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Doğan E, Sydow K, Heiden SE, Eger E, Wassilew G, Proctor RA, Bohnert JA, Idelevich EA, Schaufler K, Becker K. Klebsiella pneumoniae exhibiting a phenotypic hyper-splitting phenomenon including the formation of small colony variants. Front Cell Infect Microbiol 2024; 14:1372704. [PMID: 38601740 PMCID: PMC11004228 DOI: 10.3389/fcimb.2024.1372704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Abstract
In this study, we characterized a Klebsiella pneumoniae strain in a patient with shrapnel hip injury, which resulted in multiple phenotypic changes, including the formation of a small colony variant (SCV) phenotype. Although already described since the 1960s, there is little knowledge about SCV phenotypes in Enterobacteriaceae. The formation of SCVs has been recognized as a bacterial strategy to evade host immune responses and compromise the efficacy of antimicrobial therapies, leading to persistent and recurrent courses of infections. In this case, 14 isolates with different resisto- and morpho-types were distinguished from the patient's urine and tissue samples. Whole genome sequencing revealed that all isolates were clonally identical belonging to the K. pneumoniae high-risk sequence type 147. Subculturing the SCV colonies consistently resulted in the reappearance of the initial SCV phenotype and three stable normal-sized phenotypes with distinct morphological characteristics. Additionally, an increase in resistance was observed over time in isolates that shared the same colony appearance. Our findings highlight the complexity of bacterial behavior by revealing a case of phenotypic "hyper-splitting" in a K. pneumoniae SCV and its potential clinical significance.
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Affiliation(s)
- Eyüp Doğan
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Katharina Sydow
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research Helmholtz Center for Infection Research (HZI), Greifswald, Germany
| | - Stefan E. Heiden
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research Helmholtz Center for Infection Research (HZI), Greifswald, Germany
| | - Elias Eger
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research Helmholtz Center for Infection Research (HZI), Greifswald, Germany
| | - Georgi Wassilew
- Center for Orthopedics, Trauma Surgery and Rehabilitation Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Richard A. Proctor
- Departments of Medical Microbiology/Immunology and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Jürgen A. Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Evgeny A. Idelevich
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Katharina Schaufler
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research Helmholtz Center for Infection Research (HZI), Greifswald, Germany
- University Medicine Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
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Matsumoto T, Hashimoto M, Huang WC, Teng CH, Niwa T, Yamada M, Negishi T. Molecular characterization of a carbon dioxide-dependent Proteus mirabilis small-colony variant isolated from a clinical specimen. J Infect Chemother 2024:S1341-321X(24)00072-2. [PMID: 38442770 DOI: 10.1016/j.jiac.2024.02.031] [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: 01/24/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
INTRODUCTION Carbon dioxide-dependent Proteus mirabilis has been isolated from clinical specimens. It is not clear whether mutations in carbonic anhydrase are responsible for the carbon dioxide dependence of P. mirabilis. The pathogenicity of carbon dioxide-dependent P. mirabilis also remains unclear. The purpose of this study was to determine the cause carbon dioxide dependence of P. mirabilis and its pathogenicity. METHODS The DNA sequence of can encoding carbonic anhydrase of a carbon dioxide-dependent P. mirabilis small colony variant (SCV) isolate was analyzed. To confirm that impaired carbonic anhydrase activity is responsible for the formation of the carbon dioxide-dependent SCV phenotype of P. mirabilis, we performed complementation experiments using plasmids with intact can. Additionally, mouse infection experiments were performed to confirm the change in virulence due to the mutation of carbonic anhydrase. RESULTS We found that the can gene of the carbon dioxide-dependent P. mirabilis SCV isolate showed had a frameshift mutation with a deletion of 1 bp (c. 173delC). The can of P. mirabilis encodes carbonic anhydrase was also found to function in Escherichia coli. The cause of the carbon dioxide-dependent SCV phenotype of P. mirabilis was an abnormality in carbonic anhydrase. Nevertheless, no changes were observed in virulence due to the mutation of carbonic anhydrase in mouse infection experiments. CONCLUSIONS The can gene is essential for the growth of P. mirabilis in ambient air. The mechanisms underlying this fitness advantage in terms of infection warrant further investigation.
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Affiliation(s)
- Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Maebashi, Japan; Department of Biomedical Laboratory Sciences, Shinshu University School of Medicine, School of Health Sciences, Shinshu University, Matsumoto, Japan.
| | - Masayuki Hashimoto
- Institute of Molecular Medicine, College of Medicine, National Cheng-Kung University, Tainan City, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chun Huang
- Institute of Molecular Medicine, College of Medicine, National Cheng-Kung University, Tainan City, Taiwan
| | - Ching-Hao Teng
- Institute of Molecular Medicine, College of Medicine, National Cheng-Kung University, Tainan City, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Takahiko Niwa
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Maebashi, Japan; Department of Clinical Laboratory, Gunma University Hospital, Maebashi, Japan
| | - Mariko Yamada
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Maebashi, Japan
| | - Tatsuya Negishi
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
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Ryan H, Ballard E, Stockwell RE, Duplancic C, Thomson RM, Smith K, Bell SC. A systematic review of the clinical impact of small colony variants in patients with cystic fibrosis. BMC Pulm Med 2023; 23:323. [PMID: 37658311 PMCID: PMC10474644 DOI: 10.1186/s12890-023-02611-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Cystic fibrosis (CF) is a life-limiting disorder that is characterised by respiratory tract inflammation that is mediated by a range of microbial pathogens. Small colony variants (SCVs) of common respiratory pathogens are being increasingly recognised in CF. The aim of this systematic review is to investigate the prevalence of SCVs, clinical characteristics and health outcomes for patients with CF, and laboratory diagnostic features of SCVs compared to non-small colony variants (NCVs) for a range of Gram-positive and Gram-negative respiratory pathogens. METHODS A literature search was conducted (PubMed, Web of Science, Embase and Scopus) in April 2020 to identify articles of interest. Data pertaining to demographic characteristics of participants, diagnostic criteria of SCVs, SCV prevalence and impact on lung function were extracted from included studies for analysis. RESULTS Twenty-five of 673 studies were included in the systematic review. Individuals infected with SCVs of Staphylococcus aureus (S. aureus) were more likely to have had prior use of the broad-spectrum antibiotic trimethoprim sulfamethoxazole (p < 0.001), and the prevalence of SCVs in patients infected with S. aureus was estimated to be 19.3% (95% CI: 13.5% to 25.9%). Additionally, patients infected with SCVs of Gram-negative and Gram-positive pathogens were identified to have a lower forced expiratory volume in one second percentage predicted (-16.8, 95% CI: -23.2 to -10.4) than those infected by NCVs. Gram-positive SCVs were commonly described as small and non-haemolytic, grown on Mannitol salt or blood agar for 24 h at 35°C and confirmed using tube coagulase testing. CONCLUSION The findings of this systematic review demonstrate that SCVs of S. aureus have a high prevalence in the CF community, and that the occurrence of SCVs in Gram-positive and Gram-negative pathogens is linked to poorer respiratory function. Further investigation is necessary to determine the effect of infection by SCVs on the CF population.
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Affiliation(s)
- Harrigan Ryan
- Centre for Children's Health Research, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
| | - Emma Ballard
- Statistics Unit, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Rebecca E Stockwell
- Centre for Children's Health Research, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, QLD, Australia
| | - Christine Duplancic
- Centre for Children's Health Research, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
| | - Rachel M Thomson
- Respiratory Research Group, Gallipoli Medical Research Foundation, Greenslopes, QLD, Australia
| | - Kimberley Smith
- Centre for Children's Health Research, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
| | - Scott C Bell
- Centre for Children's Health Research, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia.
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, QLD, Australia.
- Translational Research Institute, Woolloongabba, QLD, Australia.
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Ding X, Fu X, Euphrasie D, Ferroni A, Sermet-Gaudelus I, Charbit A, Coureuil M, Jamet A. Genomic analysis of Staphylococcus aureus sequential isolates from lungs of patients with cystic fibrosis. Microbes Infect 2023; 25:105124. [PMID: 36871931 DOI: 10.1016/j.micinf.2023.105124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/07/2023]
Abstract
Staphylococcus aureus is the predominant pathogen in children with cystic fibrosis (CF) in France and, around 80% of them harbored S. aureus in their lungs. This study investigated virulence and antimicrobial resistance-associated genes and within-host evolution polymorphisms in 14 S. aureus persistent clones from 14 chronically infected CF children. For each of the 14 patients, we compared genomes of two isogenic sequential isolates separated by 2-9 years. All isolates were methicillin-sensitive and harbored the immune evasion gene cluster, whereas half of them harbored the enterotoxin gene cluster. Most clones were capsule type 8 (8/14) and accessory gene regulator (agr)-specificity group 1 (9/14). We identified convergent mutations in genes involved in carbohydrate metabolism, cell wall metabolism, genetic information processing and adhesion, which are likely to play important role in intracellular invasion and persistence. Further explorations relying notably on proteomics will contribute to improve our understanding of the mechanisms at play in the striking long-term persistence ability of S. aureus.
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Affiliation(s)
- Xiongqi Ding
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Xiali Fu
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Daniel Euphrasie
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Agnes Ferroni
- Department of Clinical Microbiology, Necker-Enfants Malades Hospital, AP-HP Centre Université de Paris, F75015 Paris, France
| | - Isabelle Sermet-Gaudelus
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Alain Charbit
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Mathieu Coureuil
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Anne Jamet
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France; Department of Clinical Microbiology, Necker-Enfants Malades Hospital, AP-HP Centre Université de Paris, F75015 Paris, France.
