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Thiriet-Rupert S, Josse J, Perez-Pascual D, Tasse J, Andre C, Abad L, Lebeaux D, Ghigo JM, Laurent F, Beloin C. Analysis of In-Patient Evolution of Escherichia coli Reveals Potential Links to Relapse of Bone and Joint Infections. J Infect Dis 2024; 229:1546-1556. [PMID: 38041851 DOI: 10.1093/infdis/jiad528] [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: 06/02/2023] [Revised: 11/03/2023] [Accepted: 11/29/2023] [Indexed: 12/04/2023] Open
Abstract
Bone and joint infections (BJIs) are difficult to treat and affect a growing number of patients, in which relapses are observed in 10-20% of case. These relapses, which call for prolonged antibiotic treatment and increase resistance emergence risk, may originate from ill-understood adaptation of the pathogen to the host. Here, we investigated 3 pairs of Escherichia coli strains from BJI cases and their relapses to unravel adaptations within patients. Whole-genome comparison presented evidence for positive selection and phenotypic characterization showed that biofilm formation remained unchanged, contrary to what is usually described in such cases. Although virulence was not modified, we identified the loss of 2 virulence factors contributing to immune system evasion in one of the studied strains. Other strategies, including global growth optimization and colicin production, likely allowed the strains to outcompete competitors. This work highlights the variety of strategies allowing in-patient adaptation in BJIs.
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Affiliation(s)
| | - Jérôme Josse
- Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - David Perez-Pascual
- Genetics of Biofilms Laboratory, Institut Pasteur, Université de Paris-Cité, Paris, France
| | - Jason Tasse
- Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Camille Andre
- Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Lélia Abad
- Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - David Lebeaux
- Genetics of Biofilms Laboratory, Institut Pasteur, Université de Paris-Cité, Paris, France
- Département de Maladies Infectieuses et Tropicales, AP-HP, Hôpital Saint-Louis, Lariboisière, Paris, France
- FHU PROTHEE (Prosthetic joint infections: innovative strategies to overcome a medico-surgical challenge) Group
| | - Jean-Marc Ghigo
- Genetics of Biofilms Laboratory, Institut Pasteur, Université de Paris-Cité, Paris, France
| | - Frédéric Laurent
- Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, Université de Paris-Cité, Paris, France
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Shepherd MJ, Fu T, Harrington NE, Kottara A, Cagney K, Chalmers JD, Paterson S, Fothergill JL, Brockhurst MA. Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance. Nat Rev Microbiol 2024:10.1038/s41579-024-01041-1. [PMID: 38689039 DOI: 10.1038/s41579-024-01041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/02/2024]
Abstract
The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.
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Affiliation(s)
- Matthew J Shepherd
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
| | - Taoran Fu
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Niamh E Harrington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anastasia Kottara
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Kendall Cagney
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joanne L Fothergill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
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3
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Meumann EM, Limmathurotsakul D, Dunachie SJ, Wiersinga WJ, Currie BJ. Burkholderia pseudomallei and melioidosis. Nat Rev Microbiol 2024; 22:155-169. [PMID: 37794173 DOI: 10.1038/s41579-023-00972-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Burkholderia pseudomallei, the causative agent of melioidosis, is found in soil and water of tropical and subtropical regions globally. Modelled estimates of the global burden predict that melioidosis remains vastly under-reported, and a call has been made for it to be recognized as a neglected tropical disease by the World Health Organization. Severe weather events and environmental disturbance are associated with increased case numbers, and it is anticipated that, in some regions, cases will increase in association with climate change. Genomic epidemiological investigations have confirmed B. pseudomallei endemicity in newly recognized regions, including the southern United States. Melioidosis follows environmental exposure to B. pseudomallei and is associated with comorbidities that affect the immune response, such as diabetes, and with socioeconomic disadvantage. Several vaccine candidates are ready for phase I clinical trials. In this Review, we explore the global burden, epidemiology and pathophysiology of B. pseudomallei as well as current diagnostics, treatment recommendations and preventive measures, highlighting research needs and priorities.
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Affiliation(s)
- Ella M Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Northern Territory, Australia.
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Willem J Wiersinga
- Division of Infectious Diseases, Center for Experimental Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Northern Territory, Australia
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4
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Dekker JP. Within-Host Evolution of Bacterial Pathogens in Acute and Chronic Infection. ANNUAL REVIEW OF PATHOLOGY 2024; 19:203-226. [PMID: 37832940 DOI: 10.1146/annurev-pathmechdis-051122-111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Bacterial pathogens undergo remarkable adaptive change in response to the selective forces they encounter during host colonization and infection. Studies performed over the past few decades have demonstrated that many general evolutionary processes can be discerned during the course of host adaptation, including genetic diversification of lineages, clonal succession events, convergent evolution, and balanced fitness trade-offs. In some cases, elevated mutation rates resulting from mismatch repair or proofreading deficiencies accelerate evolution, and active mobile genetic elements or phages may facilitate genome plasticity. The host immune response provides another critical component of the fitness landscapes guiding adaptation, and selection operating on pathogens at this level may lead to immune evasion and the establishment of chronic infection. This review summarizes recent advances in this field, with a special focus on different forms of bacterial genome plasticity in the context of infection, and considers clinical consequences of adaptive changes for the host.
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Affiliation(s)
- John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA;
- National Institutes of Health Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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5
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Ramamoorthy S, Pena M, Ghosh P, Liao YY, Paret M, Jones JB, Potnis N. Transcriptome profiling of type VI secretion system core gene tssM mutant of Xanthomonas perforans highlights regulators controlling diverse functions ranging from virulence to metabolism. Microbiol Spectr 2024; 12:e0285223. [PMID: 38018859 PMCID: PMC10782981 DOI: 10.1128/spectrum.02852-23] [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: 07/14/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE T6SS has received attention due to its significance in mediating interorganismal competition through contact-dependent release of effector molecules into prokaryotic and eukaryotic cells. Reverse-genetic studies have indicated the role of T6SS in virulence in a variety of plant pathogenic bacteria, including the one studied here, Xanthomonas. However, it is not clear whether such effect on virulence is merely due to a shift in the microbiome-mediated protection or if T6SS is involved in a complex virulence regulatory network. In this study, we conducted in vitro transcriptome profiling in minimal medium to decipher the signaling pathways regulated by tssM-i3* in X. perforans AL65. We show that TssM-i3* regulates the expression of a suite of genes associated with virulence and metabolism either directly or indirectly by altering the transcription of several regulators. These findings further expand our knowledge on the intricate molecular circuits regulated by T6SS in phytopathogenic bacteria.
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Affiliation(s)
- Sivakumar Ramamoorthy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Michelle Pena
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Palash Ghosh
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Ying-Yu Liao
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Mathews Paret
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
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Mikucki A, Kahler CM. Microevolution and Its Impact on Hypervirulence, Antimicrobial Resistance, and Vaccine Escape in Neisseria meningitidis. Microorganisms 2023; 11:3005. [PMID: 38138149 PMCID: PMC10745880 DOI: 10.3390/microorganisms11123005] [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: 11/06/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Neisseria meningitidis is commensal of the human pharynx and occasionally invades the host, causing the life-threatening illness invasive meningococcal disease. The meningococcus is a highly diverse and adaptable organism thanks to natural competence, a propensity for recombination, and a highly repetitive genome. These mechanisms together result in a high level of antigenic variation to invade diverse human hosts and evade their innate and adaptive immune responses. This review explores the ways in which this diversity contributes to the evolutionary history and population structure of the meningococcus, with a particular focus on microevolution. It examines studies on meningococcal microevolution in the context of within-host evolution and persistent carriage; microevolution in the context of meningococcal outbreaks and epidemics; and the potential of microevolution to contribute to antimicrobial resistance and vaccine escape. A persistent theme is the idea that the process of microevolution contributes to the development of new hyperinvasive meningococcal variants. As such, microevolution in this species has significant potential to drive future public health threats in the form of hypervirulent, antibiotic-resistant, vaccine-escape variants. The implications of this on current vaccination strategies are explored.
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Affiliation(s)
- August Mikucki
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
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7
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Izydorczyk C, Waddell BJ, Thornton CS, Conly JM, Rabin HR, Somayaji R, Surette MG, Church DL, Parkins MD. Stenotrophomonas maltophilia natural history and evolution in the airways of adults with cystic fibrosis. Front Microbiol 2023; 14:1205389. [PMID: 37396351 PMCID: PMC10308010 DOI: 10.3389/fmicb.2023.1205389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction Stenotrophomonas maltophilia is an opportunistic pathogen infecting persons with cystic fibrosis (pwCF) and portends a worse prognosis. Studies of S. maltophilia infection dynamics have been limited by cohort size and follow-up. We investigated the natural history, transmission potential, and evolution of S. maltophilia in a large Canadian cohort of 321 pwCF over a 37-year period. Methods One-hundred sixty-two isolates from 74 pwCF (23%) were typed by pulsed-field gel electrophoresis, and shared pulsotypes underwent whole-genome sequencing. Results S. maltophilia was recovered at least once in 82 pwCF (25.5%). Sixty-four pwCF were infected by unique pulsotypes, but shared pulsotypes were observed between 10 pwCF. In chronic carriage, longer time periods between positive sputum cultures increased the likelihood that subsequent isolates were unrelated. Isolates from individual pwCF were largely clonal, with differences in gene content being the primary source of genetic diversity objectified by gene content differences. Disproportionate progression of CF lung disease was not observed amongst those infected with multiple strains over time (versus a single) or amongst those with shared clones (versus strains only infecting one patient). We did not observe evidence of patient-to-patient transmission despite relatedness between isolates. Twenty-four genes with ≥ 2 mutations accumulated over time were identified across 42 sequenced isolates from all 11 pwCF with ≥ 2 sequenced isolates, suggesting a potential role for these genes in adaptation of S. maltophilia to the CF lung. Discussion Genomic analyses suggested common, indirect sources as the origins of S. maltophilia infections in the clinic population. The information derived from a genomics-based understanding of the natural history of S. maltophilia infection within CF provides unique insight into its potential for in-host evolution.
