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Campos ACC, Andrade NL, Ferdous M, Chlebowicz MA, Santos CC, Correal JCD, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Rossen JWA. Corrigendum: Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil. Front Microbiol 2020; 11:599031. [PMID: 33193282 PMCID: PMC7662894 DOI: 10.3389/fmicb.2020.599031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/15/2020] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2018.00243.].
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Affiliation(s)
- Ana Carolina C Campos
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nathália L Andrade
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mithila Ferdous
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Carla C Santos
- Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Julio C D Correal
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Jerome R Lo Ten Foe
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ana Cláudia P Rosa
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo V Damasco
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Doenças Infecciosas e Parasitárias, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Fleres G, Couto N, Schuele L, Chlebowicz MA, Mendes CI, van der Sluis LWM, Rossen JWA, Friedrich AW, García-Cobos S. Detection of a novel mcr-5.4 gene variant in hospital tap water by shotgun metagenomic sequencing. J Antimicrob Chemother 2020; 74:3626-3628. [PMID: 31504580 PMCID: PMC6857192 DOI: 10.1093/jac/dkz363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Giuseppe Fleres
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Monika A Chlebowicz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Catarina I Mendes
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Luc W M van der Sluis
- Center of Dentistry and Oral Hygiene, University Medical Center Groningen, 9712 CP Groningen, The Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Alex W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Silvia García-Cobos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
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3
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Miro E, Rossen JWA, Chlebowicz MA, Harmsen D, Brisse S, Passet V, Navarro F, Friedrich AW, García-Cobos S. Core/Whole Genome Multilocus Sequence Typing and Core Genome SNP-Based Typing of OXA-48-Producing Klebsiella pneumoniae Clinical Isolates From Spain. Front Microbiol 2020; 10:2961. [PMID: 32082262 PMCID: PMC7005014 DOI: 10.3389/fmicb.2019.02961] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/09/2019] [Indexed: 11/17/2022] Open
Abstract
Whole-genome sequencing (WGS)-based typing methods have emerged as promising and highly discriminative epidemiological tools. In this study, we combined gene-by-gene allele calling and core genome single nucleotide polymorphism (cgSNP) approaches to investigate the genetic relatedness of a well-characterized collection of OXA-48-producing Klebsiella pneumoniae isolates. We included isolates from the predominant sequence type ST405 (n = 31) OXA-48-producing K. pneumoniae clone and isolates from ST101 (n = 3), ST14 (n = 1), ST17 (n = 1), and ST1233 (n = 1), obtained from eight Catalan hospitals. Core-genome multilocus sequence typing (cgMLST) schemes from Institut Pasteur’s BIGSdb-Kp (634 genes) and SeqSphere+ (2,365 genes), and a SeqSphere+ whole-genome MLST (wgMLST) scheme (4,891 genes) were used. Allele differences or allelic mismatches and the genetic distance, as the proportion of allele differences, were used to interpret the results from a gene-by-gene approach, whereas the number of SNPs was used for the cgSNP analysis. We observed between 0–10 and 0–14 allele differences among the predominant ST405 using cgMLST and wgMLST from SeqSphere+, respectively, and <2 allelic mismatches when using Institut Pasteur’s BIGSdb-Kp cgMLST scheme. For ST101, we observed 14 and 54 allele differences when using cgMLST and wgMLST SeqSphere+, respectively, and 2–5 allelic mismatches for BIGSdb-Kp cgMLST. A low genetic distance (<0.0035, a previously established threshold for epidemiological link) was generally in concordance with a low number of allele differences (<8) when using the SeqSphere+ cgMLST scheme. The cgSNP analysis showed 6–29 SNPs in isolates with identical allelic SeqSphere+ cgMLST profiles and 16–61 cgSNPs among ST405 isolates. Furthermore, comparison of WGS-based typing results with previously obtained MLST and pulsed-field gel electrophoresis (PFGE) data showed some differences, demonstrating the different molecular principles underlying these techniques. In conclusion, the use of the different WGS-based typing methods that were used to elucidate the genetic relatedness of clonal OXA-48-producing K. pneumoniae all led to the same conclusions. Furthermore, threshold parameters in WGS-based typing methods should be applied with caution and should be used in combination with clinical epidemiological data and population and species characteristics.