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Kocer K, Boudour-Halil D, Chanthalangsy Q, Sähr A, Heeg K, Boutin S, Nurjadi D. Genomic Modification of TonB and Emergence of Small-Colony Phenotype in VIM- and NDM-Producing Escherichia coli following Cefiderocol Exposure In Vitro. Antimicrob Agents Chemother 2023; 67:e0011823. [PMID: 37022155 PMCID: PMC10190670 DOI: 10.1128/aac.00118-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/07/2023] [Indexed: 04/07/2023] Open
Abstract
Knowledge on resistance mechanisms toward cefiderocol, a novel siderophore-conjugated cephalosporin antibiotic, is still limited. Although the presence of New-Delhi metallo-β-lactamase has been demonstrated to facilitate the resistance development toward cefiderocol via siderophore receptor mutations in Enterobacter cloacae and Klebsiella pneumoniae, the impact of metallo-β-lactamases on facilitating such mutations in Escherichia coli is not yet elucidated. Our study aimed to study the effect of the presence of various β-lactamases, such as NDM-5, VIM-1, KPC-2, and OXA-48, on the development of cefiderocol resistance in E. coli. To this end, we performed liquid mating to transfer these β-lactamases onto a defined K-12 E. coli background (J53) and exposed these transconjugants to increasing cefiderocol concentrations in a serial passage experiment. Cefiderocol-resistant isolates were genotyped by whole-genome sequencing to investigate the underlying resistance mechanism. Cefiderocol-resistant isolates emerged only in isolates producing VIM-1 and NDM-5 metallo-β-lactamase, but not in those producing the serine β-lactamases KPC-2 and OXA-48. We observed two distinct morphological changes of the J53 E. coli strain exhibiting reduced colony size after insertions of transposable elements in the tonB gene leading to alterations in the TonB binding site and morphological changes consistent with the small-colony variant (SCV) phenotype due to mutations in the hemB and hemH genes. Passaging experiments suggested that these phenotypes were highly plastic. The SCV phenotype is attributed to immune evasion and decreased susceptibility toward antibiotics. The emergence of SCV following cefiderocol exposure may have clinical implications for bacterial clearance and warrants further investigation.
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Affiliation(s)
- Kaan Kocer
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Deniz Boudour-Halil
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Quan Chanthalangsy
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Aline Sähr
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Klaus Heeg
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Sébastien Boutin
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg-Lübeck-Borstel-Riems, Germany
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Zirbes CF, Pitcher NJ, Davis JC, Bartels AR, Krogh JD, Teresi M, Farber T, Milavetz F, Pamatmat AJ, Rozen AL, Reinhardt LD, Boyken L, Singh SB, Twait E, Reeb VC, Ford BA, Fischer AJ. Staphylococcus aureus detection from CF respiratory samples is improved using alternative media. J Cyst Fibros 2022; 21:888-889. [PMID: 35491319 PMCID: PMC10152491 DOI: 10.1016/j.jcf.2022.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
Affiliation(s)
- Christian F Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Nicholas J Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Joseph C Davis
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Alyssa R Bartels
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Justin D Krogh
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Mary Teresi
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Tyler Farber
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Francesca Milavetz
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Anthony J Pamatmat
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Alexis L Rozen
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Lindsey D Reinhardt
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Linda Boyken
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Sachinkumar B Singh
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Erik Twait
- State Hygienic Laboratory at the University of Iowa, Coralville, IA, United States
| | - Valérie C Reeb
- State Hygienic Laboratory at the University of Iowa, Coralville, IA, United States
| | - Bradley A Ford
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Anthony J Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States.
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Jakovljev A, Afset JE, Haugum K, Steinum HO, Gresdal Rønning T, Samuelsen Ø, Ås CG. Phenotypic and genotypic characterisation of thymine auxotrophy in Escherichia coli isolated from a patient with recurrent bloodstream infection. PLoS One 2022; 17:e0270256. [PMID: 35802671 PMCID: PMC9269972 DOI: 10.1371/journal.pone.0270256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/08/2022] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Thymine auxotrophic in vitro mutants of Escherichia coli were first reported in the mid-20th century. Later, thymine-dependent clinical strains of E. coli as well as other Enterobacterales, Enterococcus faecalis and Staphylococcus aureus have been recognized as the cause of persistent and recurrent infections. OBJECTIVES The aim of this study was to characterize the phenotype and investigate the molecular basis of thymine auxotrophy in ten E. coli isolates obtained at different time points from a patient with recurrent bloodstream infection (BSI) due to a chronic aortic graft infection treated with Trimethoprim/sulfamethoxazole (TMP-SMX). METHODS Clinical data was obtained from hospital records. Growth characterization and antimicrobial susceptibility testing to TMP-SMX was performed on M9 agar and in MH broth with different thymine concentrations (0.5, 2, 5, 10 and 20 μg/mL), on Mueller-Hinton (MH) and blood agar. Whole genome sequencing (WGS) was performed on all E. coli isolates. RESULTS E. coli were isolated from ten consecutive BSI episodes from a patient with chronic aortic graft infection. Six of these isolates were resistant to TMP-SMX when assayed on blood agar. Growth experiments with added thymine confirmed that these isolates were thymine-dependent (thy-), and revealed growth defects (slower growth rate and smaller colony size) in these isolates relative to thy+ isolates (n = 4). WGS indicated that all isolates were of the same clonal lineage of sequence type 7358. Genomic analysis revealed a G172C substitution in thyA in all TMP-SMX resistant isolates, while mutations affecting genes involved in the deoxyribose salvage pathway (deoB and deoC) were identified in eight isolates. CONCLUSION This case highlights the risk of resistance development to TMP-SMX, especially for long-term treatment, and the possible pitfalls in detection of growth-deficient subpopulations from chronic infections, which could lead to treatment failure.
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Affiliation(s)
- Aleksandra Jakovljev
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Egil Afset
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kjersti Haugum
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Harald Otto Steinum
- Department of Infectious Diseases, Clinic of Internal Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Torunn Gresdal Rønning
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ørjan Samuelsen
- Department of Microbiology and Infection Control, Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - Christina Gabrielsen Ås
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail:
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Tang Q, Precit MR, Thomason MK, Blanc SF, Ahmed-Qadri F, McFarland AP, Wolter DJ, Hoffman LR, Woodward JJ. Thymidine starvation promotes c-di-AMP-dependent inflammation during pathogenic bacterial infection. Cell Host Microbe 2022; 30:961-974.e6. [PMID: 35439435 DOI: 10.1016/j.chom.2022.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/01/2022] [Accepted: 03/23/2022] [Indexed: 11/03/2022]
Abstract
Antimicrobials can impact bacterial physiology and host immunity with negative treatment outcomes. Extensive exposure to antifolate antibiotics promotes thymidine-dependent Staphylococcus aureus small colony variants (TD-SCVs), commonly associated with worse clinical outcomes. We show that antibiotic-mediated disruption of thymidine synthesis promotes elevated levels of the bacterial second messenger cyclic di-AMP (c-di-AMP), consequently inducing host STING activation and inflammation. An initial antibiotic screen in Firmicutes revealed that c-di-AMP production was largely driven by antifolate antibiotics targeting dihydrofolate reductase (DHFR), which promotes folate regeneration required for thymidine biosynthesis. Additionally, TD-SCVs exhibited excessive c-di-AMP production and STING activation in a thymidine-dependent manner. Murine lung infection with TD-SCVs revealed STING-dependent elevation of proinflammatory cytokines, causing higher airway neutrophil infiltration and activation compared with normal-colony S. aureus and hemin-dependent SCVs. Collectively, our results suggest that thymidine metabolism disruption in Firmicutes leads to elevated c-di-AMP-mediated STING-dependent inflammation, with potential impacts on antibiotic usage and infection outcomes.
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Affiliation(s)
- Qing Tang
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Mimi R Precit
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Maureen K Thomason
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Sophie F Blanc
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Fariha Ahmed-Qadri
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Adelle P McFarland
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Daniel J Wolter
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA.
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Rumpf C, Lange J, Schwartbeck B, Kahl BC. Staphylococcus aureus and Cystic Fibrosis-A Close Relationship. What Can We Learn from Sequencing Studies? Pathogens 2021; 10:pathogens10091177. [PMID: 34578208 PMCID: PMC8466686 DOI: 10.3390/pathogens10091177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023] Open
Abstract
Staphylococcus aureus is next to Pseudomonas aeruginosa the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant S. aureus clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. S. aureus is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. S. aureus is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant S. aureus are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using S. aureus isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or spa-sequence typing (spa-typing) to follow the population dynamics of S. aureus, elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of S. aureus with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of S. aureus and its evolution in the airways of individuals with CF.
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10
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Long DR, Wolter DJ, Lee M, Precit M, McLean K, Holmes E, Penewit K, Waalkes A, Hoffman LR, Salipante SJ. Polyclonality, Shared Strains, and Convergent Evolution in Chronic Cystic Fibrosis Staphylococcus aureus Airway Infection. Am J Respir Crit Care Med 2021; 203:1127-1137. [PMID: 33296290 DOI: 10.1164/rccm.202003-0735oc] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rationale: Staphylococcus aureus is the most common respiratory pathogen isolated from patients with cystic fibrosis (CF) in the United States. Although modes of acquisition and genetic adaptation have been described for Pseudomonas aeruginosa, resulting in improved diagnosis and treatment, these features remain more poorly defined for S. aureus.Objectives: To characterize the molecular epidemiology and genetic adaptation of S. aureus during chronic CF airway infection and in response to antibiotic therapy.Methods: We performed whole-genome sequencing of 1,382 S. aureus isolates collected longitudinally over a mean 2.2 years from 246 children with CF at five U.S. centers between 2008 and 2017. Results were integrated with clinical and demographic data to characterize bacterial population dynamics and identify common genetic targets of in vivo adaptation.Measurements and Main Results: Results showed that 45.5% of patients carried multiple, coexisting S. aureus lineages, often having different antibiotic susceptibility profiles. Adaptation during the course of infection commonly occurred in a set of genes related to persistence and antimicrobial resistance. Individual sequence types demonstrated wide geographic distribution, and we identified limited strain-sharing among children linked by common household or clinical exposures. Unlike P. aeruginosa, S. aureus genetic diversity was unconstrained, with an ongoing flow of new genetic elements into the population of isolates from children with CF.Conclusions: CF airways are frequently coinfected by multiple, genetically distinct S. aureus lineages, indicating that current clinical procedures for sampling isolates and selecting antibiotics are likely inadequate. Strains can be shared by patients in close domestic or clinical contact and can undergo convergent evolution in key persistence and antimicrobial-resistance genes, suggesting novel diagnostic and therapeutic approaches for future study.
