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Gand M, Navickaite I, Bartsch LJ, Grützke J, Overballe-Petersen S, Rasmussen A, Otani S, Michelacci V, Matamoros BR, González-Zorn B, Brouwer MSM, Di Marcantonio L, Bloemen B, Vanneste K, Roosens NHCJ, AbuOun M, De Keersmaecker SCJ. Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes. Front Microbiol 2024; 15:1336532. [PMID: 38659981 PMCID: PMC11042533 DOI: 10.3389/fmicb.2024.1336532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/29/2024] [Indexed: 04/26/2024] Open
Abstract
Metagenomic sequencing is a promising method that has the potential to revolutionize the world of pathogen detection and antimicrobial resistance (AMR) surveillance in food-producing environments. However, the analysis of the huge amount of data obtained requires performant bioinformatics tools and databases, with intuitive and straightforward interpretation. In this study, based on long-read metagenomics data of chicken fecal samples with a spike-in mock community, we proposed confidence levels for taxonomic identification and AMR gene detection, with interpretation guidelines, to help with the analysis of the output data generated by KMA, a popular k-mer read alignment tool. Additionally, we demonstrated that the completeness and diversity of the genomes present in the reference databases are key parameters for accurate and easy interpretation of the sequencing data. Finally, we explored whether KMA, in a two-step procedure, can be used to link the detected AMR genes to their bacterial host chromosome, both detected within the same long-reads. The confidence levels were successfully tested on 28 metagenomics datasets which were obtained with sequencing of real and spiked samples from fecal (chicken, pig, and buffalo) or food (minced beef and food enzyme products) origin. The methodology proposed in this study will facilitate the analysis of metagenomics sequencing datasets for KMA users. Ultimately, this will contribute to improvements in the rapid diagnosis and surveillance of pathogens and AMR genes in food-producing environments, as prioritized by the EU.
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Affiliation(s)
- Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Indre Navickaite
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Lee-Julia Bartsch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Astrid Rasmussen
- Bacterial Reference Center, Statens Serum Institute, Copenhagen, Denmark
| | - Saria Otani
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Bruno González-Zorn
- Department of Animal Health, Complutense University of Madrid, Madrid, Spain
| | - Michael S. M. Brouwer
- Wageningen Bioveterinary Research Part of Wageningen University and Research, Lelystad, Netherlands
| | - Lisa Di Marcantonio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Bram Bloemen
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
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Dankittipong N, Alderliesten JB, Van den Broek J, Dame-Korevaar MA, Brouwer MSM, Velkers FC, Bossers A, de Vos CJ, Wagenaar JA, Stegeman JA, Fischer EAJ. Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producing Escherichia coli between broiler chickens. Prev Vet Med 2023; 219:105998. [PMID: 37647719 DOI: 10.1016/j.prevetmed.2023.105998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/19/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
The emergence of carbapenemase-producing Enterobacteriaceae (CPE) is a threat to public health, because of their resistance to clinically important carbapenem antibiotics. The emergence of CPE in meat-producing animals is particularly worrying because consumption of meat contaminated with resistant bacteria comparable to CPE, such as extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, contributed to colonization in humans worldwide. Currently, no data on the transmission of CPE in livestock is available. We performed a transmission experiment to quantify the transmission of CPE between broilers to fill this knowledge gap and to compare the transmission rates of CPE and other antibiotic-resistant E. coli. A total of 180 Ross 308 broiler chickens were distributed over 12 pens on the day of hatch (day 0). On day 5, half of the 10 remaining chickens in each pen were orally inoculated with 5·102 colony-forming units of CPE, ESBL, or chloramphenicol-resistant E. coli (catA1). To evaluate the effect of antibiotic treatment, amoxicillin was given twice daily in drinking water in 6 of the 12 pens from days 2-6. Cloacal swabs of all animals were taken to determine the number of infectious broilers. We used a Bayesian hierarchical model to quantify the transmission of the E. coli strains. E. coli can survive in the environment and serve as a reservoir. Therefore, the susceptible-infectious transmission model was adapted to account for the transmission of resistant bacteria from the environment. In addition, the caecal microbiome was analyzed on day 5 and at the end of the experiment on day 14 to assess the relationship between the caecal microbiome and the transmission rates. The transmission rates of CPE were 52 - 68 per cent lower compared to ESBL and catA1, but it is not clear if these differences were caused by differences between the resistance genes or by other differences between the E. coli strains. Differences between the groups in transmission rates and microbiome diversity did not correspond to each other, indicating that differences in transmission rates were probably not caused by major differences in the community structure in the caecal microbiome. Amoxicillin treatment from day 2-6 increased the transmission rate more than three-fold in all inoculums. It also increased alpha-diversity compared to untreated animals on day 5, but not on day 14, suggesting only a temporary effect. Future research could incorporate more complex transmission models with different species of resistant bacteria into the Bayesian hierarchical model.
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Affiliation(s)
- Natcha Dankittipong
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jesse B Alderliesten
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jan Van den Broek
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - M Anita Dame-Korevaar
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Michael S M Brouwer
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Francisca C Velkers
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Alex Bossers
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Clazien J de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands.
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Jamin C, Brouwer MSM, Veldman KT, Beuken E, Witteveen S, Landman F, Heddema E, Savelkoul PHM, van Alphen L, Hendrickx APA. Mobile colistin resistance mcr-4.3- and mcr-4.6-harbouring plasmids in livestock- and human-retrieved Enterobacterales in the Netherlands. JAC Antimicrob Resist 2023; 5:dlad053. [PMID: 37153697 PMCID: PMC10155863 DOI: 10.1093/jacamr/dlad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Affiliation(s)
| | | | - Kees T Veldman
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Erik Beuken
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sandra Witteveen
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Fabian Landman
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Edou Heddema
- Department of Medical Microbiology and Infection Control, Zuyderland Medical Center, Sittard-Geleen/Heerlen, The Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands
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Brouwer MSM, Zandbergen Van Essen A, Kant A, Rapallini M, Harders F, Bossers A, Wullings B, Wit B, Veldman KT. Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat. J Antimicrob Chemother 2023:7185845. [PMID: 37248737 DOI: 10.1093/jac/dkad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/05/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND As WGS comes of age, changes in EU legislation implemented in 2021 allow its usage for systematic monitoring of ESBL-producing Escherichia coli from livestock and meat, replacing phenotypic testing. Presently, phenotypic testing correlates well with antimicrobial resistance predicted from WGS data. WGS has added value in the wealth of additional information that is present in the data. OBJECTIVES In this study we have detected the resistance phenotypes for a panel of antimicrobials while also analysing the molecular epidemiology of ESBL-producing E. coli. METHODS Susceptibility testing was performed with broth microdilution of selectively isolated E. coli. Short-read WGS was performed in parallel and phenotypes predicted based on the sequence data, which was also used to determine the phylogeny of the isolates. RESULTS The phenotypically determined resistance and the predicted resistance correlated 90%-100% for the different antimicrobial classes. Furthermore, clonal relationships were detected amongst ESBL-producing E. coli within livestock sectors and the meat produced by this sector. CONCLUSIONS Further implementation of WGS analysis of ESBL/AmpC-producing E. coli within the AMR monitoring programme of EU member states and global surveillance programmes will contribute to determining the attribution of livestock in the prevalence of ESBL/AmpC-encoding E. coli in humans.