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Affiliation(s)
- Elisenda Miro
- Department of Microbiology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Monika A Chlebowicz
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Dag Harmsen
- Department of Periodontology and Restorative Dentistry, University of Münster, Münster, Germany
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Ferran Navarro
- Department of Microbiology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - S García-Cobos
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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4
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Zhou X, Chlebowicz MA, Bathoorn E, Rosema S, Couto N, Lokate M, Arends JP, Friedrich AW, Rossen JWA. Elucidating vancomycin-resistant Enterococcus faecium outbreaks: the role of clonal spread and movement of mobile genetic elements. J Antimicrob Chemother 2019; 73:3259-3267. [PMID: 30219855 DOI: 10.1093/jac/dky349] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/06/2018] [Indexed: 12/27/2022] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a nosocomial pathogen worldwide. The dissemination of VREfm is due to both clonal spread and spread of mobile genetic elements (MGEs) such as transposons. Objectives We aimed to combine vanB-carrying transposon data with core-genome MLST (cgMLST) typing and epidemiological data to understand the pathways of transmission in nosocomial outbreaks. Methods Retrospectively, 36 VREfm isolates obtained from 34 patients from seven VREfm outbreak investigations in 2014 were analysed. Isolates were sequenced on a MiSeq and a MinION instrument. De novo assembly was performed in CLC Genomics Workbench and the hybrid assemblies were obtained through Unicycler v0.4.1. Ridom SeqSphere+ was used to extract MLST and cgMLST data. Detailed analysis of each transposon and their integration points was performed using the Artemis Comparison Tool (ACT) and multiple blast analyses. Results Four different vanB transposons were found among the isolates. cgMLST divided ST80 isolates into three cluster types (CTs); CT16, CT104 and CT106. ST117 isolates were divided into CT24, CT103 and CT105. Within VREfm isolates belonging to CT103, two different vanB transposons were found. In contrast, VREfm isolates belonging to CT104 and CT106 harboured an identical vanB transposon. Conclusions cgMLST provides a high discriminatory power for the epidemiological analysis of VREfm. However, additional transposon analysis is needed to detect horizontal gene transfer. Combining these two methods allows investigation of both clonal spread as well as the spread of MGEs. This leads to new insights and thereby better understanding of the complex transmission routes in VREfm outbreaks.
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Affiliation(s)
- X Zhou
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - M A Chlebowicz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - E Bathoorn
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - S Rosema
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - N Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - M Lokate
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - J P Arends
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - A W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - J W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
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5
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Gabarrini G, Palma Medina LM, Stobernack T, Prins RC, du Teil Espina M, Kuipers J, Chlebowicz MA, Rossen JWA, van Winkelhoff AJ, van Dijl JM. There's no place like OM: Vesicular sorting and secretion of the peptidylarginine deiminase of Porphyromonas gingivalis. Virulence 2018; 9:456-464. [PMID: 29505395 PMCID: PMC5955434 DOI: 10.1080/21505594.2017.1421827] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The oral pathogen Porphyromonas gingivalis is one of the major periodontal agents and it has been recently hailed as a potential cause of the autoimmune disease rheumatoid arthritis. In particular, the peptidylarginine deiminase enzyme of P. gingivalis (PPAD) has been implicated in the citrullination of certain host proteins and the subsequent appearance of antibodies against citrullinated proteins, which might play a role in the etiology of rheumatoid arthritis. The aim of this study was to investigate the extracellular localization of PPAD in a large panel of clinical P. gingivalis isolates. Here we show that all isolates produced PPAD. In most cases PPAD was abundantly present in secreted outer membrane vesicles (OMVs) that are massively produced by P. gingivalis, and to minor extent in a soluble secreted state. Interestingly, a small subset of clinical isolates showed drastically reduced levels of the OMV-bound PPAD and secreted most of this enzyme in the soluble state. The latter phenotype is strictly associated with a lysine residue at position 373 in PPAD, implicating the more common glutamine residue at this position in PPAD association with OMVs. Further, one isolate displayed severely restricted vesiculation. Together, our findings show for the first time that neither the major association of PPAD with vesicles, nor P. gingivalis vesiculation per se, are needed for P. gingivalis interactions with the human host.
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Affiliation(s)
- Giorgio Gabarrini
- a Center for Dentistry and Oral Hygiene , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands.,b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Laura M Palma Medina
- b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Tim Stobernack
- b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Rianne C Prins
- b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Marines du Teil Espina
- b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Jeroen Kuipers
- c Department of Cell Biology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Monika A Chlebowicz
- b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - John W A Rossen
- b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Arie Jan van Winkelhoff
- a Center for Dentistry and Oral Hygiene , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands.,b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Jan Maarten van Dijl
- b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
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Desmet S, Nepal S, van Dijl JM, Van Ranst M, Chlebowicz MA, Rossen JW, Van Houdt JKJ, Maes P, Lagrou K, Bathoorn E. Antibiotic Resistance Plasmids Cointegrated into a Megaplasmid Harboring the blaOXA-427 Carbapenemase Gene. Antimicrob Agents Chemother 2018; 62:e01448-17. [PMID: 29311088 PMCID: PMC5826099 DOI: 10.1128/aac.01448-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 12/21/2017] [Indexed: 11/20/2022] Open
Abstract
OXA-427 is a new class D carbapenemase encountered in different species of Enterobacteriaceae in a Belgian hospital. To study the dispersal of this gene, we performed a comparative analysis of two plasmids containing the blaOXA-427 gene, isolated from a Klebsiella pneumoniae strain and an Enterobacter cloacae complex strain. The two IncA/C2 plasmids containing blaOXA-427 share the same backbone; in the K. pneumoniae strain, however, this plasmid is cointegrated into an IncFIb plasmid, forming a 321-kb megaplasmid with multiple multiresistance regions.