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Affiliation(s)
- Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine
| | - Daniel J Wolter
- Department of Pediatrics.,Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington
| | | | | | - Kathryn McLean
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Elizabeth Holmes
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Lucas R Hoffman
- Department of Pediatrics.,Department of Microbiology, and.,Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
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11
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Bogut A, Magryś A. The road to success of coagulase-negative staphylococci: clinical significance of small colony variants and their pathogenic role in persistent infections. Eur J Clin Microbiol Infect Dis 2021; 40:2249-2270. [PMID: 34296355 PMCID: PMC8520507 DOI: 10.1007/s10096-021-04315-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/09/2021] [Indexed: 01/14/2023]
Abstract
Bacterial small colony variants represent an important aspect of bacterial variability. They are naturally occurring microbial subpopulations with distinctive phenotypic and pathogenic traits, reported for many clinically important bacteria. In clinical terms, SCVs tend to be associated with persistence in host cells and tissues and are less susceptible to antibiotics than their wild-type (WT) counterparts. The increased tendency of SCVs to reside intracellularly where they are protected against the host immune responses and antimicrobial drugs is one of the crucial aspects linking SCVs to recurrent or chronic infections, which are difficult to treat. An important aspect of the SCV ability to persist in the host is the quiescent metabolic state, reduced immune response and expression a changed pattern of virulence factors, including a reduced expression of exotoxins and an increased expression of adhesins facilitating host cell uptake. The purpose of this review is to describe in greater detail the currently available data regarding CoNS SCV and, in particular, their clinical significance and possible mechanisms by which SCVs contribute to the pathogenesis of the chronic infections. It should be emphasized that in spite of an increasing clinical significance of this group of staphylococci, the number of studies unraveling the mechanisms of CoNS SCVs formation and their impact on the course of the infectious process is still scarce, lagging behind the studies on S. aureus SCVs.
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Affiliation(s)
- Agnieszka Bogut
- Chair and Department of Medical Microbiology, Medical University of Lublin, ul. Chodźki 1, 20-093, Lublin, Poland
| | - Agnieszka Magryś
- Chair and Department of Medical Microbiology, Medical University of Lublin, ul. Chodźki 1, 20-093, Lublin, Poland.
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12
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Association of Diverse Staphylococcus aureus Populations with Pseudomonas aeruginosa Coinfection and Inflammation in Cystic Fibrosis Airway Infection. mSphere 2021; 6:e0035821. [PMID: 34160233 PMCID: PMC8265651 DOI: 10.1128/msphere.00358-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Staphylococcus aureus is one of the most common pathogens isolated from the airways of cystic fibrosis (CF) patients and often persists for extended periods. There is limited knowledge about the diversity of S. aureus in CF. We hypothesized that increased diversity of S. aureus would impact CF lung disease. Therefore, we conducted a 1-year observational prospective study with 14 patients with long-term S. aureus infection. From every sputum, 40 S. aureus isolates were chosen and characterized in terms of phenotypic appearance (size, hemolysis, mucoidy, and pigmentation), important virulence traits such as nuclease activity, biofilm formation, and molecular typing by spa sequence typing. Data about coinfection with Pseudomonas aeruginosa and clinical parameters such as lung function, exacerbation, and inflammatory markers in blood (C-reactive protein [CRP], interleukin 6 [IL-6], and S100A8/9 [calprotectin]) were collected. From 58 visits of 14 patients, 2,319 S. aureus isolates were distinguished into 32 phenotypes (PTs) and 50 spa types. The Simpson diversity index (SDI) was used to calculate the phenotypic and genotypic diversity, revealing a high diversity of PTs ranging from 0.19 to 0.87 among patients, while the diversity of spa types of isolates was less pronounced. The SDI of PTs was positively associated with P. aeruginosa coinfection and inflammatory parameters, with IL-6 being the most sensitive parameter. Also, coinfection with P. aeruginosa was associated with mucoid S. aureus and S. aureus with high nuclease activity. Our analyses showed that in CF patients with long-term S. aureus airway infection, a highly diverse and dynamic S. aureus population was present and associated with P. aeruginosa coinfection and inflammation. IMPORTANCE Staphylococcus aureus can persist for extended periods in the airways of people with cystic fibrosis (CF) in spite of antibiotic therapy and high numbers of neutrophils, which fail to eradicate this pathogen. Therefore, S. aureus needs to adapt to this hostile niche. There is only limited knowledge about the diversity of S. aureus in respiratory specimens. We conducted a 1-year prospective study with 14 patients with long-term S. aureus infection and investigated 40 S. aureus isolates from every sputum in terms of phenotypic appearance, nuclease activity, biofilm formation, and molecular typing. Data about coinfection with Pseudomonas aeruginosa and clinical parameters such as lung function, exacerbation, and inflammatory markers in blood were collected. Thirty-two phenotypes (PTs) and 50 spa types were distinguished. Our analyses revealed that in CF patients with long-term S. aureus airway infection, a highly diverse and dynamic S. aureus population was associated with P. aeruginosa coinfection and inflammation.
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13
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14
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Watanabe Y, Oikawa N, Hariu M, Seki M. Evaluation of agar culture plates to efficiently identify small colony variants of methicillin-resistant Staphylococcus aureus. Infect Drug Resist 2019; 12:1743-1748. [PMID: 31417291 PMCID: PMC6593740 DOI: 10.2147/idr.s207057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/22/2019] [Indexed: 11/23/2022] Open
Abstract
Background: Small-colony variants of methicillin-resistant Staphylococcus aureus (SCV-MRSA) recently were described as slow-growing, thymidine-dependent strains; typically, SCV-MRSA were isolated from patients receiving sulfamethoxazole-trimethoprim, but detection of these strains frequently was delayed because of their small colony size and slow growth. Bacteremia cases due to SCV-MRSA sometimes become lethal when the initiation of treatment with intravenous anti-methicillin-resistant Staphylococcus aureus (MRSA) drugs starts too late. Methods: Here, we evaluated the use of general MRSA-specific agar plates in Japan, including MS-CFX, X-MRSA, and CHROMagar, for the efficient detection of SCV-MRSA, including the comparative detection efficiencies of these media for stock strains and clinical isolates. Results: Among the three MRSA-specific agar plates that were tested, X-MRSA and CHROMagar showed similar detection efficiencies for both 24 and 48 hrs culturing; in contrast, MS-CFS did not permit the detection of SCV-MRSA in stock strains. For clinical isolates of SCV-MRSA, X-MRSA plates permitted detection of the smallest and slowest-growing colonies of SCV-MRSA at 48 hrs of culturing; in contrast, CHROMagar and MS-CFX sometimes did not identify SCV-MRSA at 24 and 48 hrs. Conclusion: Optimization of media and incubation times will be necessary for efficient identification for SCV-MRSA, which would prevent delays in diagnosis and treatment with anti-MRSA drugs.
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Affiliation(s)
- Yuji Watanabe
- Division of Infectious Diseases and Infection Control.,Laboratory for Clinical Microbiology, Tohoku Medical and Pharmaceutical University Hospital, Sendai City, Miyagi, Japan
| | - Nozomi Oikawa
- Division of Infectious Diseases and Infection Control.,Laboratory for Clinical Microbiology, Tohoku Medical and Pharmaceutical University Hospital, Sendai City, Miyagi, Japan
| | - Maya Hariu
- Division of Infectious Diseases and Infection Control.,Laboratory for Clinical Microbiology, Tohoku Medical and Pharmaceutical University Hospital, Sendai City, Miyagi, Japan
| | - Masafumi Seki
- Division of Infectious Diseases and Infection Control
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15
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Kittinger C, Toplitsch D, Folli B, Masoud Landgraf L, Zarfel G. Phenotypic Stability of Staphylococcus Aureus Small Colony Variants (SCV) Isolates from Cystic Fibrosis (CF) Patients. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16111940. [PMID: 31159295 PMCID: PMC6603916 DOI: 10.3390/ijerph16111940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/23/2022]
Abstract
One of the most interesting features of Staphylococcus aureus is its ability to switch to a small colony variant (SCV). This switch allows the pathogen to survive periods of antibiotic treatment or pressure from the immune system of the host and further enables it to start the infection once again after the environmental stress declines. However, so far only little is known about this reversion back to the more virulent wild type phenotype. Therefore, this study aimed to analyze the frequency of reversion to the wild type phenotype of thymidine auxotroph S. aureus SCV isolates (TD-SCVs) obtained from patients with cystic fibrosis (CF). With the use of single cell starting cultures, the occurrence of the thymidine prototroph revertants was monitored. The underlying mutational cause of the SCVs and subsequent revertants were analyzed by sequencing the gene coding for thymidylate synthase (ThyA), whose mutations are known to produce thymidine auxotroph S. aureus SCV. In our study, the underlying mutational cause for the switch to the TD-SCV phenotype was primarily point mutations. Out of twelve isolates, seven isolates showed an occurrence of revertants with a frequency ranging from 90.06% to 0.16%. This high variability in the frequency of reversion to the wild type was not expected. However, this variability in the frequency of reversion may also be the key to successful re-infection of the host. Sometimes quick reversion to the wild type proves necessary for survival, whereas other times, staying hidden for a bit longer leads to success in re-colonization of the host.
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Affiliation(s)
- Clemens Kittinger
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria.
| | - Daniela Toplitsch
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria.
| | - Bettina Folli
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria.
| | - Lilian Masoud Landgraf
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria.
| | - Gernot Zarfel
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria.
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16
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The prevalence of Staphylococcus aureus with mucoid phenotype in the airways of patients with cystic fibrosis-A prospective study. Int J Med Microbiol 2019; 309:283-287. [PMID: 31122879 DOI: 10.1016/j.ijmm.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/10/2019] [Accepted: 05/10/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is one of the most frequently isolated pathogens in the respiratory tract of CF patients. Recently, we characterized peculiar mucoid S. aureus isolates, which are excessive biofilm formers and which carried a 5bp-deletion within the intergenic region of the ica operon. In this prospective study, we determined the prevalence of mucoid S. aureus-isolates in the airways of CF-patients during a 3-months period. METHODS We analyzed specimens (sputa, throat swabs) from 81 CF patients who attended two CF centers in Münster, Germany. Ten S. aureus isolates were randomly picked from every S. aureus-positive airway specimen and evaluated for mucoidy using Congo Red agar and phenotypic tests. Mucoid isolates were characterized by spa sequence typing, biofilm production and sequencing of the intergenic region of the ica operon to screen for the 5bp-deletion. RESULTS In 7 of 81 examined patients (8.6%), we detected mucoid S. aureus phenotypes (37 out of 1050 isolates; 3.5%). Twenty-five mucoid isolates carried the 5bp-deletion. Mucoid isolates produced excessive biofilm and were significantly more resistant to certain antibiotics. CONCLUSIONS In our prospective study, mucoid S. aureus was present in 8.6% of S. aureus-positive CF-patients. In 6 of 7 patients, mucoid isolates carried the 5bp-deletion, indicating that also other so far not identified mechanisms cause excessive biofilm formation. Further studies are necessary to ascertain the clinical impact of mucoid S. aureus phenotypes on the severity of the CF disease.