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Affiliation(s)
- Conrad Izydorczyk
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Barbara J. Waddell
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Christina S. Thornton
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
| | - John M. Conly
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
- Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary and Alberta Health Services, Calgary, AB, Canada
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
| | - Harvey R. Rabin
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
| | - Ranjani Somayaji
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
- Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary and Alberta Health Services, Calgary, AB, Canada
| | - Michael G. Surette
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Deirdre L. Church
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
- Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary and Alberta Health Services, Calgary, AB, Canada
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
| | - Michael D. Parkins
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
- Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary and Alberta Health Services, Calgary, AB, Canada
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8
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Fen SHY, Tandhavanant S, Phunpang R, Ekchariyawat P, Saiprom N, Chewapreecha C, Seng R, Thiansukhon E, Morakot C, Sangsa N, Chayangsu S, Chuananont S, Tanwisaid K, Silakun W, Buasi N, Chaisuksant S, Hompleum T, Chetchotisakd P, Day NPJ, Chantratita W, Lertmemongkolchai G, West TE, Chantratita N. Antibiotic susceptibility of clinical Burkholderia pseudomallei isolates in northeast Thailand during 2015-2018 and the genomic characterization of β-lactam-resistant isolates. Antimicrob Agents Chemother 2023; 95:AAC.02230-20. [PMID: 33593842 PMCID: PMC8092913 DOI: 10.1128/aac.02230-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023] Open
Abstract
Melioidosis is an often fatal infection in tropical regions caused by an environmental bacterium, Burkholderia pseudomallei Current recommended melioidosis treatment requires intravenous β-lactam antibiotics such as ceftazidime (CAZ), meropenem (MEM) or amoxicillin-clavulanic acid (AMC) and oral trimethoprim-sulfamethoxazole. Emerging antibiotic resistance could lead to therapy failure and high mortality. We performed a prospective multicentre study in northeast Thailand during 2015-2018 to evaluate antibiotic susceptibility and characterize β-lactam resistance in clinical B. pseudomallei isolates. Collection of 1,317 B. pseudomallei isolates from patients with primary and relapse infections were evaluated for susceptibility to CAZ, imipenem (IPM), MEM and AMC. β-lactam resistant isolates were confirmed by broth microdilution method and characterized by whole genome sequence analysis, penA expression and β-lactamase activity. The resistant phenotype was verified via penA mutagenesis. All primary isolates were IPM-susceptible but we observed two CAZ-resistant and one CAZ-intermediate resistant isolates, two MEM-less susceptible isolates, one AMC-resistant and two AMC-intermediate resistant isolates. One of 13 relapse isolates was resistant to both CAZ and AMC. Two isolates were MEM-less susceptible. Strains DR10212A (primary) and DR50054E (relapse) were multi-drug resistant. Genomic and mutagenesis analyses supplemented with gene expression and β-lactamase analyses demonstrated that CAZ-resistant phenotype was caused by PenA variants: P167S (N=2) and penA amplification (N=1). Despite the high mortality rate in melioidosis, our study revealed that B. pseudomallei isolates had a low frequency of β-lactam resistance caused by penA alterations. Clinical data suggest that resistant variants may emerge in patients during antibiotic therapy and be associated with poor response to treatment.
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Affiliation(s)
- Shirley Hii Yi Fen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Peeraya Ekchariyawat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Wellcome Sanger Institute, Hinxton, UK
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Chumpol Morakot
- Department of Medicine, Mukdahan Hospital, Mukdahan, Thailand
| | | | | | | | | | | | - Noppol Buasi
- Department of Medicine, Sisaket Hospital, Sisaket, Thailand
| | | | - Tanin Hompleum
- Department of Surgery, Khon Kaen Hospital, Khon Kaen, Thailand
| | - Ploenchan Chetchotisakd
- Department of Medicine, Srinagarind Hospital, Faculty of Medicine and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Center for Tropical Medicine and Global Health, University of Oxford, UK
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Bangkok, Thailand
| | - Ganjana Lertmemongkolchai
- Department of Clinical Immunology, Faculty of Associated Medical Science, Khon Kaen University, Khon Kaen, Thailand
- The Centre for Research and Development of Medical Diagnostic Laboratories, Khon Kaen University, Khon Kaen, Thailand
| | - T Eoin West
- Division of Pulmonary, Critical Care & Sleep Medicine, Harborview Medical Center
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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9
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Usui M, Yoshii Y, Thiriet-Rupert S, Ghigo JM, Beloin C. Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance. Commun Biol 2023; 6:275. [PMID: 36928386 PMCID: PMC10020551 DOI: 10.1038/s42003-023-04601-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial antibiotic resistance is a global health concern of increasing importance and intensive study. Although biofilms are a common source of infections in clinical settings, little is known about the development of antibiotic resistance within biofilms. Here, we use experimental evolution to compare selection of resistance mutations in planktonic and biofilm Escherichia coli populations exposed to clinically relevant cycles of lethal treatment with the aminoglycoside amikacin. Consistently, mutations in sbmA, encoding an inner membrane peptide transporter, and fusA, encoding the essential elongation factor G, are rapidly selected in biofilms, but not in planktonic cells. This is due to a combination of enhanced mutation rate, increased adhesion capacity and protective biofilm-associated tolerance. These results show that the biofilm environment favors rapid evolution of resistance and provide new insights into the dynamic evolution of antibiotic resistance in biofilms.
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Affiliation(s)
- Masaru Usui
- Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan.
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France.
| | - Yutaka Yoshii
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Stanislas Thiriet-Rupert
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Christophe Beloin
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France.
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10
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Somprasong N, Hagen JP, Sahl JW, Webb JR, Hall CM, Currie BJ, Wagner DM, Keim P, Schweizer HP. A conserved active site PenA β-lactamase Ambler motif specific for Burkholderia pseudomallei/B. mallei is likely responsible for intrinsic amoxicillin-clavulanic acid sensitivity and facilitates a simple diagnostic PCR assay for melioidosis. Int J Antimicrob Agents 2023; 61:106714. [PMID: 36640845 DOI: 10.1016/j.ijantimicag.2023.106714] [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: 05/31/2022] [Revised: 11/23/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
Burkholderia pseudomallei is a soil- and water-dwelling Gram-negative bacterium that causes melioidosis in humans and animals. Amoxicillin-clavulanic acid (AMC) susceptibility has been hailed as an integral part of the screening algorithm for identification of B. pseudomallei, but the molecular basis for the inherent AMC susceptibility of this bacterium remains undefined. This study showed that B. pseudomallei (and the closely-related B. mallei) wild-type strains are the only Burkholderia spp. that contain a 70STSK73 PenA Ambler motif. This motif was present in >99.5% of 1820 analysed B. pseudomallei strains and 100% of 83 analysed B. mallei strains, and is proposed as the likely cause for their inherent AMC sensitivity. The authors developed a polymerase chain reaction (PCR) assay that specifically amplifies the penA70ST(S/F)K73-containing region from B. pseudomallei and B. mallei, but not from the remaining B. pseudomallei complex species or the 70STFK73 region from the closely-related penB of B. cepacia complex species. The abundance and purity of the 193-bp PCR fragment from putative B. pseudomallei isolates from clinical and environmental samples is likely sufficient for reliable confirmation of the presence of B. pseudomallei. The PCR assay is designed to be especially suited for use in resource-constrained areas. While not further explored in this study, the assay may allow diagnosis of putative B. mallei in culture isolates from animal and human samples.
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Affiliation(s)
- Nawarat Somprasong
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Johannah P Hagen
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Carina M Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Infectious Diseases and Northern Territory Medical Programme, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Herbert P Schweizer
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
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11
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Rep Med 2023; 4:100943. [PMID: 36791724 PMCID: PMC9906997 DOI: 10.1016/j.xcrm.2023.100943] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, CT, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott C Roberts
- Infectious Disease, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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12
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Seng R, Phunpang R, Saiprom N, Dulsuk A, Chewapreecha C, Thaipadungpanit J, Batty EM, Chantratita W, West TE, Chantratita N. Phenotypic and genetic alterations of Burkholderia pseudomallei in patients during relapse and persistent infections. Front Microbiol 2023; 14:1103297. [PMID: 36814569 PMCID: PMC9939903 DOI: 10.3389/fmicb.2023.1103297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/09/2023] [Indexed: 02/09/2023] Open
Abstract
The bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a severe tropical disease associated with high mortality and relapse and persistent infections. Treatment of melioidosis requires prolonged antibiotic therapy; however, little is known about relapse and persistent infections, particularly the phenotypic and genetic alterations of B. pseudomallei in patients. In this study, we performed pulsed-field gel electrophoresis (PFGE) to compare the bacterial genotype between the initial isolate and the subsequent isolate from each of 23 suspected recurrent and persistent melioidosis patients in Northeast Thailand. We used whole-genome sequencing (WGS) to investigate multilocus sequence types and genetic alterations of within-host strain pairs. We also investigated the bacterial phenotypes associated with relapse and persistent infections, including multinucleated giant cell (MNGC) formation efficiency and intracellular multiplication. We first identified 13 (1.2%) relapse, 7 (0.7%) persistent, and 3 (0.3%) reinfection patients from 1,046 survivors. Each of the 20 within-host strain pairs from patients with relapse and persistent infections shared the same genotype, suggesting that the subsequent isolates arise from the infecting isolate. Logistic regression analysis of clinical data revealed regimen and duration of oral antibiotic therapies as risk factors associated with relapse and persistent infections. WGS analysis demonstrated 17 within-host genetic alteration events in 6 of 20 paired isolates, including a relatively large deletion and 16 single-nucleotide polymorphism (stocktickerSNP) mutations distributed across 12 genes. In 1 of 20 paired isolates, we observed significantly increased cell-to-cell fusion and intracellular replication in the second isolate compared with the initial isolate from a patient with persistent infection. WGS analysis suggested that a non-synonymous mutation in the tssB-5 gene, which encoded an essential component of the type VI secretion system, may be associated with the increased intracellular replication and MNGC formation efficiency of the second isolate of the patient. This information provides insights into genetic and phenotypic alterations in B. pseudomallei in human melioidosis, which may represent a bacterial strategy for persistent and relapse infections.
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Affiliation(s)
- Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Adul Dulsuk
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Janjira Thaipadungpanit
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Elizabeth M. Batty
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - T. Eoin West
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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13
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Grote A, Earl AM. Within-host evolution of bacterial pathogens during persistent infection of humans. Curr Opin Microbiol 2022; 70:102197. [PMID: 36063686 DOI: 10.1016/j.mib.2022.102197] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 01/25/2023]
Abstract
Many bacterial pathogens can form persistent infections, providing an infectious reservoir, which allows for infection of new hosts. Currently, the molecular mechanisms and evolutionary dynamics driving persistence are still not well-understood. High-throughput sequencing methods have enabled the study of within-host evolution of persistent bacterial pathogens, revealing common trends among bacterial species in how they adapt to persist. We will focus on trends emerging from longitudinal human-cohort studies, including i) genome-size reduction, ii) metabolic adaptation to the host, iii) antimicrobial resistance, iv) changes in virulence and the bacterial cell surface, and v) hypermutation, and comment on where the field should focus going forward.
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Affiliation(s)
- Alexandra Grote
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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14
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Synthesis and study of new siderophore analog-ciprofloxacin conjugates with antibiotic activities against Pseudomonas aeruginosa and Burkholderia spp. Eur J Med Chem 2022; 245:114921. [DOI: 10.1016/j.ejmech.2022.114921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022]
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15
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Planet PJ. Adaptation and Evolution of Pathogens in the Cystic Fibrosis Lung. J Pediatric Infect Dis Soc 2022; 11:S23-S31. [PMID: 36069898 PMCID: PMC9451014 DOI: 10.1093/jpids/piac073] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023]
Abstract
As opposed to acute respiratory infections, the persistent bacterial infections of the lung that characterize cystic fibrosis (CF) provide ample time for bacteria to evolve and adapt. The process of adaptation is recorded in mutations that accumulate over time in the genomes of the infecting bacteria. Some of these mutations lead to obvious phenotypic differences such as antibiotic resistance or the well-known mucoid phenotype of Pseudomonas aeruginosa. Other mutations may be just as important but harder to detect such as increased mutation rates, cell surface changes, and shifts in metabolism and nutrient acquisition. Remarkably, many of the adaptations occur again and again in different patients, signaling that bacteria are adapting to solve specific challenges in the CF respiratory tract. This parallel evolution even extends across distinct bacterial species. This review addresses the bacterial systems that are known to change in long-term CF infections with a special emphasis on cross-species comparisons. Consideration is given to how adaptation may impact health in CF, and the possible evolutionary mechanisms that lead to the repeated parallel adaptations.