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Affiliation(s)
- Stefanie Desmet
- Department of Microbiology and Immunology, Laboratory of Clinical Bacteriology and Mycology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Suruchi Nepal
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Marc Van Ranst
- Department of Microbiology and Immunology, Laboratory of Clinical Bacteriology and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Monika A Chlebowicz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - John W Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Jeroen K J Van Houdt
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Piet Maes
- Department of Microbiology and Immunology, Laboratory of Clinical Bacteriology and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Katrien Lagrou
- Department of Microbiology and Immunology, Laboratory of Clinical Bacteriology and Mycology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Erik Bathoorn
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
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Campos ACC, Andrade NL, Ferdous M, Chlebowicz MA, Santos CC, Correal JCD, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Rossen JWA. Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil. Front Microbiol 2018; 9:243. [PMID: 29503639 PMCID: PMC5821075 DOI: 10.3389/fmicb.2018.00243] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/31/2018] [Indexed: 01/09/2023] Open
Abstract
Urinary tract infections (UTIs) are often caused by Escherichia coli. Their increasing resistance to broad-spectrum antibiotics challenges the treatment of UTIs. Whereas, E. coli ST131 is often multidrug resistant (MDR), ST69 remains susceptible to antibiotics such as cephalosporins. Both STs are commonly linked to community and nosocomial infections. E. coli phylogenetic groups B2 and D are associated with virulence and resistance profiles making them more pathogenic. Little is known about the population structure of E. coli isolates obtained from urine samples of hospitalized patients in Brazil. Therefore, we characterized E. coli isolated from urine samples of patients hospitalized at the university and three private hospitals in Rio de Janeiro, using whole genome sequencing. A high prevalence of E. coli ST131 and ST69 was found, but other lineages, namely ST73, ST648, ST405, and ST10 were also detected. Interestingly, isolates could be divided into two groups based on their antibiotic susceptibility. Isolates belonging to ST131, ST648, and ST405 showed a high resistance rate to all antibiotic classes tested, whereas isolates belonging to ST10, ST73, ST69 were in general susceptible to the antibiotics tested. Additionally, most ST69 isolates, normally resistant to aminoglycosides, were susceptible to this antibiotic in our population. The majority of ST131 isolates were ESBL-producing and belonged to serotype O25:H4 and the H30-R subclone. Previous studies showed that this subclone is often associated with more complicated UTIs, most likely due to their high resistance rate to different antibiotic classes. Sequenced isolates could be classified into five phylogenetic groups of which B2, D, and F showed higher resistance rates than groups A and B1. No significant difference for the predicted virulence genes scores was found for isolates belonging to ST131, ST648, ST405, and ST69. In contrast, the phylogenetic groups B2, D and F showed a higher predictive virulence score compared to phylogenetic groups A and B1. In conclusion, despite the diversity of E. coli isolates causing UTIs, clonal groups O25:H4-B2-ST131 H30-R, O1:H6-B2-ST648, and O102:H6-D-ST405 were the most prevalent. The emergence of highly virulent and MDR E. coli in Brazil is of high concern and requires more attention from the health authorities.
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Affiliation(s)
- Ana Carolina C Campos
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nathália L Andrade
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mithila Ferdous
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Carla C Santos
- Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Julio C D Correal
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Jerome R Lo Ten Foe
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ana Cláudia P Rosa
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo V Damasco
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Doenças Infecciosas e Parasitárias, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Gabarrini G, Chlebowicz MA, Vega Quiroz ME, Veloo ACM, Rossen JWA, Harmsen HJM, Laine ML, van Dijl JM, van Winkelhoff AJ. Conserved Citrullinating Exoenzymes in Porphyromonas Species. J Dent Res 2018; 97:556-562. [PMID: 29298553 DOI: 10.1177/0022034517747575] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Porphyromonas gingivalis is one of the major oral pathogens implicated in the widespread inflammatory disorder periodontitis. Moreover, in recent years, P. gingivalis has been associated with the autoimmune disease rheumatoid arthritis. The peptidylarginine deiminase enzyme of P. gingivalis (PPAD) is a major virulence factor that catalyzes the citrullination of both bacterial and host proteins, potentially contributing to production of anticitrullinated protein antibodies. Considering that these antibodies are very specific for rheumatoid arthritis, PPAD appears to be a link between P. gingivalis, periodontitis, and the autoimmune disorder rheumatoid arthritis. PPAD was thus far considered unique among prokaryotes, with P. gingivalis being the only bacterium known to produce and secrete it. To challenge this hypothesis, we investigated the possible secretion of PPAD by 11 previously collected Porphyromonas isolates from a dog, 2 sheep, 3 cats, 4 monkeys, and a jaguar with periodontitis. Our analyses uncovered the presence of secreted PPAD homologues in 8 isolates that were identified as Porphyromonas gulae (from a dog, monkeys, and cats) and Porphyromonas loveana (from sheep). In all 3 PPAD-producing Porphyromonas species, the dominant form of the secreted PPAD was associated with outer membrane vesicles, while a minor fraction was soluble. Our results prove for the first time that the citrullinating PPAD exoenzyme is not unique to only 1 prokaryotic species. Instead, we show that PPAD is produced by at least 2 other oral pathogens.