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17
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Langhanki L, Berger P, Treffon J, Catania F, Kahl BC, Mellmann A. In vivo competition and horizontal gene transfer among distinct Staphylococcus aureus lineages as major drivers for adaptational changes during long-term persistence in humans. BMC Microbiol 2018; 18:152. [PMID: 30348081 PMCID: PMC6198438 DOI: 10.1186/s12866-018-1308-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/09/2018] [Indexed: 02/08/2023] Open
Abstract
Background The airways of the majority of adolescent cystic fibrosis (CF) patients are persistently colonized or infected by Staphylococcus aureus. Using whole genome sequencing, we studied the evolutionary traits within a S. aureus population in the airways of a CF patient hypothesizing that horizontal gene transfer (HGT) and inter-bacterial interaction play a major role in adaptation during long-term persistence. Results Whole genome sequencing of 21 S. aureus isolates spanning 13 years resulted in seven lineages defined by the spa types t012, t021, t331, t338, t364, t056, and t2351. Of these, the successfully persisting lineages t012 and t021 were closely related suggesting the evolution of t021 from t012, which was further corroborated by a nearly identical, syntenic set of mobile genetic elements. During transformation from t012 to t021, an increase of genomic changes including HGT from other S. aureus lineages was detected. Conclusions In summary, our in vivo data enabled us to conceptualize an evolutionary model showing the impact of HGT and inter-bacterial interaction on bacterial long-term adaptation to the human host during CF. Electronic supplementary material The online version of this article (10.1186/s12866-018-1308-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lars Langhanki
- Institute of Hygiene, University Hospital Münster, Robert-Koch Straße 41, Münster, 48149, Germany
| | - Petya Berger
- Institute of Hygiene, University Hospital Münster, Robert-Koch Straße 41, Münster, 48149, Germany
| | - Janina Treffon
- Institute of Med. Microbiology, University Hospital Muenster, Domagkstraße 10, 48149, Münster, Germany
| | - Francesco Catania
- Institute for Evolution and Biodiversity Muenster, Hüfferstraße 1, 48149, Münster, Germany
| | - Barbara C Kahl
- Institute of Med. Microbiology, University Hospital Muenster, Domagkstraße 10, 48149, Münster, Germany
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Münster, Robert-Koch Straße 41, Münster, 48149, Germany.
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Negishi T, Matsumoto T, Horiuchi K, Kasuga E, Natori T, Matsuoka M, Ogiwara N, Sugano M, Uehara T, Nagano N, Honda T. Characterization of clinically isolated thymidine-dependent small-colony variants of Escherichia coli producing extended-spectrum β-lactamase. J Med Microbiol 2017; 67:33-39. [PMID: 29143727 DOI: 10.1099/jmm.0.000634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Thymidine-dependent small-colony variants (TD-SCVs) are difficult to detect or test for antimicrobial susceptibility. We investigated the characteristics of clonal TD-SCVs of Escherichia coli, both with and without blaCTX-M-3, isolated from a patient. METHODOLOGY Mutation in the thyA gene was analysed by sequencing, and morphological abnormalities in the colonies and cells of the isolates were examined. Additionally, conjugational transfer experiments were performed to prove the horizontal transferability of plasmids harbouring resistance genes. RESULTS The TD-SCVs contained a single nucleotide substitution in the thyA gene, c.62G>A, corresponding to p.Arg21His. Morphologically, their colonies were more translucent and flattened than those of the wild-type strain. In addition, cells of the TD-SCVs were swollen and elongated, sometimes with abnormal and incomplete divisions; a large amount of cell debris was also observed. Changing c.62G>A back to the wild-type sequence reversed these abnormalities. Conjugational transfer experiments showed that the TD-SCV of E. coli with blaCTX-M-3 failed to transfer blaCTX-M-3 to E. coli CSH2. However, the TD-SCV of E. coli without blaCTX-M-3 experimentally received the plasmid encoding blaSHV-18 from Klebsiella pneumoniae ATCC 700603 and transferred it to E. coli CSH2. CONCLUSION Mutation in the thyA gene causes morphological abnormalities in the colonies and cells of E. coli, as well as inducing thymidine auxotrophy. In addition, TD-SCVs horizontally transmit plasmids encoding resistance genes. It is important to detect TD-SCVs based on their characteristics because they serve as reservoirs of transferable antibiotic resistance plasmids.
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Affiliation(s)
- Tatsuya Negishi
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.,Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514, Japan
| | - Kazuki Horiuchi
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Eriko Kasuga
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Tatsuya Natori
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Mina Matsuoka
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Naoko Ogiwara
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Mitsutoshi Sugano
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takeshi Uehara
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Noriyuki Nagano
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takayuki Honda
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
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Kubistova L, Dvoracek L, Tkadlec J, Melter O, Licha I. Environmental Stress Affects the Formation of Staphylococcus aureus Persisters Tolerant to Antibiotics. Microb Drug Resist 2017; 24:547-555. [PMID: 28813617 DOI: 10.1089/mdr.2017.0064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ability to form persisters has been observed in many microorganisms, including Staphylococcus aureus, mainly in the context of chronic infections and the pathogenicity of these microbes. In our research, we have demonstrated that salt or oxidative stress could play a role in the formation of S. aureus persisters outside the host's intracellular interface. We pre-exposed planktonic growing bacterial culture to an oxidative or salt stress and monitored the dynamics of persister formation after ciprofloxacin and gentamicin treatment. In parallel, using the quantitative PCR (qPCR) approach, we determined the expression level of the stress sigma factor SigB. The pre-exposure of bacteria to salt stress caused a 1-2.5 order of magnitude increase in persister formation in the bacterial population after antibiotic exposure, depending on the type and concentration of the antibiotic used. In contrast, oxidative stress only minimally influenced the formation of persisters, without correlation to the antibiotic type and concentration. We have demonstrated that both stress and antibiotic exposure increase the expression of sigB in bacterial populations from very early on. And that the expression level of sigB differs with the type of antibiotic and stress, but no correlation was observed between persister formation and sigB expression. The method used could be helpful in testing the ability that strains can have, to form persisters.
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Affiliation(s)
- Lucie Kubistova
- 1 Department of Genetics and Microbiology, Faculty of Science, Charles University , Prague, Czech Republic
| | - Lukas Dvoracek
- 1 Department of Genetics and Microbiology, Faculty of Science, Charles University , Prague, Czech Republic
| | - Jan Tkadlec
- 2 Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University , Prague, Czech Republic .,3 Department of Medical Microbiology, Motol University Hospital , Prague, Czech Republic
| | - Oto Melter
- 2 Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University , Prague, Czech Republic .,3 Department of Medical Microbiology, Motol University Hospital , Prague, Czech Republic
| | - Irena Licha
- 1 Department of Genetics and Microbiology, Faculty of Science, Charles University , Prague, Czech Republic
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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Rapid Acquisition of Linezolid Resistance in Methicillin-Resistant Staphylococcus aureus: Role of Hypermutation and Homologous Recombination. PLoS One 2016; 11:e0155512. [PMID: 27182700 PMCID: PMC4868352 DOI: 10.1371/journal.pone.0155512] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/30/2016] [Indexed: 01/01/2023] Open
Abstract
Background We previously reported the case of a 64-year-old man with mediastinitis caused by Staphylococcus aureus in which the infecting bacterium acquired linezolid resistance after only 14 days treatment with linezolid. We therefore investigated relevant clinical isolates for possible mechanisms of this rapid acquisition of linezolid resistance. Methods Using clinical S. aureus isolates, we assessed the in vitro mutation rate and performed stepwise selection for linezolid resistance. To investigate homologous recombination, sequences were determined for each of the 23S ribosomal RNA (23S rRNA) loci; analyzed sequences spanned the entirety of each 23S rRNA gene, including domain V, as well as the 16S-23S intergenic spacer regions. We additionally performed next-generation sequencing on clinical strains to identify single-nucleotide polymorphisms compared to the N315 genome. Results Strains isolated from the patient prior to linezolid exposure (M5-M7) showed higher-level linezolid resistance than N315, and the pre-exposure strain (M2) exhibited more rapid acquisition of linezolid resistance than did N315. However, the mutation rates of these and contemporaneous clinical isolates were similar to those of N315, and the isolates did not exhibit any mutations in hypermutation-related genes. Sequences of the 23S rRNA genes and 16S-23S intergenic spacer regions were identical among the pre- and post-exposure clinical strains. Notably, all of the pre-exposure isolates harbored a recQ missense mutation (Glu69Asp) with respect to N315; such a lesion may have affected short sequence recombination (facilitating, for example, recombination among rrn loci). We hypothesize that this mechanism contributed to rapid acquisition of linezolid resistance. Conclusions Hypermutation and homologous recombination of the ribosomal RNA genes, including 23S rRNA genes, appear not to have been sources of the accelerated acquisition of linezolid resistance observed in our clinical case. Increased frequency of short sequence recombination may have resulted from a recQ variant in the infecting organism.
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Saiman L, Siegel JD, LiPuma JJ, Brown RF, Bryson EA, Chambers MJ, Downer VS, Fliege J, Hazle LA, Jain M, Marshall BC, O’Malley C, Pattee SR, Potter-Bynoe G, Reid S, Robinson KA, Sabadosa KA, Schmidt HJ, Tullis E, Webber J, Weber DJ. Infection Prevention and Control Guideline for Cystic Fibrosis: 2013 Update. Infect Control Hosp Epidemiol 2016; 35 Suppl 1:S1-S67. [DOI: 10.1086/676882] [Citation(s) in RCA: 270] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The 2013 Infection Prevention and Control (IP&C) Guideline for Cystic Fibrosis (CF) was commissioned by the CF Foundation as an update of the 2003 Infection Control Guideline for CF. During the past decade, new knowledge and new challenges provided the following rationale to develop updated IP&C strategies for this unique population:1.The need to integrate relevant recommendations from evidence-based guidelines published since 2003 into IP&C practices for CF. These included guidelines from the Centers for Disease Control and Prevention (CDC)/Healthcare Infection Control Practices Advisory Committee (HICPAC), the World Health Organization (WHO), and key professional societies, including the Infectious Diseases Society of America (IDSA) and the Society for Healthcare Epidemiology of America (SHEA). During the past decade, new evidence has led to a renewed emphasis on source containment of potential pathogens and the role played by the contaminated healthcare environment in the transmission of infectious agents. Furthermore, an increased understanding of the importance of the application of implementation science, monitoring adherence, and feedback principles has been shown to increase the effectiveness of IP&C guideline recommendations.2.Experience with emerging pathogens in the non-CF population has expanded our understanding of droplet transmission of respiratory pathogens and can inform IP&C strategies for CF. These pathogens include severe acute respiratory syndrome coronavirus and the 2009 influenza A H1N1. Lessons learned about preventing transmission of methicillin-resistantStaphylococcus aureus(MRSA) and multidrug-resistant gram-negative pathogens in non-CF patient populations also can inform IP&C strategies for CF.
