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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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Stubberfield E, AbuOun M, Card RM, Welchman D, Anjum MF. Molecular characterization of antimicrobial resistance in Brachyspira species isolated from UK chickens: Identification of novel variants of pleuromutilin and beta-lactam resistance genes. Vet Microbiol 2024; 290:109992. [PMID: 38306769 DOI: 10.1016/j.vetmic.2024.109992] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 12/21/2023] [Accepted: 01/10/2024] [Indexed: 02/04/2024]
Abstract
Brachyspira species are Gram negative, anaerobic bacteria that colonise the gut of many animals, including poultry. In poultry, Brachyspira species can be commensal (B. innocens, B. murdochii, 'B. pulli') or pathogenic (B. pilosicoli, B. intermedia, B. alvinipulli or rarely B. hyodysenteriae), the latter causing avian intestinal spirochaetosis (AIS). Antimicrobial therapy options for treatment is limited, frequently involving administration of the pleuromutilin, tiamulin, in water. In this study 38 Brachyspira isolates from chickens in the UK, representing both commensal and pathogenic species, were whole genome sequenced to identify antimicrobial resistance (AMR) mechanisms and the minimum inhibitory concentration (MIC) to a number of antimicrobials was also determined. We identified several new variants of blaOXA in B. pilosicoli and B. pulli isolates, and variations in tva which led to two new tva variants in B.murdochii and B.pulli. A number of isolates also harboured mutations known to encode AMR in the 16S and 23S rRNA genes. The percentage of isolates that were genotypically multi-drug resistance (MDR) was 16%, with the most common resistance profile being: tetracycline, pleuromutilin and beta-lactam, which were found in three 'B. pulli' and one B. pilosicoli. There was good correlation with the genotype and the corresponding antibiotic MIC phenotypes: pleuromutilins (tiamulin and valnemulin), macrolides (tylosin and tylvalosin), lincomycin and doxycycline. The occurrence of resistance determinants identified in this study in pathogenic Brachyspira, especially those which were MDR, is likely to impact treatment of AIS and clearance of infections on farm.
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Affiliation(s)
- Emma Stubberfield
- Animal and Plant Health Agency Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Manal AbuOun
- Animal and Plant Health Agency Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK.
| | - Roderick M Card
- Animal and Plant Health Agency Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - David Welchman
- Animal and Plant Health Agency Winchester, Itchen Abbas, Winchester SO21 1BX, UK
| | - Muna F Anjum
- Animal and Plant Health Agency Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
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Duggett N, AbuOun M, Stubberfield E, Turner O, Randall L, Horton R, Nunez-Garcia J, Gates D, Chanter J, Teale C, Anjum MF. Genomic surveillance of extended-spectrum cephalosporin-resistant Escherichia coli isolated from poultry in the UK from 2016 to 2020. Front Microbiol 2024; 14:1335173. [PMID: 38352060 PMCID: PMC10861728 DOI: 10.3389/fmicb.2023.1335173] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 02/16/2024] Open
Abstract
Introduction Surveillance is vital for monitoring the increasing risk of antimicrobial resistance (AMR) in bacteria leading to failures in humans and animals to treat infections. In a One Health context, AMR bacteria from livestock and food can transfer through the food chain to humans, and vice versa, which can be characterized in detail through genomics. We investigated the critical aspects of AMR and the dynamics of AMR in poultry in the UK. Methods In this study, we performed whole genome sequencing for genomic characterization of 761 extended-spectrum cephalosporinases (ESCs) harboring Escherichia coli isolated from poultry caeca and meat through EU harmonized monitoring of AMR in zoonotic and commensal bacteria from 2016 and 2018 and UK national monitoring in 2020. Results The most common ESC in 2016 and 2018 was blaCTX-M-1; however, 2020 had a greater diversity of ESCs with blaCTX-M-55 dominant in chickens and blaCTX-M-15 more prevalent in turkeys. Co-resistance to sulphonamides, tetracycline, and trimethoprim was widespread, and there were several positive correlations between the sequence types (STs) and ESC genes. We identified certain AMR genotypes and STs that were frequent each year but not as successful in subsequent years, e.g., ST350 harboring blaCTX-M-1, sul2, and tetA-v4.Phylogenetic comparison of isolates prevalent in our panel with global ones from the same STs available in public databases showed that isolates from the UK generally clustered together, suggesting greater within-country than between-country transmission. Discussion We conclude that future genomic surveillance of indicator organisms will be invaluable as it will enable detailed comparisons of AMR between and within neighboring countries, potentially identifying the most successful sequence types, plasmids, or emerging threats.
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Affiliation(s)
- Nicholas Duggett
- Animal and Plant Health Agency, Addlestone, United Kingdom
- Animal and Plant Health Agency, Thirsk Veterinary Investigation Centre, Thirsk, United Kingdom
| | - Manal AbuOun
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | | | - Olivia Turner
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Luke Randall
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Robert Horton
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | | | - Daisy Gates
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Jeremy Chanter
- Animal and Plant Health Agency, Starcross Veterinary Investigation Centre, Exeter, United Kingdom
| | - Chris Teale
- Animal and Plant Health Agency, Veterinary Investigation Centre, Shrewsbury, United Kingdom
| | - Muna F. Anjum
- Animal and Plant Health Agency, Addlestone, United Kingdom
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Davies TJ, Swann J, Sheppard AE, Pickford H, Lipworth S, AbuOun M, Ellington MJ, Fowler PW, Hopkins S, Hopkins KL, Crook DW, Peto TEA, Anjum MF, Walker AS, Stoesser N. Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli. Microb Genom 2023; 9:001151. [PMID: 38100178 PMCID: PMC10763500 DOI: 10.1099/mgen.0.001151] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Several bioinformatics genotyping algorithms are now commonly used to characterize antimicrobial resistance (AMR) gene profiles in whole-genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly Escherichia coli, is of major importance, because this is a common pathogen. However, robust comparisons of different genotyping approaches on relevant simulated and large real-life WGS datasets are lacking. Here, we used both simulated datasets and a large set of real E. coli WGS data (n=1818 isolates) to systematically investigate genotyping methods in greater detail. Simulated constructs and real sequences were processed using four different bioinformatic programs (ABRicate, ARIBA, KmerResistance and SRST2, run with the ResFinder database) and their outputs compared. For simulation tests where 3079 AMR gene variants were inserted into random sequence constructs, KmerResistance was correct for 3076 (99.9 %) simulations, ABRicate for 3054 (99.2 %), ARIBA for 2783 (90.4 %) and SRST2 for 2108 (68.5 %). For simulation tests where two closely related gene variants were inserted into random sequence constructs, KmerResistance identified the correct alleles in 35 338/46 318 (76.3 %) simulations, ABRicate identified them in 11 842/46 318 (25.6 %) simulations, ARIBA identified them in 1679/46 318 (3.6 %) simulations and SRST2 identified them in 2000/46 318 (4.3 %) simulations. In real data, across all methods, 1392/1818 (76 %) isolates had discrepant allele calls for at least 1 gene. In addition to highlighting areas for improvement in challenging scenarios, (e.g. identification of AMR genes at <10× coverage, identifying multiple closely related AMR genes present in the same sample), our evaluations identified some more systematic errors that could be readily soluble, such as repeated misclassification (i.e. naming) of genes as shorter variants of the same gene present within the reference resistance gene database. Such naming errors accounted for at least 2530/4321 (59 %) of the discrepancies seen in real data. Moreover, many of the remaining discrepancies were likely 'artefactual', with reporting of cut-off differences accounting for at least 1430/4321 (33 %) discrepants. Whilst we found that comparing outputs generated by running multiple algorithms on the same dataset could identify and resolve these algorithmic artefacts, the results of our evaluations emphasize the need for developing new and more robust genotyping algorithms to further improve accuracy and performance.
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Affiliation(s)
- Timothy J. Davies
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Anna E. Sheppard
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Hayleigh Pickford
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Samuel Lipworth
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Manal AbuOun
- Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - Matthew J. Ellington
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Division, UK Health Security Agency, London, UK
| | | | - Susan Hopkins
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Division, UK Health Security Agency, London, UK
| | - Katie L. Hopkins
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Derrick W. Crook
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Timothy E. A. Peto
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Muna F. Anjum
- Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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Deza-Cruz I, Vilar MJ, Velasova M, AbuOun M, Anjum MF, Smith RP. Antimicrobial resistance of Escherichia coli in the UK: comparison of single vs. pooled samples from healthy pigs. Lett Appl Microbiol 2023; 76:ovad123. [PMID: 37942558 DOI: 10.1093/lambio/ovad123] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/04/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
This study compared the antimicrobial resistance (AMR) of Escherichia coli detected from single samples vs. pooled samples at herd level. The national monitoring dataset included isolates from one sample per pig holding, whereas the research study included isolates from pooled samples of 10 pigs per holding. In both datasets, caecal samples were collected from healthy pigs randomly selected at slaughterhouses and plated on non-selective and antibiotic selective media. Resistance against a panel of nine antibiotics was compared between datasets by generalized linear mixed effects models (GLMMs) and by bootstrapped generalized linear model (GLM) to account for pooling. The highest proportion of resistant E. coli was observed against tetracycline and ampicillin in both datasets. In non-selective media, single and pooled samples showed similar results, but the bootstrapped GLM detected significantly lower resistance to ciprofloxacin and nalidixic acid in the national dataset. In selective media, a significantly greater proportion of resistant isolates was observed in the research dataset for ceftazidime (OR: 0.05, 95%CI = 0.01-0.42) and nalidixic acid (OR: 0.15, 95%CI = 0.05-0.51). The results suggest that one sample per holding provides similar information on AMR at herd level as pooled samples for most of the tested antibiotics, although less resistance to ciprofloxacin, ceftazidime, and nalidixic acid was detected.
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Affiliation(s)
- Iñaki Deza-Cruz
- Department of Veterinary Epidemiology and Public Health, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, United Kingdom
| | - María J Vilar
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Martina Velasova
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey KT15 3NB, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey KT15 3NB, United Kingdom
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Lopez-Garcia AV, AbuOun M, Nunez-Garcia J, Nale JY, Gaylov EE, Phothaworn P, Sukjoi C, Thiennimitr P, Malik DJ, Korbsrisate S, Clokie MRJ, Anjum MF. Corrigendum: Pathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens. Front Microbiol 2023; 14:1221779. [PMID: 37614593 PMCID: PMC10443699 DOI: 10.3389/fmicb.2023.1221779] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2023.1166615.].
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Affiliation(s)
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Javier Nunez-Garcia
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Janet Y. Nale
- Department of Veterinary and Animal Science, Scotland's Rural College, Inverness, United Kingdom
| | - Edouard E. Gaylov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Preeda Phothaworn
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chutikarn Sukjoi
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Danish J. Malik
- Department of Chemical Engineering, Loughborough University, Loughborough, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
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Lopez-Garcia AV, AbuOun M, Nunez-Garcia J, Nale JY, Gaylov EE, Phothaworn P, Sukjoi C, Thiennimitr P, Malik DJ, Korbsrisate S, Clokie MRJ, Anjum MF. Pathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens. Front Microbiol 2023; 14:1166615. [PMID: 37234523 PMCID: PMC10206635 DOI: 10.3389/fmicb.2023.1166615] [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: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 05/28/2023] Open
Abstract
Salmonella is a food-borne pathogen often linked to poultry sources, causing gastrointestinal infections in humans, with the numbers of multidrug resistant (MDR) isolates increasing globally. To gain insight into the genomic diversity of common serovars and their potential contribution to disease, we characterized antimicrobial resistance genes, and virulence factors encoded in 88 UK and 55 Thai isolates from poultry; the presence of virulence genes was detected through an extensive virulence determinants database compiled in this study. Long-read sequencing of three MDR isolates, each from a different serovar, was used to explore the links between virulence and resistance. To augment current control methods, we determined the sensitivity of isolates to 22 previously characterized Salmonella bacteriophages. Of the 17 serovars included, Salmonella Typhimurium and its monophasic variants were the most common, followed by S. Enteritidis, S. Mbandaka, and S. Virchow. Phylogenetic analysis of Typhumurium and monophasic variants showed poultry isolates were generally distinct from pigs. Resistance to sulfamethoxazole and ciprofloxacin was highest in isolates from the UK and Thailand, respectively, with 14-15% of all isolates being MDR. We noted that >90% of MDR isolates were likely to carry virulence genes as diverse as the srjF, lpfD, fhuA, and stc operons. Long-read sequencing revealed the presence of global epidemic MDR clones in our dataset, indicating they are possibly widespread in poultry. The clones included MDR ST198 S. Kentucky, harboring a Salmonella Genomic Island-1 (SGI)-K, European ST34 S. 1,4,[5],12:i:-, harboring SGI-4 and mercury-resistance genes, and a S. 1,4,12:i:- isolate from the Spanish clone harboring an MDR-plasmid. Testing of all isolates against a panel of bacteriophages showed variable sensitivity to phages, with STW-77 found to be the most effective. STW-77 lysed 37.76% of the isolates, including serovars important for human clinical infections: S. Enteritidis (80.95%), S. Typhimurium (66.67%), S. 1,4,[5],12:i:- (83.3%), and S. 1,4,12: i:- (71.43%). Therefore, our study revealed that combining genomics and phage sensitivity assays is promising for accurately identifying and providing biocontrols for Salmonella to prevent its dissemination in poultry flocks and through the food chain to cause infections in humans.