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Affiliation(s)
- Michael S M Brouwer
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Alieda Zandbergen Van Essen
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Arie Kant
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Michel Rapallini
- Department of Bacteriology, Molecular Biology and AMR, Wageningen Food Safety Research part of Wageningen University and Research, Akkermaalsbos 2, Wageningen, The Netherlands
| | - Frank Harders
- Department of Bioinformatics, Epidemiology and Animal Models, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Alex Bossers
- Department of Bioinformatics, Epidemiology and Animal Models, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Bart Wullings
- Department of Bacteriology, Molecular Biology and AMR, Wageningen Food Safety Research part of Wageningen University and Research, Akkermaalsbos 2, Wageningen, The Netherlands
| | - Ben Wit
- Department of Food Safety, Netherlands Food and Consumer Product Safety Authority (NVWA), Catharijnesingel 59, Utrecht, The Netherlands
| | - Kees T Veldman
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
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Perestrelo S, Amaro A, Brouwer MSM, Clemente L, Ribeiro Duarte AS, Kaesbohrer A, Karpíšková R, Lopez-Chavarrias V, Morris D, Prendergast D, Pista A, Silveira L, Skarżyńska M, Slowey R, Veldman KT, Zając M, Burgess C, Alvarez J. Building an International One Health Strain Level Database to Characterise the Epidemiology of AMR Threats: ESBL—AmpC Producing E. coli as An Example—Challenges and Perspectives. Antibiotics (Basel) 2023; 12:antibiotics12030552. [PMID: 36978419 PMCID: PMC10044432 DOI: 10.3390/antibiotics12030552] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the top public health threats nowadays. Among the most important AMR pathogens, Escherichia coli resistant to extended spectrum cephalosporins (ESC-EC) is a perfect example of the One Health problem due to its global distribution in animal, human, and environmental sources and its resistant phenotype, derived from the carriage of plasmid-borne extended-spectrum and AmpC β-lactamases, which limits the choice of effective antimicrobial therapies. The epidemiology of ESC-EC infection is complex as a result of the multiple possible sources involved in its transmission, and its study would require databases ideally comprising information from animal (livestock, companion, wildlife), human, and environmental sources. Here, we present the steps taken to assemble a database with phenotypic and genetic information on 10,763 ESC-EC isolates retrieved from multiple sources provided by 13 partners located in eight European countries, in the frame of the DiSCoVeR Joint Research project funded by the One Health European Joint Programme (OH-EJP), along with its strengths and limitations. This database represents a first step to help in the assessment of different geographical and temporal trends and transmission dynamics in animals and humans. The work performed highlights aspects that should be considered in future international efforts, such as the one presented here.
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Affiliation(s)
- Sara Perestrelo
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany
| | - Ana Amaro
- Laboratory of Bacteriology and Micology, National Institute of Agrarian and Veterinary Research, National Reference for Animal Health, 2780-157 Oeiras, Portugal
| | - Michael S. M. Brouwer
- Department of Bacteriology, Host Pathogen Interaction & Diagnostics, Wageningen Bioveterinary Research, Part of Wageningen University & Research, 8221 Lelystad, The Netherlands
| | - Lurdes Clemente
- Laboratory of Bacteriology and Micology, National Institute of Agrarian and Veterinary Research, National Reference for Animal Health, 2780-157 Oeiras, Portugal
| | | | - Annemarie Kaesbohrer
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany
- Veterinary Public Health and Epidemiology, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Renata Karpíšková
- Department of Public Health, Medical Faculty, Masaryk University, 625 000 Brno, Czech Republic
| | | | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, H91 TK33 Galway, Ireland
| | - Deirdre Prendergast
- Backweston Laboratory Campus, Department of Agriculture, Food and the Marine, W23 X3PH Celbridge, Ireland
| | - Angela Pista
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Leonor Silveira
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, 24-100 Pulawy, Poland
| | - Rosemarie Slowey
- Backweston Laboratory Campus, Department of Agriculture, Food and the Marine, W23 X3PH Celbridge, Ireland
| | - Kees T. Veldman
- Department of Bacteriology, Host Pathogen Interaction & Diagnostics, Wageningen Bioveterinary Research, Part of Wageningen University & Research, 8221 Lelystad, The Netherlands
| | - Magdalena Zając
- Department of Microbiology, National Veterinary Research Institute, 24-100 Pulawy, Poland
| | - Catherine Burgess
- Food Safety Department, Teagasc Food Research Centre Ashtown, D15 DY05 Dublin, Ireland
| | - Julio Alvarez
- VISAVET Health Surveillance Centre, Universidad Complutense, 28040 Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Universidad Complutense, Avda. Puerta de Hierro S/N, 28040 Madrid, Spain
- Correspondence:
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6
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Schouls LM, Veldman K, Brouwer MSM, Dierikx C, Witteveen S, van Santen-Verheuvel M, Hendrickx APA, Landman F, Hengeveld P, Wullings B, Rapallini M, Wit B, van Duijkeren E. cfr and fexA genes in methicillin-resistant Staphylococcus aureus from humans and livestock in the Netherlands. Commun Med 2022; 2:135. [PMID: 36317053 PMCID: PMC9616846 DOI: 10.1038/s43856-022-00200-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 05/20/2022] [Accepted: 10/06/2022] [Indexed: 11/09/2022] Open
Abstract
Background Although the Netherlands is a country with a low endemic level of methicillin-resistant Staphylococcus aureus (MRSA), a national MRSA surveillance has been in place since 1989. In 2003 livestock emerged as a major reservoir of MRSA and currently livestock-associated MRSA (clonal complex CC398) make up 25% of all surveillance isolates. To assess possible transfer of resistant strains or resistance genes, MRSA obtained from humans and animals were characterized in detail. Methods The sequenced genomes of 6327 MRSA surveillance isolates from humans and from 332 CC398 isolates from livestock-related samples were analyzed and resistance genes were identified. Several isolates were subjected to long-read sequencing to reconstruct chromosomes and plasmids. Results Here we show the presence of the multi-resistance gene cfr in seven CC398 isolates obtained from humans and in one CC398 isolate from a pig-farm dust sample. Cfr induces resistance against five antibiotic classes, which is true for all but two isolates. The isolates are genetically unrelated, and in seven of the isolates cfr are located on distinct plasmids. The fexA gene is found in 3.9% surveillance isolates and in 7.5% of the samples from livestock. There is considerable sequence variation of fexA and geographic origin of the fexA alleles. Conclusions The rare cfr and fexA resistance genes are found in MRSA from humans and animals in the Netherlands, but there is no evidence for spread of resistant strains or resistance plasmids. The proportion of cfr-positive MRSA is low, but its presence is worrying and should be closely monitored.
