1
|
Olorunleke SO, Kirchner M, Duggett N, Stevens K, Chah KF, Nwanta JA, Brunton LA, Anjum MF. Rapid detection and molecular epidemiology of β-lactamase producing Enterobacteriaceae isolated from food animals and in-contact humans in Nigeria. PLoS One 2024; 19:e0289190. [PMID: 38603727 PMCID: PMC11008865 DOI: 10.1371/journal.pone.0289190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/02/2024] [Indexed: 04/13/2024] Open
Abstract
The emergence and spread of β-lactamase-producing Enterobacteriaceae poses a significant threat to public health, necessitating the rapid detection and investigation of the molecular epidemiology of these pathogens. We modified a multiplex real-time (RT)-PCR to concurrently detect β-lactamase genes (blaCTX-M, blaTEM, and blaSHV) and Enterobacteriaceae 16S ribosomal RNA. qPCR probes and primers were validated using control isolates, and the sensitivity and specificity assessed. The optimised multiplex qPCR was used to screen 220 non-clinical Enterobacteriaceae from food animals and in-contact humans in Southeast Nigeria selected on cefotaxime-supplemented agar plates. Binary logistic regression was used to explore factors associated with the presence of the blaTEM and blaSHV genes in these isolates, and a subset of isolates from matched sampling sites and host species were whole genome sequenced, and their antimicrobial resistance (AMR) and plasmid profiles determined. The sensitivity and specificity of the qPCR assay was 100%. All isolates (220/220) were positive for Enterobacteriaceae ribosomal 16S rRNA and blaCTX-M, while 66.4% (146/220) and 9% (20/220) were positive for blaTEM and blaSHV, respectively. The prevalence of blaTEM and blaSHV varied across different sampling sites (farm, animal market and abattoirs). Isolates from Abia state were more likely to harbour blaTEM (OR = 2.3, p = 0.04) and blaSHV (OR = 5.12,p = 0.01) than isolates from Ebonyi state; blaTEM was more likely to be detected in isolates from food animals than humans (OR = 2.34, p = 0.03), whereas the reverse was seen for blaSHV (OR = 7.23, p = 0.02). Furthermore, Klebsiella and Enterobacter isolates harboured more AMR genes than Escherichia coli, even though they were isolated from the same sample. We also identified pan resistant Klebsiella harbouring resistance to ten classes of antimicrobials and disinfectant. Therefore, we recommend ESKAPE pathogens are included in AMR surveillance in future and suggest qPCRs be utilised for rapid screening of Enterobacteriaceae from human and animal sources.
Collapse
Affiliation(s)
- Solomon Olabiyi Olorunleke
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria Nsukka, Enugu, Nigeria
| | - Miranda Kirchner
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
| | - Nicholas Duggett
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, United Kingdom
| | - Kim Stevens
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Kennedy F. 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, Surrey, United Kingdom
| |
Collapse
|
2
|
Anjum MF, Duggett N, Sheldon E, Sharma M, Smith RP, Teale CJ. Genomics to detect transmission of livestock-associated methicillin-resistant Staphylococcus aureus from UK pigs in abattoirs during slaughter. J Antimicrob Chemother 2024:dkae052. [PMID: 38442335 DOI: 10.1093/jac/dkae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Livestock-associated MRSA (LA-MRSA) transmission/cross-contamination can occur at abattoir through colonized pigs, increasing occupational hazards and health concerns for workers. To assess this risk we used genomics to identify LA-MRSA lineages present in batches of pigs sent to slaughter and distribution of clones. METHODS WGS was performed on 85 LA-MRSA previously isolated from six abattoirs from 105 batches of pigs sent from 100 UK farms. spa typing and MLST were performed on all isolates. A mashtree tree was constructed to compare genomes of the LA-MRSA with 1281 global isolates from livestock and humans. A phylogenetic tree and pairwise SNP distance matrices were built from whole genomes of 109 isolates closest to those from abattoirs to compare evolutionary relationships and identify clones. RESULTS All abattoir isolates belonged to CC398 and were mainly of spa type t011, although other spa types were present. Phylogenetic analysis confirmed the abattoir isolates were most closely related to each other and to pig LA-MRSA from across Europe, indicating a common evolutionary origin with related lineages colonizing UK pigs.Comparison of genomes using SNPs suggested between one and four clones were transferring between pigs from different batches. Transmission likely occurred on farm premises, during transportation, and/or within abattoirs through contact with contaminated surfaces in lairage or post-stunning. CONCLUSIONS Genomics forensically identified related isolates/clones circulating in pigs at slaughter, showing contamination occurs often. Results suggest that further genomic tracking will identify hotspots, and improvements in measures such as biosecurity and disinfection will help reduce risk for workers.