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Affiliation(s)
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Javier Nunez-Garcia
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Janet Y. Nale
- Department of Veterinary and Animal Science, Scotland's Rural College, Inverness, United Kingdom
| | - Edouard E. Gaylov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Preeda Phothaworn
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chutikarn Sukjoi
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Danish J. Malik
- Department of Chemical Engineering, Loughborough University, Loughborough, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
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Matlock W, Lipworth S, Chau KK, AbuOun M, Barker L, Kavanagh J, Andersson M, Oakley S, Morgan M, Crook DW, Read DS, Anjum M, Shaw LP, Stoesser N. Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK. eLife 2023; 12:e85302. [PMID: 36961866 DOI: 10.7554/elife.85302] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, the extent of plasmid sharing and evolution between Enterobacterales causing human infections and other niches remains unclear, including the emergence of resistance plasmids. Dense, unselected sampling is essential to developing our understanding of plasmid epidemiology and designing appropriate interventions to limit the emergence and dissemination of plasmid-associated AMR. We established a geographically and temporally restricted collection of human bloodstream infection (BSI)-associated, livestock-associated (cattle, pig, poultry, and sheep faeces, farm soils) and wastewater treatment work (WwTW)-associated (influent, effluent, waterways upstream/downstream of effluent outlets) Enterobacterales. Isolates were collected between 2008 and 2020 from sites <60 km apart in Oxfordshire, UK. Pangenome analysis of plasmid clusters revealed shared 'backbones', with phylogenies suggesting an intertwined ecology where well-conserved plasmid backbones carry diverse accessory functions, including AMR genes. Many plasmid 'backbones' were seen across species and niches, raising the possibility that plasmid movement between these followed by rapid accessory gene change could be relatively common. Overall, the signature of identical plasmid sharing is likely to be a highly transient one, implying that plasmid movement might be occurring at greater rates than previously estimated, raising a challenge for future genomic One Health studies.
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Affiliation(s)
- William Matlock
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Samuel Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Manal AbuOun
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Sarah Oakley
- Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Marcus Morgan
- Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Trust, Oxford, United Kingdom
- NIHR Biomedical Research Centre, Oxford, United Kingdom
| | - Daniel S Read
- Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Muna Anjum
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Liam P Shaw
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Trust, Oxford, United Kingdom
- NIHR Biomedical Research Centre, Oxford, United Kingdom
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Smith RP, May HE, AbuOun M, Stubberfield E, Gilson D, Chau KK, Crook DW, Shaw LP, Read DS, Stoesser N, Vilar MJ, Anjum MF. A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone. Front Microbiol 2023; 14:1070340. [PMID: 36998408 PMCID: PMC10043416 DOI: 10.3389/fmicb.2023.1070340] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/23/2023] [Indexed: 03/15/2023] Open
Abstract
IntroductionThere are concerns that antimicrobial usage (AMU) is driving an increase in multi-drug resistant (MDR) bacteria so treatment of microbial infections is becoming harder in humans and animals. The aim of this study was to evaluate factors, including usage, that affect antimicrobial resistance (AMR) on farm over time.MethodsA population of 14 cattle, sheep and pig farms within a defined area of England were sampled three times over a year to collect data on AMR in faecal Enterobacterales flora; AMU; and husbandry or management practices. Ten pooled samples were collected at each visit, with each comprising of 10 pinches of fresh faeces. Up to 14 isolates per visit were whole genome sequenced to determine presence of AMR genes.ResultsSheep farms had very low AMU in comparison to the other species and very few sheep isolates were genotypically resistant at any time point. AMR genes were detected persistently across pig farms at all visits, even on farms with low AMU, whereas AMR bacteria was consistently lower on cattle farms than pigs, even for those with comparably high AMU. MDR bacteria was also more commonly detected on pig farms than any other livestock species.DiscussionThe results may be explained by a complex combination of factors on pig farms including historic AMU; co-selection of AMR bacteria; variation in amounts of antimicrobials used between visits; potential persistence in environmental reservoirs of AMR bacteria; or importation of pigs with AMR microbiota from supplying farms. Pig farms may also be at increased risk of AMR due to the greater use of oral routes of group antimicrobial treatment, which were less targeted than cattle treatments; the latter mostly administered to individual animals. Also, farms which exhibited either increasing or decreasing trends of AMR across the study did not have corresponding trends in their AMU. Therefore, our results suggest that factors other than AMU on individual farms are important for persistence of AMR bacteria on farms, which may be operating at the farm and livestock species level.
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Affiliation(s)
- Richard P. Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
- *Correspondence: Richard P. Smith,
| | - Hannah E. May
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Daniel Gilson
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Kevin K. Chau
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Derrick W. Crook
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom
- Molecular Ecology Group, UK Centre of Ecology and Hydrology (UKCEH), Wallingford, United Kingdom
| | - Liam P. Shaw
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Daniel S. Read
- Molecular Ecology Group, UK Centre of Ecology and Hydrology (UKCEH), Wallingford, United Kingdom
| | - Nicole Stoesser
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom
- Molecular Ecology Group, UK Centre of Ecology and Hydrology (UKCEH), Wallingford, United Kingdom
| | - Maria Jose Vilar
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
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Nale JY, Ahmed B, Haigh R, Shan J, Phothaworn P, Thiennimitr P, Garcia A, AbuOun M, Anjum MF, Korbsrisate S, Galyov EE, Malik DJ, Clokie MR. Activity of a Bacteriophage Cocktail to Control Salmonella Growth Ex Vivo in Avian, Porcine, and Human Epithelial Cell Cultures. Phage (New Rochelle) 2023; 4:11-25. [PMID: 37214653 PMCID: PMC10196083 DOI: 10.1089/phage.2023.0001] [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] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We examined the activity of phages to control the growth of chicken and swine Salmonella strains in avian (CHIC-8E11), porcine (IPEC-1), and human (HT-29) cell cultures. We optimized a six-phage cocktail by selecting the five most effective myoviruses and a siphovirus that have optimal lysis on prevalent serovars. We observed ∼20% of 7 log10 PFU/well phage and 3-6 log10 CFU bacterial adhesions, and 3-5 log10 CFU bacterial invasion per 2 cm2 of the cultured cells at 2 h post-treatment. The invasive bacteria when plated had a variable reduced susceptibility to the phages. After phage application at an MOI of 10, the prophylaxis regimen had better efficacy at controlling bacterial growth with an up to 6 log10 CFU/well reduction as compared with the 1-2 log10 CFU/well bacterial reduction observed in the remedial and coinfection regimens. Our data support the development of these phages to control salmonellosis in chickens, pigs, and humans.
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Affiliation(s)
- Janet Y. Nale
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, North Faculty, Scotland's Rural College, Inverness, United Kingdom
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Buthainah Ahmed
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Richard Haigh
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Respiratory Science, University of Leicester, Leicester, United Kingdom
| | - Jinyu Shan
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Preeda Phothaworn
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Centre of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
- Center of Multidisciplinary Technology for Advanced Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Angela Garcia
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Edouard E. Galyov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Danish J. Malik
- Department of Chemical Engineering, Loughborough University, Loughborough, United Kingdom
| | - Martha R.J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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11
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Sukjoi C, Buddhasiri S, Tantibhadrasapa A, Kaewsakhorn T, Phothaworn P, Nale JY, Lopez-Garcia AV, AbuOun M, Anjum MF, Malik DJ, Galyov EE, Clokie MRJ, Korbsrisate S, Thiennimitr P. Therapeutic effects of oral administration of lytic Salmonella phages in a mouse model of non-typhoidal salmonellosis. Front Microbiol 2022; 13:955136. [DOI: 10.3389/fmicb.2022.955136] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
Acute non-typhoidal salmonellosis (NTS) caused by a Gram-negative bacterium Salmonella enterica serovar Typhimurium (S. Tm) is one of the most common bacterial foodborne diseases worldwide. Bacteriophages (phages) can specifically target and lyse their host bacteria, including the multidrug-resistant strains, without collateral damage to other bacteria in the community. However, the therapeutic use of Salmonella phages in vivo is still poorly investigated. Salmonella phages ST-W77 and SE-W109 have previously been shown by our group to be useful for biocontrol properties. Here, we tested whether phages ST-W77 and SE-W109 can reduce Salmonella invasion into cultured human cells and confer a therapeutic benefit for acute NTS in a mammalian host. Human colonocytes, T84 cells, were treated with phages ST-W77, SE-W109, and its combination for 5 min before S. Tm infection. Gentamicin protection assays demonstrated that ST-W77 and SE-W109 significantly reduced S. Tm invasion and inflammatory response in human colonocytes. Next, streptomycin-pretreated mice were orally infected with S. Tm (108 CFU/mouse) and treated with a single or a combination of ST-W77 and SE-W109 (1010 PFU/mouse for 4 days) by oral feeding. Our data showed that phage-treated mice had lower S. Tm numbers and tissue inflammation compared to the untreated mice. Our study also revealed that ST-W77 and SE-W109 persist in the mouse gut lumen, but not in systemic sites. Together, these data suggested that Salmonella phages ST-W77 and SE-W109 could be further developed as an alternative approach for treating an acute NTS in mammalian hosts.
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Nunez-Garcia J, AbuOun M, Storey N, Brouwer MS, Delgado-Blas JF, Mo SS, Ellaby N, Veldman KT, Haenni M, Châtre P, Madec JY, Hammerl JA, Serna C, Getino M, La Ragione R, Naas T, Telke AA, Glaser P, Sunde M, Gonzalez-Zorn B, Ellington MJ, Anjum MF. Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance. Sci Rep 2022; 12:14372. [PMID: 35999234 PMCID: PMC9396611 DOI: 10.1038/s41598-022-16760-9] [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: 02/11/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance (AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436 Escherichia coli were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype–phenotype associations. No significant differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations. The study also revealed limitations of in-silico technology on detecting resistance to certain antimicrobials due to lack of specific fine-tuning options in bioinformatics tool or a lack of representation of resistance mechanisms in reference databases. Lastly, we noted user friendliness of tools was also an important consideration. Therefore, our recommendations are timely for widespread standardisation of bioinformatics for genomic diagnostics and surveillance globally.
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Affiliation(s)
| | - M AbuOun
- Animal and Plant Health Agency (APHA), Weybridge, UK
| | - N Storey
- Animal and Plant Health Agency (APHA), Weybridge, UK
| | - M S Brouwer
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | | | - S S Mo
- Norwegian Veterinary Institute (NVI), Oslo, Norway
| | - N Ellaby
- Public Health England (PHE), London, UK
| | - K T Veldman
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - M Haenni
- Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Maisons-Alfort, France
| | - P Châtre
- Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Maisons-Alfort, France
| | - J Y Madec
- Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Maisons-Alfort, France
| | - J A Hammerl
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - C Serna
- Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - M Getino
- University of Surrey (UoS), Guildford, UK
| | | | - T Naas
- Assistance Publique Hopitaux de Paris, Paris, France
| | - A A Telke
- Norwegian Veterinary Institute (NVI), Oslo, Norway
| | - P Glaser
- Institute Pasteur, EERA Unit, Paris, France
| | - M Sunde
- Norwegian Veterinary Institute (NVI), Oslo, Norway
| | | | | | - M F Anjum
- Animal and Plant Health Agency (APHA), Weybridge, UK. .,University of Surrey (UoS), Guildford, UK.