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Affiliation(s)
- Leo M. Schouls
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), Bilthoven, The Netherlands
| | - Kees Veldman
- grid.4818.50000 0001 0791 5666Wageningen Bioveterinary Research (WBVR), Bacteriology, Host Pathogen Interaction & Diagnostics, Lelystad, The Netherlands
| | - Michael S. M. Brouwer
- grid.4818.50000 0001 0791 5666Wageningen Bioveterinary Research (WBVR), Bacteriology, Host Pathogen Interaction & Diagnostics, Lelystad, The Netherlands
| | - Cindy Dierikx
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Zoonoses and Environmental Microbiology (Z&O), Bilthoven, The Netherlands
| | - Sandra Witteveen
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), Bilthoven, The Netherlands
| | - Marga van Santen-Verheuvel
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), Bilthoven, The Netherlands
| | - Antoni P. A. Hendrickx
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), Bilthoven, The Netherlands
| | - Fabian Landman
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), Bilthoven, The Netherlands
| | - Paul Hengeveld
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Zoonoses and Environmental Microbiology (Z&O), Bilthoven, The Netherlands
| | - Bart Wullings
- grid.4818.50000 0001 0791 5666Wageningen Food Safety Research, Team Bacteriology, Molecular Biology & AMR, Wageningen, The Netherlands
| | - Michel Rapallini
- grid.4818.50000 0001 0791 5666Wageningen Food Safety Research, Team Bacteriology, Molecular Biology & AMR, Wageningen, The Netherlands
| | - Ben Wit
- grid.435742.30000 0001 0726 7822Netherlands Food and Consumer Product Safety Authority (NVWA), Food safety, Apeldoorn, The Netherlands
| | - Engeline van Duijkeren
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Zoonoses and Environmental Microbiology (Z&O), Bilthoven, The Netherlands
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Börjesson S, Brouwer MSM, Östlund E, Eriksson J, Elving J, Karlsson Lindsjö O, Engblom LI. Detection of an IMI-2 carbapenemase-producing Enterobacter asburiae at a Swedish feed mill. Front Microbiol 2022; 13:993454. [PMID: 36338068 PMCID: PMC9634252 DOI: 10.3389/fmicb.2022.993454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
Occurrence of multidrug resistant Enterobacteriaceae in livestock is of concern as they can spread to humans. A potential introduction route for these bacteria to livestock could be animal feed. We therefore wanted to identify if Escherichia spp., Enterobacter spp., Klebsiella spp., or Raoutella spp. with transferable resistance to extended spectrum cephalosporins, carbapenems or colistin could be detected in the environment at feed mills in Sweden. A second aim was to compare detected isolates to previous described isolates from humans and animals in Sweden to establish relatedness which could indicate a potential transmission between sectors and feed mills as a source for antibiotic resistant bacteria. However, no isolates with transferable resistance to extended-cephalosporins or colistin could be identified, but one isolate belonging to the Enterobacter cloacae complex was shown to be carbapenem-resistant and showing carbapenemase-activity. Based on sequencing by both short-read Illumina and long-read Oxford Nanopore MinIon technologies it was shown that this isolate was an E. asburiae carrying a blaIMI-2 gene on a 216 Kbp plasmid, designated pSB89A/IMI-2, and contained the plasmid replicons IncFII, IncFIB, and a third replicon showing highest similarity to the IncFII(Yp). In addition, the plasmid contained genes for various functions such as plasmid segregation and stability, plasmid transfer and arsenical transport, but no additional antibiotic resistance genes. This isolate and the pSB89A/IMI-2 was compared to three human clinical isolates positive for blaIMI-2 available from the Swedish antibiotic monitoring program Swedres. It was shown that one of the human isolates carried a plasmid similar with regards to gene content to the pSB89A/IMI-2 except for the plasmid transfer system, but that the order of genes was different. The pSB89A/IMI-2 did however share the same transfer system as the blaIMI-2 carrying plasmids from the other two human isolates. The pSB89A/IMI-2 was also compared to previously published plasmids carrying blaIMI-2, but no identical plasmids could be identified. However, most shared part of the plasmid transfer system and DNA replication genes, and the blaIMI-2 gene was located next the transcription regulator imiR. The IS3-family insertion element downstream of imiR in the pSB89A was also related to the IS elements in other blaIMI-carrying plasmids.
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Affiliation(s)
- Stefan Börjesson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- *Correspondence: Stefan Börjesson,
| | - Michael S. M. Brouwer
- Department of Bacteriology, Host-Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Emma Östlund
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Jenny Eriksson
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Josefine Elving
- Department of Chemistry, Environment and Feed Hygiene, National Veterinary Institute (SVA), Uppsala, Sweden
| | | | - Linda I. Engblom
- Department of Chemistry, Environment and Feed Hygiene, National Veterinary Institute (SVA), Uppsala, Sweden
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Cárdenas-Rey I, Bello Gonzalez TDJ, van der Goot J, Ceccarelli D, Bouwhuis G, Schillemans D, Jurburg SD, Veldman KT, de Visser JAGM, Brouwer MSM. Succession in the caecal microbiota of developing broilers colonised by extended-spectrum β-lactamase-producing Escherichia coli. Anim Microbiome 2022; 4:51. [PMID: 35986389 PMCID: PMC9389726 DOI: 10.1186/s42523-022-00199-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 07/26/2022] [Indexed: 11/11/2022] Open
Abstract
Background Broilers are among the most common and dense poultry production systems, where antimicrobials have been used extensively to promote animal health and performance. The continuous usage of antimicrobials has contributed to the appearance of resistant bacteria, such as extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec). Here, we studied the ESBL-Ec prevalence and successional dynamics of the caecal microbiota of developing broilers in a commercial flock during their production life cycle (0–35 days). Broilers were categorised as ESBL-Ec colonised (ESBL-Ec+) or ESBL-Ec non-colonised (ESBL-Ec−) by selective culturing. Using 16S rRNA gene sequencing, we i. compared the richness, evenness and composition of the caecal microbiota of both broilers’ groups and ii. assessed the combined role of age and ESBL-Ec status on the broilers’ caecal microbiota. Results From day two, we observed an increasing linear trend in the proportions of ESBL-Ec throughout the broilers' production life cycle, X2 (1, N = 12) = 28.4, p < 0.001. Over time, the caecal microbiota richness was consistently higher in ESBL-Ec− broilers, but significant differences between both broilers’ groups were found exclusively on day three (Wilcoxon rank-sum test, p = 0.016). Bray–Curtis distance-based RDA (BC-dbRDA) showed no explanatory power of ESBL-Ec status, while age explained 14% of the compositional variation of the caecal microbiota, F (2, 66) = 6.47, p = 0.001. Conclusions This study assessed the role of ESBL-Ec in the successional dynamics of the caecal microbiota in developing broilers and showed that the presence of ESBL-Ec is associated with mild but consistent reductions in alpha diversity and with transient bacterial compositional differences. We also reported the clonal spread of ESBL-Ec and pointed to the farm environment as a likely source for ESBLs. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00199-4.