Collapse
Affiliation(s)
- Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - Nicholas Duggett
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - Ewart Sheldon
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - Meenaxi Sharma
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, UK
| | - Chris J Teale
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Muloi DM, Jauneikaite E, Anjum MF, Essack SY, Singleton DA, Kasudi MR, Wade MJ, Egyir B, Nunn JG, Midega JT, Peacock SJ, Feasey NA, Baker KS, Zadoks RN. Exploiting genomics for antimicrobial resistance surveillance at One Health interfaces. Lancet Microbe 2023; 4:e1056-e1062. [PMID: 37977165 DOI: 10.1016/s2666-5247(23)00284-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
The intersection of human, animal, and ecosystem health at One Health interfaces is recognised as being of key importance in the evolution and spread of antimicrobial resistance (AMR) and represents an important, and yet rarely realised opportunity to undertake vital AMR surveillance. A working group of international experts in pathogen genomics, AMR, and One Health convened to take part in a workshop series and online consultation focused on the opportunities and challenges facing genomic AMR surveillance in a range of settings. Here we outline the working group's discussion of the potential utility, advantages of, and barriers to, the implementation of genomic AMR surveillance at One Health interfaces and propose a series of recommendations for addressing these challenges. Embedding AMR surveillance at One Health interfaces will require the development of clear beneficial use cases, especially in low-income and middle-income countries. Evidence of directionality, risks to human and animal health, and potential trade implications were also identified by the working group as key issues. Addressing these challenges will be vital to enable genomic surveillance technology to reach its full potential for assessing the risk of transmission of AMR between the environment, animals, and humans at One Health interfaces.
Collapse
Affiliation(s)
- Dishon M Muloi
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, New Haw, UK
| | - Sabiha Y Essack
- Antimicrobial Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - David A Singleton
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Mitchelle R Kasudi
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| | - Matthew J Wade
- Data Analytics and Surveillance Group, UK Health Security Agency, London, UK; School of Engineering, Newcastle University, Newcastle-upon-Tyne, UK
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | | | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Chichiri, Blantyre, Malawi
| | - Kate S Baker
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Ruth N Zadoks
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camden, NSW, Australia; School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| |
Collapse
|
6
|
Wheeler NE, Price V, Cunningham-Oakes E, Tsang KK, Nunn JG, Midega JT, Anjum MF, Wade MJ, Feasey NA, Peacock SJ, Jauneikaite E, Baker KS. Innovations in genomic antimicrobial resistance surveillance. Lancet Microbe 2023; 4:e1063-e1070. [PMID: 37977163 DOI: 10.1016/s2666-5247(23)00285-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Whole-genome sequencing of antimicrobial-resistant pathogens is increasingly being used for antimicrobial resistance (AMR) surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology; however, routine adoption of these technologies is challenging, particularly in low-income and middle-income countries. As part of a wider series of workshops and online consultations, a group of experts in AMR pathogen genomics and computational tool development conducted a situational analysis, identifying the following under-used innovations in genomic AMR surveillance: clinical metagenomics, environmental metagenomics, gene or plasmid tracking, and machine learning. The group recommended developing cost-effective use cases for each approach and mapping data outputs to clinical outcomes of interest to justify additional investment in capacity, training, and staff required to implement these technologies. Harmonisation and standardisation of methods, and the creation of equitable data sharing and governance frameworks, will facilitate successful implementation of these innovations.
Collapse
Affiliation(s)
- Nicole E Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, Edgbaston, UK
| | - Vivien Price
- Department of Clinical Infection, Immunology and Microbiology, Liverpool Centre for Global Health Research, University of Liverpool, Liverpool, UK
| | - Edward Cunningham-Oakes
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kara K Tsang
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - Matthew J Wade
- Data Analytics and Surveillance Group, UK Health Security Agency, London, UK; School of Engineering, Newcastle University, Newcastle-upon-Tyne, UK
| | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Chichiri, Blantyre, Malawi
| | | | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Kate S Baker
- Centre for Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.].