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Affiliation(s)
- G Gabarrini
- 1 Center for Dentistry and Oral Hygiene, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,2 Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - M A Chlebowicz
- 2 Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - M E Vega Quiroz
- 2 Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - A C M Veloo
- 2 Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - J W A Rossen
- 2 Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - H J M Harmsen
- 2 Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - M L Laine
- 3 Department of Periodontology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University, Amsterdam, the Netherlands
| | - J M van Dijl
- 2 Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - A J van Winkelhoff
- 1 Center for Dentistry and Oral Hygiene, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,2 Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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9
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García-Pérez AN, de Jong A, Junker S, Becher D, Chlebowicz MA, Duipmans JC, Jonkman MF, van Dijl JM. From the wound to the bench: exoproteome interplay between wound-colonizing Staphylococcus aureus strains and co-existing bacteria. Virulence 2018; 9:363-378. [PMID: 29233035 PMCID: PMC5955179 DOI: 10.1080/21505594.2017.1395129] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/09/2017] [Accepted: 10/15/2017] [Indexed: 11/16/2022] Open
Abstract
Wound-colonizing microorganisms can form complex and dynamic polymicrobial communities where pathogens and commensals may co-exist, cooperate or compete with each other. The present study was aimed at identifying possible interactions between different bacteria isolated from the same chronic wound of a patient with the genetic blistering disease epidermolysis bullosa (EB). Specifically, this involved two different isolates of the human pathogen Staphylococcus aureus, and isolates of Bacillus thuringiensis and Klebsiella oxytoca. Particular focus was attributed to interactions of S. aureus with the two other species, because of the high staphylococcal prevalence among chronic wounds. Intriguingly, upon co-cultivation, none of the wound isolates inhibited each other's growth. Since the extracellular proteome of bacterial pathogens is a reservoir of virulence factors, the exoproteomes of the staphylococcal isolates in monoculture and co-culture with B. thuringiensis and K. oxytoca were characterized by Mass Spectrometry to explore the inherent relationships between these co-exisiting bacteria. This revealed a massive reduction in the number of staphylococcal exoproteins upon co-culturing with K. oxytoca or B. thuringiensis. Interestingly, this decrease was particularly evident for extracellular proteins with a predicted cytoplasmic localization, which were recently implicated in staphylococcal virulence and epidemiology. Furthermore, our exoproteome analysis uncovered potential cooperativity between the two different S. aureus isolates. Altogether, the observed exoproteome variations upon co-culturing are indicative of unprecedented adaptive mechanisms that set limits to the production of secreted staphylococcal virulence factors.
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Affiliation(s)
- Andrea N. García-Pérez
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, the Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, AG Groningen, the Netherlands
| | - Sabryna Junker
- Institute for Microbiology, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, Germany
| | - Monika A. Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, the Netherlands
| | - José C. Duipmans
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, RB Groningen, the Netherlands
| | - Marcel F. Jonkman
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, RB Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, the Netherlands
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10
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Giordano C, Barnini S, Tsioutis C, Chlebowicz MA, Scoulica EV, Gikas A, Rossen JW, Friedrich AW, Bathoorn E. Expansion of KPC-producing Klebsiella pneumoniae with various mgrB mutations giving rise to colistin resistance: the role of ISL3 on plasmids. Int J Antimicrob Agents 2017; 51:260-265. [PMID: 29097338 DOI: 10.1016/j.ijantimicag.2017.10.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 10/06/2017] [Accepted: 10/21/2017] [Indexed: 11/19/2022]
Abstract
mcr-1 has been reported as the first plasmid-encoded gene conferring colistin resistance. In KPC-producing Klebsiella pneumoniae (KPC-KP), however, colistin resistance is rapidly emerging through other mechanisms. Resistance is frequently due to disruption of the mgrB gene by insertion sequences, e.g. ISL3. The aim of this study was to investigate the expansion of mgrB-mutated KPC-KP isolates. In addition, the localisation and targets of ISL3 sequences within the core and accessory genome of common KPC-KP lineages were identified. A total of 29 clinical K. pneumoniae isolates collected from Italian patients were randomly selected. Whole genome sequences were analysed for resistance genes, plasmids and insertion sequences. In addition, 27 colistin-resistant KPC-KP isolates from a previous study from Crete (Greece) were assessed. Clonal expansion of KPC-KP isolates with various mutations in mgrB among all lineages was observed. In two Italian MLST ST512 isolates and eight Greek ST258 isolates, an identical copy of ISL3 was inserted in mgrB nucleotide position 133. ISL3, a transposable restriction-modification system of 8154 nucleotides, was located on pKpQIL-like plasmids and may transpose into the chromosome. In four isolates, chromosomal integration of ISL3 in diverse inner membrane proteins other than mgrB was identified. Colistin resistance is most often explained by clonal expansion of isolates with mutated mgrB. pKpQIL-like plasmids, which are omnipresent in KPC-KP, carry insertion sequences such as ISL3 that have mgrB as a target hotspot for transposition. Transposition of insertion sequences from plasmids and subsequent clonal expansion may contribute to the emerging colistin resistance in KPC-KP.