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Bello Gonzalez TD, Kant A, Dijkstra Q, Marcato F, van Reenen K, Veldman KT, Brouwer MSM. Changes in Fecal Carriage of Extended-Spectrum β-Lactamase Producing Enterobacterales in Dutch Veal Calves by Clonal Spread of Klebsiella pneumoniae. Front Microbiol 2022; 13:866674. [PMID: 35814663 PMCID: PMC9260047 DOI: 10.3389/fmicb.2022.866674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/31/2022] [Accepted: 05/31/2022] [Indexed: 01/14/2023] Open
Abstract
This study aimed to characterize the changes in fecal carriage of Extended-Spectrum β-Lactamase (ESBL) producing Enterobacterales (ESBL-PE) in a single Dutch veal calves. During the rearing period at the Dutch veal farm, a decrease in fecal carriage of cefotaxime-resistant Escherichia coli isolates was observed after 2 weeks at the veal farm, while an increase of cefotaxime-resistant Klebsiella pneumoniae isolates was demonstrated. E. coli and K. pneumoniae were isolated from rectal swabs collected from 110 veal calves in week 2, 6, 10, 18, and 24 after their arrival at the farm. ESBL-PE isolates were selectively cultured and identified by MALDI-TOF. ESBL genes were characterized by RT-PCR, PCRs, and amplicon sequencing. A total of 80 E. coli and 174 K. pneumoniae strains were isolated from 104 out of 110 veal calves. The prevalence of ESBL-E. coli decreased from week 2 (61%) to week 6 (7%), while an unexpected increase in ESBL-K. pneumoniae colonization was detected in week 6 (80%). The predominant ESBL genes detected in E. coli isolates were blaCTX-M-15 and the non-ESBL gene blaTEM-1a, while in K. pneumoniae blaCTX-M-14 gene was detected in all isolates. Four cefotaxime-resistant K. pneumoniae isolates were randomly selected and characterized in deep by transformation, PCR-based replicon typing, and whole-genome sequencing (WGS). The clonal relatedness of a subgroup of nine animals carrying K. pneumoniae ESBL genes was investigated by Multi Locus sequence typing (MLST). In four ESBL-K. pneumoniae isolates, blaCTX-M-14 was located on IncFIIK and IncFIINK plasmid replicons and the isolates were multi-drug resistant (MDR). MLST demonstrated a clonal spread of ESBL-K. pneumoniae ST107. To the best of our knowledge, this is the first study to report a change in fecal carriage of ESBL-PE over time in the same veal calf during the rearing period.
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Affiliation(s)
- Teresita d.J. Bello Gonzalez
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
- *Correspondence: Teresita d.J. Bello Gonzalez,
| | - Arie Kant
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Quillan Dijkstra
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Francesca Marcato
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Kees van Reenen
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Kees T. Veldman
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Michael S. M. Brouwer
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
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10
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Ciuria S, Brouwer MSM, de Gier MM, van Zeeland Y, Bossers A, Prähauser B, Schädler J, Hatt JM, Heijne M, Borel N. Chlamydia caviae in Swiss and Dutch Guinea Pigs-Occurrence and Genetic Diversity. Pathogens 2021; 10:pathogens10101230. [PMID: 34684177 PMCID: PMC8539544 DOI: 10.3390/pathogens10101230] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/09/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022] Open
Abstract
Chlamydia (C.) caviae is a known pathogen in guinea pigs, causing conjunctivitis, respiratory infections and abortions. Recently, a C. caviae-induced zoonotic link was identified as the etiology of severe community-acquired pneumonia in humans. Here, 784 conjunctival and rectal swabs originating from 260 guinea pigs and 110 rabbits from 64 husbandries in Switzerland, as well as 200 composite conjunctival swabs originating from 878 guinea pigs from 37 husbandries in The Netherlands were examined by real-time PCR followed by conventional PCR and sequencing. Chlamydiaceae were detected in 2.3% (18/784) and 12.5% (25/200) of all Swiss and Dutch samples, respectively. An overall C. caviae occurrence was detected in 2.7% (7/260) and 8.9% (78/878) of all Swiss and Dutch guinea pigs, respectively. OmpA genotyping of 64 C. caviae-positive samples resulted in 33 sequences sharing 100% nucleotide identity with the strains isolated from the zoonotic transmission cases in The Netherlands. However, all ompA sequences of this study were distinct from the C. caviae GPIC reference strain. C. caviae was not detected in rabbits but C. psittaci genotype A was identified in guinea pigs and rabbits, raising concerns about the importance of these animal species as novel zoonotic sources for C. psittaci.
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Affiliation(s)
- Silvia Ciuria
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland; (S.C.); (B.P.)
- Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland
| | - Michael S. M. Brouwer
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (M.S.M.B.); (A.B.); (M.H.)
| | - Marende M. de Gier
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (M.M.d.G.); (Y.v.Z.)
| | - Yvonne van Zeeland
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (M.M.d.G.); (Y.v.Z.)
| | - Alex Bossers
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (M.S.M.B.); (A.B.); (M.H.)
| | - Barbara Prähauser
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland; (S.C.); (B.P.)
- Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland
| | - Julia Schädler
- National Reference Centre for Poultry and Rabbit Diseases, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland;
| | - Jean-Michel Hatt
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland;
| | - Marloes Heijne
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (M.S.M.B.); (A.B.); (M.H.)
| | - Nicole Borel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zürich, Switzerland; (S.C.); (B.P.)