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13
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Olorunleke SO, Kirchner M, Duggett N, AbuOun M, Okorie-Kanu OJ, Stevens K, Card RM, Chah KF, Nwanta JA, Brunton LA, Anjum MF. Molecular characterization of extended spectrum cephalosporin resistant Escherichia coli isolated from livestock and in-contact humans in Southeast Nigeria. Front Microbiol 2022; 13:937968. [PMID: 35935201 PMCID: PMC9354541 DOI: 10.3389/fmicb.2022.937968] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/05/2022] [Indexed: 11/20/2022] Open
Abstract
The rise in antimicrobial resistance (AMR) in bacteria is reducing therapeutic options for livestock and human health, with a paucity of information globally. To fill this gap, a One-Health approach was taken by sampling livestock on farms (n = 52), abattoir (n = 8), and animal markets (n = 10), and in-contact humans in Southeast Nigeria. Extended spectrum cephalosporin (ESC)-resistant (ESC-R) Escherichia coli was selectively cultured from 975 healthy livestock faecal swabs, and hand swabs from in-contact humans. Antimicrobial susceptibility testing (AST) was performed on all ESC-R E. coli. For isolates showing a multi-drug resistance (MDR) phenotype (n = 196), quantitative real-time PCR (qPCR) was performed for confirmation of extended-spectrum β-lactamase (ESBL) and carbapenemase genes. Whole-genome sequencing (WGS) was performed on a subset (n = 157) for detailed molecular characterisation. The results showed ESC-R E. coli was present in 41.2% of samples, with AST results indicating 48.8% of isolates were phenotypically MDR. qPCR confirmed presence of ESBL genes, with blaCTX-M present in all but others in a subset [blaTEM (62.8%) and blaSHV (0.5%)] of isolates; none harboured transferable carbapenemase genes. Multi-locus sequence typing identified 34 Sequence Types (ST) distributed among different sampling levels; ST196 carrying blaCTX-M-55 was predominant in chickens. Large numbers of single nucleotide polymorphisms (SNPs) in the core genome of isolates, even within the same clade by phylogenetic analysis, indicated high genetic diversity. AMR genotyping indicated the predominant blaCTX-M variant was blaCTX-M-15 (87.9%), although blaCTX-M-55, blaCTX-M-64, and blaCTX-M-65 were present; it was notable that blaCTX-M-1, common in livestock, was absent. Other predominant AMR genes included: sul2, qnrS1, strB, blaTEM-1b, tetA-v2, and dfrA14, with prevalence varying according to host livestock species. A blaCTX-M-15 harbouring plasmid from livestock isolates in Ebonyi showed high sequence identity to one from river/sewage water in India, indicating this ESBL plasmid to be globally disseminated, being present beyond the river environment. In conclusion, ESC-R E. coli was widespread in livestock and in-contact humans from Southeast Nigeria. WGS data indicated the isolates were genetically highly diverse, probably representing true diversity of wild type E. coli; they were likely to be MDR with several harbouring blaCTX-M-15. Surprisingly, human isolates had highest numbers of AMR genes and pigs the least.
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Affiliation(s)
- Solomon O. Olorunleke
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka, Enugu, Nigeria
- Department of Animal Science, Ebonyi State University, Abakaliki, Nigeria
| | - Miranda Kirchner
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Nicholas Duggett
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- School of Health and Life Science, Teesside University, Middlesbrough, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Onyinye J. Okorie-Kanu
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka, Enugu, Nigeria
| | - Kim Stevens
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Roderick M. Card
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Kennedy Foinkfu Chah
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu, Nigeria
| | - John A. Nwanta
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka, Enugu, Nigeria
| | - Lucy A. Brunton
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- *Correspondence: Muna F. Anjum
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Perrin-Guyomard A, Granier SA, Slettemeås JS, Anjum M, Randall L, AbuOun M, Pauly N, Irrgang A, Hammerl JA, Kjeldgaard JS, Hammerum A, Franco A, Skarżyńska M, Kamińska E, Wasyl D, Dierikx C, Börjesson S, Geurts Y, Haenni M, Veldman K. Multicentre evaluation of a selective isolation protocol for detection of mcr-positive E. coli and Salmonella spp. in food-producing animals and meat. Lett Appl Microbiol 2022; 75:224-233. [PMID: 35388505 PMCID: PMC9544698 DOI: 10.1111/lam.13717] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 12/01/2022]
Abstract
This study was conducted to evaluate the performance of a screening protocol to detect and isolate mcr‐positive Escherichia coli and Salmonella spp. from animal caecal content and meat samples. We used a multicentre approach involving 12 laboratories from nine European countries. All participants applied the same methodology combining a multiplex PCR performed on DNA extracted from a pre‐enrichment step, followed by a selective culture step on three commercially available chromogenic agar plates. The test panel was composed of two negative samples and four samples artificially contaminated with E. coli and Salmonella spp. respectively harbouring mcr‐1 or mcr‐3 and mcr‐4 or mcr‐5 genes. PCR screening resulted in a specificity of 100% and a sensitivity of 83%. Sensitivity of each agar medium to detect mcr‐positive colistin‐resistant E. coli or Salmonella spp. strains was 86% for CHROMID® Colistin R, 75% for CHROMagarTM COL‐APSE and 70% for COLISTIGRAM. This combined method was effective to detect and isolate most of the E. coli or Salmonella spp. strains harbouring different mcr genes from food‐producing animals and food products and might thus be used as a harmonized protocol for the screening of mcr genes in food‐producing animals and food products in Europe.
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Affiliation(s)
- Agnès Perrin-Guyomard
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères Laboratory, France
| | - Sophie A Granier
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères Laboratory, France
| | | | - Muna Anjum
- Animal and Plant Health Agency, United Kingdom
| | | | | | - Natalie Pauly
- German Federal Institute for Risk Assessment, Germany
| | | | | | | | | | - Alessia Franco
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Italy
| | | | | | | | - Cindy Dierikx
- National Institute for Public Health and the Environment, the Netherlands
| | - Stefan Börjesson
- National Veterinary Institute (SVA), Sweden and Public Health Agency of Sweden, Sweden
| | - Yvon Geurts
- Wageningen Bioveterinary Research, the Netherlands
| | - Marisa Haenni
- Lyon University - French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Lyon laboratory, France
| | - Kees Veldman
- Wageningen Bioveterinary Research, the Netherlands
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Storey N, Cawthraw S, Turner O, Rambaldi M, Lemma F, Horton R, Randall L, Duggett NA, AbuOun M, Martelli F, Anjum MF. Use of genomics to explore AMR persistence in an outdoor pig farm with low antimicrobial usage. Microb Genom 2022; 8:000782. [PMID: 35344479 PMCID: PMC9176276 DOI: 10.1099/mgen.0.000782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Indexed: 01/05/2023] Open
Abstract
Food animals may be reservoirs of antimicrobial resistance (AMR) passing through the food chain, but little is known about AMR prevalence in bacteria when selective pressure from antimicrobials is low or absent. We monitored antimicrobial-resistant Escherichia coli over 1 year in a UK outdoor pig farm with low antimicrobial usage (AMU) compared to conventional pig farms in the United Kingdom. Short and selected long-read whole-genome sequencing (WGS) was performed to identify AMR genes, phylogeny and mobile elements in 385 E. coli isolates purified mainly from pig and some seagull faeces. Generally, low levels of antimicrobial-resistant E. coli were present, probably due to low AMU. Those present were likely to be multi-drug resistant (MDR) and belonging to particular Sequence Types (STs) such as ST744, ST88 or ST44, with shared clones (<14 Single Nucleotide Polymorphisms (SNPs) apart) isolated from different time points indicating epidemiological linkage within pigs of different ages, and between pig and the wild bird faeces. Although importance of horizontal transmission of AMR is well established, there was limited evidence of plasmid-mediated dissemination between different STs. Non-conjugable MDR plasmids or large AMR gene-bearing transposons were stably integrated within the chromosome and remained associated with particular STs/clones over the time period sampled. Heavy metal resistance genes were also detected within some genetic elements. This study highlights that although low levels of antimicrobial-resistant E. coli correlates with low AMU, a basal level of MDR E. coli can still persist on farm potentially due to transmission and recycling of particular clones within different pig groups. Environmental factors such as wild birds and heavy metal contaminants may also play important roles in the recycling and dissemination, and hence enabling persistence of MDR E. coli. All such factors need to be considered as any rise in AMU on low usage farms, could in future, result in a significant increase in their AMR burden.
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Affiliation(s)
- Nathaniel Storey
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- Great Ormond Street Hospital for Children, London WC1N 3JH, UK
| | - Shaun Cawthraw
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Olivia Turner
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Margherita Rambaldi
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- University of Bologna, Via Zamboni, 33, 40126 Bologna BO, Italy
| | - Fabrizio Lemma
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Robert Horton
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Luke Randall
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Nicholas A. Duggett
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- Teeside University, Campus Heart, Middlesbrough TS1 3BX, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Francesca Martelli
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Muna F. Anjum
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- *Correspondence: Muna F. Anjum,
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Martelli F, AbuOun M, Cawthraw S, Storey N, Turner O, Ellington M, Nair S, Painset A, Teale C, Anjum MF. Detection of the transferable tigecycline resistance gene tet(X4) in Escherichia coli from pigs in the United Kingdom. J Antimicrob Chemother 2021; 77:846-848. [PMID: 34897485 DOI: 10.1093/jac/dkab439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/25/2021] [Indexed: 01/10/2023] Open
Affiliation(s)
- Francesca Martelli
- Bacteriology Department, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Manal AbuOun
- Bacteriology Department, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Shaun Cawthraw
- Bacteriology Department, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Nathaniel Storey
- Bacteriology Department, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Olivia Turner
- Bacteriology Department, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Matthew Ellington
- HCAI & AMR Division, National Infection Service, UKHSA, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Satheesh Nair
- Gastrointestinal Pathogens Unit, Gastrointestinal Bacteria Reference Unit, National Infection Service, UKHSA, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Anais Painset
- Gastrointestinal Pathogens Unit, Gastrointestinal Bacteria Reference Unit, National Infection Service, UKHSA, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Christopher Teale
- Bacteriology Department, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Muna F Anjum
- Bacteriology Department, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
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17
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AbuOun M, Jones H, Stubberfield E, Gilson D, Shaw LP, Hubbard ATM, Chau KK, Sebra R, Peto TEA, Crook DW, Read DS, Gweon HS, Walker AS, Stoesser N, Smith RP, Anjum MF, On Behalf Of The Rehab Consortium. A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage. Microb Genom 2021; 7. [PMID: 34609275 PMCID: PMC8627209 DOI: 10.1099/mgen.0.000630] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Enterobacterales from livestock are potentially important reservoirs for antimicrobial resistance (AMR) to pass through the food chain to humans, thereby increasing the AMR burden and affecting our ability to tackle infections. In this study 168 isolates from four genera of the order Enterobacterales, primarily Escherichia coli, were purified from livestock (cattle, pigs and sheep) faeces from 14 farms in the United Kingdom. Their genomes were resolved using long- and short-read sequencing to analyse AMR genes and their genetic context, as well as to explore the relationship between AMR burden and on-farm antimicrobial usage (AMU), in the three months prior to sampling. Although E. coli isolates were genomically diverse, phylogenetic analysis using a core-genome SNP tree indicated pig isolates to generally be distinct from sheep isolates, with cattle isolates being intermediates. Approximately 28 % of isolates harboured AMR genes, with the greatest proportion detected in pigs, followed by cattle then sheep; pig isolates also harboured the highest number of AMR genes per isolate. Although 90 % of sequenced isolates harboured diverse plasmids, only 11 % of plasmids (n=58 out of 522) identified contained AMR genes, with 91 % of AMR plasmids being from pig, 9 % from cattle and none from sheep isolates; these results indicated that pigs were a principle reservoir of AMR genes harboured by plasmids and likely to be involved in their horizontal transfer. Significant associations were observed between AMU (mg kg−1) and AMR. As both the total and the numbers of different antimicrobial classes used on-farm increased, the risk of multi-drug resistance (MDR) in isolates rose. However, even when AMU on pig farms was comparatively low, pig isolates had increased likelihood of being MDR; harbouring relatively more resistances than those from other livestock species. Therefore, our results indicate that AMR prevalence in livestock is not only influenced by recent AMU on-farm but also livestock-related factors, which can influence the AMR burden in these reservoirs and its plasmid mediated transmission.
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Affiliation(s)
- Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Hannah Jones
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Daniel Gilson
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Liam P Shaw
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alasdair T M Hubbard
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Kevin K Chau
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert Sebra
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mt Sinai, Mt Sinai, New York, USA
| | - Tim E A Peto
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick W Crook
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in partnership with Public Health England (PHE), Oxford, UK
| | - Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford, UK
| | - H Soon Gweon
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford, UK.,School of Biological Sciences, University of Reading, UK
| | - A Sarah Walker
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in partnership with Public Health England (PHE), Oxford, UK
| | - Nicole Stoesser
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in partnership with Public Health England (PHE), Oxford, UK
| | - Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, UK
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18
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Stubberfield E, Sheldon J, Card RM, AbuOun M, Rogers J, Williamson S, Kay GL, Pallen MJ, Anjum MF. Whole-Genome Sequencing of Brachyspira hyodysenteriae Isolates From England and Wales Reveals Similarities to European Isolates and Mutations Associated With Reduced Sensitivity to Antimicrobials. Front Microbiol 2021; 12:713233. [PMID: 34531838 PMCID: PMC8439570 DOI: 10.3389/fmicb.2021.713233] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/09/2021] [Indexed: 11/24/2022] Open
Abstract
Brachyspira hyodysenteriae is the principal cause of swine dysentery, a disease that threatens economic productivity of pigs in many countries as it can spread readily within and between farms, and only a small number of antimicrobials are authorized for treatment of pigs. In this study, we performed whole-genome sequencing (WGS) of 81 B. hyodysenteriae archived at the Animal and Plant Health Agency (APHA) from diagnostic submissions and herd monitoring in England and Wales between 2004 and 2015. The resulting genome sequences were analyzed alongside 34 genomes we previously published. Multi-locus sequence typing (MLST) showed a diverse population with 32 sequence types (STs) among the 115 APHA isolates, 25 of them identified only in England; while also confirming that the dominant European clonal complexes, CC8 and CC52, were common in the United Kingdom. A core-genome SNP tree typically clustered the isolates by ST, with isolates from some STs detected only within a specific region in England, although others were more widespread, suggesting transmission between different regions. Also, some STs were more conserved in their core genome than others, despite these isolates being from different holdings, regions and years. Minimum inhibitory concentrations to commonly used antimicrobials (Tiamulin, Valnemulin, Doxycycline, Lincomycin, Tylosin, Tylvalosin) were determined for 82 of the genome-sequenced isolates; genomic analysis revealed mutations generally correlated well with the corresponding resistance phenotype. There was a major swine dysentery intervention program in 2009–2010, and antimicrobial survival curves showed a significant reduction in sensitivity to tiamulin and valnemulin in isolates collected in and after 2010, compared to earlier isolates. This correlated with a significant increase in post-2009 isolates harboring the pleuromutilin resistance gene tva(A), which if present, may facilitate higher levels of resistance. The reduction in susceptibility of Brachyspira from diagnostic submissions to pleuromutilins, emphasizes the need for prudent treatment, control and eradication strategies.