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Ramsay KA, Stockwell RE, Bell SC, Kidd TJ. Infection in cystic fibrosis: impact of the environment and climate. Expert Rev Respir Med 2016; 10:505-19. [PMID: 26949990 DOI: 10.1586/17476348.2016.1162715] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In many countries numbers of adults with cystic fibrosis (CF) exceed that of children, with median survival predicted to surpass 50 years. Increasing longevity is, in part, due to intensive therapies including eradication of early infection and suppressive therapies and pulmonary exacerbations. Initial infections with common CF pathogens are thought to arise from the natural environment. We review the impact of climate and environment on infection in CF. Specifically, several studies indicate that higher ambient temperatures, proximity to the equator and the summer season may be linked to the increased prevalence of Pseudomonas aeruginosa in people with CF. The environment may also play an important role in the acquisition of Gram negative organisms other than P. aeruginosa. There is emerging data suggesting that climatic and environmental factors are likely to impact on the risk of infection with NTM and fungi in people which are found extensively throughout the natural environment.
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Affiliation(s)
- K A Ramsay
- a Lung Bacteria Group , QIMR Berghofer Medical Research Institute , Brisbane , Australia.,b Child Health Research Centre, The University of Queensland , Brisbane , Australia.,c School of Medicine , The University of Queensland , Brisbane , Australia
| | - R E Stockwell
- a Lung Bacteria Group , QIMR Berghofer Medical Research Institute , Brisbane , Australia
| | - S C Bell
- a Lung Bacteria Group , QIMR Berghofer Medical Research Institute , Brisbane , Australia.,c School of Medicine , The University of Queensland , Brisbane , Australia.,d Adult Cystic Fibrosis Centre , The Prince Charles Hospital , Brisbane , Australia
| | - T J Kidd
- b Child Health Research Centre, The University of Queensland , Brisbane , Australia.,e Centre for Infection and Immunity , Queen's University Belfast , Belfast , UK.,f School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Australia
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Vestergaard M, Paulander W, Ingmer H. Activation of the SOS response increases the frequency of small colony variants. BMC Res Notes 2015; 8:749. [PMID: 26643526 PMCID: PMC4672542 DOI: 10.1186/s13104-015-1735-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/24/2015] [Indexed: 02/07/2023] Open
Abstract
Background In Staphylococcus aureus sub-populations of slow-growing cells forming small colony variants (SCVs) are associated with persistent and recurrent infections that are difficult to eradicate with antibiotic therapies. In SCVs that are resistant towards aminoglycosides, mutations have been identified in genes encoding components of the respiratory chain. Given the high frequencies of SCVs isolated clinically it is vital to understand the conditions that promote or select for SCVs. Results In this study we have examined how exposure to sub-inhibitory concentrations of antibiotics with different mechanism of action influence the formation of SCVs that are resistant to otherwise lethal concentrations of the aminoglycoside, gentamicin. We found that exposure of S. aureus to fluoroquinolones and mitomycin C increased the frequency of gentamicin resistant SCVs, while other antibiotic classes failed to do so. The higher proportion of SCVs in cultures exposed to fluoroquinolones and mitomycin C compared to un-exposed cultures correlate with an increased mutation rate monitored by rifampicin resistance and followed induction of the SOS DNA damage response. Conclusion Our observations suggest that environmental stimuli, including antimicrobials that reduce replication fidelity, increase the formation of SCVs through activation of the SOS response and thereby potentially promote persistent infections that are difficult to treat.
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Affiliation(s)
- Martin Vestergaard
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark.
| | - Wilhelm Paulander
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark.
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark.
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25
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Bartoli C, Lamichhane JR, Berge O, Varvaro L, Morris CE. Mutability in Pseudomonas viridiflava as a programmed balance between antibiotic resistance and pathogenicity. MOLECULAR PLANT PATHOLOGY 2015; 16:860-9. [PMID: 25649542 PMCID: PMC6638476 DOI: 10.1111/mpp.12243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mutable bacterial cells are defective in their DNA repair system and often have a phenotype different from that of their wild-type counterparts. In human bacterial pathogens, the mutable and hypermutable phenotypes are often associated with general antibiotic resistance. Here, we quantified the occurrence of mutable cells in Pseudomonas viridiflava, a phytopathogenic bacterium in the P. syringae complex with a broad host range and capacity to live as a saprophyte. Two phenotypic variants (transparent and mucoid) were produced by this bacterium. The transparent variant had a mutator phenotype, showed general antibiotic resistance and could not induce disease on the plant species tested (bean). In contrast, the mucoid variant did not display mutability or resistance to antibiotics and was capable of inducing disease on bean. Both the transparent and mucoid variants were less fit when grown in vitro, whereas, in planta, both of the variants and wild-types attained similar population densities. Given the importance of the methyl-directed mismatch repair system (MMR) in the occurrence of mutable and hypermutable cells in human bacterial pathogens, we investigated whether mutations in mut genes were associated with mutator transparent cells in P. viridiflava. Our results showed no mutations in MMR genes in any of the P. viridiflava cells tested. Here, we report that a high mutation rate and antibiotic resistance are inversely correlated with pathogenicity in P. viridiflava, but are not associated with mutations in MMR. In addition, P. viridiflava variants differ from variants produced by other phytopathogenic bacteria in the absence of reversion to the wild-type phenotype.
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Affiliation(s)
- Claudia Bartoli
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), Tuscia University, 01100, Viterbo, Italy
- INRA, UR0407 Pathologie Végétale, F-84143, Montfavet cedex, France
| | - Jay Ram Lamichhane
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), Tuscia University, 01100, Viterbo, Italy
- INRA, UR0407 Pathologie Végétale, F-84143, Montfavet cedex, France
| | - Odile Berge
- INRA, UR0407 Pathologie Végétale, F-84143, Montfavet cedex, France
| | - Leonardo Varvaro
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), Tuscia University, 01100, Viterbo, Italy
| | - Cindy E Morris
- INRA, UR0407 Pathologie Végétale, F-84143, Montfavet cedex, France
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26
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Johns BE, Purdy KJ, Tucker NP, Maddocks SE. Phenotypic and Genotypic Characteristics of Small Colony Variants and Their Role in Chronic Infection. Microbiol Insights 2015; 8:15-23. [PMID: 26448688 PMCID: PMC4581789 DOI: 10.4137/mbi.s25800] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/09/2015] [Accepted: 08/13/2015] [Indexed: 01/02/2023] Open
Abstract
Small colony variant (SCV) bacteria arise spontaneously within apparently homogeneous microbial populations, largely in response to environmental stresses, such as antimicrobial treatment. They display unique phenotypic characteristics conferred in part by heritable genetic changes. Characteristically slow growing, SCVs comprise a minor proportion of the population from which they arise but persist by virtue of their inherent resilience and host adaptability. Consequently, SCVs are problematic in chronic infection, where antimicrobial treatment is administered during the acute phase of infection but fails to eradicate SCVs, which remain within the host causing recurrent or chronic infection. This review discusses some of the phenotypic and genotypic changes that enable SCVs to successfully proliferate within the host environment as potential pathogens and strategies that could ameliorate the resolution of infection where SCVs are present.
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Affiliation(s)
- Benjamin E Johns
- Department of Biomedical Science, Cardiff School of Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - Kevin J Purdy
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Sarah E Maddocks
- Department of Biomedical Science, Cardiff School of Health Sciences, Cardiff Metropolitan University, Cardiff, UK
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Thymidine-Dependent Staphylococcus aureus Small-Colony Variants Are Induced by Trimethoprim-Sulfamethoxazole (SXT) and Have Increased Fitness during SXT Challenge. Antimicrob Agents Chemother 2015; 59:7265-72. [PMID: 26369968 DOI: 10.1128/aac.00742-15] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/04/2015] [Indexed: 11/20/2022] Open
Abstract
Trimethoprim-sulfamethoxazole (SXT) is a possible alternative for the treatment of community- and hospital-acquired methicillin-resistant Staphylococcus aureus (MRSA) due to the susceptibility of most MRSA strains to the drug. However, after long-term treatment with SXT, thymidine-dependent (TD) SXT-resistant small-colony variants (SCVs) emerge. In TD-SCVs, mutations of thymidylate synthase ([TS] thyA) occur. Until now, it has never been systematically investigated that SXT is triggering the induction and/or selection of TD-SCVs. In our study, we performed induction, reversion, and competition experiments in vitro and in vivo using a chronic mouse pneumonia model to determine the impact of SXT on the emergence of TD-SCVs. SCVs were characterized by light and transmission electron microscopy (TEM) and auxotrophism testing. Short-term exposure of S. aureus to SXT induced the TD-SCV phenotype in S. aureus SH1000, while selection of TD-SCVs with thyA mutations occurred after long-term exposure. In reversion experiments with clinical and laboratory TD-SCVs, all revertants carried compensating mutations at the initially identified mutation site. Competition experiments in vitro and in vivo revealed a survival and growth advantage of the ΔthyA mutant under low-thymidine availability and SXT exposure although this advantage was less profound in vivo. Our results show that SXT induces the TD-SCV phenotype after short-term exposure, while long-term exposure selects for thyA mutations, which provide an advantage for TD-SCVs under specified conditions. Thus, our results further an understanding of the dynamic processes occurring during SXT exposure with induction and selection of S. aureus TD-SCVs.
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28
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Khodursky A, Guzmán EC, Hanawalt PC. Thymineless Death Lives On: New Insights into a Classic Phenomenon. Annu Rev Microbiol 2015; 69:247-63. [PMID: 26253395 DOI: 10.1146/annurev-micro-092412-155749] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The primary mechanisms by which bacteria lose viability when deprived of thymine have been elusive for over half a century. Early research focused on stalled replication forks and the deleterious effects of uracil incorporation into DNA from thymidine-deficient nucleotide pools. The initiation of the replication cycle and origin-proximal DNA degradation during thymine starvation have now been quantified via whole-genome microarrays and other approaches. These advances have fostered innovative models and informative experiments in bacteria since this topic was last reviewed. Given that thymineless death is similar in mammalian cells and that certain antibacterial and chemotherapeutic drugs elicit thymine deficiency, a mechanistic understanding of this phenomenon might have valuable biomedical applications.