- Correspondence: ; Tel.: +41-44-6358563
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11
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Pallares-Vega R, Macedo G, Brouwer MSM, Hernandez Leal L, van der Maas P, van Loosdrecht MCM, Weissbrodt DG, Heederik D, Mevius D, Schmitt H. Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains. Front Microbiol 2021; 12:656250. [PMID: 34349732 PMCID: PMC8326584 DOI: 10.3389/fmicb.2021.656250] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 01/20/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmid-mediated dissemination of antibiotic resistance among fecal Enterobacteriaceae in natural ecosystems may contribute to the persistence of antibiotic resistance genes in anthropogenically impacted environments. Plasmid transfer frequencies measured under laboratory conditions might lead to overestimation of plasmid transfer potential in natural ecosystems. This study assessed differences in the conjugative transfer of an IncP-1 (pKJK5) plasmid to three natural Escherichia coli strains carrying extended-spectrum beta-lactamases, by filter mating. Matings were performed under optimal laboratory conditions (rich LB medium and 37°C) and environmentally relevant temperatures (25, 15 and 9°C) or nutrient regimes mimicking environmental conditions and limitations (synthetic wastewater and soil extract). Under optimal nutrient conditions and temperature, two recipients yielded high transfer frequencies (5 × 10-1) while the conjugation frequency of the third strain was 1000-fold lower. Decreasing mating temperatures to psychrophilic ranges led to lower transfer frequencies, albeit all three strains conjugated under all the tested temperatures. Low nutritive media caused significant decreases in transconjugants (-3 logs for synthetic wastewater; -6 logs for soil extract), where only one of the strains was able to produce detectable transconjugants. Collectively, this study highlights that despite less-than-optimal conditions, fecal organisms may transfer plasmids in the environment, but the transfer of pKJK5 between microorganisms is limited mainly by low nutrient conditions.
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Affiliation(s)
- Rebeca Pallares-Vega
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gonçalo Macedo
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Michael S. M. Brouwer
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Lucia Hernandez Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
| | - Peter van der Maas
- Van Hall Larenstein, University of Applied Sciences, Leeuwarden, Netherlands
| | | | - David G. Weissbrodt
- Department Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Dik Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
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12
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Hesp A, Veldman K, Brouwer MSM, Wagenaar JA, Mevius D, van Schaik G. Latent class analysis to assess whole-genome sequencing versus broth microdilution for monitoring antimicrobial resistance in livestock. Prev Vet Med 2021; 193:105406. [PMID: 34147959 DOI: 10.1016/j.prevetmed.2021.105406] [Citation(s) in RCA: 1] [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: 01/14/2021] [Revised: 04/29/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance (AMR) monitoring in animals is performed in commensal Escherichia coli, and other microorganisms relevant for human or veterinary health. Due to advances in the field and major reductions in cost, it is expected that whole-genome sequencing (WGS)-based antimicrobial susceptibility testing (AST) will (partly) replace culture-based AST. So far, no studies have been performed without using culture-based AST as the gold standard. Our aim was to use Bayesian latent class analysis to evaluate the accuracy of susceptibility testing of commensal E. coli by WGS-based AST versus culture-based AST as this test does not assume a gold standard. OpenBUGS was used to model two independent tests in three animal populations (N = 150, 50 bacterial isolates per population): veal calves, pigs, and broilers. This resulted in the first estimation of sensitivity and specificity of WGS-based AST versus culture-based AST to detect AMR without a gold standard. Both methods had high sensitivity (>0.92, lowest limit probability interval: 0.76) and specificity was generally high for both methods for all antimicrobial classes except for aminoglycosides and macrolides. We compared WGS results for different length and identity settings (%) of gene alignment and found few differences between the 60/90, 90/90 and 95/95 settings. We recommend to further investigate sensitivity and specificity of WGS-based AST by means of latent class analysis, especially for low-prevalent resistance.
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Affiliation(s)
- Ayla Hesp
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
| | - Kees Veldman
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Michael S M Brouwer
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Dik Mevius
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Gerdien van Schaik
- Royal GD, Deventer, the Netherlands; Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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13
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Brouwer MSM, Goodman RN, Kant A, Mevius D, Newire E, Roberts AP, Veldman KT. Mobile colistin resistance gene mcr-1 detected on an IncI1 plasmid in Escherichia coli from meat. J Glob Antimicrob Resist 2020; 23:145-148. [PMID: 32889139 DOI: 10.1016/j.jgar.2020.08.018] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/20/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Mobile colistin resistance (mcr) genes encoded on conjugative plasmids, although described only relatively recently, have been reported globally both in humans and livestock. The genes are often associated with the insertion sequence ISApl1 that can transpose the genes to novel genetic locations. Since its first report, multiple variants of mcr have been discovered in a variety of genetic locations in Escherichia coli, in plasmids and integrated into the chromosome. METHODS Using hybrid assembly of short-read and long-read whole-genome sequencing data, the presence ofmcr-1 was confirmed on an IncI1 plasmid in E. coli. In vitro conjugation assays were performed to determine the potential to transfer between strains. Genetic comparison with previously reported IncI1 plasmids was performed. RESULTS The genomic sequence identified thatmcr-1 is present on a complete IncI1 plasmid. Comparison with previously reported extended-spectrum β-lactamase (ESBL)-encoding plasmids from E. coli in the Netherlands from the same time period indicated a distinct lineage for this plasmid. CONCLUSIONS The observation ofmcr-1 on an IncI1 plasmid confirms that the genetic region of this gene is actively transposed between genetic locations. This active transposition has consequences for the study of the epidemiology of mcr in populations.
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Affiliation(s)
| | | | - Arie Kant
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Dik Mevius
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Enas Newire
- Institute of Systems, Molecular & Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | | | - Kees T Veldman
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
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14
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Rozwandowicz M, Brouwer MSM, Mughini-Gras L, Wagenaar JA, Gonzalez-Zorn B, Mevius DJ, Hordijk J. Successful Host Adaptation of IncK2 Plasmids. Front Microbiol 2019; 10:2384. [PMID: 31681238 PMCID: PMC6803427 DOI: 10.3389/fmicb.2019.02384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 06/20/2019] [Accepted: 10/01/2019] [Indexed: 01/15/2023] Open
Abstract
The IncK plasmid group can be divided into two separate lineages named IncK1 and IncK2. IncK2 is found predominantly in poultry while IncK1 was reported in various mammals, including animals and humans. The physiological basis of this distinction is not known. In this manuscript we examined fitness cost of IncK1 and IncK2 plasmids at 37 and 42°C, which resembles mammalian and chicken body temperatures, respectively. We analyzed conjugation frequency, plasmid copy number and plasmid fitness cost in direct competition. Additionally, we measured levels of σ-32 in Escherichia coli carrying either wild type or conjugation-deficient IncK plasmids. The results show that IncK2 plasmids have a higher conjugation frequency and lower copy number at 42°C compared to IncK1. While the overall fitness cost to the host bacterium of IncK2 plasmids was higher than that of IncK1, it was not affected by the temperature while the fitness cost of IncK1 was shown to increase at 42°C compared to 37°C. These differences correlate with an increased expression of σ-32, a regulator of heat-shock protein expression, in E. coli with IncK2 compared to cells containing IncK1. This effect was not seen in cells containing conjugation deficient plasmids. Therefore, it is hypothesized that the assembly of the functional T4S may lead to these increased levels of σ–32. Increased activation of CpxR at 42°C may explain why IncK2 plasmids, and not IncK1, are predominantly found in chicken isolates.