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Affiliation(s)
- Cesira Giordano
- Bacteriology Unit, Azienda Ospedaliero-Universitaria Pisana, via Paradisa 2, 56124, Pisa, Italy
| | - Simona Barnini
- Bacteriology Unit, Azienda Ospedaliero-Universitaria Pisana, via Paradisa 2, 56124, Pisa, Italy
| | - Constantinos Tsioutis
- Department of Internal Medicine, Infectious Diseases Unit, University Hospital of Heraklion, Voutes, 71110, Heraklion, Crete, Greece; School of Medicine, European University Cyprus, 6 Diogenis Street, Engomi, Nicosia 1516, Cyprus
| | - Monika A Chlebowicz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Effie V Scoulica
- School of Medicine, European University Cyprus, 6 Diogenis Street, Engomi, Nicosia 1516, Cyprus
| | - Achilleas Gikas
- School of Medicine, European University Cyprus, 6 Diogenis Street, Engomi, Nicosia 1516, Cyprus
| | - John W Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Alexander W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Erik Bathoorn
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands.
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11
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Bošnjak Z, Chlebowicz MA, Mareković I, Rezo Vranješ V, Rossen JW, Budimir A. First report of OXA-48-producing Escherichia coli in Croatia and confirmed intergenic transfer of a plasmid-carrying blaOXA-48 from Klebsiella pneumoniae. Infect Dis (Lond) 2017; 50:313-316. [PMID: 29069970 DOI: 10.1080/23744235.2017.1395067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Zrinka Bošnjak
- a Department of Clinical and Molecular Microbiology and School of Medicine , University Hospital Center Zagreb , Zagreb , Croatia
| | - Monika A Chlebowicz
- b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Ivana Mareković
- a Department of Clinical and Molecular Microbiology and School of Medicine , University Hospital Center Zagreb , Zagreb , Croatia
| | - Violeta Rezo Vranješ
- a Department of Clinical and Molecular Microbiology and School of Medicine , University Hospital Center Zagreb , Zagreb , Croatia
| | - John W Rossen
- b Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Ana Budimir
- a Department of Clinical and Molecular Microbiology and School of Medicine , University Hospital Center Zagreb , Zagreb , Croatia
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12
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Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, Kooistra-Smid AMD, Raangs EC, Rosema S, Veloo ACM, Zhou K, Friedrich AW, Rossen JWA. Reprint of "Application of next generation sequencing in clinical microbiology and infection prevention". J Biotechnol 2017; 250:2-10. [PMID: 28495072 DOI: 10.1016/j.jbiotec.2017.03.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 12/13/2022]
Abstract
Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test. In this review, a general introduction to NGS is presented, including the library preparation and the major characteristics of the most common NGS platforms, such as the MiSeq (Illumina) and the Ion PGM™ (ThermoFisher). An overview of the software used for NGS data analyses used at the medical microbiology diagnostic laboratory in the University Medical Center Groningen in The Netherlands is given. Furthermore, applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans. Finally, we share our vision on the use of NGS in personalised microbiology in the near future, pointing out specific requirements.