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Affiliation(s)
- Paul J Planet
- Corresponding Author: Paul J. Planet, MD, PhD, 3615 Civic Center Blvd, Philadelphia, PA 19104. E-mail:
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16
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Wongpalee SP, Thananchai H, Chewapreecha C, Roslund HB, Chomkatekaew C, Tananupak W, Boonklang P, Pakdeerat S, Seng R, Chantratita N, Takarn P, Khamnoi P. Highly specific and sensitive detection of Burkholderia pseudomallei genomic DNA by CRISPR-Cas12a. PLoS Negl Trop Dis 2022; 16:e0010659. [PMID: 36037185 PMCID: PMC9423629 DOI: 10.1371/journal.pntd.0010659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
Detection of Burkholderia pseudomallei, a causative bacterium for melioidosis, remains a challenging undertaking due to long assay time, laboratory requirements, and the lack of specificity and sensitivity of many current assays. In this study, we are presenting a novel method that circumvents those issues by utilizing CRISPR-Cas12a coupled with isothermal amplification to identify B. pseudomallei DNA from clinical isolates. Through in silico search for conserved CRISPR-Cas12a target sites, we engineered the CRISPR-Cas12a to contain a highly specific spacer to B. pseudomallei, named crBP34. The crBP34-based detection assay can detect as few as 40 copies of B. pseudomallei genomic DNA while discriminating against other tested common pathogens. When coupled with a lateral flow dipstick, the assay readout can be simply performed without the loss of sensitivity and does not require expensive equipment. This crBP34-based detection assay provides high sensitivity, specificity and simple detection method for B. pseudomallei DNA. Direct use of this assay on clinical samples may require further optimization as these samples are complexed with high level of human DNA. Melioidosis is a fatal infectious disease caused by a Gram-negative bacterium called Burkholderia pseudomallei. The bacteria can be found in many parts of the world, especially in the tropical and subtropical regions. Infection displays a variety of symptoms such as pneumonia, organ abscess and septicemia. The latter can lead to death within 24–48 hours if not properly diagnosed and treated. Rapid and accurate diagnosis, consequently, are essential for saving patients’ lives. Currently, culturing B. pseudomallei is a gold standard diagnostic method, but the assay turnaround time is 2–4 days, and the result could be of low sensitivity. Other detection methods such as real-time PCR and serological assays are limited by availability of equipment and by low specificity in endemic areas, respectively. For these reasons, in this study we developed a specific, sensitive and rapid detection assay for B. pseudomallei DNA, that is based on CRISPR-Cas12a system. The CRISPR-Cas12a is a protein-RNA complex that recognizes DNA. The RNA can be reprogramed to guide the detection of any DNA of interest, which in our case B. pseudomallei genomic DNA. Our data showed that this assay exhibited a 100% specificity to B. pseudomallei while discriminating against 10 other pathogens and human. The assay can detect B. pseudomallei DNA in less than one hour and does not require sophisticated equipment.
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Affiliation(s)
- Somsakul Pop Wongpalee
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
| | - Hathairat Thananchai
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Claire Chewapreecha
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Henrik B. Roslund
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Chalita Chomkatekaew
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Warunya Tananupak
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phumrapee Boonklang
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sukritpong Pakdeerat
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Piyawan Takarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phadungkiat Khamnoi
- Microbiology Unit, Diagnostic Laboratory, Maharaj Nakorn Chiang Mai Hospital, Chiang Mai, Thailand
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17
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.06.29.22276868. [PMID: 35794895 PMCID: PMC9258298 DOI: 10.1101/2022.06.29.22276868] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral loads. During the infection, we found an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately two-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution led to the emergence and persistence of at least three genetically distinct genotypes suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, using unique molecular indexes for accurate intrahost viral sequencing, we tracked the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, ultimately providing opportunity for the emergence of genetically divergent and potentially highly transmissible variants as seen with Delta and Omicron.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Correspondence: (C.C.) and (N.D.G.)
| | - Anne M. Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A. Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I. Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Correspondence: (C.C.) and (N.D.G.)
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18
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Abstract
Microbes are constantly evolving. Laboratory studies of bacterial evolution increase our understanding of evolutionary dynamics, identify adaptive changes, and answer important questions that impact human health. During bacterial infections in humans, however, the evolutionary parameters acting on infecting populations are likely to be much more complex than those that can be tested in the laboratory. Nonetheless, human infections can be thought of as naturally occurring in vivo bacterial evolution experiments, which can teach us about antibiotic resistance, pathogenesis, and transmission. Here, we review recent advances in the study of within-host bacterial evolution during human infection and discuss practical considerations for conducting such studies. We focus on 2 possible outcomes for de novo adaptive mutations, which we have termed "adapt-and-live" and "adapt-and-die." In the adapt-and-live scenario, a mutation is long lived, enabling its transmission on to other individuals, or the establishment of chronic infection. In the adapt-and-die scenario, a mutation is rapidly extinguished, either because it carries a substantial fitness cost, it arises within tissues that block transmission to new hosts, it is outcompeted by more fit clones, or the infection resolves. Adapt-and-die mutations can provide rich information about selection pressures in vivo, yet they can easily elude detection because they are short lived, may be more difficult to sample, or could be maladaptive in the long term. Understanding how bacteria adapt under each of these scenarios can reveal new insights about the basic biology of pathogenic microbes and could aid in the design of new translational approaches to combat bacterial infections.
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Affiliation(s)
- Matthew J. Culyba
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Daria Van Tyne
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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19
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Meumann EM, Kaestli M, Mayo M, Ward L, Rachlin A, Webb JR, Kleinecke M, Price EP, Currie BJ. Emergence of Burkholderia pseudomallei Sequence Type 562, Northern Australia. Emerg Infect Dis 2021; 27:1057-1067. [PMID: 33754984 PMCID: PMC8007296 DOI: 10.3201/eid2704.202716] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since 2005, the range of Burkholderia pseudomallei sequence type 562 (ST562) has expanded in northern Australia. During 2005–2019, ST562 caused melioidosis in 61 humans and 3 animals. Cases initially occurred in suburbs surrounding a creek before spreading across urban Darwin, Australia and a nearby island community. In urban Darwin, ST562 caused 12% (53/440) of melioidosis cases, a proportion that increased during the study period. We analyzed 2 clusters of cases with epidemiologic links and used genomic analysis to identify previously unassociated cases. We found that ST562 isolates from Hainan Province, China, and Pingtung County, Taiwan, were distantly related to ST562 strains from Australia. Temporal genomic analysis suggested a single ST562 introduction into the Darwin region in ≈1988. The origin and transmission mode of ST562 into Australia remain uncertain.
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20
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Gatt YE, Margalit H. Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. Mol Biol Evol 2021; 38:1101-1121. [PMID: 33118035 PMCID: PMC7947768 DOI: 10.1093/molbev/msaa278] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Within-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge toward similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. Although the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure, or function were changed in other species utilizing the same adaptive strategy (e.g., mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa) and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.
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Affiliation(s)
- Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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21
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Schnetterle M, Gorgé O, Nolent F, Boughammoura A, Sarilar V, Vigier C, Guillier S, Koch L, Degand N, Ramisse V, Tichadou X, Girleanu M, Favier AL, Valade E, Biot F, Neulat-Ripoll F. Genomic and RT-qPCR analysis of trimethoprim-sulfamethoxazole and meropenem resistance in Burkholderia pseudomallei clinical isolates. PLoS Negl Trop Dis 2021; 15:e0008913. [PMID: 33592059 PMCID: PMC7909661 DOI: 10.1371/journal.pntd.0008913] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 02/26/2021] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
Background Melioidosis is an endemic disease in southeast Asia and northern Australia caused by the saprophytic bacteria Burkholderia pseudomallei, with a high mortality rate. The clinical presentation is multifaceted, with symptoms ranging from acute septicemia to multiple chronic abscesses. Here, we report a chronic case of melioidosis in a patient who lived in Malaysia in the 70s and was suspected of contracting tuberculosis. Approximately 40 years later, in 2014, he was diagnosed with pauci-symptomatic melioidosis during a routine examination. Four strains were isolated from a single sample. They showed divergent morphotypes and divergent antibiotic susceptibility, with some strains showing resistance to trimethoprim-sulfamethoxazole and fluoroquinolones. In 2016, clinical samples were still positive for B. pseudomallei, and only one type of strain, showing atypical resistance to meropenem, was isolated. Principal findings We performed whole genome sequencing and RT-qPCR analysis on the strains isolated during this study to gain further insights into their differences. We thus identified two types of resistance mechanisms in these clinical strains. The first one was an adaptive and transient mechanism that disappeared during the course of laboratory sub-cultures; the second was a mutation in the efflux pump regulator amrR, associated with the overexpression of the related transporter. Conclusion The development of such mechanisms may have a clinical impact on antibiotic treatment. Indeed, their transient nature could lead to an undiagnosed resistance. Efflux overexpression due to mutation leads to an important multiple resistance, reducing the effectiveness of antibiotics during treatment. B. pseudomallei is a Gram-negative bacterium that causes melioidosis, a tropical disease. The mortality rate is high, the treatment long and harsh, and the therapeutic arsenal is limited due to the natural resistance of the bacteria to antibiotics. Eleven percent of melioidosis cases are chronic. Here, we studied a chronic melioidosis case in a French male patient who lived in Malaysia in the 70s. B. pseudomallei was identified in 2014 and in a relapse in 2016. Analysis revealed several strains from the same clinical sample with different morphotypes and divergent antibiotic-resistance profiles. Two atypical multidrug resistance profiles were observed for two strains: one possessed multiple resistance to trimethoprim-sulfamethoxazole, fluoroquinolones, and chloramphenicol and the other multiple resistance to fluoroquinolones and meropenem. Trimethoprim-sulfamethoxazole or meropenem resistance have rarely been described in clinical cases and are probably underdiagnosed. Here, we show that trimethoprim-sulfamethoxazole resistance can be transient in clinical strains and easily lost in the laboratory after sub-culture during identification, resulting in an underestimation of trimethoprim-sulfamethoxazole resistance and therapeutic failure. We also identified a mutation in the AmrAB-OprA efflux pump regulator, leading to high level meropenem resistance, but this resistance is also transient.
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Affiliation(s)
- Marine Schnetterle
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
- Ecole du Val de Grace, Paris, France
| | - Olivier Gorgé
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Flora Nolent
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Aïda Boughammoura
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Véronique Sarilar
- Molecular Biology Unit, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Cécile Vigier
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Sophie Guillier
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Lionel Koch
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
- Ecole du Val de Grace, Paris, France
| | - Nicolas Degand
- Laboratoire de bactériologie, Hôpital de l’Archet, Centre Hospitalier Universitaire de Nice, Nice, France
| | - Vincent Ramisse
- DGA MNRBC- Le Bouchet, Division Biologie, ABIO, Vert-le-Petit, France
| | - Xavier Tichadou
- DGA MNRBC- Le Bouchet, Division Biologie, ABIO, Vert-le-Petit, France
| | - Maria Girleanu
- Imagery Unit, Departement of plateforms and technology research, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Anne-Laure Favier
- Imagery Unit, Departement of plateforms and technology research, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Eric Valade
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
- Ecole du Val de Grace, Paris, France
| | - Fabrice Biot
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Fabienne Neulat-Ripoll
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
- * E-mail:
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Chomkatekaew C, Boonklang P, Sangphukieo A, Chewapreecha C. An Evolutionary Arms Race Between Burkholderia pseudomallei and Host Immune System: What Do We Know? Front Microbiol 2021; 11:612568. [PMID: 33552023 PMCID: PMC7858667 DOI: 10.3389/fmicb.2020.612568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
A better understanding of co-evolution between pathogens and hosts holds promise for better prevention and control strategies. This review will explore the interactions between Burkholderia pseudomallei, an environmental and opportunistic pathogen, and the human host immune system. B. pseudomallei causes "Melioidosis," a rapidly fatal tropical infectious disease predicted to affect 165,000 cases annually worldwide, of which 89,000 are fatal. Genetic heterogeneities were reported in both B. pseudomallei and human host population, some of which may, at least in part, contribute to inter-individual differences in disease susceptibility. Here, we review (i) a multi-host-pathogen characteristic of the interaction; (ii) selection pressures acting on B. pseudomallei and human genomes with the former being driven by bacterial adaptation across ranges of ecological niches while the latter are driven by human encounter of broad ranges of pathogens; (iii) the mechanisms that generate genetic diversity in bacterial and host population particularly in sequences encoding proteins functioning in host-pathogen interaction; (iv) reported genetic and structural variations of proteins or molecules observed in B. pseudomallei-human host interactions and their implications in infection outcomes. Together, these predict bacterial and host evolutionary trajectory which continues to generate genetic diversity in bacterium and operates host immune selection at the molecular level.