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Affiliation(s)
- Arkady Khodursky
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108;
| | - Elena C Guzmán
- Departamento de Bioquímica Biología Molecular y Genética, Universidad de Extremadura, 06071 Badajoz, Spain;
| | - Philip C Hanawalt
- Department of Biology, Stanford University, Stanford, California 94305;
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29
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Tkadlec J, Vařeková E, Pantůček R, Doškař J, Růžičková V, Botka T, Fila L, Melter O. Characterization ofStaphylococcus aureusStrains Isolated from Czech Cystic Fibrosis Patients: High Rate of Ribosomal Mutation Conferring Resistance to MLSBAntibiotics as a Result of Long-Term and Low-Dose Azithromycin Treatment. Microb Drug Resist 2015; 21:416-23. [DOI: 10.1089/mdr.2014.0276] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Jan Tkadlec
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Eva Vařeková
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Doškař
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Vladislava Růžičková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tibor Botka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Libor Fila
- Department of Pneumology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Oto Melter
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
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30
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Altered Competitive Fitness, Antimicrobial Susceptibility, and Cellular Morphology in a Triclosan-Induced Small-Colony Variant of Staphylococcus aureus. Antimicrob Agents Chemother 2015; 59:4809-16. [PMID: 26033734 DOI: 10.1128/aac.00352-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/24/2015] [Indexed: 01/16/2023] Open
Abstract
Staphylococcus aureus can produce small-colony variants (SCVs) that express various phenotypes. While their significance is unclear, SCV propagation may be influenced by relative fitness, antimicrobial susceptibility, and the underlying mechanism. We have investigated triclosan-induced generation of SCVs in six S. aureus strains, including methicillin-resistant S. aureus (MRSA). Parent strains (P0) were repeatedly passaged on concentration gradients of triclosan using a solid-state exposure system to generate P10. P10 was subsequently passaged without triclosan to generate X10. Susceptibility to triclosan and 7 antibiotics was assessed at all stages. For S. aureus ATCC 6538, SCVs were further characterized by determining microbicide susceptibility and competitive fitness. Cellular morphology was examined using electron microscopy, and protein expression was evaluated through proteomics. Triclosan susceptibility in all SCVs (which could be generated from 4/6 strains) was markedly decreased, while antibiotic susceptibility was significantly increased in the majority of cases. An SCV of S. aureus ATCC 6538 exhibited significantly increased susceptibility to all tested microbicides. Cross-wall formation was impaired in this bacterium, while expression of FabI, a target of triclosan, and IsaA, a lytic transglycosylase involved in cell division, was increased. The P10 SCV was 49% less fit than P0. In summary, triclosan exposure of S. aureus produced SCVs in 4/6 test bacteria, with decreased triclosan susceptibility but with generally increased antibiotic susceptibility. An SCV derived from S. aureus ATCC 6538 showed reduced competitive fitness, potentially due to impaired cell division. In this SCV, increased FabI expression could account for reduced triclosan susceptibility, while IsaA may be upregulated in response to cell division defects.
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31
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Long SW, Olsen RJ, Mehta SC, Palzkill T, Cernoch PL, Perez KK, Musick WL, Rosato AE, Musser JM. PBP2a mutations causing high-level Ceftaroline resistance in clinical methicillin-resistant Staphylococcus aureus isolates. Antimicrob Agents Chemother 2014; 58:6668-74. [PMID: 25155594 PMCID: PMC4249384 DOI: 10.1128/aac.03622-14] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/16/2014] [Indexed: 12/25/2022] Open
Abstract
Ceftaroline is the first member of a novel class of cephalosporins approved for use in the United States. Although prior studies have identified eight ceftaroline-resistant methicillin-resistant Staphylococcus aureus (MRSA) isolates in Europe and Asia with MICs ranging from 4 to 8 mg/liter, high-level resistance to ceftaroline (>32 mg/liter) has not been described in MRSA strains isolated in the United States. We isolated a ceftaroline-resistant (MIC > 32 mg/liter) MRSA strain from the blood of a cystic fibrosis patient and five MRSA strains from the respiratory tract of this patient. Whole-genome sequencing identified two amino acid-altering mutations uniquely present in the ceftaroline-binding pocket of the transpeptidase region of penicillin-binding protein 2a (PBP2a) in ceftaroline-resistant isolates. Biochemical analyses and the study of isogenic mutant strains confirmed that these changes caused ceftaroline resistance. Thus, we identified the molecular mechanism of ceftaroline resistance in the first MRSA strain with high-level ceftaroline resistance isolated in the United States.
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Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Shrenik C Mehta
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Patricia L Cernoch
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Katherine K Perez
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
| | - William L Musick
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
| | - Adriana E Rosato
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
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32
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Dalhoff A. Pharmacokinetics and pharmacodynamics of aerosolized antibacterial agents in chronically infected cystic fibrosis patients. Clin Microbiol Rev 2014; 27:753-82. [PMID: 25278574 PMCID: PMC4187638 DOI: 10.1128/cmr.00022-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacteria adapt to growth in lungs of patients with cystic fibrosis (CF) by selection of heterogeneously resistant variants that are not detected by conventional susceptibility testing but are selected for rapidly during antibacterial treatment. Therefore, total bacterial counts and antibiotic susceptibilities are misleading indicators of infection and are not helpful as guides for therapy decisions or efficacy endpoints. High drug concentrations delivered by aerosol may maximize efficacy, as decreased drug susceptibilities of the pathogens are compensated for by high target site concentrations. However, reductions of the bacterial load in sputum and improvements in lung function were within the same ranges following aerosolized and conventional therapies. Furthermore, the use of conventional pharmacokinetic/pharmacodynamic (PK/PD) surrogates correlating pharmacokinetics in serum with clinical cure and presumed or proven eradication of the pathogen as a basis for PK/PD investigations in CF patients is irrelevant, as minimization of systemic exposure is one of the main objectives of aerosolized therapy; in addition, bacterial pathogens cannot be eradicated, and chronic infection cannot be cured. Consequently, conventional PK/PD surrogates are not applicable to CF patients. It is nonetheless obvious that systemic exposure of patients, with all its sequelae, is minimized and that the burden of oral treatment for CF patients suffering from chronic infections is reduced.
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Affiliation(s)
- Axel Dalhoff
- University Medical Center Schleswig-Holstein, Institute for Infection Medicine, Kiel, Germany
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33
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Champion EA, Miller MB, Popowitch EB, Hobbs MM, Saiman L, Muhlebach MS. Antimicrobial susceptibility and molecular typing of MRSA in cystic fibrosis. Pediatr Pulmonol 2014; 49:230-7. [PMID: 23765686 DOI: 10.1002/ppul.22815] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 04/05/2013] [Indexed: 11/11/2022]
Abstract
OBJECTIVES The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in cystic fibrosis (CF) patients in the United States is approximately 25%. Little is known about the relative proportion of hospital- versus community-associated strains or the antimicrobial susceptibility of MRSA in different CF centers. We hypothesized that the majority of MRSA isolates obtained from children with CF are those endemic in the hospital and that those associated with community acquisition (SCCmec IV) would be more resistant than typically seen in non-CF MRSA isolates. METHODS We studied MRSA strains from seven pediatric CF centers to determine the clonal distribution based on DNA sequencing of the staphylococcal protein A gene (spa typing), the type of staphylococcal chromosomal cassette mec (SCCmec), and the proportion of strains with Panton-Valentine leukocidin (PVL). Antimicrobial susceptibility to systemic and topical antibiotics was compared between different MRSA types. RESULTS We analyzed 277 MRSA isolates from unique patients (mean age 11.15 ± 4.77 years, 55% male). Seventy % of isolates were SCCmec II PVL negative and the remainder SCCmec IV. Overall 17% MRSA strains were PVL positive (all SCCmec IV). Spa typing of 118 isolates showed most of the SCCmec II strains being t002, while SCCmec IV PVL positive isolates were t008, and SCCmec IV PVL negative isolates represented a variety of spa-types. The proportions of SCCmec II strains and spa-types were similar among centers. Overall rates of resistance to trimethoprim-sulfamethoxazole (4%), tetracycline (7%), tigecycline (0.4%), linezolid (0.4%) as well as fosfomycin (0.4%), fusidic acid (3%), and mupirocin (1%) were low. No strains were resistant to vancomycin. SCCmec II strains had higher rates of resistance to ciprofloxacin and clindamycin (P < 0.001) than SCCmec IV strains. CONCLUSIONS In this U.S. study, most MRSA isolates in the pediatric CF population were SCCmec II PVL negative. Rates of resistance were low, including to older and orally available antibiotics such as trimethoprim-sulfamethoxazole.
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Affiliation(s)
- E A Champion
- Division of Pediatric Pulmonology, Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina
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34
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Woappi Y, Gabani P, Singh A, Singh OV. Antibiotrophs: The complexity of antibiotic-subsisting and antibiotic-resistant microorganisms. Crit Rev Microbiol 2014; 42:17-30. [PMID: 24495094 DOI: 10.3109/1040841x.2013.875982] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Widespread overuse of antibiotics has led to the emergence of numerous antibiotic-resistant bacteria; among these are antibiotic-subsisting strains capable of surviving in environments with antibiotics as the sole carbon source. This unparalleled expansion of antibiotic resistance reveals the potent and diversified resistance abilities of certain bacterial strains. Moreover, these strains often possess hypermutator phenotypes and virulence transmissibility competent for genomic and proteomic propagation and pathogenicity. Pragmatic and prospicient approaches will be necessary to develop efficient therapeutic methods against such bacteria and to understand the extent of their genomic adaptability. This review aims to reveal the niches of these antibiotic-catabolizing microbes and assesses the underlying factors linking natural microbial antibiotic production, multidrug resistance, and antibiotic-subsistence.
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Affiliation(s)
- Yvon Woappi
- a Division of Biological and Health Sciences , University of Pittsburgh , Bradford , PA , USA and
| | - Prashant Gabani
- a Division of Biological and Health Sciences , University of Pittsburgh , Bradford , PA , USA and
| | - Arya Singh
- b Department of Computer Science , Texas State University , San Marcos , TX , USA
| | - Om V Singh
- a Division of Biological and Health Sciences , University of Pittsburgh , Bradford , PA , USA and
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35
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Chaves F. [Infections due to small colony variants of Staphylococcus aureus: clinical and microbiological implications]. Enferm Infecc Microbiol Clin 2013; 32:67-9. [PMID: 24360833 DOI: 10.1016/j.eimc.2013.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 10/31/2013] [Indexed: 11/15/2022]
Affiliation(s)
- Fernando Chaves
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, España.
