 (COVID-19) is of increasing interest, however their kinetics, response to current COVID-related treatments, association with disease severity and comparison with other disease states associated with potential cytokine storm (CS) such as Staphylococcus aureus bacteraemia (SAB) are ill-defined. Methods A cohort of 55 hospitalized SARS-CoV-2 positive patients was prospectively recruited - blood sampling was performed at baseline, post-treatment and hospital discharge. Serum IL-6, C-reactive protein (CRP) and other laboratory investigations were compared between treatment groups and across timepoints. Acute serum IL-6 and CRP levels were then compared to those with suspected COVID-19 (SCOVID) and age and sex matched patients with SAB and patients hospitalized for any non-infectious condition (NIC). Results IL-6 was elevated at admission in the SARS-CoV-2 cohort but at lower levels compared to matched SAB patients. Median (IQR) IL-6 at admission was 73.89 pg/mL (30.9, 126.39) in SARS-CoV-2 compared to 92.76 pg/mL (21.75, 246.55) in SAB (p=0.017); 12.50 pg/mL (3.06, 35.77) in patients with NIC; and 95.51 pg/mL (52.17, 756.67) in SCOVID. Median IL-6 and CRP levels decreased between admission and discharge timepoints. This reduction was amplified in patients treated with remdesivir and/or dexamethasone. CRP and bedside vital signs were the strongest predictors of COVID-19 severity. Conclusions Knowledge of the kinetics of IL-6 did not offer enhanced predictive value for disease severity in COVID-19 over common investigations such as CRP and vital signs.
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Affiliation(s)
- Ana Copaescu
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia
- Clinical Immunology and Allergy, Department of Medicine, McGill University Health Center, Montréal, QC, Canada
- The Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Fiona James
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia
| | - Effie Mouhtouris
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia
| | - Sara Vogrin
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC, Australia
| | - Olivia C. Smibert
- Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, VIC, Australia
| | - Claire L. Gordon
- Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
| | - George Drewett
- Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, VIC, Australia
| | - Natasha E. Holmes
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia
- Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, VIC, Australia
- Department of Critical Care, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia
| | - Jason A. Trubiano
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia
- Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, VIC, Australia
- Department of Oncology, Sir Peter MacCallum Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- The National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Parkville, VIC, Australia
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15
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Parente CS, Sandland-Taylor LE, Akhtar W. Diagnostic challenge: an atypical presentation of infective endocarditis. BMJ Case Rep 2021; 14:e239994. [PMID: 33495170 PMCID: PMC7839874 DOI: 10.1136/bcr-2020-239994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2021] [Indexed: 01/27/2023] Open
Abstract
It is recognised that infective endocarditis is frequently a challenging diagnosis to make, as it may present with a range of non-specific symptoms. A middle-aged man was admitted with an 8-day history of profuse non-bloody diarrhoea and vomiting. He had no medical history and no identifiable risk factors for infective endocarditis, and so this in combination with the patient's atypical symptoms presented a diagnostic challenge. The patient was eventually diagnosed with a Staphylococcus aureus right-sided infective endocarditis. This case report explores the events which led to this diagnosis and demonstrates a number of unique learning points. It also highlights the importance of maintaining an open mind and being prepared to revise an initial diagnosis in the face of medical uncertainty.
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Affiliation(s)
| | | | - Waheed Akhtar
- Lincolnshire Heart Centre, United Lincolnshire Hospitals NHS Trust, Lincoln, Lincolnshire, UK
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16
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Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in Staphylococcus aureus. mBio 2020; 11:mBio.02882-20. [PMID: 33293382 PMCID: PMC7733948 DOI: 10.1128/mbio.02882-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antistaphylococcal penicillins such as oxacillin are the key antibiotics in the treatment of invasive methicillin-susceptible Staphylococcus aureus (MSSA) infections; however, mec gene-independent resistance adaptation can cause treatment failure. Despite its clinical relevance, the basis of this phenomenon remains poorly understood. Here, we investigated the genomic adaptation to oxacillin at an unprecedented scale using a large collection of 503 clinical mec-negative isolates and 30 in vitro-adapted isolates from independent oxacillin exposures. By combining comparative genomics, evolutionary convergence, and genome-wide association analysis, we found 21 genetic loci associated with low-level oxacillin resistance, underscoring the polygenic nature of this phenotype. Evidence of adaptation was particularly strong for the c-di-AMP signal transduction pathways (gdpP and dacA) and in the clpXP chaperone-protease complex. The role of mutations in gdpP in conferring low-level oxacillin resistance was confirmed by allele-swapping experiments. We found that resistance to oxacillin emerges at high frequency in vitro (median, 2.9 × 10-6; interquartile range [IQR], 1.9 × 10-6 to 3.9 × 10-6), which is consistent with a recurrent minimum inhibitory concentration (MIC) increase across the global phylogeny of clinical isolates. Nevertheless, adaptation in clinical isolates appears sporadically, with no stably adapted lineages, suggesting a high fitness cost of resistance, confirmed by growth assessment of mutants in rich media. Our data provide a broader understanding of the emergence and dynamics of oxacillin resistance adaptation in S. aureus and a framework for future surveillance of this clinically important phenomenon.IMPORTANCE The majority of Staphylococcus aureus strains causing human disease are methicillin-susceptible (MSSA) and can be treated with antistaphylococcal penicillins (such as oxacillin). While acquisition of the mec gene represents the main resistance mechanism to oxacillin, S. aureus can acquire low-level resistance through adaptive mutations in other genes. In this study, we used genomic approaches to understand the basis of S. aureus adaption to oxacillin and its dynamic at the population level. By combining a genome analysis of clinical isolates from persistent MSSA infections, in vitro selection of oxacillin resistance, and genome-wide association analysis on a large collection of isolates, we identified 21 genes linked to secondary oxacillin resistance. Adaptive mutations in these genes were easy to select when S. aureus was exposed to oxacillin, but they also came at a substantial cost in terms of bacterial fitness, suggesting that this phenotype emerges preferentially in the setting of sustained antibiotic exposure.