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Affiliation(s)
| | | | - Apiwat Sangphukieo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Wellcome Sanger Institute, Hinxton, United Kingdom
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Faucher C, Mazana V, Kardacz M, Parthuisot N, Ferdy JB, Duneau D. Step-Specific Adaptation and Trade-Off over the Course of an Infection by GASP Mutation Small Colony Variants. mBio 2021; 12:e01399-20. [PMID: 33436427 PMCID: PMC7845629 DOI: 10.1128/mbio.01399-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/17/2020] [Indexed: 11/20/2022] Open
Abstract
During an infection, parasites face a succession of challenges, each decisive for disease outcome. The diversity of challenges requires a series of parasite adaptations to successfully multiply and transmit from host to host. Thus, the pathogen genotypes that succeed during one step might be counterselected in later stages of the infection. Using the bacterium Xenorhabdus nematophila and adult Drosophila melanogaster flies as hosts, we showed that such step-specific adaptations, here linked to GASP (i.e., growth advantage in stationary phase) mutations in the X. nematophila master gene regulator lrp, exist and can trade off with each other. We found that nonsense lrp mutations had lowered the ability to resist the host immune response, while all classes of mutations in lrp were associated with a decrease in the ability to proliferate during early infection. We demonstrate that reduced proliferation of X. nematophila best explains diminished virulence in this infection model. Finally, decreased proliferation during the first step of infection is accompanied by improved proliferation during late infection, suggesting a trade-off between the adaptations to each step. Step-specific adaptations could play a crucial role in the chronic phase of infections in any disease organisms that show similar small colony variants (SCVs) to X. nematophilaIMPORTANCE Within-host evolution has been described in many bacterial diseases, and the genetic basis behind the adaptations has stimulated a lot of interest. Yet, the studied adaptations are generally focused on antibiotic resistance and rarely on the adaptation to the environment given by the host, and the potential trade-offs hindering adaptations to each step of the infection are rarely considered. Those trade-offs are key to understanding intrahost evolution and thus the dynamics of the infection. However, understanding these trade-offs supposes a detailed study of host-pathogen interactions at each step of the infection process, with an adapted methodology for each step. Using Drosophila melanogaster as the host and the bacterium Xenorhabdus nematophila, we investigated the bacterial adaptations resulting from GASP mutations known to induce the small colony variant (SCV) phenotype positively selected within the host over the course of an infection, as well as the trade-off between step-specific adaptations.
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Affiliation(s)
- Christian Faucher
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Vincent Mazana
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Marion Kardacz
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Nathalie Parthuisot
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Jean-Baptiste Ferdy
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - David Duneau
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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Madden DE, Webb JR, Steinig EJ, Currie BJ, Price EP, Sarovich DS. Taking the next-gen step: Comprehensive antimicrobial resistance detection from Burkholderia pseudomallei. EBioMedicine 2020; 63:103152. [PMID: 33285499 PMCID: PMC7724162 DOI: 10.1016/j.ebiom.2020.103152] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/18/2020] [Accepted: 11/16/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a major threat to human health. Whole-genome sequencing holds great potential for AMR identification; however, there remain major gaps in accurately and comprehensively detecting AMR across the spectrum of AMR-conferring determinants and pathogens. METHODS Using 16 wild-type Burkholderia pseudomallei and 25 with acquired AMR, we first assessed the performance of existing AMR software (ARIBA, CARD, ResFinder, and AMRFinderPlus) for detecting clinically relevant AMR in this pathogen. B. pseudomallei was chosen due to limited treatment options, high fatality rate, and AMR caused exclusively by chromosomal mutation (i.e. single-nucleotide polymorphisms [SNPs], insertions-deletions [indels], copy-number variations [CNVs], inversions, and functional gene loss). Due to poor performance with existing tools, we developed ARDaP (Antimicrobial Resistance Detection and Prediction) to identify the spectrum of AMR-conferring determinants in B. pseudomallei. FINDINGS CARD, ResFinder, and AMRFinderPlus failed to identify any clinically-relevant AMR in B. pseudomallei; ARIBA identified AMR encoded by SNPs and indels that were manually added to its database. However, none of these tools identified CNV, inversion, or gene loss determinants, and ARIBA could not differentiate AMR determinants from natural genetic variation. In contrast, ARDaP accurately detected all SNP, indel, CNV, inversion, and gene loss AMR determinants described in B. pseudomallei (n≈50). Additionally, ARDaP accurately predicted three previously undescribed determinants. In mixed strain data, ARDaP identified AMR to as low as ~5% allelic frequency. INTERPRETATION Existing AMR software packages are inadequate for chromosomal AMR detection due to an inability to detect resistance conferred by CNVs, inversions, and functional gene loss. ARDaP overcomes these major shortcomings. Further, ARDaP enables AMR prediction from mixed sequence data down to 5% allelic frequency, and can differentiate natural genetic variation from AMR determinants. ARDaP databases can be constructed for any microbial species of interest for comprehensive AMR detection. FUNDING National Health and Medical Research Council (BJC, EPP, DSS); Australian Government (DEM, ES); Advance Queensland (EPP, DSS).
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Affiliation(s)
- Danielle E Madden
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia; Sunshine Coast Health Institute, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Tiwi, Northern Territory, Australia
| | - Eike J Steinig
- Australian Institute of Tropical and Health Medicine, James Cook University, Townsville, Queensland, Australia
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Tiwi, Northern Territory, Australia; Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Tiwi, Northern Territory, Australia
| | - Erin P Price
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia; Sunshine Coast Health Institute, Sunshine Coast University Hospital, Birtinya, Queensland, Australia; Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Tiwi, Northern Territory, Australia
| | - Derek S Sarovich
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia; Sunshine Coast Health Institute, Sunshine Coast University Hospital, Birtinya, Queensland, Australia; Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Tiwi, Northern Territory, Australia.
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25
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Hassan AA, Dos Santos SC, Cooper VS, Sá-Correia I. Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung. Front Microbiol 2020; 11:574626. [PMID: 33101250 PMCID: PMC7545829 DOI: 10.3389/fmicb.2020.574626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
During chronic respiratory infections of cystic fibrosis (CF) patients, bacteria adaptively evolve in response to the nutritional and immune environment as well as influence other infecting microbes. The present study was designed to gain insights into the genetic mechanisms underlying adaptation and diversification by the two most prevalent pathogenic species of the Burkholderia cepacia complex (Bcc), B. cenocepacia and B. multivorans. Herein, we study the evolution of both of these species during coinfection of a CF patient for 4.4 years using genome sequences of 9 B. multivorans and 11 B. cenocepacia. This co-infection spanned at least 3 years following initial infection by B. multivorans and ultimately ended in the patient's death by cepacia syndrome. Both species acquired several mutations with accumulation rates of 2.08 (B. cenocepacia) and 2.27 (B. multivorans) SNPs/year. Many of the mutated genes are associated with oxidative stress response, transition metal metabolism, defense mechanisms against antibiotics, and other metabolic alterations consistent with the idea that positive selection might be driven by the action of the host immune system, antibiotic therapy and low oxygen and iron concentrations. Two orthologous genes shared by B. cenocepacia and B. multivorans were found to be under strong selection and accumulated mutations associated with lineage diversification. One gene encodes a nucleotide sugar dehydratase involved in lipopolysaccharide O-antigen (OAg) biosynthesis (wbiI). The other gene encodes a putative two-component regulatory sensor kinase protein required to sense and adapt to oxidative- and heavy metal- inducing stresses. This study contributes to understanding of shared and species-specific evolutionary patterns of B. cenocepacia and B. multivorans evolving in the same CF lung environment.
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Affiliation(s)
- A Amir Hassan
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Sandra C Dos Santos
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Abstract
The regulation and timely expression of bacterial genes during infection is critical for a pathogen to cause an infection. Bacteria have multiple mechanisms to regulate gene expression in response to their environment, one of which is two-component systems (TCS). TCS have two components. One component is a sensory histidine kinase (HK) that autophosphorylates when activated by a signal. The activated sensory histidine kinase then transfers the phosphoryl group to the second component, the response regulator, which activates transcription of target genes. The genus Burkholderia contains members that cause human disease and are often extensively resistant to many antibiotics. The Burkholderia cepacia complex (BCC) can cause severe lung infections in patients with cystic fibrosis (CF) or chronic granulomatous disease (CGD). BCC members have also recently been associated with several outbreaks of bacteremia from contaminated pharmaceutical products. Separate from the BCC is Burkholderia pseudomallei, which is the causative agent of melioidosis, a serious disease that occurs in the tropics, and a potential bioterrorism weapon. Bioinformatic analysis of sequenced Burkholderia isolates predicts that most strains have at least 40 TCS. The vast majority of these TCS are uncharacterized both in terms of the signals that activate them and the genes that are regulated by them. This review will highlight TCS that have been described to play a role in virulence in either the BCC or B. pseudomallei Since many of these TCS are involved in virulence, TCS are potential novel therapeutic targets, and elucidating their function is critical for understanding Burkholderia pathogenesis.
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27
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Burkholderia pseudomallei pathogenesis and survival in different niches. Biochem Soc Trans 2020; 48:569-579. [PMID: 32167134 DOI: 10.1042/bst20190836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 01/16/2023]
Abstract
Burkholderia pseudomallei (Bp) is the causative agent of melioidosis, a disease of the tropics with high clinical mortality rates. To date, no vaccines are approved for melioidosis and current treatment relies on antibiotics. Conversely, common misdiagnosis and high pathogenicity of Bp hamper efforts to fight melioidosis. This bacterium can be isolated from a wide range of niches such as waterlogged fields, stagnant water bodies, salt water bodies and from human and animal clinical specimens. Although extensive studies have been undertaken to elucidate pathogenesis mechanisms of Bp, little is known about how a harmless soil bacterium adapts to different environmental conditions, in particular, the shift to a human host to become a highly virulent pathogen. The bacterium has a large genome encoding an armory of factors that assist the pathogen in surviving under stressful conditions and assuming its role as a deadly intracellular pathogen. This review presents an overview of what is currently known about how the pathogen adapts to different environments. With in-depth understanding of Bp adaptation and survival, more effective therapies for melioidosis can be developed by targeting related genes or proteins that play a major role in the bacteria's survival.