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36
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Miskinyte M, Sousa A, Ramiro RS, de Sousa JAM, Kotlinowski J, Caramalho I, Magalhães S, Soares MP, Gordo I. The genetic basis of Escherichia coli pathoadaptation to macrophages. PLoS Pathog 2013; 9:e1003802. [PMID: 24348252 PMCID: PMC3861542 DOI: 10.1371/journal.ppat.1003802] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 10/14/2013] [Indexed: 12/25/2022] Open
Abstract
Antagonistic interactions are likely important driving forces of the evolutionary process underlying bacterial genome complexity and diversity. We hypothesized that the ability of evolved bacteria to escape specific components of host innate immunity, such as phagocytosis and killing by macrophages (MΦ), is a critical trait relevant in the acquisition of bacterial virulence. Here, we used a combination of experimental evolution, phenotypic characterization, genome sequencing and mathematical modeling to address how fast, and through how many adaptive steps, a commensal Escherichia coli (E. coli) acquire this virulence trait. We show that when maintained in vitro under the selective pressure of host MΦ commensal E. coli can evolve, in less than 500 generations, virulent clones that escape phagocytosis and MΦ killing in vitro, while increasing their pathogenicity in vivo, as assessed in mice. This pathoadaptive process is driven by a mechanism involving the insertion of a single transposable element into the promoter region of the E. coli yrfF gene. Moreover, transposition of the IS186 element into the promoter of Lon gene, encoding an ATP-dependent serine protease, is likely to accelerate this pathoadaptive process. Competition between clones carrying distinct beneficial mutations dominates the dynamics of the pathoadaptive process, as suggested from a mathematical model, which reproduces the observed experimental dynamics of E. coli evolution towards virulence. In conclusion, we reveal a molecular mechanism explaining how a specific component of host innate immunity can modulate microbial evolution towards pathogenicity.
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Affiliation(s)
| | - Ana Sousa
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | | | - Iris Caramalho
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Unidade de Imunologia Clínica, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Sara Magalhães
- Centro Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | | | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail:
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Bogut A, Niedźwiadek J, Kozioł-Montewka M, Strzelec-Nowak D, Blacha J, Mazurkiewicz T, Marczyński W, Plewik D. Characterization of Staphylococcus epidermidis and Staphyloccocus warneri small-colony variants associated with prosthetic-joint infections. J Med Microbiol 2013; 63:176-185. [PMID: 24257683 DOI: 10.1099/jmm.0.066068-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We determined the frequency of isolation of staphylococcal small-colony variants (SCVs) from 31 culture-positive patients undergoing revision of total hip prosthesis for aseptic loosening or presumed prosthetic-joint infection (PJI). We analysed auxotrophy of cultured SCVs, their antimicrobial susceptibility profiles and their biofilm-forming capacity. Eight SCV strains were cultivated from six (19 %) patients. All SCVs were coagulase-negative staphylococci (CNS) with Staphylococcus epidermidis as the predominant species; there was also one Staphylococcus warneri SCV. The SCVs were auxotrophic for haemin, with one strain additionally auxotrophic for menadione. We noted the presence of two phenotypically (differences concerning antimicrobial susceptibility) and genetically distinct SCV strains in one patient, as well as the growth of two genetically related SCVs that differed in terms of their morphology and the type of auxotrophy in another. Seven out of eight SCVs were resistant to meticillin and gentamicin. In addition, antibiotic sensitivity testing revealed three multidrug-resistant SCV-normal-morphology isolate pairs. One S. epidermidis SCV harboured icaADBC genes and was found to be a proficient biofilm producer. This paper highlights the involvement of CNS SCVs in the aetiology of PJIs, including what is believed to be the first report of a S. warneri SCV. These subpopulations must be actively sought in the routine diagnosis of implant-associated infections. Moreover, in view of the phenotypic and genetic diversity of some SCV pairs, particular attention should be paid to the investigation of all types of observed colony morphologies, and isolates should be subjected to antimicrobial susceptibility testing.
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Affiliation(s)
- Agnieszka Bogut
- Department of Medical Microbiology, Medical University of Lublin, Chodźki 1 Street, 20-093 Lublin, Poland
| | - Justyna Niedźwiadek
- Department of Medical Microbiology, Medical University of Lublin, Chodźki 1 Street, 20-093 Lublin, Poland
| | - Maria Kozioł-Montewka
- Department of Medical Microbiology, Medical University of Lublin, Chodźki 1 Street, 20-093 Lublin, Poland
| | - Dagmara Strzelec-Nowak
- Department of Medical Microbiology, Medical University of Lublin, Chodźki 1 Street, 20-093 Lublin, Poland
| | - Jan Blacha
- Orthopaedics and Traumatology Ward, Clinical Hospital No. 4, Jaczewskiego 8 Street, 20-954 Lublin, Poland
| | - Tomasz Mazurkiewicz
- Orthopaedics and Traumatology Ward, Clinical Hospital No. 4, Jaczewskiego 8 Street, 20-954 Lublin, Poland
| | - Wojciech Marczyński
- Orthopaedics Ward, Public Clinical Hospital of Prof. Adam Gruca, Konarskiego 13 Street, 05-400 Otwock, Poland
| | - Dorota Plewik
- Research Centre for Innovation, Pope John Paul II State School of Higher Education in Biała Podlaska, Sidorska 105 Street, 21-500 Biała Podlaska, Poland
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Kubota N, Kuzumoto K, Hidaka E, Yoshizawa K, Yumoto K, Oana K, Ogiso Y, Nakamura T, Kawakami Y. First isolation of oleate-dependent Enterococcus faecalis small-colony variants from the umbilical exudate of a paediatric patient with omphalitis. J Med Microbiol 2013; 62:1883-1890. [PMID: 24072765 DOI: 10.1099/jmm.0.062752-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An oleate-dependent Enterococcus faecalis isolate representing small-colony variants (SCVs) was isolated from the umbilical exudate of a 31-month-old Japanese male patient in Nagano Children's Hospital, Azumino, Japan. The patient had been suffering from recurrent omphalitis since early infancy. The initial E. faecalis SCV isolate formed small colonies on sheep blood agar plates and tiny colonies on chocolate and modified Drigalski agar, although no visible growth was observed in HK-semi solid medium after 48 h incubation in ambient air. Moreover, the SCV isolate, the colonial morphology of which was reminiscent of Streptococcus species, could not be identified using the MicroScan WalkAway-40 and API 20 Strep systems, both of which yielded profile numbers that did not correspond to any bacterial species, probably as a result of insufficient growth of the isolate. The SCV isolate was subsequently identified as E. faecalis based on its morphological, cultural and biochemical properties, and this was confirmed by sequencing the 16S rRNA gene of the organism. Investigations revealed that the addition of oleate, an unsaturated fatty acid, enabled the isolate to grow on every medium with normal-sized colony morphology. Although it has long been known that long-chain fatty acids, especially unsaturated oleic acid, have a major inhibitory effect on the growth of a variety of microorganisms, including not only mycobacteria but also streptococci, this is, to the best of our knowledge, the first clinical isolation of an oleate-dependent E. faecalis SCV isolate. In addition, oleic acid might be considered to affect the cell membrane permeability of carbohydrates or antimicrobial agents such as β-lactams.
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Affiliation(s)
- Noriko Kubota
- Department of Laboratory Medicine, Nagano Children's Hospital, Azumino 399-8288, Japan
| | - Kei Kuzumoto
- Department of Laboratory Medicine, Nagano Children's Hospital, Azumino 399-8288, Japan
| | - Eiko Hidaka
- Department of Laboratory Medicine, Nagano Children's Hospital, Azumino 399-8288, Japan
| | - Katsumi Yoshizawa
- Department of Surgery, Nagano Children's Hospital, Azumino 399-8288, Japan
| | - Kayoko Yumoto
- Department of Laboratory Medicine, Nagano Children's Hospital, Azumino 399-8288, Japan
| | - Kozue Oana
- Division of Clinical Microbiology, Department of Biomedical Laboratory Sciences, School of Health Sciences, Shinshu University School of Medicine, Matsumoto 390-8621, Japan.,Division of Infection Control and Microbiological Regulation, Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Matsumoto 390-8621, Japan
| | - Yoshifumi Ogiso
- Department of Infection Control, Nagano Children's Hospital, Azumino 399-8288, Japan.,Department of Laboratory Medicine, Nagano Children's Hospital, Azumino 399-8288, Japan
| | - Tomohiko Nakamura
- Department of Infection Control, Nagano Children's Hospital, Azumino 399-8288, Japan
| | - Yoshiyuki Kawakami
- Division of Clinical Microbiology, Department of Biomedical Laboratory Sciences, School of Health Sciences, Shinshu University School of Medicine, Matsumoto 390-8621, Japan.,Division of Infection Control and Microbiological Regulation, Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Matsumoto 390-8621, Japan
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[Small-colony variants of Staphylococcus aureus: Usefulness of various test for diagnosis and susceptibility study]. Enferm Infecc Microbiol Clin 2013; 32:96-8. [PMID: 24054970 DOI: 10.1016/j.eimc.2013.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 06/11/2013] [Accepted: 06/17/2013] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Small colony variants of Staphylococcus aureus (SCVSA) are a sub-population with special features. METHODS The phenotypic features and antibiotic susceptibility of four clinical isolates SCVSA were studied. RESULTS Colonies grew in the usual culture media, except in Mueller Hinton. All isolates were resistant to ciprofloxacin and co-trimoxazole. DISCUSSION As SCVSA are isolated with low frequency, it is necessary to determine the optimal methods for their identification and antibiotic susceptibility study.