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Affiliation(s)
- Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Jonathan Sheldon
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Roderick M Card
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Jon Rogers
- Animal and Plant Health Agency, Bury St Edmunds, United Kingdom
| | | | - Gemma L Kay
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich, United Kingdom.,Norwich Medical School, University of East Anglia, Norwich, United Kingdom.,School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom.,School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
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19
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Matlock W, Chau KK, AbuOun M, Stubberfield E, Barker L, Kavanagh J, Pickford H, Gilson D, Smith RP, Gweon HS, Hoosdally SJ, Swann J, Sebra R, Bailey MJ, Peto TEA, Crook DW, Anjum MF, Read DS, Walker AS, Stoesser N, Shaw LP. Genomic network analysis of environmental and livestock F-type plasmid populations. ISME J 2021; 15:2322-2335. [PMID: 33649550 PMCID: PMC8319146 DOI: 10.1038/s41396-021-00926-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/08/2021] [Accepted: 02/03/2021] [Indexed: 12/02/2022]
Abstract
F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.
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Affiliation(s)
- William Matlock
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | | | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hayleah Pickford
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Gilson
- Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | | | - H Soon Gweon
- UK Centre for Ecology & Hydrology, Wallingford, UK
- University of Reading, Reading, UK
| | | | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert Sebra
- Icahn Institute of Data Science and Genomic Technology, Mt Sinai, NY, USA
| | | | - Timothy E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU in Healthcare-Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU in Healthcare-Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Muna F Anjum
- Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | | | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU in Healthcare-Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- NIHR HPRU in Healthcare-Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Liam P Shaw
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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20
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AbuOun M, O'Connor HM, Stubberfield EJ, Nunez-Garcia J, Sayers E, Crook DW, Smith RP, Anjum MF. Corrigendum: Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain. Front Microbiol 2021; 12:693940. [PMID: 34122397 PMCID: PMC8194817 DOI: 10.3389/fmicb.2021.693940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/06/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership With Public Health England (PHE), Oxford, United Kingdom
| | - Heather M O'Connor
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Emma J Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Javier Nunez-Garcia
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Ellie Sayers
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Derick W Crook
- National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership With Public Health England (PHE), Oxford, United Kingdom.,Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership With Public Health England (PHE), Oxford, United Kingdom
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21
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Shaw LP, Chau KK, Kavanagh J, AbuOun M, Stubberfield E, Gweon HS, Barker L, Rodger G, Bowes MJ, Hubbard ATM, Pickford H, Swann J, Gilson D, Smith RP, Hoosdally SJ, Sebra R, Brett H, Peto TEA, Bailey MJ, Crook DW, Read DS, Anjum MF, Walker AS, Stoesser N. Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. Sci Adv 2021; 7:eabe3868. [PMID: 33837077 PMCID: PMC8034854 DOI: 10.1126/sciadv.abe3868] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/22/2021] [Indexed: 05/07/2023]
Abstract
Escherichia coli and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.
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Affiliation(s)
- Liam P Shaw
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.
| | - Kevin K Chau
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - James Kavanagh
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - H Soon Gweon
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
- School of Biological Sciences, University of Reading, Reading RG6 6AS, UK
| | - Leanne Barker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Gillian Rodger
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Mike J Bowes
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Alasdair T M Hubbard
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Hayleah Pickford
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Daniel Gilson
- Department of Epidemiological Sciences, The Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Richard P Smith
- Department of Epidemiological Sciences, The Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Sarah J Hoosdally
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, 333 Ludlow Street, North Tower, 8th floor, Stamford, CT 06902, USA
| | - Howard Brett
- Thames Water Utilities, Clearwater Court, Vastern Road, Reading RG1 8DB, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Mark J Bailey
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
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22
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Foster G, AbuOun M, Pizzi R, Tennant B, McCall M, Anjum MF. Isolation of the human-associated bla CTX-M-15-harbouring Klebsiella pneumoniae ST307 from a tortoise in the UK. Access Microbiol 2021; 2:acmi000172. [PMID: 33490868 PMCID: PMC7818245 DOI: 10.1099/acmi.0.000172] [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: 07/09/2020] [Accepted: 09/15/2020] [Indexed: 11/18/2022] Open
Abstract
The ST307 multidrug-resistant CTX-M-15-producing Klebsiella pneumoniae is an emerging pathogen, which has become disseminated worldwide in humans but is rarely reported from other reservoirs. We report the first isolation of K. pneumoniae from an animal in Europe and also from a reptile, a captive tortoise, whose death it probably caused. Detection of this clone from an animal adds to evidence of niche expansion in non-human environments, where it may amplify, recycle and become of greater public health concern.
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Affiliation(s)
| | - Manal AbuOun
- Animal and Plant Health Agency, New Haw, Surrey, KT15 3NB, UK
| | - Romain Pizzi
- Zoological Medicine Ltd, 40 Charlton Grove, Roslin, EH25 9NX, UK
| | - Bryn Tennant
- SRUC Veterinary Services, Penicuik, Midlothian, EH26 0PZ, UK
| | - Margaret McCall
- SRUC Veterinary Services, Penicuik, Midlothian, EH26 0PZ, UK
| | - Muna F Anjum
- Animal and Plant Health Agency, New Haw, Surrey, KT15 3NB, UK
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23
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Nale JY, Vinner GK, Lopez VC, Thanki AM, Phothaworn P, Thiennimitr P, Garcia A, AbuOun M, Anjum MF, Korbsrisate S, Galyov EE, Malik DJ, Clokie MRJ. An Optimized Bacteriophage Cocktail Can Effectively Control Salmonella in vitro and in Galleria mellonella. Front Microbiol 2021; 11:609955. [PMID: 33552020 PMCID: PMC7858669 DOI: 10.3389/fmicb.2020.609955] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 09/24/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022] Open
Abstract
Salmonella spp. is a leading cause of gastrointestinal enteritis in humans where it is largely contracted via contaminated poultry and pork. Phages can be used to control Salmonella infection in the animals, which could break the cycle of infection before the products are accessible for consumption. Here, the potential of 21 myoviruses and a siphovirus to eliminate Salmonella in vitro and in vivo was examined with the aim of developing a biocontrol strategy to curtail the infection in poultry and swine. Together, the phages targeted the twenty-three poultry and ten swine prevalent Salmonella serotype isolates tested. Although individual phages significantly reduced bacterial growth of representative isolates within 6 h post-infection, bacterial regrowth occurred 1 h later, indicating proliferation of resistant strains. To curtail bacteriophage resistance, a novel three-phage cocktail was developed in vitro, and further investigated in an optimized Galleria mellonella larva Salmonella infection model colonized with representative swine, chicken and laboratory strains. For all the strains examined, G. mellonella larvae given phages 2 h prior to bacterial exposure (prophylactic regimen) survived and Salmonella was undetectable 24 h post-phage treatment and throughout the experimental time (72 h). Administering phages with bacteria (co-infection), or 2 h post-bacterial exposure (remedial regimen) also improved survival (73-100% and 15-88%, respectively), but was less effective than prophylaxis application. These pre-livestock data support the future application of this cocktail for further development to effectively treat Salmonella infection in poultry and pigs. Future work will focus on cocktail formulation to ensure stability and incorporation into feeds and used to treat the infection in target animals.
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Affiliation(s)
- Janet Y Nale
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Gurinder K Vinner
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Viviana C Lopez
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Anisha M Thanki
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Preeda Phothaworn
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Angela Garcia
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Danish J Malik
- Department of Chemical Engineering, Loughborough University, Loughborough, United Kingdom
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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24
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AbuOun M, O'Connor HM, Stubberfield EJ, Nunez-Garcia J, Sayers E, Crook DW, Smith RP, Anjum MF. Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain. Front Microbiol 2020; 11:861. [PMID: 32523560 PMCID: PMC7261845 DOI: 10.3389/fmicb.2020.00861] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 05/15/2019] [Accepted: 04/09/2020] [Indexed: 12/18/2022] Open
Abstract
Combatting antimicrobial resistant (AMR) using a One-Health approach is essential as various bacteria, including Escherichia coli, a common bacteria, are becoming increasingly resistant and livestock may be a reservoir. The AMR gene content of 492 E. coli, isolated from 56 pig farms across Great Britain in 2014–2015, and purified on antibiotic selective and non-selective plates, was determined using whole genome sequencing (WGS). The E. coli were phylogenetically diverse harboring a variety of AMR profiles with widespread resistance to “old” antibiotics; isolates harbored up to seven plasmid Inc-types. None showed concurrent resistance to third-generation cephalosporins, fluoroquinolones and clinically relevant aminoglycosides, although ∼3% harbored AMR genes to both the former two. Transferable resistance to carbapenem and colistin were absent, and six of 117 E. coli STs belonged to major types associated with human disease. Prevalence of genotypically MDR E. coli, gathered from non-selective media was 35% and that of extended-spectrum-beta-lactamase E. coli was low (∼2% from non-selective). Approximately 72.6% of E. coli from ciprofloxacin plates and only 8.5% from the other plates harbored fluoroquinolone resistance due to topoisomerase mutations; the majority were MDR. In fact, multivariable analysis confirmed E. coli purified from CIP enrichment plates were more likely to be MDR, and suggested MDR isolates were also more probable from farms with high antibiotic usage, specialist finisher farms, and farms emptying their manure pits only after each batch. Additionally, farms from the South East were more likely to have MDR E. coli, whereas farms in Yorkshire and the Humber were less likely. Future investigations will determine whether suggested improvements such as better biosecurity or lower antimicrobial use decreases MDR E. coli on pig farms. Although this study focuses on pig farms, we believe the methodology and findings can be applied more widely to help livestock farmers in the United Kingdom and elsewhere to tackle AMR.
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Affiliation(s)
- Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom
| | - Heather M O'Connor
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Emma J Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Javier Nunez-Garcia
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Ellie Sayers
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Derick W Crook
- National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom.,Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom
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Duff JP, AbuOun M, Bexton S, Rogers J, Turton J, Woodford N, Irvine R, Anjum M, Teale C. Resistance to carbapenems and other antibiotics in Klebsiella pneumoniae found in seals indicates anthropogenic pollution. Vet Rec 2020; 187:154. [PMID: 32327551 DOI: 10.1136/vr.105440] [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: 05/01/2019] [Revised: 09/10/2019] [Accepted: 01/29/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND The beta-lactamase enzyme OXA-48 has spread widely in recent years in Enterobacteriaceae associated with man, disseminated primarily on incompatibility group L/M plasmids. OXA-48 confers resistance to carbapenems, important antimicrobials for treating highly resistant bacterial infections in humans. This enzyme has rarely been detected in bacteria from animals. Furthermore, the use of carbapenem compounds is not permitted in food-producing animals in Europe and to our knowledge has not been reported in food-producing animals globally. METHODS Bacterial isolates from lesions in stranded, free-living, juvenile common seals (Phoca vitulina) were identified. Antimicrobial susceptibility testing and whole genome sequencing analysis were used to characterise antimicrobial resistance genes carried by the bacteria. RESULTS Here, we report the detection of Klebsiella pneumoniae subspecies pneumoniae carrying the bla OXA-48 gene on an incompatibility group L/M plasmid from an infection in a common seal. CONCLUSION Evidence is accruing that marine mammals may be infected with bacteria originating from anthropogenic sources, such as human sewage, contaminating the environment.