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28
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Somprasong N, Hall CM, Webb JR, Sahl JW, Wagner DM, Keim P, Currie BJ, Schweizer HP. Burkholderia ubonensis Meropenem Resistance: Insights into Distinct Properties of Class A β-Lactamases in Burkholderia cepacia Complex and Burkholderia pseudomallei Complex Bacteria. mBio 2020; 11:e00592-20. [PMID: 32291300 PMCID: PMC7157819 DOI: 10.1128/mbio.00592-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Burkholderia pseudomallei, the founding member of the B. pseudomallei complex (Bpc), is a biothreat agent and causes melioidosis, a disease whose treatment mainly relies on ceftazidime and meropenem. The concern is that B. pseudomallei could enhance its drug resistance repertoire by the acquisition of DNA from resistant near-neighbor species. Burkholderia ubonensis, a member of the B. cepacia complex (Bcc), is commonly coisolated from environments where B. pseudomallei is present. Unlike B. pseudomallei, in which significant primary carbapenem resistance is rare, it is not uncommon in B. ubonensis, but the underlying mechanisms are unknown. We established that carbapenem resistance in B. ubonensis is due to an inducible class A PenB β-lactamase, as has been shown for other Bcc bacteria. Inducibility is not sufficient for high-level resistance but also requires other determinants, such as a PenB that is more robust than that present in susceptible isolates, as well as other resistance factors. Curiously and diagnostic for the two complexes, both Bpc and Bcc bacteria contain distinct annotated PenA class A β-lactamases. However, the protein from Bcc bacteria is missing its essential active-site serine and, therefore, is not a β-lactamase. Regulated expression of a transcriptional penB'-lacZ (β-galactosidase) fusion in the B. pseudomallei surrogate B. thailandensis confirms that although Bpc bacteria lack an inducible β-lactamase, they contain the components required for responding to aberrant peptidoglycan synthesis resulting from β-lactam challenge. Understanding the diversity of antimicrobial resistance in Burkholderia species is informative about how the challenges arising from potential resistance transfer between them can be met.IMPORTANCEBurkholderia pseudomallei causes melioidosis, a tropical disease that is highly fatal if not properly treated. Our data show that, in contrast to B. pseudomallei, B. ubonensis β-lactam resistance is fundamentally different because intrinsic resistance is mediated by an inducible class A β-lactamase. This includes resistance to carbapenems. Our work demonstrates that studies with near-neighbor species are informative about the diversity of antimicrobial resistance in Burkholderia and can also provide clues about the potential of resistance transfer between bacteria inhabiting the same environment. Knowledge about potential adverse challenges resulting from the horizontal transfer of resistance genes between members of the two complexes enables the design of effective countermeasures.
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Affiliation(s)
- Nawarat Somprasong
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Carina M Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jessica R Webb
- Global and Tropical Heath Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bart J Currie
- Global and Tropical Heath Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia
- Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Herbert P Schweizer
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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Pearson T, Sahl JW, Hepp CM, Handady K, Hornstra H, Vazquez AJ, Settles E, Mayo M, Kaestli M, Williamson CHD, Price EP, Sarovich DS, Cook JM, Wolken SR, Bowen RA, Tuanyok A, Foster JT, Drees KP, Kidd TJ, Bell SC, Currie BJ, Keim P. Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection. PLoS Pathog 2020; 16:e1008298. [PMID: 32134991 PMCID: PMC7077878 DOI: 10.1371/journal.ppat.1008298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/17/2020] [Accepted: 01/02/2020] [Indexed: 12/14/2022] Open
Abstract
Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314’s sputum despite intensive initial therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314’s airways over a >16-year period, and also sampled the patient’s home environment, recovering six closely related B. pseudomallei isolates from the household water system. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a strictly clonal mode of genetic inheritance. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successful lineage through the first four years and two lineages after that. Overall, the evolution of this population is nonadaptive and best explained by genetic drift. However, some genetic and phenotypic changes are consistent with in situ adaptation. Using a mouse model, P314 isolates caused greatly reduced morbidity and mortality compared to the environmental isolates. Additionally, potentially adaptive phenotypes emerged and included differences in the O-antigen, capsular polysaccharide, motility, and colony morphology. The >13-year co-existence of two long-lived lineages presents interesting hypotheses that can be tested in future studies to provide additional insights into selective pressures, niche differentiation, and microbial adaptation. This unusual melioidosis case presents a rare example of the evolutionary progression towards commensalism by a highly virulent pathogen within a single human host. Pathogens frequently jump between different hosts, and associated adaptation may lead to the emergence of new infectious agents. Such host-jumping evolution is witnessed through endpoint analyses but these cannot capture genetic changes in lineages that have gone extinct. In this study, we have identified and monitored an example of the evolution of a bacterium often deadly to its mammalian host, in an unprecedented case whereby disease lessened through time and the pathogen became a part of the commensal human flora. We used genomic analyses to characterize more than 16 years of this evolutionary process and the stepwise mutations that control pathogen interactions with the patient. Soon after infection, mutational changes occurred that allowed the bacterium to remain in the airways without causing disease. This shift towards avirulence was determined based on clinical data and virulence testing in an animal model. In addition, mutations occurred that contributed to the persistence of the bacteria in the patient's lungs. Finally, we found evidence for the evolutionary emergence and persistence of two distinct lineages of the bacterium over the last 13 years, presenting interesting questions about niche utilization. Bacteria are ubiquitous in the human body and almost all are beneficial or benign. In this study, we document the evolutionary conversion of a normally deadly bacterium towards a commensal.
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Affiliation(s)
- Talima Pearson
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Crystal M. Hepp
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Karthik Handady
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie Hornstra
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Adam J. Vazquez
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erik Settles
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Charles H. D. Williamson
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erin P. Price
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Derek S. Sarovich
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Cook
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Spenser R. Wolken
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Colorado, United States of America
| | - Apichai Tuanyok
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey T. Foster
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Kevin P. Drees
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Timothy J. Kidd
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Scott C. Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, and QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Infectious Diseases Department and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Paul Keim
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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Duplantier AJ, Shurtleff AC, Miller C, Chiang CY, Panchal RG, Sunay M. Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges. DRUG DISCOVERY TARGETING DRUG-RESISTANT BACTERIA 2020. [PMCID: PMC7258707 DOI: 10.1016/b978-0-12-818480-6.00007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Research to discover and develop antibacterial and antiviral drugs with potent activity against pathogens of biothreat concern presents unique methodological and process-driven challenges. Herein, we review laboratory approaches for finding new antibodies, antibiotics, and antiviral molecules for pathogens of biothreat concern. Using high-throughput screening techniques, molecules that directly inhibit a pathogen’s entry, replication, or growth can be identified. Alternatively, molecules that target host proteins can be interesting targets for development when countering biothreat pathogens, due to the modulation of the host immune response or targeting proteins that interfere with the pathways required by the pathogen for replication. Monoclonal and cocktail antibody therapies approved by the Food and Drug Administration for countering anthrax and under development for treatment of Ebola virus infection are discussed. A comprehensive tabular review of current in vitro, in vivo, pharmacokinetic and efficacy datasets has been presented for biothreat pathogens of greatest concern. Finally, clinical trials and animal rule or traditional drug approval pathways are also reviewed. Opinions; interpretations; conclusions; and recommendations are those of the authors and are not necessarily endorsed by the US Army.
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Papanikolaou IC, Tsenempi XA. Tropical Lung Diseases. HUNTER'S TROPICAL MEDICINE AND EMERGING INFECTIOUS DISEASES 2020. [PMCID: PMC7152421 DOI: 10.1016/b978-0-323-55512-8.00001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Lung disease is common in the tropics; lower respiratory tract infections are a major cause of mortality, especially in children under 5 years of age. The World Health Organization has launched strategies to tackle this killer of children. Infections, including tuberculosis and drug-resistant tuberculosis, find vulnerable hosts in the tropics where human immunodeficiency virus co-infection is widespread, especially in India and sub-Saharan Africa. Parasitic infections can cause pulmonary manifestations (e.g., pleural effusion and cavitary lesions). Blood and pulmonary eosinophilia are common in such infections. Non-communicable lung disease such as chronic obstructive pulmonary disease and lung cancer associated with tobacco use, contribute to mortality, particularly where there is poor access to health structures. Pneumonia is a major cause of death in the tropics, especially in children under 5 years old. Symptoms and physical examination determine care-seeking behaviors and clinical management. Most new tuberculosis cases occur in the tropics, often with human immunodeficiency virus (HIV) co-infection. Parasitic infections can manifest as wheezing, eosinophilic pneumonia, pleural effusion, and cavitary lesions. The impact of non-communicable disease (e.g., chronic obstructive pulmonary disease [COPD] and lung cancer) on mortality is projected to rise in low- and middle-income countries.
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Sarovich DS, Webb JR, Pitman MC, Viberg LT, Mayo M, Baird RW, Robson JM, Currie BJ, Price EP. Raising the Stakes: Loss of Efflux Pump Regulation Decreases Meropenem Susceptibility in Burkholderia pseudomallei. Clin Infect Dis 2019; 67:243-250. [PMID: 29394337 DOI: 10.1093/cid/ciy069] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/29/2018] [Indexed: 02/06/2023] Open
Abstract
Background Burkholderia pseudomallei, the causative agent of the high-mortality disease melioidosis, is a gram-negative bacterium that is naturally resistant to many antibiotics. There is no vaccine for melioidosis, and effective eradication is reliant on biphasic and prolonged antibiotic administration. The carbapenem drug meropenem is the current gold standard option for treating severe melioidosis. Intrinsic B. pseudomallei resistance toward meropenem has not yet been documented; however, resistance could conceivably develop over the course of infection, leading to prolonged sepsis and treatment failure. Methods We examined our 30-year clinical collection of melioidosis cases to identify B. pseudomallei isolates with reduced meropenem susceptibility. Isolates were subjected to minimum inhibitory concentration (MIC) testing toward meropenem. Paired isolates from patients who had evolved decreased susceptibility were subjected to whole-genome sequencing. Select agent-compliant genetic manipulation was carried out to confirm the molecular mechanisms conferring resistance. Results We identified 11 melioidosis cases where B. pseudomallei isolates developed decreased susceptibility toward meropenem during treatment, including 2 cases not treated with this antibiotic. Meropenem MICs increased from 0.5-0.75 µg/mL to 3-8 µg/mL. Comparative genomics identified multiple mutations affecting multidrug resistance-nodulation-division (RND) efflux pump regulators, with concomitant overexpression of their corresponding pumps. All cases were refractory to treatment despite aggressive, targeted therapy, and 2 were associated with a fatal outcome. Conclusions This study confirms the role of RND efflux pumps in decreased meropenem susceptibility in B. pseudomallei. These findings have important ramifications for the diagnosis, treatment, and management of life-threatening melioidosis cases.