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17
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Karer M, Kussmann M, Ratzinger F, Obermueller M, Reischer V, Winkler H, Kriz R, Burgmann H, Jilma B, Lagler H. Different Types of Coagulase Are Associated With 28-Day Mortality in Patients With Staphylococcus aureus Bloodstream Infections. Front Cell Infect Microbiol 2020; 10:236. [PMID: 32509602 PMCID: PMC7248564 DOI: 10.3389/fcimb.2020.00236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/24/2020] [Indexed: 11/13/2022] Open
Abstract
Background:Staphylococcus aureus (S. aureus), a leading cause of bacteremia and infective endocarditis, exploits the human coagulation system by using a wide range of specific virulence factors. However, the impact of these host-pathogen interactions on the outcome of patients with Staphylococcus aureus bacteremia (SAB) remains unclear. Methods: A total of 178 patients with S. aureus bacteremia were included and analyzed regarding bacterial factors (coa gene size, vWbp, clfA, clfB, fnbA, fnbB, fib) and clinical parameters. A stepwise multivariate Cox regression model and a Partitioning Around Medoids (PAM) cluster algorithm were used for statistical analysis. Results: Patients' risk factors for 28-day mortality were creatinine (OR 1.49, p < 0.001), age (OR 1.9, p < 0.002), fibrinogen (OR 0.44, p < 0.004), albumin (OR 0.63, p < 0.02), hemoglobin (OR 0.59, p < 0.03), and CRP (OR 1.72, p < 0.04). Five distinct bacterial clusters with different mortality rates were unveiled, whereof two showed a 2-fold increased mortality and an accumulation of specific coagulase gene sizes, 547-base pairs and 660-base pairs. Conclusions: Based on the data obtained in the present study an association of coagulase gene size and fib regarding 28-day mortality was observed in patients with S. aureus bloodstream infections. Further animal and prospective clinical studies are needed to confirm our preliminary findings.
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Affiliation(s)
- Matthias Karer
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Manuel Kussmann
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Franz Ratzinger
- Division of Medical and Chemical Laboratory Diagnostics, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.,Ihr Labor, Medical Diagnostics Laboratories, Vienna, Austria
| | - Markus Obermueller
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Veronika Reischer
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Heidemarie Winkler
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Richard Kriz
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Heinz Burgmann
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Bernd Jilma
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Heimo Lagler
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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18
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Giulieri SG, Tong SYC, Williamson DA. Using genomics to understand meticillin- and vancomycin-resistant Staphylococcus aureus infections. Microb Genom 2020; 6:e000324. [PMID: 31913111 PMCID: PMC7067033 DOI: 10.1099/mgen.0.000324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
Resistance to meticillin and vancomycin in Staphylococcus aureus significantly complicates the management of severe infections like bacteraemia, endocarditis or osteomyelitis. Here, we review the molecular mechanisms and genomic epidemiology of resistance to these agents, with a focus on how genomics has provided insights into the emergence and evolution of major meticillin-resistant S. aureus clones. We also provide insights on the use of bacterial whole-genome sequencing to inform management of S. aureus infections and for control of transmission at the hospital and in the community.