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Affiliation(s)
- Marta Rozwandowicz
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | | | - Lapo Mughini-Gras
- National Institute for Public Health and the Environment, Bilthoven, Netherlands.,Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit, Department of Animal Health and VISAVET, Complutense University of Madrid, Madrid, Spain
| | - Dik J Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Joost Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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15
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Rozwandowicz M, Brouwer MSM, Fischer J, Wagenaar JA, Gonzalez-Zorn B, Guerra B, Mevius DJ, Hordijk J. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother 2019; 73:1121-1137. [PMID: 29370371 DOI: 10.1093/jac/dkx488] [Citation(s) in RCA: 484] [Impact Index Per Article: 96.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacterial antimicrobial resistance (AMR) is constantly evolving and horizontal gene transfer through plasmids plays a major role. The identification of plasmid characteristics and their association with different bacterial hosts provides crucial knowledge that is essential to understand the contribution of plasmids to the transmission of AMR determinants. Molecular identification of plasmid and strain genotypes elicits a distinction between spread of AMR genes by plasmids and dissemination of these genes by spread of bacterial clones. For this reason several methods are used to type the plasmids, e.g. PCR-based replicon typing (PBRT) or relaxase typing. Currently, there are 28 known plasmid types in Enterobacteriaceae distinguished by PBRT. Frequently reported plasmids [IncF, IncI, IncA/C, IncL (previously designated IncL/M), IncN and IncH] are the ones that bear the greatest variety of resistance genes. The purpose of this review is to provide an overview of all known AMR-related plasmid families in Enterobacteriaceae, the resistance genes they carry and their geographical distribution.
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Affiliation(s)
- M Rozwandowicz
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - M S M Brouwer
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Fischer
- Department of Biological Safety, Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - J A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - B Gonzalez-Zorn
- Department of Animal Health and VISAVET, Complutense University of Madrid, Madrid, Spain
| | - B Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - D J Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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16
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Jurburg SD, Brouwer MSM, Ceccarelli D, van der Goot J, Jansman AJM, Bossers A. Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession. Microbiologyopen 2019; 8:e00821. [PMID: 30828985 PMCID: PMC6741130 DOI: 10.1002/mbo3.821] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [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: 10/25/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 01/11/2023] Open
Abstract
The fine‐scale temporal dynamics of the chicken gut microbiome are unexplored, but thought to be critical for chicken health and productivity. Here, we monitored the fecal microbiome of healthy chickens on days 1–7, 10, 14, 21, 28, and 35 after hatching, and performed 16S rRNA amplicon sequencing in order to obtain a high‐resolution census of the fecal microbiome over time. In the period studied, the fecal microbiomes of the developing chickens showed a linear‐log increase in community richness and consistent shifts in community composition. Three successional stages were detected: the first stage was dominated by vertically transmitted or rapidly colonizing taxa including Streptococcus and Escherichia/Shigella; in the second stage beginning on day 4, these taxa were displaced by rapid‐growing taxa including Lachnospiraceae and Ruminococcus‐like species variants; and in the third stage, starting on day 10, slow‐growing, specialist taxa including Candidatus Arthrobacter and Romboutsia were detected. The patterns of displacement and the previously reported ecological characteristics of many of the dominant taxa observed suggest that resource competition plays an important role in regulating successional dynamics in the developing chicken gut. We propose that the boundaries between successional stages (3–4 and 14–21 days after hatching) may be optimal times for microbiome interventions.
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Affiliation(s)
- Stephanie D Jurburg
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands.,German Centre for Integrative Biodiversity Research iDiv (Halle/Jena/Leipzig), Leipzig, Germany
| | - Michael S M Brouwer
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Jeanet van der Goot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | | | - Alex Bossers
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
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17
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Liakopoulos A, van der Goot J, Bossers A, Betts J, Brouwer MSM, Kant A, Smith H, Ceccarelli D, Mevius D. Genomic and functional characterisation of IncX3 plasmids encoding bla SHV-12 in Escherichia coli from human and animal origin. Sci Rep 2018; 8:7674. [PMID: 29769695 PMCID: PMC5955891 DOI: 10.1038/s41598-018-26073-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 07/21/2017] [Accepted: 05/03/2018] [Indexed: 01/09/2023] Open
Abstract
The blaSHV-12 β-lactamase gene is one of the most prevalent genes conferring resistance to extended-spectrum β-lactams in Enterobacteriaceae disseminating within and between reservoirs, mostly via plasmid-mediated horizontal gene transfer. Yet, studies regarding the biology of plasmids encoding blaSHV-12 are very limited. In this study, we revealed the emergence of IncX3 plasmids alongside IncI1α/γ in blaSHV-12 in animal-related Escherichia coli isolates. Four representative blaSHV-12-encoding IncX3 plasmids were selected for genome sequencing and further genetic and functional characterization. We report here the first complete sequences of IncX3 plasmids of animal origin and show that IncX3 plasmids exhibit remarkable synteny in their backbone, while the major differences lie in their blaSHV-12-flanking region. Our findings indicate that plasmids of this subgroup are conjugative and highly stable, while they exert no fitness cost on their bacterial host. These favourable features might have contributed to the emergence of IncX3 amongst SHV-12-producing E. coli in the Netherlands, highlighting the epidemic potential of these plasmids.
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Affiliation(s)
- Apostolos Liakopoulos
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands. .,Institute of Biology, University of Leiden, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| | - Jeanet van der Goot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Alex Bossers
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Jonathan Betts
- Department of Bacteriology, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Michael S M Brouwer
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Arie Kant
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Hilde Smith
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Liakopoulos A, Geurts Y, Dierikx CM, Brouwer MSM, Kant A, Wit B, Heymans R, van Pelt W, Mevius DJ. Extended-Spectrum Cephalosporin-Resistant Salmonella enterica serovar Heidelberg Strains, the Netherlands(1). Emerg Infect Dis 2018; 22:1257-61. [PMID: 27314180 PMCID: PMC4918182 DOI: 10.3201/eid2207.151377] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Extended-spectrum cephalosporin-resistant Salmonella enterica serovar Heidelberg strains (JF6X01.0022/XbaI.0251, JF6X01.0326/XbaI.1966, JF6X01.0258/XbaI.1968, and JF6X01.0045/XbaI.1970) have been identified in the United States with pulsed-field gel electrophoresis. Our examination of isolates showed introduction of these strains in the Netherlands and highlight the need for active surveillance and intervention strategies by public health organizations.