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Affiliation(s)
- Derek S Sarovich
- Global and Tropical Health Division, Menzies School of Health Research, Tiwi, Northern Territory.,Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Tiwi, Northern Territory
| | - Matthew C Pitman
- Department of Territory Pathology, Royal Darwin Hospital, Tiwi, Northern Territory.,Infectious Diseases, Royal Darwin Hospital, Tiwi, Northern Territory
| | - Linda T Viberg
- Global and Tropical Health Division, Menzies School of Health Research, Tiwi, Northern Territory
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Tiwi, Northern Territory
| | - Robert W Baird
- Department of Territory Pathology, Royal Darwin Hospital, Tiwi, Northern Territory.,Infectious Diseases, Royal Darwin Hospital, Tiwi, Northern Territory
| | | | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Tiwi, Northern Territory.,Infectious Diseases, Royal Darwin Hospital, Tiwi, Northern Territory.,Northern Territory Medical Program, Royal Darwin Hospital, Tiwi, Australia
| | - Erin P Price
- Global and Tropical Health Division, Menzies School of Health Research, Tiwi, Northern Territory.,Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland
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Shearer JD, Saylor ML, Butler CM, Treston AM, Heine HS, Chirakul S, Schweizer HP, Louie A, Drusano GL, Zumbrun SD, Warfield KL. GC-072: A Novel Therapeutic Candidate for Oral Treatment of Melioidosis and Infections Caused by Select Biothreat Pathogens. Antimicrob Agents Chemother 2019; 63:AAC.00834-19. [PMID: 31548183 PMCID: PMC6879241 DOI: 10.1128/aac.00834-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/13/2019] [Indexed: 12/03/2022] Open
Abstract
Burkholderia pseudomallei (B. pseudomallei), the etiological agent of melioidosis, is a Gram-negative bacterium with additional concern as a biothreat pathogen. The mortality rate from B. pseudomallei varies depending on the type of infection and extent of available health care, but in the case of septicemia left untreated it can range from 50 - 90%. Current therapy for melioidosis is biphasic, consisting of parenteral acute-phase treatment for two weeks or longer, followed by oral eradication-phase treatment lasting several months. An effective oral therapeutic for outpatient treatment of acute-phase melioidosis is needed. GC-072 is a potent, 4-oxoquinolizine antibiotic with selective inhibitory activity against bacterial topoisomerases. GC-072 has demonstrated in vitro potency against susceptible and drug-resistant strains of B. pseudomallei and is also active against Burkholderia mallei, Bacillus anthracis, Yersinia pestis, and Francisella tularensis GC-072 is bactericidal both extra- and intracellularly, with rapid killing noted within a few hours and reduced development of resistance compared to ceftazidime. GC-072, delivered intragastrically to mimic oral administration, promoted dose-dependent survival in mice using lethal inhalational models of B. pseudomallei infection following exposure to a 24 or 339 LD50 challenge with B. pseudomallei strain 1026b. Overall, GC-072 appears to be a strong candidate for first-line, oral treatment of melioidosis.
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Affiliation(s)
| | | | | | | | - Henry S Heine
- Institute for Therapeutic Innovation, University of Florida, College of Medicine, Orlando, FL
| | - Sunisa Chirakul
- Emerging Pathogens Institute, University of Florida, College of Medicine, Gainesville, FL
| | - Herbert P Schweizer
- Institute for Therapeutic Innovation, University of Florida, College of Medicine, Orlando, FL
- Emerging Pathogens Institute, University of Florida, College of Medicine, Gainesville, FL
| | - Arnold Louie
- Institute for Therapeutic Innovation, University of Florida, College of Medicine, Orlando, FL
| | - George L Drusano
- Institute for Therapeutic Innovation, University of Florida, College of Medicine, Orlando, FL
| | - Steven D Zumbrun
- United States Army Medical Research Institute of Infectious Diseases, Frederick MD
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Aziz A, Sarovich DS, Nosworthy E, Beissbarth J, Chang AB, Smith-Vaughan H, Price EP, Harris TM. Molecular Signatures of Non-typeable Haemophilus influenzae Lung Adaptation in Pediatric Chronic Lung Disease. Front Microbiol 2019; 10:1622. [PMID: 31379777 PMCID: PMC6646836 DOI: 10.3389/fmicb.2019.01622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/01/2019] [Indexed: 12/03/2022] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi), an opportunistic pathogen of the upper airways of healthy children, can infect the lower airways, driving chronic lung disease. However, the molecular basis underpinning NTHi transition from a commensal to a pathogen is not clearly understood. Here, we performed comparative genomic and transcriptomic analyses of 12 paired, isogenic NTHi strains, isolated from the nasopharynx (NP) and bronchoalveolar lavage (BAL) of 11 children with chronic lung disease, to identify convergent molecular signatures associated with lung adaptation. Comparative genomic analyses of the 12 NP-BAL pairs demonstrated that five were genetically identical, with the remaining seven differing by only 1 to 3 mutations. Within-patient transcriptomic analyses identified between 2 and 58 differentially expressed genes in 8 of the 12 NP-BAL pairs, including pairs with no observable genomic changes. Whilst no convergence was observed at the gene level, functional enrichment analysis revealed significant under-representation of differentially expressed genes belonging to Coenzyme metabolism, Function unknown, Translation, ribosomal structure, and biogenesis Cluster of Orthologous Groups categories. In contrast, Carbohydrate transport and metabolism, Cell motility and secretion, Intracellular trafficking and secretion, and Energy production categories were over-represented. This observed trend amongst genetically unrelated NTHi strains provides evidence of convergent transcriptional adaptation of NTHi to pediatric airways that deserves further exploration. Understanding the pathoadaptative mechanisms that NTHi employs to infect and persist in the lower pediatric airways is essential for devising targeted diagnostics and treatments aimed at minimizing disease severity, and ultimately, preventing NTHi lung infections and subsequent chronic lung disease in children.
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Affiliation(s)
- Ammar Aziz
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Derek S. Sarovich
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Elizabeth Nosworthy
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Anne B. Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Department of Respiratory and Sleep Medicine, Children’s Health Queensland, Queensland University of Technology, Brisbane, QLD, Australia
| | - Heidi Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Erin P. Price
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Tegan M. Harris
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
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Price EP, Sarovich DS. The Scourge of Antibiotic-resistant Infections in Cystic Fibrosis. Trends Microbiol 2019; 27:289-291. [PMID: 30709708 DOI: 10.1016/j.tim.2019.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 01/17/2019] [Indexed: 11/15/2022]
Abstract
Bacterial infections are the primary cause of respiratory decline and mortality in cystic fibrosis (CF) patients. In a recent study, Diaz Caballero and colleagues [1] (PLoS Pathog. 2018;14:e1007453) catalogued the molecular adaptation of a decade-long Burkholderia multivorans infection in a Canadian CF patient, which evolved to become resistant towards multiple classes of antibiotics.
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Affiliation(s)
- Erin P Price
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia; Sunshine Coast Health Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia.
| | - Derek S Sarovich
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia; Sunshine Coast Health Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
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Aziz A, Sarovich DS, Harris TM, Kaestli M, McRobb E, Mayo M, Currie BJ, Price EP. Suspected cases of intracontinental Burkholderia pseudomallei sequence type homoplasy resolved using whole-genome sequencing. Microb Genom 2019; 3. [PMID: 29208140 PMCID: PMC5729916 DOI: 10.1099/mgen.0.000139] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Burkholderia pseudomallei is a Gram-negative environmental bacterium that causes melioidosis, a disease of high mortality in humans and animals. Multilocus sequence typing (MLST) is a popular and portable genotyping method that has been used extensively to characterise the genetic diversity of B. pseudomallei populations. MLST has been central to our understanding of the underlying phylogeographical signal present in the B. pseudomallei genome, revealing distinct populations on both the intra- and the inter-continental level. However, due to its high recombination rate, it is possible for B. pseudomallei isolates to share the same multilocus sequence type (ST) despite being genetically and geographically distinct, with two cases of ‘ST homoplasy’ recently reported between Cambodian and Australian B. pseudomallei isolates. This phenomenon can dramatically confound conclusions about melioidosis transmission patterns and source attribution, a critical issue for bacteria such as B. pseudomallei that are of concern due to their potential for use as bioweapons. In this study, we used whole-genome sequencing to identify the first reported instances of intracontinental ST homoplasy, which involved ST-722 and ST-804 B. pseudomallei isolates separated by large geographical distances. In contrast, a third suspected homoplasy case was shown to be a true long-range (460 km) dispersal event between a remote Australian island and the Australian mainland. Our results show that, whilst a highly useful and portable method, MLST can occasionally lead to erroneous conclusions about isolate origin and disease attribution. In cases where a shared ST is identified between geographically distant locales, whole-genome sequencing should be used to resolve strain origin.
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Affiliation(s)
- Ammar Aziz
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Derek S Sarovich
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia.,2Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Tegan M Harris
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Mirjam Kaestli
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia.,3Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Australia
| | - Evan McRobb
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Mark Mayo
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Bart J Currie
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Erin P Price
- 2Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
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Chirakul S, Somprasong N, Norris MH, Wuthiekanun V, Chantratita N, Tuanyok A, Schweizer HP. Burkholderia pseudomallei acquired ceftazidime resistance due to gene duplication and amplification. Int J Antimicrob Agents 2019; 53:582-588. [PMID: 30639528 DOI: 10.1016/j.ijantimicag.2019.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/13/2018] [Accepted: 01/06/2019] [Indexed: 10/27/2022]
Abstract
Ceftazidime (CAZ) is the antibiotic of choice for the treatment of Burkholderia pseudomallei infection (melioidosis). The chromosomally-encoded PenA β-lactamase possesses weak cephalosporinase activity. The wild-type penA gene confers clinically significant CAZ resistance only when overexpressed due to a promoter mutation, transcriptional antitermination or by gene duplication and amplification (GDA). Here we characterise a reversible 33-kb GDA event involving wild-type penA in a CAZ-resistant B. pseudomallei clinical isolate from Thailand. We show that duplication arises from exchanges between short (<10 bp) chromosomal sequences, which in this example consist of 4-bp repeats flanked by 3-bp inverted repeats. GDA involving β-lactamases may be a common CAZ resistance mechanism in B. pseudomallei.
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Affiliation(s)
- Sunisa Chirakul
- Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, Institute for Therapeutic Innovation, University of Florida, Gainesville, FL, USA
| | - Nawarat Somprasong
- Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, Institute for Therapeutic Innovation, University of Florida, Gainesville, FL, USA
| | - Michael H Norris
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Apichai Tuanyok
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Herbert P Schweizer
- Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, Institute for Therapeutic Innovation, University of Florida, Gainesville, FL, USA.
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Diaz Caballero J, Clark ST, Wang PW, Donaldson SL, Coburn B, Tullis DE, Yau YCW, Waters VJ, Hwang DM, Guttman DS. A genome-wide association analysis reveals a potential role for recombination in the evolution of antimicrobial resistance in Burkholderia multivorans. PLoS Pathog 2018; 14:e1007453. [PMID: 30532201 PMCID: PMC6300292 DOI: 10.1371/journal.ppat.1007453] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/19/2018] [Accepted: 11/02/2018] [Indexed: 01/05/2023] Open
Abstract
Cystic fibrosis (CF) lung infections caused by members of the Burkholderia cepacia complex, such as Burkholderia multivorans, are associated with high rates of mortality and morbidity. We performed a population genomics study of 111 B. multivorans sputum isolates from one CF patient through three stages of infection including an early incident isolate, deep sampling of a one-year period of chronic infection occurring weeks before a lung transplant, and deep sampling of a post-transplant infection. We reconstructed the evolutionary history of the population and used a lineage-controlled genome-wide association study (GWAS) approach to identify genetic variants associated with antibiotic resistance. We found the incident isolate was basally related to the rest of the strains and more susceptible to antibiotics from three classes (β-lactams, aminoglycosides, quinolones). The chronic infection isolates diversified into multiple, distinct genetic lineages and showed reduced antimicrobial susceptibility to the same antibiotics. The post-transplant reinfection isolates derived from the same source as the incident isolate and were genetically distinct from the chronic isolates. They also had a level of susceptibility in between that of the incident and chronic isolates. We identified numerous examples of potential parallel pathoadaptation, in which multiple mutations were found in the same locus or even codon. The set of parallel pathoadaptive loci was enriched for functions associated with virulence and resistance. Our GWAS analysis identified statistical associations between a polymorphism in the ampD locus with resistance to β-lactams, and polymorphisms in an araC transcriptional regulator and an outer membrane porin with resistance to both aminoglycosides and quinolones. Additionally, these three loci were independently mutated four, three and two times, respectively, providing further support for parallel pathoadaptation. Finally, we identified a minimum of 14 recombination events, and observed that loci carrying putative parallel pathoadaptations and polymorphisms statistically associated with β-lactam resistance were over-represented in these recombinogenic regions. Cystic fibrosis (CF) is the most common lethal genetic disorder affecting individuals of European descent. Most CF patients die at a young age due to chronic lung infections. Among the organisms involved in these infections are bacteria from the Burkholderia cepacia complex (BCC), which are strongly associated with poor clinical prognosis. This study examines how the most prevalent BCC species among CF patients, B. multivorans, evolves within a single CF patient by studying the first B. multivorans isolate recovered from the patient, one hundred isolates recovered over a one year period during the chronic infection phase, and an additional ten isolates recovered after the reinfection of the transplanted lungs. We found that B. multivorans diversify phenotypically and genetically within the CF lung over the course of the infection, and evolves into a complex population during the chronic infection phase. We found that isolates collected from the post-transplant reinfection were more closely related to descendants of the original isolate rather than those recovered in the chronic infection. We identify genetic variants statistically associated with resistance to the antibiotics, and showed that some of these variants were found in regions that show patterns of recombination (genetic exchange) between strains. We also found that genes which were mutated multiple times during overall infection were more likely to be found in regions showing signals consistent with recombination. The presence of multiple independent mutations in a gene is a very strong signal that the gene helps bacteria adapt to their environment. Overall, this study provides insight into how pathogens adapt to the host during long-term infections, specific genes associated with antibiotic resistance, and the origin of new and recurrent infections.