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Affiliation(s)
- Ruud H Deurenberg
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Natacha Couto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Mithila Ferdous
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Silvia García-Cobos
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Anna M D Kooistra-Smid
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands; Certe, Department of Medical Microbiology, Groningen, The Netherlands
| | - Erwin C Raangs
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Sigrid Rosema
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Alida C M Veloo
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Kai Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
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13
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Amissah NA, Chlebowicz MA, Ablordey A, Tetteh CS, Prah I, van der Werf TS, Friedrich AW, van Dijl JM, Stienstra Y, Rossen JW. Virulence potential of Staphylococcus aureus isolates from Buruli ulcer patients. Int J Med Microbiol 2017; 307:223-232. [PMID: 28442219 DOI: 10.1016/j.ijmm.2017.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/01/2017] [Accepted: 04/13/2017] [Indexed: 12/27/2022] Open
Abstract
Buruli ulcer (BU) is a necrotizing infection of the skin and subcutaneous tissue caused by Mycobacterium ulcerans. BU wounds may also be colonized with other microorganisms including Staphylococcus aureus. This study aimed to characterize the virulence factors of S. aureus isolated from BU patients. Previously sequenced genomes of 21 S. aureus isolates from BU patients were screened for the presence of virulence genes. The results show that all S. aureus isolates harbored on their core genomes genes for known virulence factors like α-hemolysin, and the α- and β-phenol soluble modulins. Besides the core genome virulence genes, mobile genetic elements (MGEs), i.e. prophages, genomic islands, pathogenicity islands and a Staphylococcal cassette chromosome (SCC) were found to carry different combinations of virulence factors, among them genes that are known to encode factors that promote immune evasion, superantigens and Panton-Valentine Leucocidin. The present observations imply that the S. aureus isolates from BU patients harbor a diverse repertoire of virulence genes that may enhance bacterial survival and persistence in the wound environment and potentially contribute to delayed wound healing.
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Affiliation(s)
- Nana Ama Amissah
- Department of Internal Medicine/Infectious Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.
| | - Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Caitlin S Tetteh
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Isaac Prah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Tjip S van der Werf
- Department of Internal Medicine/Infectious Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ymkje Stienstra
- Department of Internal Medicine/Infectious Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John W Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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14
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Yan X, Li Z, Chlebowicz MA, Tao X, Ni M, Hu Y, Li Z, Grundmann H, Murray S, Pascoe B, Sheppard SK, Bo X, van Dijl JM, Du P, Zhang M, You Y, Yu X, Meng F, Wang S, Zhang J. Genetic features of livestock-associated Staphylococcus aureus ST9 isolates from Chinese pigs that carry the lsa(E) gene for quinupristin/dalfopristin resistance. Int J Med Microbiol 2016; 306:722-729. [PMID: 27528592 DOI: 10.1016/j.ijmm.2016.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/04/2016] [Accepted: 08/09/2016] [Indexed: 11/16/2022] Open
Abstract
Whole-genome sequencing (WGS) was used to investigate the genetic features of the recently identified lsa(E) gene in porcine S. aureus ST9 isolates. Three quinupristin/dalfopristin-resistant isolates harboring the lsa(E) gene (two MRSA and one MSSA) were sequenced. Phylogenetic analysis of 184S. aureus genomes showed that ST9 porcine isolates belong to a distinct sequence cluster. Further analysis showed that all isolates were deficient in the recently described type IV restriction-modification system and SCCmec type XII was identified in the two MRSA isolates, which included a rare class C2 mec gene complex. A 24kb ΨSCC fragment was found in the MRSA and MSSA isolates sharing 99% nucleotide sequence homology with the ΨSCCJCSC6690 (O-2) element of a ST9 MRSA isolate from Thailand (accession number AB705453). Comparison of these ST9 isolates with 181 publically available S. aureus genomes identified 24 genes present in all (100%) ST9 isolates, that were absent from the most closely related human isolate. Our analysis suggests that the sequenced quinupristin/dalfopristin-resistant ST9 lineage represent a reservoir of mobile genetic elements associated with resistance and virulence features.
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Affiliation(s)
- Xiaomei Yan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zongwei Li
- Beijing Institution of Radiation Medicine, Beijing, China
| | - Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Xiaoxia Tao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Ming Ni
- Beijing Institution of Radiation Medicine, Beijing, China
| | - Yuan Hu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhen Li
- Beijing Institution of Radiation Medicine, Beijing, China
| | - Hajo Grundmann
- Department of Infection Prevention and Hospital Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - Susan Murray
- Swansea University Medical School, Institute of Life Sciences, Swansea University, Singleton Park, Swansea, UK
| | - Ben Pascoe
- Swansea University Medical School, Institute of Life Sciences, Swansea University, Singleton Park, Swansea, UK; The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Samuel K Sheppard
- Swansea University Medical School, Institute of Life Sciences, Swansea University, Singleton Park, Swansea, UK; The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Xiaochen Bo
- Beijing Institution of Radiation Medicine, Beijing, China
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Pengcheng Du
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Minli Zhang
- Beijing Institution of Radiation Medicine, Beijing, China
| | - Yuanhai You
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaojie Yu
- Heilongjiang provincial Centre for Disease Control and Prevention, Harbin, China
| | - Fanliang Meng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Shengqi Wang
- Beijing Institution of Radiation Medicine, Beijing, China.