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Affiliation(s)
- James Paul Duff
- Animal Plant and Health Agency (APHA), Diseases of Wildlife Scheme, APHA Penrith Veterinary Investigation Centre, Penrith, UK
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | | | - Jon Rogers
- Animal and Plant Health Agency Bury St Edmunds Veterinary Investigation Centre, Bury St Edmunds, UK
| | - Jane Turton
- National Infection Service, Public Health England, London, UK
| | - Neil Woodford
- National Infection Service, Public Health England, London, UK
| | - Richard Irvine
- Surveillance Intelligence Unit, Animal and Plant Health Agency, Weybridge, UK
| | - Muna Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - Christopher Teale
- Animal Plant and Health Agency Shrewsbury Veterinary Investigation Centre, Shrewsbury, UK
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26
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Stubberfield E, AbuOun M, Sayers E, O'Connor HM, Card RM, Anjum MF. Use of whole genome sequencing of commensal Escherichia coli in pigs for antimicrobial resistance surveillance, United Kingdom, 2018. Euro Surveill 2019; 24:1900136. [PMID: 31847943 PMCID: PMC6918588 DOI: 10.2807/1560-7917.es.2019.24.50.1900136] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 02/19/2019] [Accepted: 08/01/2019] [Indexed: 12/19/2022] Open
Abstract
BackgroundSurveillance of commensal Escherichia coli, a possible reservoir of antimicrobial resistance (AMR) genes, is important as they pose a risk to human and animal health. Most surveillance activities rely on phenotypic characterisation, but whole genome sequencing (WGS) presents an alternative.AimIn this retrospective study, we tested 515 E. coli isolated from pigs to evaluate the use of WGS to predict resistance phenotype.MethodsMinimum inhibitory concentration (MIC) was determined for nine antimicrobials of clinical and veterinary importance. Deviation from wild-type, fully-susceptible MIC was assessed using European Committee on Antimicrobial Susceptibility Testing (EUCAST) epidemiological cut-off (ECOFF) values. Presence of AMR genes and mutations were determined using APHA SeqFinder. Statistical two-by-two table analysis and Cohen's kappa (k) test were applied to assess genotype and phenotype concordance.ResultsOverall, correlation of WGS with susceptibility to the nine antimicrobials was 98.9% for test specificity, and 97.5% for the positive predictive value of a test. The overall kappa score (k = 0.914) indicated AMR gene presence was highly predictive of reduced susceptibility and showed excellent correlation with MIC. However, there was variation for each antimicrobial; five showed excellent correlation; four very good and one moderate. Suggested ECOFF adjustments increased concordance between genotypic data and kappa values for four antimicrobials.ConclusionWGS is a powerful tool for accurately predicting AMR that can be used for national surveillance purposes. Additionally, it can detect resistance genes from a wider panel of antimicrobials whose phenotypes are currently not monitored but may be of importance in the future.
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Affiliation(s)
- Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
| | - Ellie Sayers
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
- University of East Anglia/Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Heather M O'Connor
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
| | - Roderick M Card
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
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27
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Gweon HS, Shaw LP, Swann J, De Maio N, AbuOun M, Niehus R, Hubbard ATM, Bowes MJ, Bailey MJ, Peto TEA, Hoosdally SJ, Walker AS, Sebra RP, Crook DW, Anjum MF, Read DS, Stoesser N. The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples. Environ Microbiome 2019; 14:7. [PMID: 33902704 PMCID: PMC8204541 DOI: 10.1186/s40793-019-0347-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/28/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, 'ResPipe'. RESULTS Taxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve < 1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike of Thermus thermophilus DNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment. CONCLUSIONS Sequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available ( https://gitlab.com/hsgweon/ResPipe ).
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Affiliation(s)
- H Soon Gweon
- Harborne Building, School of Biological Sciences, University of Reading, Reading, RG6 6AS, UK.
- Centre for Ecology & Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK.
| | - Liam P Shaw
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola De Maio
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, KT15 3NB, UK
| | - Rene Niehus
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Mike J Bowes
- Centre for Ecology & Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Mark J Bailey
- Centre for Ecology & Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit (HPRU) in Healthcare-associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | | | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit (HPRU) in Healthcare-associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Robert P Sebra
- Department of Genetics and Genomics, Icahn School of Medicine at Mt Sinai, New York, NY, USA
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit (HPRU) in Healthcare-associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, KT15 3NB, UK
| | - Daniel S Read
- Centre for Ecology & Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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28
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Giles M, Cawthraw SA, AbuOun M, Thomas CM, Munera D, Waldor MK, La Ragione RM, Ritchie JM. Host-specific differences in the contribution of an ESBL IncI1 plasmid to intestinal colonization by Escherichia coli O104:H4. J Antimicrob Chemother 2019; 73:1579-1585. [PMID: 29506073 DOI: 10.1093/jac/dky037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 01/18/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives To assess stability and contribution of a large ESBL-encoding IncI1 plasmid to intestinal colonization by Escherichia coli O104:H4 in two different mammalian hosts. Methods Specific-pathogen-free 3-4-day-old New Zealand White rabbits and conventionally reared 6-week-old weaned lambs were orally infected with WT E. coli O104:H4 or the ESBL-plasmid-cured derivative, and the recovery of bacteria in intestinal homogenates and faeces monitored over time. Results Carriage of the ESBL plasmid had differing impacts on E. coli O104:H4 colonization of the two experimental hosts. The plasmid-cured strain was recovered at significantly higher levels than WT during late-stage colonization of rabbits, but at lower levels than WT in sheep. Regardless of the animal host, the ESBL plasmid was stably maintained in virtually all in vivo passaged bacteria that were examined. Conclusions These findings suggest that carriage of ESBL plasmids has distinct effects on the host bacterium depending upon the animal species it encounters and demonstrates that, as for E. coli O157:H7, ruminants could represent a potential transmission reservoir.
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Affiliation(s)
- M Giles
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - S A Cawthraw
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - M AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - C M Thomas
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - D Munera
- Division of Infectious Diseases, Brigham and Women's Hospital/Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - M K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital/Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - R M La Ragione
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - J M Ritchie
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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29
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De Maio N, Shaw LP, Hubbard A, George S, Sanderson ND, Swann J, Wick R, AbuOun M, Stubberfield E, Hoosdally SJ, Crook DW, Peto TEA, Sheppard AE, Bailey MJ, Read DS, Anjum MF, Walker AS, Stoesser N. Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes. Microb Genom 2019; 5:e000294. [PMID: 31483244 PMCID: PMC6807382 DOI: 10.1099/mgen.0.000294] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [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: 01/31/2019] [Accepted: 08/19/2019] [Indexed: 01/23/2023] Open
Abstract
Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the family Enterobacteriaceae, as these frequently have highly plastic, repetitive genetic structures, and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. We de novo assembled genomes using the hybrid assembler Unicycler and compared different read processing strategies, as well as comparing to long-read-only assembly with Flye followed by short-read polishing with Pilon. Hybrid assembly with either PacBio or ONT reads facilitated high-quality genome reconstruction, and was superior to the long-read assembly and polishing approach evaluated with respect to accuracy and completeness. Combining ONT and Illumina reads fully resolved most genomes without additional manual steps, and at a lower consumables cost per isolate in our setting. Automated hybrid assembly is a powerful tool for complete and accurate bacterial genome assembly.
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Affiliation(s)
- Nicola De Maio
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Liam P. Shaw
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alasdair Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | | | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ryan Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, KT15 3NB, UK
| | - Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, KT15 3NB, UK
| | | | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Timothy E. A. Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Anna E. Sheppard
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Mark J. Bailey
- Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - Daniel S. Read
- Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, KT15 3NB, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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30
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Mensah N, Tang Y, Cawthraw S, AbuOun M, Fenner J, Thomson NR, Mather AE, Petrovska-Holmes L. Determining antimicrobial susceptibility in Salmonella enterica serovar Typhimurium through whole genome sequencing: a comparison against multiple phenotypic susceptibility testing methods. BMC Microbiol 2019; 19:148. [PMID: 31266463 PMCID: PMC6604184 DOI: 10.1186/s12866-019-1520-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 11/30/2018] [Accepted: 06/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background UK public health organisations perform routine antimicrobial susceptibility tests (ASTs) to characterise the potential for antimicrobial resistance in Salmonella enterica serovars. Genetic determinants of these resistance mechanisms are detectable by whole genome sequencing (WGS), however the viability of WGS-based genotyping as an alternative resistance screening tool remains uncertain. We compared WGS-based genotyping, disk diffusion and agar dilution to the broth microdilution reference AST for 102 Salmonella enterica serovar Typhimurium (S. Typhimurium) isolates across 11 antimicrobial compounds. Results Genotyping concordance, interpreted using epidemiological cut-offs (ECOFFs), was 89.8% (1007/1122) with 0.83 sensitivity and 0.96 specificity. For seven antimicrobials interpreted using Salmonella clinical breakpoints, genotyping produced 0.84 sensitivity and 0.88 specificity. Although less accurate than disk diffusion (0.94 sensitivity, 0.93 specificity) and agar dilution (0.83 sensitivity, 0.98 specificity), genotyping performance improved to 0.89 sensitivity and 0.97 specificity when two antimicrobials with relatively high very major error rates were excluded (streptomycin and sulfamethoxazole). Conclusions An 89.8% concordance from WGS-based AST predictions using ECOFF interpretations suggest that WGS would serve as an effective screening tool for the tracking of antimicrobial resistance mechanisms in S. Typhimurium. For use as a standalone clinical diagnostic screen, further work is required to reduce the error rates for specific antimicrobials. Electronic supplementary material The online version of this article (10.1186/s12866-019-1520-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nana Mensah
- Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, UK
| | - Yue Tang
- Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, UK
| | - Shaun Cawthraw
- Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, UK
| | - Jackie Fenner
- Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, UK
| | | | - Alison E Mather
- University of Cambridge, Cambridge, Cambridgeshire, UK.,Present Address: Quadram Institute Bioscience, Norwich, Norfolk, UK.,University of East Anglia, Norwich, Norfolk, UK
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AbuOun M, Stubberfield EJ, Duggett NA, Kirchner M, Dormer L, Nunez-Garcia J, Randall LP, Lemma F, Crook DW, Teale C, Smith RP, Anjum MF. mcr-1 and mcr-2 (mcr-6.1) variant genes identified in Moraxella species isolated from pigs in Great Britain from 2014 to 2015. J Antimicrob Chemother 2018; 73:2904. [PMID: 30053008 DOI: 10.1093/jac/dky272] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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32
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Sharma M, AbuOun M, Nunez-Garcia J, Rogers J, Welchman D, Teale C, Anjum MF, Kearns AM, Pichon B, Foster G, Robb A, McMillan M. MRSA spa type t899 from food animals in the UK. Vet Rec 2018; 182:697-698. [PMID: 29907724 DOI: 10.1136/vr.k2576] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Meenaxi Sharma
- Animal and Plant Health Agency, New Haw, Surrey KT15 3NB
| | - Manal AbuOun
- Animal and Plant Health Agency, New Haw, Surrey KT15 3NB
| | | | - Jon Rogers
- Animal and Plant Health Agency, New Haw, Surrey KT15 3NB
| | - David Welchman
- Animal and Plant Health Agency, New Haw, Surrey KT15 3NB
| | | | - Muna F Anjum
- Animal and Plant Health Agency, New Haw, Surrey KT15 3NB
| | - Angela M Kearns
- National Infection Service, Public Health England, Colindale, London NW9 5EQ
| | - Bruno Pichon
- National Infection Service, Public Health England, Colindale, London NW9 5EQ
| | | | - Andrew Robb
- Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow G31 2ER
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33
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Card RM, Stubberfield E, Rogers J, Nunez-Garcia J, Ellis RJ, AbuOun M, Strugnell B, Teale C, Williamson S, Anjum MF. Identification of a New Antimicrobial Resistance Gene Provides Fresh Insights Into Pleuromutilin Resistance in Brachyspira hyodysenteriae, Aetiological Agent of Swine Dysentery. Front Microbiol 2018; 9:1183. [PMID: 29971045 PMCID: PMC6018095 DOI: 10.3389/fmicb.2018.01183] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 03/02/2018] [Accepted: 05/15/2018] [Indexed: 11/30/2022] Open
Abstract
Brachyspira hyodysenteriae is the aetiological agent of swine dysentery, a globally distributed disease that causes profound economic loss, impedes the free trade and movement of animals, and has significant impact on pig health. Infection is generally treated with antibiotics of which pleuromutilins, such as tiamulin, are widely used for this purpose, but reports of resistance worldwide threaten continued effective control. In Brachyspira hyodysenteriae pleuromutilin resistance has been associated with mutations in chromosomal genes encoding ribosome-associated functions, however the dynamics of resistance acquisition are poorly understood, compromising stewardship efforts to preserve pleuromutilin effectiveness. In this study we undertook whole genome sequencing (WGS) and phenotypic susceptibility testing of 34 UK field isolates and 3 control strains to investigate pleuromutilin resistance in Brachyspira hyodysenteriae. Genome-wide association studies identified a new pleuromutilin resistance gene, tva(A) (tiamulin valnemulin antibiotic resistance), encoding a predicted ABC-F transporter. In vitro culture of isolates in the presence of inhibitory or sub-inhibitory concentrations of tiamulin showed that tva(A) confers reduced pleuromutilin susceptibility that does not lead to clinical resistance but facilitates the development of higher-level resistance via mutations in genes encoding ribosome-associated functions. Genome sequencing of antibiotic-exposed isolates identified both new and previously described mutations in chromosomal genes associated with reduced pleuromutilin susceptibility, including the 23S rRNA gene and rplC, which encodes the L3 ribosomal protein. Interesting three antibiotic-exposed isolates harboured mutations in fusA, encoding Elongation Factor G, a gene not previously associated with pleuromutilin resistance. A longitudinal molecular epidemiological examination of two episodes of swine dysentery at the same farm indicated that tva(A) contributed to development of tiamulin resistance in vivo in a manner consistent with that seen experimentally in vitro. The in vitro studies further showed that tva(A) broadened the mutant selection window and raised the mutant prevention concentration above reported in vivo antibiotic concentrations obtained when administered at certain doses. We show how the identification and characterisation of tva(A), a new marker for pleuromutilin resistance, provides evidence to inform treatment regimes and reduce the development of resistance to this class of highly important antimicrobial agents.