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Small colony variants (SCVs) of Staphylococcus aureus--a bacterial survival strategy. INFECTION GENETICS AND EVOLUTION 2013; 21:515-22. [PMID: 23722021 DOI: 10.1016/j.meegid.2013.05.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 05/11/2013] [Accepted: 05/18/2013] [Indexed: 01/28/2023]
Abstract
Small colony variants (SCVs) of Staphylococcus aureus have been implicated in chronic recurrent infections and have therefore gained renewed interest during the last decade. Moreover, SCVs have been shown to be part of the regular growth cycle, are highly dynamic or stable and can be selected during various harsh conditions. As such, the emergence of SCVs has been described not only in human, but also in veterinary medicine as well as in food microbiology. SCVs are characterized by impaired growth, down-regulation of genes for metabolism and virulence, while sigB and genes important for persistence and biofilm formation are up-regulated. Furthermore, SCVs are resistant to various antibiotics such as aminoglycosides, trimethoprim-sulfamethoxazole, fluorquinolones, fusidic acid or even to antiseptics such as triclosan. An underlying mechanism has been determined for hemin-, menadione- and thymidine-dependent SCVs as well as for SCVs which are impaired in their stress response. SCVs are optimized for persistence in the host. They are able to reverse and thereby constitute a highly dynamic subpopulation of S. aureus. Such phenotype switching constitutes an integral part of the infection process enabling the bacteria to hide inside the host cell without eliciting a strong host response.
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41
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Wang S, Wu C, Shen J, Wu Y, Wang Y. Hypermutable Staphylococcus aureus strains present at high frequency in subclinical bovine mastitis isolates are associated with the development of antibiotic resistance. Vet Microbiol 2013; 165:410-5. [PMID: 23642648 DOI: 10.1016/j.vetmic.2013.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 03/29/2013] [Accepted: 04/01/2013] [Indexed: 10/27/2022]
Abstract
Hypermutable bacterial strains with greatly elevated spontaneous mutation rates have been described at high frequencies in various clinically important species, particularly in cystic fibrosis (CF) patients. It has been suggested that such strains can play a major role in the development of chronic respiratory infections. Nevertheless, little information is available regarding the potential association between hypermutation and other chronic infection settings. Here, we investigated the mutation frequencies of 261 Staphylococcus aureus isolates from bovine mastitis cases. The comparative analysis revealed that the subclinical mastitis (SM) isolates harbored significantly more hypermutators than the clinical mastitis (CM) isolates (26/141 versus 0/120, P<0.001, Fisher's exact test). Analysis of mutS and mutL genes, which are major components of the methyl mismatch repair (MMR) system, revealed that 13 of the 14 genetically unrelated hypermutators showed alterations in their deduced MutS and/or MutL amino acid sequences. The hypermutators were much more frequently found to be resistant to all of the 7 antibiotics tested (except sulfafurazole) than the nonmutators. Moreover, the proportion of hypermutators harboring multi-drug resistance was significantly higher than that of the nonmutators as well (P<0.001). Taken together, this work provides evidence that hypermutability plays an important role in antibiotic resistance development during long-term persistence of S. aureus, and reveals that the link between hypermutation and chronic infections appears not to be restricted to respiratory infections alone.
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Affiliation(s)
- Shaochen Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Alkasir R, Liu X, Zahra M, Ferreri M, Su J, Han B. Characteristics ofStaphylococcus aureusSmall Colony Variant and Its Parent Strain Isolated from Chronic Mastitis at a Dairy Farm in Beijing, China. Microb Drug Resist 2013; 19:138-45. [DOI: 10.1089/mdr.2012.0086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Rashad Alkasir
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiuquan Liu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- Animal Science and Veterinary Station, Beijing Sanyuan Group, Beijing, China
| | - Mohammad Zahra
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Miro Ferreri
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jingliang Su
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Bo Han
- College of Veterinary Medicine, China Agricultural University, Beijing, China
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Garcia LG, Lemaire S, Kahl BC, Becker K, Proctor RA, Denis O, Tulkens PM, Van Bambeke F. Antibiotic activity against small-colony variants of Staphylococcus aureus: review of in vitro, animal and clinical data. J Antimicrob Chemother 2013; 68:1455-64. [DOI: 10.1093/jac/dkt072] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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44
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Hilmi D, Parcina M, Bode K, Ostrop J, Schuett S, Heeg K, Ziebuhr W, Sommerburg O, Bekeredjian-Ding I. Functional variation reflects intra-strain diversity of Staphylococcus aureus small colony variants in the host–pathogen interaction. Int J Med Microbiol 2013; 303:61-9. [DOI: 10.1016/j.ijmm.2012.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 11/26/2012] [Accepted: 12/02/2012] [Indexed: 10/27/2022] Open
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45
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Yagci S, Hascelik G, Dogru D, Ozcelik U, Sener B. Prevalence and genetic diversity of Staphylococcus aureus small-colony variants in cystic fibrosis patients. Clin Microbiol Infect 2013; 19:77-84. [DOI: 10.1111/j.1469-0691.2011.03742.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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46
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Evolution in fast forward: a potential role for mutators in accelerating Staphylococcus aureus pathoadaptation. J Bacteriol 2012. [PMID: 23204459 DOI: 10.1128/jb.00733-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pathogen evolution and subsequent phenotypic heterogeneity during chronic infection are proposed to enhance Staphylococcus aureus survival during human infection. We tested this theory by genetically and phenotypically characterizing strains with mutations constructed in the mismatch repair (MMR) and oxidized guanine (GO) system, termed mutators, which exhibit increased spontaneous-mutation frequencies. Analysis of these mutators revealed not only strain-dependent increases in the spontaneous-mutation frequency but also shifts in mutational type and hot spots consistent with loss of GO or MMR functions. Although the GO and MMR systems are relied upon in some bacterial species to prevent reactive oxygen species-induced DNA damage, no deficit in hydrogen peroxide sensitivity was found when either of these DNA repair pathways was lost in S. aureus. To gain insight into the contribution of increased mutation supply to S. aureus pathoadaptation, we measured the rate of α-hemolysin and staphyloxanthin inactivation during serial passage. Detection of increased rates of α-hemolysin and staphyloxanthin inactivation in GO and MMR mutants suggests that these strains are capable of modifying virulence phenotypes implicated in mediating infection. Accelerated derivation of altered virulence phenotypes, combined with the absence of increased ROS sensitivity, highlights the potential of mutators to drive pathoadaptation in the host and serve as catalysts for persistent infections.
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Maduka-Ezeh AN, Greenwood-Quaintance KE, Karau MJ, Berbari EF, Osmon DR, Hanssen AD, Steckelberg JM, Patel R. Antimicrobial susceptibility and biofilm formation of Staphylococcus epidermidis small colony variants associated with prosthetic joint infection. Diagn Microbiol Infect Dis 2012; 74:224-9. [PMID: 22901790 DOI: 10.1016/j.diagmicrobio.2012.06.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 06/21/2012] [Accepted: 06/29/2012] [Indexed: 10/28/2022]
Abstract
We determined the frequency of isolation of non-aureus staphylococcal small colony variants (SCVs) from 31 patients with staphylococcal prosthetic joint infection (PJI) and described the antimicrobial susceptibility, auxotrophy, and biofilm-forming capacity of these SCVs. Eleven non-aureus SCVs were recovered, all of which were Staphylococcus epidermidis, and none of which was auxotrophic for hemin, menadione, or thymidine. Aminoglycoside resistance was detected in 5. Two were proficient, and 7 were poor, biofilm formers. With passage on antimicrobial free media, we observed a fluctuating phenotype in 3 isolates. We also noted a difference in antimicrobial susceptibility of different morphology isolates recovered from the same joints despite similar pulsed-field gel electrophoresis patterns. Our findings suggest S. epidermidis SCVs are common in PJI, and while they have a similar appearance to S. aureus SCVs, they do not necessarily share such characteristics as aminoglycoside resistance; auxotrophy for hemin, menadione, or thymidine; or enhanced biofilm formation. We also underscore the importance of antimicrobial susceptibility testing of all morphologies of isolates recovered from PJI.
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Affiliation(s)
- Awele N Maduka-Ezeh
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
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Phenotype switching is a natural consequence of Staphylococcus aureus replication. J Bacteriol 2012; 194:5404-12. [PMID: 22865841 DOI: 10.1128/jb.00948-12] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The pathogen Staphylococcus aureus undergoes phenotype switching in vivo from its normal colony phenotype (NCP) to a slow-growing, antibiotic-resistant small-colony-variant (SCV) phenotype that is associated with persistence in host cells and tissues. However, it is not clear whether phenotype switching is the result of a constitutive process that is selected for under certain conditions or is triggered by particular environmental stimuli. Examination of cultures of diverse S. aureus strains in the absence of selective pressure consistently revealed a small gentamicin-resistant SCV subpopulation that emerged during exponential-phase NCP growth and increased in number until NCP stationary phase. Treatment of replicating bacteria with the antibiotic gentamicin, which inhibited NCP but not SCV replication, resulted in an initial decrease in SCV numbers, demonstrating that SCVs arise as a consequence of NCP replication. However, SCV population expansion in the presence of gentamicin was reestablished by selection of phenotype-stable SCVs and subsequent SCV replication. In the absence of selective pressure, however, phenotype switching was bidirectional and occurred at a high frequency during NCP replication, resulting in SCV turnover. In summary, these data demonstrate that S. aureus phenotype switching occurs via a constitutive mechanism that generates a dynamic, antibiotic-resistant subpopulation of bacteria that can revert to the parental phenotype. The emergence of SCVs can therefore be considered a normal part of the S. aureus life cycle and provides an insurance policy against exposure to antibiotics that would otherwise eliminate the entire population.
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Thymidine auxotrophic Staphylococcus aureus small-colony variant endocarditis and left ventricular assist device infection. J Clin Microbiol 2012; 50:1102-5. [PMID: 22205806 DOI: 10.1128/jcm.01170-11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We describe a thymidine-dependent small-colony variant of Staphylococcus aureus associated with left ventricular assist device infection and prosthetic valve and pacemaker endocarditis.
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Abstract
Hypermutability is a phenotype characterized by a moderate to high elevation of spontaneous mutation rates and could result from DNA replication errors, defects in error correction mechanisms and many other causes. The elevated mutation rates are helpful to organisms to adapt to sudden and unforeseen threats to survival. At the same time hypermutability also leads to the generation of many deleterious mutations which offset its adaptive value and therefore disadvantageous. Nevertheless, it is very common in nature, especially among clinical isolates of pathogens. Hypermutability is inherited by indirect (second order) selection along with the beneficial mutations generated. At large population sizes and high mutation rates many cells in the population could concurrently acquire beneficial mutations of varying adaptive (fitness) values. These lineages compete with the ancestral cells and also among themselves for fixation. The one with the 'fittest' mutation gets fixed ultimately while the others are lost. This has been called 'clonal interference' which puts a speed limit on adaptation. The original clonal interference hypothesis has been modified recently. Nonheritable (transient) hypermtability conferring significant adaptive benefits also occur during stress response although its molecular basis remains controversial. The adaptive benefits of heritable hypermutability are discussed with emphasis on host-pathogen interactions.
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