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Affiliation(s)
- Julio Diaz Caballero
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Shawn T. Clark
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W. Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Sylva L. Donaldson
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Department of Medicine, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - D. Elizabeth Tullis
- Adult Cystic Fibrosis Clinic, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Yvonne C. W. Yau
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Valerie J. Waters
- Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David M. Hwang
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Emergence and Within-Host Genetic Evolution of Methicillin-Resistant Staphylococcus aureus Resistant to Linezolid in a Cystic Fibrosis Patient. Antimicrob Agents Chemother 2018; 62:AAC.00720-18. [PMID: 30275089 DOI: 10.1128/aac.00720-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 09/22/2018] [Indexed: 12/26/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infection has increased in recent years among cystic fibrosis (CF) patients. Linezolid (LZD) is one of the antistaphylococcal antibiotics widely used in this context. Although LZD resistance is rare, it has been described as often associated with long-term treatments. Thirteen MRSA strains isolated over 5 years from one CF patient were studied for LZD resistance emergence and subjected to whole-genome sequencing (WGS). Resistance emerged after three 15-day LZD therapeutic regimens over 4 months. It was associated with the mutation of G to T at position 2576 (G2576T) in all 5 rrl copies, along with a very high MIC (>256 mg/liter) and a strong increase in the generation time. Resistant strains isolated during the ensuing LZD therapeutic regimens and until 13 months after LZD stopped harbored only 3 or 4 mutated rrl copies, associated with lower MICs (8 to 32 mg/liter) and low to moderate generation time increases. Despite these differences, whole-genome sequencing allowed us to determine that all isolates, including the susceptible one isolated before LZD treatment, belonged to the same lineage. In conclusion, LZD resistance can emerge rapidly in CF patients and persist without linezolid selective pressure in colonizing MRSA strains belonging to the same lineage.
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Webb JR, Price EP, Somprasong N, Schweizer HP, Baird RW, Currie BJ, Sarovich DS. Development and validation of a triplex quantitative real-time PCR assay to detect efflux pump-mediated antibiotic resistance in Burkholderia pseudomallei. Future Microbiol 2018; 13:1403-1418. [PMID: 30256166 PMCID: PMC6190177 DOI: 10.2217/fmb-2018-0155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/23/2018] [Indexed: 01/12/2023] Open
Abstract
AIM To develop a probe-based triplex quantitative real-time PCR assay to simultaneously detect the upregulation of the efflux pumps AmrAB-OprA, BpeAB-OprB and BpeEF-OprC in Burkholderia pseudomallei strains exhibiting increased minimum inhibitory concentrations toward meropenem, doxycycline or trimethoprim-sulfamethoxazole. METHODS The triplex assay was developed and subsequently tested on RNA isolated from eight clinical and eight laboratory-generated B. pseudomallei mutants harboring efflux pump regulator mutations. RESULTS The triplex assay accurately detected efflux pump upregulation in all clinical and laboratory mutants, which corresponded with decreased antibiotic susceptibility or antibiotic resistance. CONCLUSION Rapid detection of antibiotic resistance provides clinicians with a tool to identify potential treatment failure in near real time, enabling informed alteration of treatment during an infection and improved patient outcomes.
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Affiliation(s)
- Jessica R Webb
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Erin P Price
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Nawarat Somprasong
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Herbert P Schweizer
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Robert W Baird
- Departments of Infectious Diseases & Pathology & Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Bart J Currie
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Departments of Infectious Diseases & Pathology & Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Derek S Sarovich
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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Rhodes KA, Somprasong N, Podnecky NL, Mima T, Chirakul S, Schweizer HP. Molecular determinants of Burkholderia pseudomallei BpeEF-OprC efflux pump expression. MICROBIOLOGY-SGM 2018; 164:1156-1167. [PMID: 30024368 DOI: 10.1099/mic.0.000691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Burkholderia pseudomallei, the cause of melioidosis, is intrinsically resistant to many antibiotics. Acquired multidrug resistance, including resistance to doxycycline and co-trimoxazole used for melioidosis eradication phase therapy, is mainly attributed to constitutive expression of the BpeEF-OprC efflux pump. Constitutive expression of this pump is caused by mutations affecting two highly similar LysR-type transcriptional regulators (LTTR), BpeT and BpeS, but their interaction with the regulatory region governing BpeEF-OprC expression has not yet been studied. The bpeE-bpeF-oprC genes are distally located in the llpE-bpeE-bpeF-oprC operon. The llpE gene encodes a putative lipase/esterase of unknown function. We show that in a bpeT mutant llpE is constitutively co-transcribed with bpeE-bpeF-oprC. As expected from previous studies with B. cenocepacia, deletion of llpE does not affect antibiotic efflux. Using transcriptional bpeE'-lacZ fusions, we demonstrate that the 188 bp bpeT-llpE intergenic region located between bpeT and the llpE-bpeE-bpeF-oprC operon contains regulatory elements needed for control of bpeT and llpE-bpeE-bpeF-oprC operon expression. By native polyacrylamide gel electrophoresis and electrophoretic mobility shift assays with purified recombinant BpeT and BpeS proteins, we show BpeT and BpeS form oligomers that share a 14 bp binding site overlapping the essential region required for llpE-bpeE-bpeF-oprC expression. The binding site contains the conserved T-N11-A LTTR box motif involved in binding of LysR proteins, which in concert with two other possible LTTR boxes may mediate BpeT and BpeS regulation of BpeEF-OprC expression. These studies form the basis for further investigation of BpeEF-OprC expression and regulation at the molecular level by yet unknown external stimuli.
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Affiliation(s)
- Katherine A Rhodes
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,†Present address: University of Arizona BIO5 Institute, Tucson, AZ 85721, USA
| | - Nawarat Somprasong
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Nicole L Podnecky
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,‡Present address: Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Tromsø, 9037 Tromsø, Norway
| | - Takehiko Mima
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,§Present address: Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Sunisa Chirakul
- 2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Herbert P Schweizer
- 3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
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Chirakul S, Norris MH, Pagdepanichkit S, Somprasong N, Randall LB, Shirley JF, Borlee BR, Lomovskaya O, Tuanyok A, Schweizer HP. Transcriptional and post-transcriptional regulation of PenA β-lactamase in acquired Burkholderia pseudomallei β-lactam resistance. Sci Rep 2018; 8:10652. [PMID: 30006637 PMCID: PMC6045580 DOI: 10.1038/s41598-018-28843-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/01/2018] [Indexed: 01/15/2023] Open
Abstract
Therapy of Burkholderia pseudomallei acute infections is largely limited to a few β-lactam antibiotics such as ceftazidime or meropenem. Although relatively rare, resistance emergence during therapy leads to treatment failures with high mortality rates. In the absence of acquired external resistance determinants in B. pseudomallei emergence of β-lactam resistance is invariably caused by mutational modification of genomically encoded factors. These include the deletion of the ceftazidime target penicillin-binding protein 3 or amino acid changes in the Class A PenA β-lactamase that expand its substrate spectrum, as well as penA gene duplication and amplification or its overexpression via transcriptional up-regulation. Evidence is presented that penA is co-transcribed with the upstream nlpD1 gene, that the transcriptional terminator for nlpD1 serves as a penA attenuator and that generation of a new promoter immediately upstream of the terminator/attenuator by a conserved G to A transition leads to anti-termination and thus constitutive PenA expression and extended β-lactam resistance. Further evidence obtained with the extensively β-lactam resistant clinical isolate Bp1651 shows that in addition to PenA overexpression and structural mutations other adaptive mechanisms contribute to intrinsic and acquired B. pseudomallei β-lactam resistance.
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Affiliation(s)
- Sunisa Chirakul
- University of Florida, College of Medicine, Emerging Pathogens Institute, Department of Molecular Genetics and Microbiology, Gainesville, FL, 32610, USA
| | - Michael H Norris
- University of Florida, College of Veterinary Medicine, Emerging Pathogens Institute, Department of Infectious Diseases and Immunity, Gainesville, FL, 32610, USA
| | - Sirawit Pagdepanichkit
- University of Florida, College of Medicine, Emerging Pathogens Institute, Department of Molecular Genetics and Microbiology, Gainesville, FL, 32610, USA
- Chulalongkorn University, Faculty of Veterinary Science, Department of Veterinary Public Health, Research Unit in Microbial Food Safety and Antimicrobial Resistance, Bangkok, 10330, Thailand
| | - Nawarat Somprasong
- University of Florida, College of Medicine, Emerging Pathogens Institute, Department of Molecular Genetics and Microbiology, Gainesville, FL, 32610, USA
| | - Linnell B Randall
- University of Florida, College of Medicine, Emerging Pathogens Institute, Department of Molecular Genetics and Microbiology, Gainesville, FL, 32610, USA
- Cornell University, Boyd Thompson Institute, Ithaca, NY, 14853, USA
| | - James F Shirley
- University of Florida, College of Medicine, Emerging Pathogens Institute, Department of Molecular Genetics and Microbiology, Gainesville, FL, 32610, USA
| | - Bradley R Borlee
- Colorado State University, College of Veterinary Medicine and Biomedical Sciences, Department of Microbiology, Immunology and Pathology, Fort Collins, CO, 80523, USA
| | | | - Apichai Tuanyok
- University of Florida, College of Veterinary Medicine, Emerging Pathogens Institute, Department of Infectious Diseases and Immunity, Gainesville, FL, 32610, USA
| | - Herbert P Schweizer
- University of Florida, College of Medicine, Emerging Pathogens Institute, Department of Molecular Genetics and Microbiology, Gainesville, FL, 32610, USA.