| | - Jianzhong Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
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15
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Amissah NA, Chlebowicz MA, Ablordey A, Sabat AJ, Tetteh CS, Prah I, van der Werf TS, Friedrich AW, van Dijl JM, Rossen JW, Stienstra Y. Molecular Characterization of Staphylococcus aureus Isolates Transmitted between Patients with Buruli Ulcer. PLoS Negl Trop Dis 2015; 9:e0004049. [PMID: 26360794 PMCID: PMC4567303 DOI: 10.1371/journal.pntd.0004049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/11/2015] [Indexed: 12/18/2022] Open
Abstract
Background Buruli ulcer (BU) is a skin infection caused by Mycobacterium ulcerans. The wounds of most BU patients are colonized with different microorganisms, including Staphylococcus aureus. Methodology This study investigated possible patient-to-patient transmission events of S. aureus during wound care in a health care center. S. aureus isolates from different BU patients with overlapping visits to the clinic were whole-genome sequenced and analyzed by a gene-by-gene approach using SeqSphere+ software. In addition, sequence data were screened for the presence of genes that conferred antibiotic resistance. Principal Findings SeqSphere+ analysis of whole-genome sequence data confirmed transmission of methicillin resistant S. aureus (MRSA) and methicillin susceptible S. aureus among patients that took place during wound care. Interestingly, our sequence data show that the investigated MRSA isolates carry a novel allele of the fexB gene conferring chloramphenicol resistance, which had thus far not been observed in S. aureus. Buruli ulcer (BU) is a skin infection caused by Mycobacterium ulcerans. The wounds of most BU patients are colonized with different microorganisms, including Staphylococcus aureus. This study investigated patient-to-patient transmission events during wound care in a health care center. S. aureus isolates from patients who visited the health center at the same time points were analyzed using whole-genome sequencing. Analysis of sequence data confirmed transmission of methicillin resistant S. aureus and methicillin susceptible S. aureus among patients that took place during wound care.
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Affiliation(s)
- Nana Ama Amissah
- Department of Internal Medicine/Infectious Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- * E-mail:
| | - Monika A. Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Artur J. Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Caitlin S. Tetteh
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Isaac Prah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Tjip S. van der Werf
- Department of Internal Medicine/Infectious Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alex W. Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - John W. Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ymkje Stienstra
- Department of Internal Medicine/Infectious Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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16
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Hsu LY, Harris SR, Chlebowicz MA, Lindsay JA, Koh TH, Krishnan P, Tan TY, Hon PY, Grubb WB, Bentley SD, Parkhill J, Peacock SJ, Holden MTG. Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system. Genome Biol 2015; 16:81. [PMID: 25903077 PMCID: PMC4407387 DOI: 10.1186/s13059-015-0643-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/23/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND In the past decade, several countries have seen gradual replacement of endemic multi-resistant healthcare-associated methicillin-resistant Staphylococcus aureus (MRSA) with clones that are more susceptible to antibiotic treatment. One example is Singapore, where MRSA ST239, the dominant clone since molecular profiling of MRSA began in the mid-1980s, has been replaced by ST22 isolates belonging to EMRSA-15, a recently emerged pandemic lineage originating from Europe. RESULTS We investigated the population structure of MRSA in Singaporean hospitals spanning three decades, using whole genome sequencing. Applying Bayesian phylogenetic methods we report that prior to the introduction of ST22, the ST239 MRSA population in Singapore originated from multiple introductions from the surrounding region; it was frequently transferred within the healthcare system resulting in a heterogeneous hospital population. Following the introduction of ST22 around the beginning of the millennium, this clone spread rapidly through Singaporean hospitals, supplanting the endemic ST239 population. Coalescent analysis revealed that although the genetic diversity of ST239 initially decreased as ST22 became more dominant, from 2007 onwards the genetic diversity of ST239 began to increase once more, which was not associated with the emergence of a sub-clone of ST239. Comparative genomic analysis of the accessory genome of the extant ST239 population identified that the Arginine Catabolic Mobile Element arose multiple times, thereby introducing genes associated with enhanced skin colonization into this population. CONCLUSIONS Our results clearly demonstrate that, alongside clinical practice and antibiotic usage, competition between clones also has an important role in driving the evolution of nosocomial pathogen populations.
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Affiliation(s)
- Li-Yang Hsu
- National University Health System, 1E Kent Ridge Road, NUHS Tower Block Level 10, Singapore, 119228, Singapore. .,The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 15A, UK.
| | - Simon R Harris
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 15A, UK.
| | - Monika A Chlebowicz
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 15A, UK. .,University of Groningen, Hanzeplein 1, PO Box 30001, Groningen, 9700 RB, The Netherlands.
| | - Jodi A Lindsay
- Institute of Infection and Immunity, St George's, University of London, Cranmer Terrace, London, SW17 0RE, UK.
| | - Tse-Hsien Koh
- Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.
| | - Prabha Krishnan
- Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore.
| | - Thean-Yen Tan
- Changi General Hospital, 2 Simei Street 3, Singapore, 529889, Singapore.
| | - Pei-Yun Hon
- National University Health System, 1E Kent Ridge Road, NUHS Tower Block Level 10, Singapore, 119228, Singapore.
| | - Warren B Grubb
- Curtin University of Technology, GPO Box U1987, Perth, WA, 6845, Australia.
| | - Stephen D Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 15A, UK.