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Affiliation(s)
- Roderick M Card
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Emma Stubberfield
- APHA Veterinary Investigation Centre Bury St. Edmunds, Bury St Edmunds, United Kingdom
| | - Jon Rogers
- APHA Veterinary Investigation Centre Bury St. Edmunds, Bury St Edmunds, United Kingdom
| | - Javier Nunez-Garcia
- Central Sequencing Unit, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Richard J Ellis
- Central Sequencing Unit, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Ben Strugnell
- Farm Post Mortems Ltd., Bishop Auckland, United Kingdom
| | - Christopher Teale
- APHA Veterinary Investigation Centre Shrewsbury, Shrewsbury, United Kingdom
| | - Susanna Williamson
- APHA Veterinary Investigation Centre Bury St. Edmunds, Bury St Edmunds, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
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34
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AbuOun M, Stubberfield EJ, Duggett NA, Kirchner M, Dormer L, Nunez-Garcia J, Randall LP, Lemma F, Crook DW, Teale C, Smith RP, Anjum MF. mcr-1 and mcr-2 variant genes identified in Moraxella species isolated from pigs in Great Britain from 2014 to 2015. J Antimicrob Chemother 2018; 72:2745-2749. [PMID: 29091227 DOI: 10.1093/jac/dkx286] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 07/13/2017] [Indexed: 11/14/2022] Open
Abstract
Objectives To determine the occurrence of mcr-1 and mcr-2 genes in Gram-negative bacteria isolated from healthy pigs in Great Britain. Methods Gram-negative bacteria (n = 657) isolated from pigs between 2014 and 2015 were examined by WGS. Results Variants of mcr-1 and mcr-2 were identified in Moraxella spp. isolated from pooled caecal contents of healthy pigs at slaughter collected from six farms in Great Britain. Other bacteria, including Escherichia coli from the same farms, were not detected harbouring mcr-1 or mcr-2. A Moraxella porci-like isolate, MSG13-C03, harboured MCR-1.10 with 98.7% identity to MCR-1, and a Moraxella pluranimalium-like isolate, MSG47-C17, harboured an MCR-2.2 variant with 87.9% identity to MCR-2, from E. coli; the isolates had colistin MICs of 1-2 mg/L. No intact insertion elements were identified in either MSG13-C03 or MSG47-C17, although MSG13-C03 harboured the conserved nucleotides abutting the ISApl1 composite transposon found in E. coli plasmids and the intervening ∼2.6 kb fragment showed 97% identity. Six Moraxella osloensis isolates were positive for phosphoethanolamine transferase (EptA). They shared 62%-64.5% identity to MCR-1 and MCR-2, with colistin MICs from 2 to 4 mg/L. Phylogenetic analysis indicated that MCR and EptA have evolved from a common ancestor. In addition to mcr, the β-lactamase gene, blaBRO-1, was found in both isolates, whilst the tetracycline resistance gene, tetL, was found in MSG47-C17. Conclusions Our results add further evidence for the mobilization of the mcr-pap2 unit from Moraxella via composite transposons leading to its global dissemination. The presence of mcr-pap2 from recent Moraxella isolates indicates they may comprise a reservoir for mcr.
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Affiliation(s)
- Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK.,National Institute for Health Research Health Protection Research Unit, University of Oxford in partnership with PHE, Oxford, UK
| | - Emma J Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK
| | - Nick A Duggett
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK
| | - Miranda Kirchner
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK
| | - Luisa Dormer
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK
| | - Javier Nunez-Garcia
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK
| | - Luke P Randall
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK
| | - Fabrizio Lemma
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK
| | - Derrick W Crook
- National Institute for Health Research Health Protection Research Unit, University of Oxford in partnership with PHE, Oxford, UK.,Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Christopher Teale
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK
| | - Richard P Smith
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK.,Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
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35
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Bidewell CA, Williamson SM, Rogers J, Tang Y, Ellis RJ, Petrovska L, AbuOun M. Emergence of Klebsiella pneumoniae subspecies pneumoniae as a cause of septicaemia in pigs in England. PLoS One 2018; 13:e0191958. [PMID: 29470491 PMCID: PMC5823397 DOI: 10.1371/journal.pone.0191958] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 08/29/2017] [Accepted: 01/15/2018] [Indexed: 11/18/2022] Open
Abstract
Between 2011 and 2014 outbreaks of septicaemia due to Klebsiella pneumoniae subspecies pneumoniae (Kpp) were diagnosed on thirteen English pig farms. The most consistent features were rapid deaths of pigs from ten-days-old to weaning, seasonal occurrence (May to September), affected farms being outdoor breeding herds and the location of all but one of the outbreaks in the East Anglia region in Eastern England. Molecular characterisation of the outbreak Kpp isolates showed that by multilocus sequencing all were sequence type 25 (ST25) of K2 capsular type with a combination of a 4.3kb plasmid (pKPMC25), three phage sequences and the rmpA virulence gene. No archived Kpp isolates of porcine origin pre-dating 2011 were identified as ST25. In 2013 there was the first detection of an outbreak Kpp isolate showing antimicrobial resistance to six antibiotics. Human infection with Kpp ST25 has not been reported in the UK.
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Affiliation(s)
- Cornelia A. Bidewell
- Animal and Plant Health Agency (APHA), Rougham Hill, Bury St Edmunds, Suffolk, England
| | - Susanna M. Williamson
- Animal and Plant Health Agency (APHA), Rougham Hill, Bury St Edmunds, Suffolk, England
| | - Jon Rogers
- Animal and Plant Health Agency (APHA), Rougham Hill, Bury St Edmunds, Suffolk, England
| | - Yue Tang
- APHA Weybridge, New Haw, Addlestone, Surrey, England
| | | | | | - Manal AbuOun
- APHA Weybridge, New Haw, Addlestone, Surrey, England
- * E-mail:
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36
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Duggett NA, Sayers E, AbuOun M, Ellis RJ, Nunez-Garcia J, Randall L, Horton R, Rogers J, Martelli F, Smith RP, Brena C, Williamson S, Kirchner M, Davies R, Crook D, Evans S, Teale C, Anjum MF. Occurrence and characterization of mcr-1-harbouring Escherichia coli isolated from pigs in Great Britain from 2013 to 2015. J Antimicrob Chemother 2017; 72:691-695. [PMID: 27999032 DOI: 10.1093/jac/dkw477] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/07/2016] [Indexed: 11/14/2022] Open
Abstract
Objectives To determine the occurrence of mcr-1 -harbouring Escherichia coli in archived pig material originating in Great Britain (GB) from 2013 to 2015 and characterize mcr-1 plasmids. Methods Enrichment and selective culture of 387 archived porcine caecal contents and recovery from archive of 1109 E. coli isolates to identify colistin-resistant bacteria by testing for the presence of mcr-1 by PCR and RT-PCR. mcr-1 -harbouring E. coli were characterized by WGS and compared with other available mcr-1 WGS. Results Using selective isolation following enrichment, the occurrence of mcr-1 E. coli in caeca from healthy pigs at slaughter from unique farms in GB was 0.6% (95% CI 0%-1.5%) in 2015. mcr-1 E. coli were also detected in isolates from two porcine veterinary diagnostic submissions in 2015. All isolates prior to 2015 were negative. WGS analysis of the four mcr-1 -positive E. coli indicated no other antimicrobial resistance (AMR) genes were linked to mcr-1 -plasmid-bearing contigs, despite all harbouring multiple AMR genes. The sequence similarity between mcr-1 -plasmid-bearing contigs identified and those found in GB, Chinese and South African human isolates and Danish, French and Estonian livestock-associated isolates was 90%-99%. Conclusions mcr-1- harbouring plasmids were diverse, implying transposable elements are involved in mcr-1 transmission in GB. The low number of mcr-1 -positive E. coli isolates identified suggested mcr-1 is currently uncommon in E. coli from pigs within GB. The high sequence similarity between mcr-1 plasmid draft genomes identified in pig E. coli and plasmids found in human and livestock-associated isolates globally requires further investigation to understand the full implications.
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Affiliation(s)
- Nicholas A Duggett
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Ellie Sayers
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK.,Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Richard J Ellis
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | | | - Luke Randall
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Robert Horton
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Jon Rogers
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Francesca Martelli
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Richard P Smith
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Camilla Brena
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Susanna Williamson
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Miranda Kirchner
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Robert Davies
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Derrick Crook
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 7BN, UK
| | - Sarah Evans
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Chris Teale
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
| | - Muna F Anjum
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone KT15 3NB, UK
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37
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Duff JP, Bidewell CA, Williamson SM, Teale CJ, Stidworthy MF, Bexton S, AbuOun M, Randall L, Rogers JP. Klebsiella pneumoniae
of suspected human origin from free-living common seals on the east coast of England. Vet Rec 2016; 179:652. [DOI: 10.1136/vr.104018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2016] [Indexed: 11/03/2022]
Affiliation(s)
- James Paul Duff
- APHA Penrith Veterinary Investigation Centre; Penrith Cumbria CA11 9RR
| | - C. A. Bidewell
- APHA Bury St Edmunds Veterinary Investigation Centre; Rougham Hill Bury St Edmunds IP33 2RX UK
| | - S. M. Williamson
- APHA Bury St Edmunds Veterinary Investigation Centre; Rougham Hill Bury St Edmunds IP33 2RX UK
| | - C. J. Teale
- APHA Shrewsbury Veterinary Investigation Centre; Kendal Road Harlescott Shrewsbury SY1 4HD UK
| | - M. F. Stidworthy
- International Zoo Veterinary Group, Station House; Parkwood Street Keighley West Yorkshire BD21 4NQ UK
| | - S. Bexton
- RSPCA Norfolk Wildlife Hospital; Station Road, East Winch Kings Lynn Norfolk PE32 1NR UK
| | - M. AbuOun
- Department of Bacteriology; APHA; Weybridge KT15 3NB UK
| | - L. Randall
- Department of Bacteriology; APHA; Weybridge KT15 3NB UK
| | - J. P. Rogers
- APHA Bury St Edmunds Veterinary Investigation Centre; Rougham Hill Bury St Edmunds IP33 2RX UK
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38
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Petrovska L, Mather AE, AbuOun M, Branchu P, Harris SR, Connor T, Hopkins KL, Underwood A, Lettini AA, Page A, Bagnall M, Wain J, Parkhill J, Dougan G, Davies R, Kingsley RA. Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010. Emerg Infect Dis 2016; 22:617-24. [PMID: 26982594 PMCID: PMC4806966 DOI: 10.3201/eid2204.150531] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Microevolution resulted in considerable genotypic variation. Microevolution associated with emergence and expansion of new epidemic clones of
bacterial pathogens holds the key to epidemiologic success. To determine
microevolution associated with monophasic Salmonella Typhimurium
during an epidemic, we performed comparative whole-genome sequencing and phylogenomic
analysis of isolates from the United Kingdom and Italy during 2005–2012. These
isolates formed a single clade distinct from recent monophasic epidemic clones
previously described from North America and Spain. The UK monophasic epidemic clones
showed a novel genomic island encoding resistance to heavy metals and a composite
transposon encoding antimicrobial drug resistance genes not present in other
Salmonella Typhimurium isolates, which may have contributed to
epidemiologic success. A remarkable amount of genotypic variation accumulated during
clonal expansion that occurred during the epidemic, including multiple independent
acquisitions of a novel prophage carrying the sopE gene and multiple
deletion events affecting the phase II flagellin locus. This high level of
microevolution may affect antigenicity, pathogenicity, and transmission.