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Price EP, Viberg LT, Kidd TJ, Bell SC, Currie BJ, Sarovich DS. Transcriptomic analysis of longitudinal Burkholderia pseudomallei infecting the cystic fibrosis lung. Microb Genom 2018; 4. [PMID: 29989529 PMCID: PMC6159556 DOI: 10.1099/mgen.0.000194] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The melioidosis bacterium, Burkholderia pseudomallei, is increasingly being recognised as a pathogen in patients with cystic fibrosis (CF). We have recently catalogued genome-wide variation of paired, isogenic B. pseudomallei isolates from seven Australasian CF cases, which were collected between 4 and 55 months apart. Here, we extend this investigation by documenting the transcriptomic changes in B. pseudomallei in five cases. Following growth in an artificial CF sputum medium, four of the five paired isolates exhibited significant differential gene expression (DE) that affected between 32 and 792 genes. The greatest number of DE events was observed between the strains from patient CF9, consistent with the hypermutator status of the latter strain, which is deficient in the DNA mismatch repair protein MutS. Two patient isolates harboured duplications that concomitantly increased expression of the β-lactamase-encoding gene penA, and a 35 kb deletion in another abolished expression of 29 genes. Convergent expression profiles in the chronically-adapted isolates identified two significantly downregulated and 17 significantly upregulated loci, including the resistance-nodulation-division (RND) efflux pump BpeEF-OprC, the quorum-sensing hhqABCDE operon, and a cyanide- and pyocyanin-insensitive cytochrome bd quinol oxidase. These convergent pathoadaptations lead to increased expression of pathways that may suppress competing bacterial and fungal pathogens, and that enhance survival in oxygen-restricted environments, the latter of which may render conventional antibiotics less effective in vivo. Treating chronically adapted B. pseudomallei infections with antibiotics designed to target anaerobic infections, such as the nitroimidazole class of antibiotics, may significantly improve pathogen eradication attempts by exploiting this Achilles heel.
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Affiliation(s)
- Erin P Price
- 1Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,2Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Linda T Viberg
- 2Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Timothy J Kidd
- 3Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,4School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Scott C Bell
- 3Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,5QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.,6Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, QLD, Australia
| | - Bart J Currie
- 2Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.,7Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Derek S Sarovich
- 1Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,2Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
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Kao CY, Chen JW, Liu TL, Yan JJ, Wu JJ. Comparative Genomics of Escherichia coli Sequence Type 219 Clones From the Same Patient: Evolution of the IncI1 blaCMY-Carrying Plasmid in Vivo. Front Microbiol 2018; 9:1518. [PMID: 30038606 PMCID: PMC6046403 DOI: 10.3389/fmicb.2018.01518] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
This study investigates the evolution of an Escherichia coli sequence type 219 clone in a patient with recurrent urinary tract infection, comparing isolate EC974 obtained prior to antibiotic treatment and isolate EC1515 recovered after exposure to several β-lactam antibiotics (ceftriaxone, cefixime, and imipenem). EC974 had a smooth colony morphology, while EC1515 had a rough colony morphology on sheep blood agar. RAPD-PCR analysis suggested that both isolates belonged to the same clone. Antimicrobial susceptibility tests showed that EC1515 was more resistant to piperacillin/tazobactam, cefepime, cefpirome, and ertapenem than EC974. Comparative genomic analysis was used to investigate the genetic changes of EC974 and EC1515 within the host, and showed three plasmids with replicons IncI1, P0111, and IncFII in both isolates. P0111-type plasmids pEC974-2 and pEC1515-2, contained the antibiotic resistance genes aadA2, tetA, and drfA12. IncFII-type plasmids pEC974-3 and pEC1515-3 contained the antibiotic resistance genes blaTEM−1, aadA1, aadA22, sul3, and inuF. Interestingly, blaCMY−111 and blaCMY−4 were found in very similar IncI1 plasmids that also contained aadA22 and aac(3)-IId, from isolates EC974 (pEC974-1) and EC1515 (pEC1515-1), respectively. The results showed in vivo amino acid substitutions converting blaCMY−111 to blaCMY−4 (R221W and A238V substitutions). Conjugation experiments showed a high frequency of IncI1 and IncFII plasmid co-transference. Transconjugants and DH5α cells harboring blaCMY-4 or blaCMY-111 showed higher levels of resistance to ampicillin, amoxicillin, cefazolin, cefuroxime, cefotaxime, cefixime, and ceftazidime, but not piperacillin/tazobactam, cefpime, or ertapenem. All known genes (outer membrane proteins and extended-spectrum AmpC β-lactamases) involved in ETP resistance in E. coli were identical between EC974 and EC1515. This is the first study to identify the evolution of an IncI1 plasmid within the host, and to characterize blaCMY−111 in E. coli.
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Affiliation(s)
- Cheng-Yen Kao
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, Taipei, Taiwan
| | - Jenn-Wei Chen
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tsung-Lin Liu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Jing-Jou Yan
- Department of Pathology, Cheng Ching Hospital at Chung Kang, Taichung, Taiwan
| | - Jiunn-Jong Wu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, Taipei, Taiwan
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Melioidosis: An Australian Perspective. Trop Med Infect Dis 2018; 3:tropicalmed3010027. [PMID: 30274424 PMCID: PMC6136632 DOI: 10.3390/tropicalmed3010027] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/16/2022] Open
Abstract
Burkholderia pseudomallei is endemic in northern Australia, with cases of melioidosis most commonly occurring during the wet season in individuals with diabetes, hazardous alcohol use, and chronic kidney disease. Pneumonia is the most common presentation and the majority of patients are bacteraemic—however, infection may involve almost any organ, with the skin and soft tissues, genitourinary system, visceral organs, and bone and joints affected most commonly. Central nervous system involvement is rarer, but has a high attributable mortality. Increased awareness of the disease amongst healthcare providers, ready access to appropriate antibiotic therapy and high-quality intensive care services has resulted in a sharp decline in the case fatality rate over the last 20 years. Further improvement in clinical outcomes will require a greater understanding of the disease′s pathophysiology, its optimal management, and more effective strategies for its prevention.
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Nunvar J, Capek V, Fiser K, Fila L, Drevinek P. What matters in chronic Burkholderia cenocepacia infection in cystic fibrosis: Insights from comparative genomics. PLoS Pathog 2017; 13:e1006762. [PMID: 29228063 PMCID: PMC5739508 DOI: 10.1371/journal.ppat.1006762] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/21/2017] [Accepted: 11/19/2017] [Indexed: 01/29/2023] Open
Abstract
Burkholderia cenocepacia causes severe pulmonary infections in cystic fibrosis (CF) patients. Since the bacterium is virtually untreatable by antibiotics, chronic infections persist for years and might develop into fatal septic pneumonia (cepacia syndrome, CS). To devise new strategies to combat chronic B. cenocepacia infections, it is essential to obtain comprehensive knowledge about their pathogenesis. We conducted a comparative genomic analysis of 32 Czech isolates of epidemic clone B. cenocepacia ST32 isolated from various stages of chronic infection in 8 CF patients. High numbers of large-scale deletions were found to occur during chronic infection, affecting preferentially genomic islands and nonessential replicons. Recombination between insertion sequences (IS) was inferred as the mechanism behind deletion formation; the most numerous IS group was specific for the ST32 clone and has undergone transposition burst since its divergence. Genes functionally related to transition metal metabolism were identified as hotspots for deletions and IS insertions. This functional category was also represented among genes where nonsynonymous point mutations and indels occurred parallelly among patients. Another category exhibiting parallel mutations was oxidative stress protection; mutations in catalase KatG resulted in impaired detoxification of hydrogen peroxide. Deep sequencing revealed substantial polymorphism in genes of both categories within the sputum B. cenocepacia ST32 populations, indicating extensive adaptive evolution. Neither oxidative stress response nor transition metal metabolism genes were previously reported to undergo parallel evolution during chronic CF infection. Mutations in katG and copper metabolism genes were overrepresented in patients where chronic infection developed into CS. Among professional phagocytes, macrophages use both hydrogen peroxide and copper for their bactericidal activity; our results thus tentatively point to macrophages as suspects in pathogenesis towards the fatal CS. The large Burkholderia cenocepacia populations which persist in cystic fibrosis lungs during many years of chronic infections have an inherent potential for adaptive evolution. The results provided by comparative genomics are key in understanding the processes involved. Mutational events which have taken place allow us to deductively reconstruct the history of chronic infection and to identify driving forces acting upon the bacteria. Beyond the conventional point mutation analysis of next generation sequencing data, we observed interesting phenomena such as large deletions and transposable element movement which represent another facet of adaptive evolution of B. cenocepacia during chronic infection. We also found, unexpectedly, that adaptive evolution in B. cenocepacia strain ST32 affects a set of genes conspicuously different from related species B. dolosa; these appear to be linked to host immune response. Our study provides clues to the complex puzzle of chronic B. cenocepacia infection establishment, persistence and outcome in cystic fibrosis.
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Affiliation(s)
- Jaroslav Nunvar
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Vaclav Capek
- Bioinformatics Centre, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Karel Fiser
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Libor Fila
- Department of Pneumology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
- * E-mail:
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Mechanisms of Resistance to Folate Pathway Inhibitors in Burkholderia pseudomallei: Deviation from the Norm. mBio 2017; 8:mBio.01357-17. [PMID: 28874476 PMCID: PMC5587915 DOI: 10.1128/mbio.01357-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The trimethoprim and sulfamethoxazole combination, co-trimoxazole, plays a vital role in the treatment of Burkholderia pseudomallei infections. Previous studies demonstrated that the B. pseudomallei BpeEF-OprC efflux pump confers widespread trimethoprim resistance in clinical and environmental isolates, but this is not accompanied by significant resistance to co-trimoxazole. Using the excluded select-agent strain B. pseudomallei Bp82, we now show that in vitro acquired trimethoprim versus co-trimoxazole resistance is mainly mediated by constitutive BpeEF-OprC expression due to bpeT mutations or by BpeEF-OprC overexpression due to bpeS mutations. Mutations in bpeT affect the carboxy-terminal effector-binding domain of the BpeT LysR-type activator protein. Trimethoprim resistance can also be mediated by dihydrofolate reductase (FolA) target mutations, but this occurs rarely unless BpeEF-OprC is absent. BpeS is a transcriptional regulator that is 62% identical to BpeT. Mutations affecting the BpeS DNA-binding or carboxy-terminal effector-binding domains result in constitutive BpeEF-OprC overexpression, leading to trimethoprim and sulfamethoxazole efflux and thus to co-trimoxazole resistance. The majority of laboratory-selected co-trimoxazole-resistant mutants often also contain mutations in folM, encoding a pterin reductase. Genetic analyses of these mutants established that both bpeS mutations and folM mutations contribute to co-trimoxazole resistance, although the exact role of folM remains to be determined. Mutations affecting bpeT, bpeS, and folM are common in co-trimoxazole-resistant clinical isolates, indicating that mutations affecting these genes are clinically significant. Co-trimoxazole resistance in B. pseudomallei is a complex phenomenon, which may explain why resistance to this drug is rare in this bacterium. Burkholderia pseudomallei causes melioidosis, a tropical disease that is difficult to treat. The bacterium’s resistance to antibiotics limits therapeutic options. The paucity of orally available drugs further complicates therapy. The oral drug of choice is co-trimoxazole, a combination of trimethoprim and sulfamethoxazole. These antibiotics target two distinct enzymes, FolA (dihydrofolate reductase) and FolP (dihydropteroate synthase), in the bacterial tetrahydrofolate biosynthetic pathway. Although co-trimoxazole resistance is minimized due to two-target inhibition, bacterial resistance due to folA and folP mutations does occur. Co-trimoxazole resistance in B. pseudomallei is rare and has not yet been studied. Co-trimoxazole resistance in this bacterium employs a novel strategy involving differential regulation of BpeEF-OprC efflux pump expression that determines the drug resistance profile. Contributing are mutations affecting folA, but not folP, and folM, a folate pathway-associated gene whose function is not yet well understood and which has not been previously implicated in folate inhibitor resistance in clinical isolates.
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Relationships Between Resistance and Virulence in Burkholderia pseudomallei. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0119-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Price EP, Currie BJ, Sarovich DS. Genomic Insights Into the Melioidosis Pathogen, Burkholderia pseudomallei. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0111-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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