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Brouwer MSM, Mullany P, Allan E, Roberts AP. Investigating Transfer of Large Chromosomal Regions Containing the Pathogenicity Locus Between Clostridium difficile Strains. Methods Mol Biol 2018; 1476:215-22. [PMID: 27507344 DOI: 10.1007/978-1-4939-6361-4_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The genomes of all sequenced Clostridium difficile isolates contain multiple mobile genetic elements. The chromosomally located pathogenicity locus (PaLoc), encoding the cytotoxins TcdA and TcdB, was previously hypothesized to be a mobile genetic element; however, mobility was not demonstrated. Here we describe the methods used to facilitate and detect the transfer of the PaLoc from a toxigenic strain into non-toxigenic strains of C. difficile. Although the precise mechanism of transfer has not yet been elucidated, a number of controls are described which indicate transfer occurs via a cell-to-cell-mediated conjugation-like transfer mechanism. Importantly, transfer of the PaLoc was shown to occur on large chromosomal fragments of variable sizes, indicating that homologous recombination is likely to be responsible for the insertion events.
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Affiliation(s)
- Michael S M Brouwer
- Department of Bacteriology and Epidemiology, Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands
| | - Peter Mullany
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
| | - Elaine Allan
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
| | - Adam P Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK.
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Brouwer MSM, Tagg KA, Mevius DJ, Iredell JR, Bossers A, Smith HE, Partridge SR. IncI shufflons: Assembly issues in the next-generation sequencing era. Plasmid 2015; 80:111-7. [PMID: 25952328 DOI: 10.1016/j.plasmid.2015.04.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [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: 01/19/2015] [Revised: 04/15/2015] [Accepted: 04/20/2015] [Indexed: 11/18/2022]
Abstract
The shufflon is a site-specific recombination system first identified in the IncI1 plasmid R64. The R64 shufflon consists of four segments, separated by short repeats, which are rearranged and inverted by the recombinase protein Rci, generating diversity in the C-terminal end of the PilV protein. PilV is the tip adhesin of the thin pilus structure involved in bacterial conjugation and may play a role in determining recipient cell specificity during liquid mating. The variable arrangements of the shufflon region would be expected to make plasmid assembly difficult, particularly with short-read sequencing technology, but this is not usually mentioned in recent publications reporting IncI plasmid sequences. Here we discuss the issues we encountered with assembly of IncI1 sequence data obtained from the Roche-454 and Illumina platforms and make some suggestions for assembly of the shufflon region. Comparison of shufflon segments from a collection of IncI1 plasmids from The Netherlands and Australia, together with sequences available in GenBank, suggests that the number of shufflon segments present is conserved among plasmids grouped together by plasmid multi-locus sequencing typing but the different reported arrangements of shufflon segments may not be meaningful. This analysis also indicated that the sequences of the shufflon segments are highly conserved, with very few nucleotide changes.
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Affiliation(s)
- Michael S M Brouwer
- Central Veterinary Institute of Wageningen UR, PO Box 65, 8200 AB Lelystad, The Netherlands.
| | - Kaitlin A Tagg
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, The University of Sydney and Westmead Hospital, Westmead, NSW 2145, Australia
| | - Dik J Mevius
- Central Veterinary Institute of Wageningen UR, PO Box 65, 8200 AB Lelystad, The Netherlands
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, The University of Sydney and Westmead Hospital, Westmead, NSW 2145, Australia
| | - Alex Bossers
- Central Veterinary Institute of Wageningen UR, PO Box 65, 8200 AB Lelystad, The Netherlands
| | - Hilde E Smith
- Central Veterinary Institute of Wageningen UR, PO Box 65, 8200 AB Lelystad, The Netherlands
| | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, The University of Sydney and Westmead Hospital, Westmead, NSW 2145, Australia.
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Brouwer MSM, Roberts AP, Mullany P, Allan E. In silico analysis of sequenced strains of Clostridium difficile reveals a related set of conjugative transposons carrying a variety of accessory genes. Mob Genet Elements 2014; 2:8-12. [PMID: 22754747 PMCID: PMC3383454 DOI: 10.4161/mge.19297] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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] [Indexed: 12/13/2022] Open
Abstract
The human gut pathogen Clostridium difficile contains many conjugative transposons that have an array of accessory genes. In the current study, recently sequenced genomes were analyzed to identify new putative conjugative transposons. Eleven new elements in 5 C. difficile strains were identified and all had a similar structure to the previously described elements CTn1, CTn5 and CTn7 in C. difficile strain 630. Each element identified did however contain a new set of accessory genes compared with those previously reported; including those predicted to encode ABC transporters, a toxin/antitoxin system and multiple antibiotic resistance genes.
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Affiliation(s)
- Michael S M Brouwer
- Department of Microbial Diseases; UCL Eastman Dental Institute; University College London; London, UK
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22
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Ciric L, Brouwer MSM, Mullany P, Roberts AP. Minocycline resistance in an oral Streptococcus infantis isolate is encoded by tet(S) on a novel small, low copy number plasmid. FEMS Microbiol Lett 2014; 353:106-15. [PMID: 24605990 PMCID: PMC4237122 DOI: 10.1111/1574-6968.12410] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 02/03/2014] [Revised: 02/25/2014] [Accepted: 02/25/2014] [Indexed: 11/29/2022] Open
Abstract
We have determined the genetic basis of minocycline resistance in a strain of Streptococcus infantis isolated from a healthy human oral cavity. We demonstrate that tet(S), identical to tet(S) found on the enterococcal conjugative transposon Tn6000, is responsible for the observed resistance. The gene is located on a small, low copy number plasmid and is flanked by IS1216 elements. The tet(S) gene is capable of excising from the plasmid together with one of the IS1216 elements. The plasmid contains a putative toxin/antitoxin system related to relBE. Deletion of the toxin, relE, did not result in plasmid instability but did increase the fitness of the mutant compared to the wild-type strain.