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39
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Sharma M, Nunez-Garcia J, Kearns AM, Doumith M, Butaye PR, Argudín MA, Lahuerta-Marin A, Pichon B, AbuOun M, Rogers J, Ellis RJ, Teale C, Anjum MF. Livestock-Associated Methicillin Resistant Staphylococcus aureus (LA-MRSA) Clonal Complex (CC) 398 Isolated from UK Animals belong to European Lineages. Front Microbiol 2016; 7:1741. [PMID: 27881973 PMCID: PMC5101578 DOI: 10.3389/fmicb.2016.01741] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/18/2016] [Indexed: 11/21/2022] Open
Abstract
In recent years, there has been an increase in the number of livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 recovered from S. aureus isolated animals in the UK. To determine possible origins of 12 LA-MRSA CC398 isolates collected after screening more than a thousand S. aureus animal isolates from the UK between 2013 and 2015, whole genome sequences (WGS) of CC398 European, including UK, and non-European isolates from diverse animal hosts were compared. Phylogenetic reconstruction applied to WGS data to assess genetic relatedness of all 89 isolates, clustered the 12 UK CC398 LA-MRSA within the European sub-lineages, although on different nodes; implicating multiple independent incursions into the UK, as opposed to a single introduction followed by clonal expansion. Three UK isolates from healthy pigs and one from turkey clustered within the cassette chromosome recombinases ccr C S. aureus protein A (spa)-type t011 European sub-lineage and three UK isolates from horses within the ccrA2B2 t011 European sub-lineage. The remaining UK isolates, mostly from pigs, clustered within the t034 European lineage. Presence of virulence, antimicrobial (AMR), heavy metal (HMR), and disinfectant (DR) resistance genes were determined using an in-house pipeline. Most, including UK isolates, harbored resistance genes to ≥3 antimicrobial classes in addition to β-lactams. HMR genes were detected in most European ccrC positive isolates, with >80% harboring czrC, encoding zinc and cadmium resistance; in contrast ~60% ccrC isolates within non-European lineages and 6% ccrA2B2 isolates showed this characteristic. The UK turkey MRSA isolate did not harbor φAVβ avian prophage genes (SAAV_2008 and SAAV_2009) present in US MSSA isolates from turkey and pigs. Absence of some of the major human-associated MRSA toxigenic and virulence genes in the UK LA-MRSA animal isolates was not unexpected. Therefore, we can conclude that the 12 UK LA-MRSA isolates collected in the past 2 years most likely represent separate incursions into the UK from other European countries. The presence of zinc and cadmium resistance in all nine food animal isolates (pig and poultry), which was absent from the 3 horse isolates may suggest heavy metal use/exposure has a possible role in selection of some MRSA.
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Affiliation(s)
- Meenaxi Sharma
- Department of Bacteriology, Animal and Plant Health Agency Surrey, UK
| | - Javier Nunez-Garcia
- Surveillance and Laboratory Services, Animal and Plant Health Agency Surrey, UK
| | - Angela M Kearns
- National Infection Service, Public Health England London, UK
| | - Michel Doumith
- National Infection Service, Public Health England London, UK
| | - Patrick R Butaye
- Faculty of Veterinary Medicine, University of GhentMerelbeke, Belgium; Department of Biomedical Sciences, School of Veterinary Medicine, Ross UniversityBasseterre, Saint Kitts and Nevis
| | - M Angeles Argudín
- Department of Microbiology, National Reference Centre-Staphylococcus aureus, Hôpital Erasme, Université Libre de Bruxelles Brussels, Belgium
| | | | - Bruno Pichon
- National Infection Service, Public Health England London, UK
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency Surrey, UK
| | - Jon Rogers
- Veterinary and Technical Services, Animal and Plant Health Agency Surrey, UK
| | - Richard J Ellis
- Surveillance and Laboratory Services, Animal and Plant Health Agency Surrey, UK
| | - Christopher Teale
- Department of Bacteriology, Animal and Plant Health Agency Surrey, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency Surrey, UK
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40
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Freire Martín I, Thomas CM, Laing E, AbuOun M, La Ragione RM, Woodward MJ. Curing vector for IncI1 plasmids and its use to provide evidence for a metabolic burden of IncI1 CTX-M-1 plasmid pIFM3791 on Klebsiella pneumoniae. J Med Microbiol 2016; 65:611-618. [PMID: 27166141 DOI: 10.1099/jmm.0.000271] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using a sequence-based approach we previously identified an IncI1 CTX-M-1 plasmid, pIFM3791, on a single pig farm in the UK that was harboured by Klebsiella pneumoniae, Escherichia coli and Salmonella enterica serotype 4,5,12:i:-. To test the hypothesis that the plasmid had spread rapidly into these differing host bacteria we wished to assess whether the plasmid conferred a fitness advantage. To do this an IncI1 curing vector was constructed and used to displace the IncI1 CTX-M-1 plasmids from K. pneumoniae strain B3791 and several other unrelated IncI1-harbouring strains indicating the potential wider application of the curing vector. The IncI1 CTX-M-1 plasmid was reintroduced by conjugation into the cured K. pneumoniae strain and also a naturally IncI1 plasmid free S. enterica serotype 4,5,12:i:-, S348/11. Original, cured and complemented strains were tested for metabolic competence using Biolog technology and in competitive growth, association to mammalian cells and biofilm formation experiments. The plasmid-cured K. pneumoniae strain grew more rapidly than either the original plasmid-carrying strain or plasmid-complemented strains in competition experiments. Additionally, the plasmid-cured strain was significantly better at respiring with l-sorbose as a carbon source and putrescine, γ-amino-n-butyric acid, l-alanine and l-proline as nitrogen sources. By contrast, no differences in phenotype were found when comparing plasmid-harbouring and plasmid-free S. enterica S348/11. In conclusion, the IncI1 curing vector successfully displaced multiple IncI plasmids. The IncI1 CTX-M1 plasmid conferred a growth disadvantage upon K. pneumoniae, possibly by imposing a metabolic burden, the mechanism of which remains to be determined.
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Affiliation(s)
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Emma Laing
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Roberto M La Ragione
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7AL, UK
| | - Martin J Woodward
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Park, Reading RG6 5AP, UK
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41
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Anjum MF, Duggett NA, AbuOun M, Randall L, Nunez-Garcia J, Ellis RJ, Rogers J, Horton R, Brena C, Williamson S, Martelli F, Davies R, Teale C. Colistin resistance in Salmonella and Escherichia coli isolates from a pig farm in Great Britain. J Antimicrob Chemother 2016; 71:2306-13. [PMID: 27147305 DOI: 10.1093/jac/dkw149] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/31/2016] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The objective of this study was to characterize colistin-resistant bacteria isolated from pigs on a farm in Great Britain following identification of a plasmid-borne colistin resistance mechanism in Escherichia coli from China. METHODS Phenotypic antimicrobial susceptibility testing was undertaken by broth dilution and WGS was performed to detect the presence of genes encoding resistance and virulence. Transferable colistin resistance was investigated by conjugation. RESULTS Two E. coli and one Salmonella Typhimurium variant Copenhagen were shown to be MDR, including resistance to colistin, with one E. coli and the Salmonella carrying the mcr-1 gene; all three harboured chromosomal mutations in genes conferring colistin resistance and both E. coli harboured β-lactamase resistance. The Salmonella mcr-1 plasmid was highly similar to pHNSHP45, from China, while the E. coli mcr-1 plasmid only had the ISApII and mcr-1 genes in common. The frequency of mcr-1 plasmid transfer by conjugation to recipient Enterobacteriaceae from Salmonella was low, lying between 10(-7) and 10(-9) cfu/recipient cfu. We were unable to demonstrate mcr-1 plasmid transfer from the E. coli. Plasmid profiling indicated transfer of multiple plasmids from the Salmonella resulting in some MDR transconjugants. CONCLUSIONS Identification of the mcr-1 gene in Enterobacteriaceae from pigs confirms its presence in livestock in Great Britain. The results suggest dissemination of resistance through different horizontally transferable elements. The in vitro transfer of multiple plasmids carrying colistin and other resistances from the Salmonella isolate underlines the potential for wider dissemination and recombination.
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Affiliation(s)
- Muna F Anjum
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Nicholas A Duggett
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Luke Randall
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Javier Nunez-Garcia
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Richard J Ellis
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Jon Rogers
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Robert Horton
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Camilla Brena
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Susanna Williamson
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Francesca Martelli
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Robert Davies
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Christopher Teale
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
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42
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Welchman D, Steventon A, Mawhinney I, AbuOun M. Intestinal spirochaetes (Brachyspira species) in pheasants in Great Britain. Vet Rec 2016; 178:193. [PMID: 26864024 DOI: 10.1136/vr.103496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2016] [Indexed: 11/04/2022]
Affiliation(s)
- D Welchman
- APHA Winchester, Itchen Abbas, Winchester SO21 1BX, UK
| | - A Steventon
- APHA Winchester, Itchen Abbas, Winchester SO21 1BX, UK
| | - I Mawhinney
- APHA Bury St Edmunds, Rougham Hill, Bury St Edmunds, Suffolk IP33 2RX, UK
| | - M AbuOun
- APHA Weybridge, New Haw, Addlestone Surrey KT15 3NB, UK
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43
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Diribe O, Thomas S, AbuOun M, Fitzpatrick N, La Ragione R. Genotypic relatedness and characterization of Staphylococcus pseudintermedius associated with post-operative surgical infections in dogs. J Med Microbiol 2015; 64:1074-1081. [PMID: 26449388 DOI: 10.1099/jmm.0.000110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus pseudintermedius is a commensal organism of dogs that can also be implicated in surgical site infections (SSIs) in dogs. Particularly with the recent emergence and spread of the ST71-t02-SCCmecII-III multidrug-resistant S. pseudintermedius clonal lineage (MDRSP), it is important to understand the clonal diversity of S. pseudintermedius in SSIs in dogs. The study reported here investigated the genotypic relatedness of 124 S. pseudintermedius isolates from the surgical wounds of 90 dogs admitted to a referral practice in the UK. This study also aimed to understand whether MDRSP is better adapted to survival and persistence in different environments compared with other S. pseudintermedius. Whilst no individual S. pseudintermedius clonal type was primarily responsible for S. pseudintermedius-associated SSIs in dogs, we found that MDRSP was the most represented clonal type among the isolates studied. However, we observed no difference in the level of biofilm production, susceptibility to biocides or carriage of specific virulence determinants between MDRSP and other S. pseudintermedius isolates studied. Interestingly, in the competitive fitness study, MDRSP did not outcompete any member of the other S. pseudintermedius isolates studied in each environment. Our data suggest that the determinants that promote S. pseudintermedius-associated SSIs in dogs are distributed among S. pseudintermedius as a species and are not restricted to a few clonal types. They also provide evidence to support the suggestion that MDRSP is not better adapted to survival or persistence in different environments and is no more virulent than other S. pseudintermedius isolates.
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Affiliation(s)
- Onyinye Diribe
- Animal and Plant Health Agency, Weybridge, Surrey, UK.,Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Sarah Thomas
- Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Noel Fitzpatrick
- Fitzpatrick Referrals, Halfway Lane, Godalming, Surrey, UK.,Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Roberto La Ragione
- Animal and Plant Health Agency, Weybridge, Surrey, UK.,Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
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Figueiredo R, Card R, Nunes C, AbuOun M, Bagnall MC, Nunez J, Mendonça N, Anjum MF, da Silva GJ. Virulence Characterization of Salmonella enterica by a New Microarray: Detection and Evaluation of the Cytolethal Distending Toxin Gene Activity in the Unusual Host S. Typhimurium. PLoS One 2015; 10:e0135010. [PMID: 26244504 PMCID: PMC4526557 DOI: 10.1371/journal.pone.0135010] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/16/2015] [Indexed: 11/19/2022] Open
Abstract
Salmonella enterica is a zoonotic foodborne pathogen that causes acute gastroenteritis in humans. We assessed the virulence potential of one-hundred and six Salmonella strains isolated from food animals and products. A high through-put virulence genes microarray demonstrated Salmonella Pathogenicity Islands (SPI) and adherence genes were highly conserved, while prophages and virulence plasmid genes were variably present. Isolates were grouped by serotype, and virulence plasmids separated S. Typhimurium in two clusters. Atypical microarray results lead to whole genome sequencing (WGS) of S. Infantis Sal147, which identified deletion of thirty-eight SPI-1 genes. Sal147 was unable to invade HeLa cells and showed reduced mortality in Galleria mellonella infection model, in comparison to a SPI-1 harbouring S. Infantis. Microarray and WGS of S. Typhimurium Sal199, established for the first time in S. Typhimurium presence of cdtB and other Typhi-related genes. Characterization of Sal199 showed cdtB genes were upstream of transposase IS911, and co-expressed with other Typhi-related genes. Cell cycle arrest, cytoplasmic distension, and nuclear enlargement were detected in HeLa cells infected by Sal199, but not with S. Typhimurium LT2. Increased mortality of Galleria was detected on infection with Sal199 compared to LT2. Thus, Salmonella isolates were rapidly characterized using a high through-put microarray; helping to identify unusual virulence features which were corroborated by further characterisation. This work demonstrates that the use of suitable screening methods for Salmonella virulence can help assess the potential risk associated with certain Salmonella to humans. Incorporation of such methodology into surveillance could help reduce the risk of emergence of epidemic Salmonella strains.