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 15A, UK.
| | - Sharon J Peacock
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 15A, UK. .,University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK.
| | - Matthew T G Holden
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 15A, UK. .,School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK.
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Chlebowicz MA, Mašlaňová I, Kuntová L, Grundmann H, Pantůček R, Doškař J, van Dijl JM, Buist G. The Staphylococcal Cassette Chromosome mec type V from Staphylococcus aureus ST398 is packaged into bacteriophage capsids. Int J Med Microbiol 2014; 304:764-74. [DOI: 10.1016/j.ijmm.2014.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 04/27/2014] [Accepted: 05/25/2014] [Indexed: 11/24/2022] Open
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Chlebowicz MA, Bosch T, Sabat AJ, Arends JP, Grundmann H, van Dijl JM, Buist G. Distinction of Staphylococcal Cassette Chromosome mec type V elements from Staphylococcus aureus ST398. Int J Med Microbiol 2013; 303:422-32. [PMID: 23786828 DOI: 10.1016/j.ijmm.2013.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/05/2013] [Accepted: 05/20/2013] [Indexed: 11/16/2022] Open
Abstract
Methicillin resistant S. aureus (MRSA) is a major threat for human health and well-being. In recent years, it has become clear that livestock is a potential reservoir for MRSA, most livestock-associated isolates belonging to the ST398 lineage. Importantly, ST398 strains were also reported as causative agents of severe invasive infections in humans with no evidence for livestock associations. Here we document the sequence of the J1 region of the type V (5C2&5) SCCmec element and its right chromosomal junction in the clinical PVL-positive ST398 MRSA isolate UMCG-M4. Sequence comparisons show that this SCCmec element and related type V elements from other S. aureus isolates share a common core structure, but differ substantially in the so-called J1 region. Additional PCR analyses and typing studies indicate that the J1 region of strain UMCG-M4 is specific for SCCmec elements of PVL-positive ST398 isolates. Lastly, we show that the sequenced right chromosomal junction is invariant in strains of the ST398 lineage.
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Affiliation(s)
- Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB Groningen, the Netherlands
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Glasner C, Sabat AJ, Chlebowicz MA, Vanderhaeghen W, Fetsch A, Guerra B, Huber H, Stephan R, Torres C, Butaye P, Voss A, Wulf M, van Dijl JM. High-resolution typing by MLVF unveils extensive heterogeneity of European livestock-associated methicillin-resistant Staphylococcus aureus isolates with the sequence type 398. Int J Med Microbiol 2013; 303:124-7. [DOI: 10.1016/j.ijmm.2013.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/07/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022] Open
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Ziebandt AK, Kusch H, Degner M, Jaglitz S, Sibbald MJJB, Arends JP, Chlebowicz MA, Albrecht D, Pantucek R, Doskar J, Ziebuhr W, Bröker BM, Hecker M, van Dijl JM, Engelmann S. Proteomics uncovers extreme heterogeneity in the Staphylococcus aureus exoproteome due to genomic plasticity and variant gene regulation. Proteomics 2010; 10:1634-44. [PMID: 20186749 DOI: 10.1002/pmic.200900313] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sequencing of at least 13 Staphylococcus aureus isolates has shown that genomic plasticity impacts significantly on the repertoire of virulence factors. However, genome sequencing does not reveal which genes are expressed by individual isolates. Here, we have therefore performed a comprehensive survey of the composition and variability of the S. aureus exoproteome. This involved multilocus sequence typing, virulence gene, and prophage profiling by multiplex PCR, and proteomic analyses of secreted proteins using 2-DE. Dissection of the exoproteomes of 25 clinical isolates revealed that only seven out of 63 identified secreted proteins were produced by all isolates, indicating a remarkably high exoproteome heterogeneity within one bacterial species. Most interesting, the observed variations were caused not only by genome plasticity, but also by an unprecedented variation in secretory protein production due to differences in transcriptional and post-transcriptional regulation. Our data imply that genomic studies on virulence gene conservation patterns need to be complemented by analyses of the extracellular protein pattern to assess the full virulence potential of bacterial pathogens like S. aureus. Importantly, the extensive variability of secreted virulence factors in S. aureus also suggests that development of protective vaccines against this pathogen requires a carefully selected combination of invariably produced antigens.
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