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Affiliation(s)
- Lena Ciric
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
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Corver J, Bakker D, Brouwer MSM, Harmanus C, Hensgens MP, Roberts AP, Lipman LJA, Kuijper EJ, van Leeuwen HC. Analysis of a Clostridium difficile PCR ribotype 078 100 kilobase island reveals the presence of a novel transposon, Tn6164. BMC Microbiol 2012; 12:130. [PMID: 22747711 PMCID: PMC3485107 DOI: 10.1186/1471-2180-12-130] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [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: 04/04/2012] [Accepted: 06/25/2012] [Indexed: 11/28/2022] Open
Abstract
Background Clostridium difficile is the main cause of antibiotic associated diarrhea. In the past decade, the number of C. difficile patients has increased dramatically, coinciding with the emergence of two PCR ribotypes 027 and 078. PCR ribotype 078 is also frequently found during C. difficile outbreaks in pigfarms. Previously, the genome of the PCR ribotype 078 strain M120, a human isolate, was described to contain a unique insert of 100 kilobases. Results Analysis of this insert revealed over 90 open reading frames, encoding proteins originating from transposons, phages and plasmids. The insert was shown to be a transposon (Tn6164), as evidenced by the presence of an excised and circularised molecule, containing the ligated 5’and 3’ends of the insert. Transfer of the element could not be shown through filter-mating experiments. Whole genome sequencing of PCR ribotype 078 strain 31618, isolated from a diarrheic piglet, showed that Tn6164 was not present in this strain. To test the prevalence of Tn6164, a collection of 231 Clostridium difficile PCR ribotype 078 isolates from human (n = 173) and porcine (n = 58) origin was tested for the presence of this element by PCR. The transposon was present in 9 human, tetracycline resistant isolates, originating from various countries in Europe, and none of the pig strains. Nine other strains, also tetracycline resistant human isolates, contained half of the transposon, suggesting multiple insertion steps yielding the full Tn6164. Other PCR ribotypes (n = 66) were all negative for the presence of the transposon. Multi locus variable tandem repeat analysis revealed genetic relatedness among transposon containing isolates. Although the element contained several potential antibiotic resistance genes, it did not yield a readily distinguishable phenotype. Conclusions Tn6164 is a newly described transposon, occurring sporadically in C. difficile PCR ribotype 078 strains. Although no transfer of the element could be shown, we hypothesize that the element could serve as a reservoir of antibiotic resistance genes for other bacteria. Further research is needed to investigate the transfer capabilities of the element and to substantiate the possible role of Tn6164 as a source of antibiotic resistance genes for other gut pathogens.
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Affiliation(s)
- Jeroen Corver
- Department of Medical Microbiology, Section Experimental Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands.
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Brouwer MSM, Warburton PJ, Roberts AP, Mullany P, Allan E. Genetic organisation, mobility and predicted functions of genes on integrated, mobile genetic elements in sequenced strains of Clostridium difficile. PLoS One 2011; 6:e23014. [PMID: 21876735 PMCID: PMC3158075 DOI: 10.1371/journal.pone.0023014] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 07/08/2011] [Indexed: 12/21/2022] Open
Abstract
Background Clostridium difficile is the leading cause of hospital-associated diarrhoea in the US and Europe. Recently the incidence of C. difficile-associated disease has risen dramatically and concomitantly with the emergence of ‘hypervirulent’ strains associated with more severe disease and increased mortality. C. difficile contains numerous mobile genetic elements, resulting in the potential for a highly plastic genome. In the first sequenced strain, 630, there is one proven conjugative transposon (CTn), Tn5397, and six putative CTns (CTn1, CTn2 and CTn4-7), of which, CTn4 and CTn5 were capable of excision. In the second sequenced strain, R20291, two further CTns were described. Results CTn1, CTn2 CTn4, CTn5 and CTn7 were shown to excise from the genome of strain 630 and transfer to strain CD37. A putative CTn from R20291, misleadingly termed a phage island previously, was shown to excise and to contain three putative mobilisable transposons, one of which was capable of excision. In silico probing of C. difficile genome sequences with recombinase gene fragments identified new putative conjugative and mobilisable transposons related to the elements in strains 630 and R20291. CTn5-like elements were described occupying different insertion sites in different strains, CTn1-like elements that have lost the ability to excise in some ribotype 027 strains were described and one strain was shown to contain CTn5-like and CTn7-like elements arranged in tandem. Additionally, using bioinformatics, we updated previous gene annotations and predicted novel functions for the accessory gene products on these new elements. Conclusions The genomes of the C. difficile strains examined contain highly related CTns suggesting recent horizontal gene transfer. Several elements were capable of excision and conjugative transfer. The presence of antibiotic resistance genes and genes predicted to promote adaptation to the intestinal environment suggests that CTns play a role in the interaction of C. difficile with its human host.
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Affiliation(s)
- Michael S. M. Brouwer
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, United Kingdom
| | - Philip J. Warburton
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, United Kingdom
| | - Adam P. Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, United Kingdom
| | - Peter Mullany
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, United Kingdom
| | - Elaine Allan
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, United Kingdom
- * E-mail:
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van Eijk M, Aust G, Brouwer MSM, van Meurs M, Voerman JSA, Dijke IE, Pouwels W, Sändig I, Wandel E, Aerts JMFG, Boot RG, Laman JD, Hamann J. Differential expression of the EGF-TM7 family members CD97 and EMR2 in lipid-laden macrophages in atherosclerosis, multiple sclerosis and Gaucher disease. Immunol Lett 2010; 129:64-71. [PMID: 20167235 DOI: 10.1016/j.imlet.2010.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 02/07/2010] [Accepted: 02/09/2010] [Indexed: 11/28/2022]
Abstract
The members of the epidermal growth factor (EGF)-transmembrane (TM)7 family of adhesion class G-protein coupled receptors are abundantly expressed by cells of the myeloid lineage. A detailed investigation of their expression by functional subsets of activated macrophages is still lacking. Therefore, we determined the expression of CD97, EGF module-containing mucin-like receptor (EMR)2 and EMR3 by monocyte-derived macrophages experimentally polarized in vitro. This was compared to three types of disease-associated lipid-laden macrophages displaying an alternatively activated phenotype in situ. Polarization in vitro towards classically activated M1 versus alternatively activated M2 extremes of macrophage activation did not result in a congruent regulation of EGF-TM7 receptor mRNA and protein except for a down-regulation of CD97 by IL-10. In contrast, macrophages handling lipid overload in vivo displayed differences in the expression of CD97 and EMR2. While foamy macrophages in atherosclerotic vessels expressed both CD97 and EMR2, foam cells in multiple sclerosis brain expressed CD97, but only little EMR2. Foam cell formation in vitro by oxidized LDL and myelin did not affect CD97 or EMR2 expression. Gaucher spleen cells accumulating glucosylceramide expressed very high levels of CD97 and EMR2. These findings indicate that complex cellular expression programmes rather than activation modes regulate the expression of EGF-TM7 receptors in macrophages.
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Affiliation(s)
- Marco van Eijk
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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