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Affiliation(s)
- Rui Figueiredo
- Faculty of Pharmacy and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Roderick Card
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Carla Nunes
- Faculty of Pharmacy and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Mary C. Bagnall
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Javier Nunez
- Specialist Scientific Support, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Nuno Mendonça
- Faculty of Pharmacy and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Gabriela Jorge da Silva
- Faculty of Pharmacy and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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Hayward MR, AbuOun M, La Ragione RM, Tchórzewska MA, Cooley WA, Everest DJ, Petrovska L, Jansen VAA, Woodward MJ. SPI-23 of S. Derby: role in adherence and invasion of porcine tissues. PLoS One 2014; 9:e107857. [PMID: 25238397 PMCID: PMC4169617 DOI: 10.1371/journal.pone.0107857] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 04/30/2014] [Accepted: 08/15/2014] [Indexed: 12/27/2022] Open
Abstract
Salmonella enterica serovars Derby and Mbandaka are isolated from different groups of livestock species in the UK. S. Derby is predominantly isolated from pigs and turkeys and S. Mbandaka is predominantly isolated from cattle and chickens. Alignment of the genome sequences of two isolates of each serovar led to the discovery of a new putative Salmonella pathogenicity island, SPI-23, in the chromosome sequence of S. Derby isolates. SPI-23 is 37 kb in length and contains 42 ORFs, ten of which are putative type III effector proteins. In this study we use porcine jejunum derived cell line IPEC-J2 and in vitro organ culture of porcine jejunum and colon, to characterise the association and invasion rates of S. Derby and S. Mbandaka, and tissue tropism of S. Derby respectively. We show that S. Derby invades and associates to an IPEC-J2 monolayer in significantly greater numbers than S. Mbandaka, and that S. Derby preferentially attaches to porcine jejunum over colon explants. We also show that nine genes across SPI-23 are up-regulated to a greater degree in the jejunum compared to the colon explants. Furthermore, we constructed a mutant of the highly up-regulated, pilV-like gene, potR, and find that it produces an excess of surface pili compared to the parent strain which form a strong agglutinating phenotype interfering with association and invasion of IPEC-J2 monolayers. We suggest that potR may play a role in tissue tropism.
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Affiliation(s)
- Matthew R. Hayward
- Department of Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Surrey, United Kingdom
- School of Biological Sciences, Royal Holloway University of London, Surrey, United Kingdom
- * E-mail:
| | - Manal AbuOun
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Surrey, United Kingdom
| | - Roberto M. La Ragione
- Department of Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, United Kingdom
| | | | - William A. Cooley
- Microscopy Facility, Animal Health and Veterinary Laboratories Agency, Surrey, United Kingdom
| | - David J. Everest
- Microscopy Facility, Animal Health and Veterinary Laboratories Agency, Surrey, United Kingdom
| | - Liljana Petrovska
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Surrey, United Kingdom
| | - Vincent A. A. Jansen
- School of Biological Sciences, Royal Holloway University of London, Surrey, United Kingdom
| | - Martin J. Woodward
- Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
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46
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Freire Martín I, AbuOun M, Reichel R, La Ragione RM, Woodward MJ. Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella 4,5,12:i:-, Escherichia coli and Klebsiella pneumoniae on a UK pig farm. J Antimicrob Chemother 2014; 69:2098-101. [PMID: 24729584 DOI: 10.1093/jac/dku098] [Citation(s) in RCA: 25] [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: 11/13/2022] Open
Abstract
OBJECTIVES In 2009, CTX-M Enterobacteriaceae and Salmonella isolates were recovered from a UK pig farm, prompting studies into the dissemination of the resistance and to establish any relationships between the isolates. METHODS PFGE was used to elucidate clonal relationships between isolates whilst plasmid profiling, restriction analysis, sequencing and PCR were used to characterize the CTX-M-harbouring plasmids. RESULTS Escherichia coli, Klebsiella pneumoniae and Salmonella 4,5,12:i:- and Bovismorbificans resistant to cefotaxime (n = 65) were recovered and 63 were shown by PCR to harbour a group 1 CTX-M gene. The harbouring hosts were diverse, but the group 1 CTX-M plasmids were common. Three sequenced CTX-M plasmids from E. coli, K. pneumoniae and Salmonella enterica serotype 4,5,12:i:- were identical except for seven mutations and highly similar to IncI1 plasmid ColIb-P9. Two antimicrobial resistance regions were identified: one inserted upstream of yacABC harbouring ISCR2 transposases, sul2 and floR; and the other inserted within shfB of the pilV shufflon harbouring the ISEcp1 transposase followed by blaCTX-M-1. CONCLUSIONS These data suggest that an ST108 IncI1 plasmid encoding a blaCTX-M-1 gene had disseminated across multiple genera on this farm, an example of horizontal gene transfer of the blaCTX-M-1 gene.
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Affiliation(s)
| | - Manal AbuOun
- AHVLA Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Rudolf Reichel
- AHVLA Thirsk, Station Road, Thirsk, North Yorkshire YO7 1PZ, UK
| | - Roberto M La Ragione
- AHVLA Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK School of Veterinary Medicine, Faculty of Health and Medical Sciences, Duke of Kent Building, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Martin J Woodward
- Department of Food and Nutritional Sciences, The University of Reading, Whiteknights Park, Reading RG6 5AP, UK
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Kirchner M, AbuOun M, Mafura M, Bagnall M, Hunt T, Thomas C, Weile J, Anjum MF. Cefotaxime resistant Escherichia coli collected from a healthy volunteer; characterisation and the effect of plasmid loss. PLoS One 2013; 8:e84142. [PMID: 24386342 PMCID: PMC3873979 DOI: 10.1371/journal.pone.0084142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 06/03/2013] [Accepted: 11/12/2013] [Indexed: 11/18/2022] Open
Abstract
In this study 6 CTX-M positive E. coli isolates collected during a clinical study examining the effect of antibiotic use in a human trial were analysed. The aim of the study was to analyse these isolates and assess the effect of full or partial loss of plasmid genes on bacterial fitness and pathogenicity. A DNA array was utilised to assess resistance and virulence gene carriage. Plasmids were characterised by PCR-based replicon typing and addiction system multiplex PCR. A phenotypic array and insect virulence model were utilised to assess the effect of plasmid-loss in E. coli of a large multi-resistance plasmid. All six E. coli carrying blaCTX-M-14 were detected from a single participant and were identical by pulse field gel electrophoresis and MLST. Plasmid profiling and arrays indicated absence of a large multi-drug resistance (MDR) F-replicon plasmid carrying blaTEM, aadA4, strA, strB, dfrA17/19, sul1, and tetB from one isolate. Although this isolate partially retained the plasmid it showed altered fitness characteristics e.g. inability to respire in presence of antiseptics, similar to a plasmid-cured strain. However, unlike the plasmid-cured or plasmid harbouring strains, the survival rate for Galleria mellonella infected by the former strain was approximately 5-times lower, indicating other possible changes accompanying partial plasmid loss. In conclusion, our results demonstrated that an apparently healthy individual can harbour blaCTX-M-14E. coli strains. In one such strain, isolated from the same individual, partial absence of a large MDR plasmid resulted in altered fitness and virulence characteristics, which may have implications in the ability of this strain to infect and any subsequent treatment.
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Affiliation(s)
- Miranda Kirchner
- Department of Bacteriology and Food Safety, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology and Food Safety, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
| | - Muriel Mafura
- Department of Bacteriology and Food Safety, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
| | - Mary Bagnall
- Department of Bacteriology and Food Safety, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
| | - Theresa Hunt
- Department of Bacteriology and Food Safety, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
| | - Christopher Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Jan Weile
- Institute for Laboratory and Transfusion Medicine at the Heart and Diabetes Centre, University Hospital of the Ruhr University, Bochum, Germany
| | - Muna F. Anjum
- Department of Bacteriology and Food Safety, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
- * E-mail:
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48
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Mappley LJ, Black ML, AbuOun M, Darby AC, Woodward MJ, Parkhill J, Turner AK, Bellgard MI, La T, Phillips ND, La Ragione RM, Hampson DJ. Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity. BMC Genomics 2012; 13:454. [PMID: 22947175 PMCID: PMC3532143 DOI: 10.1186/1471-2164-13-454] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [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: 06/11/2012] [Accepted: 08/22/2012] [Indexed: 11/12/2022] Open
Abstract
Background The anaerobic spirochaete Brachyspira pilosicoli causes enteric disease in avian, porcine and human hosts, amongst others. To date, the only available genome sequence of B. pilosicoli is that of strain 95/1000, a porcine isolate. In the first intra-species genome comparison within the Brachyspira genus, we report the whole genome sequence of B. pilosicoli B2904, an avian isolate, the incomplete genome sequence of B. pilosicoli WesB, a human isolate, and the comparisons with B. pilosicoli 95/1000. We also draw on incomplete genome sequences from three other Brachyspira species. Finally we report the first application of the high-throughput Biolog phenotype screening tool on the B. pilosicoli strains for detailed comparisons between genotype and phenotype. Results Feature and sequence genome comparisons revealed a high degree of similarity between the three B. pilosicoli strains, although the genomes of B2904 and WesB were larger than that of 95/1000 (~2,765, 2.890 and 2.596 Mb, respectively). Genome rearrangements were observed which correlated largely with the positions of mobile genetic elements. Through comparison of the B2904 and WesB genomes with the 95/1000 genome, features that we propose are non-essential due to their absence from 95/1000 include a peptidase, glycine reductase complex components and transposases. Novel bacteriophages were detected in the newly-sequenced genomes, which appeared to have involvement in intra- and inter-species horizontal gene transfer. Phenotypic differences predicted from genome analysis, such as the lack of genes for glucuronate catabolism in 95/1000, were confirmed by phenotyping. Conclusions The availability of multiple B. pilosicoli genome sequences has allowed us to demonstrate the substantial genomic variation that exists between these strains, and provides an insight into genetic events that are shaping the species. In addition, phenotype screening allowed determination of how genotypic differences translated to phenotype. Further application of such comparisons will improve understanding of the metabolic capabilities of Brachyspira species.
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Affiliation(s)
- Luke J Mappley
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Reading University, Addlestone, Surrey, UK.
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AbuOun M, Suthers PF, Jones GI, Carter BR, Saunders MP, Maranas CD, Woodward MJ, Anjum MF. Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain. J Biol Chem 2009; 284:29480-8. [PMID: 19690172 DOI: 10.1074/jbc.m109.005868] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Salmonella are closely related to commensal Escherichia coli but have gained virulence factors enabling them to behave as enteric pathogens. Less well studied are the similarities and differences that exist between the metabolic properties of these organisms that may contribute toward niche adaptation of Salmonella pathogens. To address this, we have constructed a genome scale Salmonella metabolic model (iMA945). The model comprises 945 open reading frames or genes, 1964 reactions, and 1036 metabolites. There was significant overlap with genes present in E. coli MG1655 model iAF1260. In silico growth predictions were simulated using the model on different carbon, nitrogen, phosphorous, and sulfur sources. These were compared with substrate utilization data gathered from high throughput phenotyping microarrays revealing good agreement. Of the compounds tested, the majority were utilizable by both Salmonella and E. coli. Nevertheless a number of differences were identified both between Salmonella and E. coli and also within the Salmonella strains included. These differences provide valuable insight into differences between a commensal and a closely related pathogen and within different pathogenic strains opening new avenues for future explorations.
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Affiliation(s)
- Manal AbuOun
- Department of Food and Environmental Safety, Veterinary Laboratories Agency (Weybridge), Addlestone, Surrey KT153NB, United Kingdom.
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50
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Pan Z, Carter B, Núñez-García J, AbuOun M, Fookes M, Ivens A, Woodward MJ, Anjum MF. Identification of genetic and phenotypic differences associated with prevalent and non-prevalent Salmonella Enteritidis phage types: analysis of variation in amino acid transport. Microbiology (Reading) 2009; 155:3200-3213. [PMID: 19574306 DOI: 10.1099/mic.0.029405-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this study, differences at the genetic level of 37 Salmonella Enteritidis strains from five phage types (PTs) were compared using comparative genomic hybridization (CGH) to assess differences between PTs. There were approximately 400 genes that differentiated prevalent (4, 6, 8 and 13a) and sporadic (11) PTs, of which 35 were unique to prevalent PTs, including six plasmid-borne genes, pefA, B, C, D, srgC and rck, and four chromosomal genes encoding putative amino acid transporters. Phenotype array studies also demonstrated that strains from prevalent PTs were less susceptible to urea stress and utilized l-histidine, l-glutamine, l-proline, l-aspartic acid, gly-asn and gly-gln more efficiently than PT11 strains. Complementation of a PT11 strain with the transporter genes from PT4 resulted in a significant increase in utilization of the amino acids and reduced susceptibility to urea stress. In epithelial cell association assays, PT11 strains were less invasive than other prevalent PTs. Most strains from prevalent PTs were better biofilm formers at 37 degrees C than at 28 degrees C, whilst the converse was true for PT11 strains. Collectively, the results indicate that genetic and corresponding phenotypic differences exist between strains of the prevalent PTs 4, 6, 8 and 13a and non-prevalent PT11 strains that are likely to provide a selective advantage for strains from the former PTs and could help them to enter the food chain and cause salmonellosis.
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Affiliation(s)
- Zhensheng Pan
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK.,Department of Food and Environmental Safety, Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Ben Carter
- Department of Food and Environmental Safety, Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Javier Núñez-García
- Department of Food and Environmental Safety, Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Manal AbuOun
- Department of Food and Environmental Safety, Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - María Fookes
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Al Ivens
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Martin J Woodward
- Department of Food and Environmental Safety, Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Muna F Anjum
- Department of Food and Environmental Safety, Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
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