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Affiliation(s)
- Stefano G. Giulieri
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Infectious Disease Department, Austin Health, Melbourne, Australia
| | - Steven Y. C. Tong
- Victorian Infectious Disease Service, Royal Melbourne Hospital, and Doherty Department University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Menzies School of Health Research, Darwin, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
- Microbiology, Royal Melbourne Hospital, Melbourne, Australia
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19
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Patton T, Jiang JH, Lundie RJ, Bafit M, Gao W, Peleg AY, O'Keeffe M. Daptomycin-resistant Staphylococcus aureus clinical isolates are poorly sensed by dendritic cells. Immunol Cell Biol 2019; 98:42-53. [PMID: 31559654 DOI: 10.1111/imcb.12295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 08/18/2019] [Accepted: 09/23/2019] [Indexed: 12/18/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) presents an increasing threat to public health, with antimicrobial resistance on the rise and infections endemic in the hospital setting. Despite a global research effort to understand and combat antimicrobial resistance, less work has focused on understanding the nuances in the immunopathogenesis of clinical strains. In particular, there is a surprising gap of knowledge in the literature pertaining to how clinical strains are recognized by dendritic cells (DCs). Here, we show that the activation of DCs is compromised in response to MRSA strains resistant to the last-line antibiotic daptomycin. We found a significant reduction in the secretion of proinflammatory cytokines including tumor necrosis factor-α, interleukin-6, regulated upon activation, normal T cell expressed, and secreted and macrophage inflammatory protein-1β, as well as decreased expression of CD80 by DCs responding to daptomycin-resistant MRSA. We further demonstrate that this phenotype is coincident with the acquisition of specific point mutations in the cardiolipin synthase gene cls2, and, partly, in the bifunctional lysylphosphatidylglycerol flippase/synthetase gene mprF, which are genes that are often mutated in clinical daptomycin-resistant strains. Therefore, throughout infection and antibiotic therapy, MRSA has the capacity to not only develop further antibiotic resistance, but also develop resistance to immunological recognition by DCs, because of single amino acid point mutations occurring under the selective pressures of both host immunity and antibiotic therapy. Understanding the diversity of clinical MRSA isolates and the nuances in their immune recognition will have important implications for future therapeutics and the treatment of these infections.
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Affiliation(s)
- Timothy Patton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Jhih-Hang Jiang
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, 3800, Australia
| | - Rachel J Lundie
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Mariam Bafit
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Wei Gao
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infectious Diseases, Melbourne, VIC, 3000, Australia
| | - Anton Y Peleg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, 3800, Australia.,Department of Infectious Diseases, The Alfred and Central Clinical School, Monash University, Melbourne, VIC, 3000, Australia
| | - Meredith O'Keeffe
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
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20
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Szubert A, Bailey SL, Cooke GS, Peto T, Llewelyn MJ, Edgeworth JD, Walker AS, Thwaites GE. Predictors of recurrence, early treatment failure and death from Staphylococcus aureus bacteraemia: Observational analyses within the ARREST trial. J Infect 2019; 79:332-340. [DOI: 10.1016/j.jinf.2019.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/26/2019] [Accepted: 08/03/2019] [Indexed: 02/05/2023]
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21
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Giulieri SG, Baines SL, Guerillot R, Seemann T, Gonçalves da Silva A, Schultz M, Massey RC, Holmes NE, Stinear TP, Howden BP. Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia. Genome Med 2018; 10:65. [PMID: 30103826 PMCID: PMC6090636 DOI: 10.1186/s13073-018-0574-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/27/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Large-scale genomic studies of within-host diversity in Staphylococcus aureus bacteraemia (SAB) are needed to understanding bacterial adaptation underlying persistence and thus refining the role of genomics in management of SAB. However, available comparative genomic studies of sequential SAB isolates have tended to focus on selected cases of unusually prolonged bacteraemia, where secondary antimicrobial resistance has developed. METHODS To understand bacterial genetic diversity during SAB more broadly, we applied whole genome sequencing to a large collection of sequential isolates obtained from patients with persistent or relapsing bacteraemia. After excluding genetically unrelated isolates, we performed an in-depth genomic analysis of point mutations and chromosome structural variants arising within individual SAB episodes. RESULTS We show that, while adaptation pathways are heterogenous and episode-specific, isolates from persistent bacteraemia have a distinctive molecular signature, characterised by a low mutation frequency and high proportion of non-silent mutations. Analysis of structural genomic variants revealed that these often overlooked genetic events are commonly acquired during SAB. We discovered that IS256 insertion may represent the most effective driver of within-host microevolution in selected lineages, with up to three new insertion events per isolate even in the absence of other mutations. Genetic mechanisms resulting in significant phenotypic changes, such as increases in vancomycin resistance, development of small colony phenotypes, and decreases in cytotoxicity, included mutations in key genes (rpoB, stp, agrA) and an IS256 insertion upstream of the walKR operon. CONCLUSIONS This study provides for the first time a large-scale analysis of within-host genomic changes during invasive S. aureus infection and describes specific patterns of adaptation that will be informative for both understanding S. aureus pathoadaptation and utilising genomics for management of complicated S. aureus 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 & Immunity, Melbourne, Australia.,Infectious Disease Department, Austin Health, Melbourne, Australia.,Infectious Diseases Service, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Doherty Institute of Infection and Immunity, Melbourne, Australia.,Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Mark Schultz
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Natasha E Holmes
- Infectious Disease Department, Austin Health, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia. .,Infectious Disease Department, Austin Health, Melbourne, Australia. .,Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Doherty Institute of Infection and Immunity, Melbourne, Australia.
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