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Orlek A, Anjum MF, Mather AE, Stoesser N, Walker AS. Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis. Sci Rep 2023; 13:2500. [PMID: 36781908 PMCID: PMC9925765 DOI: 10.1038/s41598-023-29530-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Plasmids are major vectors of bacterial antibiotic resistance, but understanding of factors associated with plasmid antibiotic resistance gene (ARG) carriage is limited. We curated > 14,000 publicly available plasmid genomes and associated metadata. Duplicate and replicate plasmids were excluded; where possible, sample metadata was validated externally (BacDive database). Using Generalised Additive Models (GAMs) we assessed the influence of 12 biotic/abiotic factors (e.g. plasmid genetic factors, isolation source, collection date) on ARG carriage, modelled as a binary outcome. Separate GAMs were built for 10 major ARG types. Multivariable analysis indicated that plasmid ARG carriage patterns across time (collection years), isolation sources (human/livestock) and host bacterial taxa were consistent with antibiotic selection pressure as a driver of plasmid-mediated antibiotic resistance. Only 0.42% livestock plasmids carried carbapenem resistance (compared with 12% human plasmids); conversely, tetracycline resistance was enriched in livestock vs human plasmids, reflecting known prescribing practices. Interpreting results using a timeline of ARG type acquisition (determined by literature review) yielded additional novel insights. More recently acquired ARG types (e.g. colistin and carbapenem) showed increases in plasmid carriage during the date range analysed (1994-2019), potentially reflecting recent onset of selection pressure; they also co-occurred less commonly with ARGs of other types, and virulence genes. Overall, this suggests that following acquisition, plasmid ARGs tend to accumulate under antibiotic selection pressure and co-associate with other adaptive genes (other ARG types, virulence genes), potentially re-enforcing plasmid ARG carriage through co-selection.
Collapse
Affiliation(s)
- Alex Orlek
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre (BRC), University of Oxford, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre (BRC), University of Oxford, Oxford, UK
| |
Collapse
|
14
|
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.
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
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,
| |
Collapse
|
18
|
Dierikx C, Börjesson S, Perrin-Guyomard A, Haenni M, Norström M, Divon HH, Ilag HK, Granier SA, Hammerum A, Kjeldgaard JS, Pauly N, Randall L, Anjum MF, Smialowska A, Franco A, Veldman K, Slettemeås JS. A European multicenter evaluation study to investigate the performance on commercially available selective agar plates for the detection of carbapenemase producing Enterobacteriaceae. J Microbiol Methods 2022; 193:106418. [PMID: 35041877 DOI: 10.1016/j.mimet.2022.106418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 12/27/2022]
Abstract
The European Food Safety Authority (EFSA) advised to prioritize monitoring carbapenemase producing Enterobacteriaceae (CPE) in food producing animals. Therefore, this study evaluated the performance of different commercially available selective agars for the detection of CPE using spiked pig caecal and turkey meat samples and the proposed EFSA cultivation protocol. Eleven laboratories from nine countries received eight samples (four caecal and four meat samples). For each matrix, three samples contained approximately 100 CFU/g CPE, and one sample lacked CPE. After overnight enrichment in buffered peptone water, broths were spread upon Brilliance™ CRE Agar (1), CHROMID® CARBA (2), CHROMagar™ mSuperCARBA™ (3), Chromatic™ CRE (4), CHROMID® OXA-48 (5) and Chromatic™ OXA-48 (6). From plates with suspected growth, one to three colonies were selected for species identification, confirmation of carbapenem resistance and detection of carbapenemase encoding genes, by methods available at participating laboratories. Of the eleven participating laboratories, seven reported species identification, susceptibility tests and genotyping on isolates from all selective agar plates. Agars 2, 4 and 5 performed best, with 100% sensitivity. For agar 3, a sensitivity of 96% was recorded, while agar 1 and 6 performed with 75% and 43% sensitivity, respectively. More background flora was noticed for turkey meat samples than pig caecal samples. Based on this limited set of samples, most commercially available agars performed adequately. The results indicate, however, that OXA-48-like and non-OXA-48-like producers perform very differently, and one should consider which CPE strains are of interest to culture when choosing agar type.
Collapse
Affiliation(s)
- Cindy Dierikx
- National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721, MA, Bilthoven, the Netherlands
| | - Stefan Börjesson
- National Veterinary Institute, SE-751 89 Uppsala, Sweden; Public Health Agency of Sweden, SE-171 82 Solna, Sweden
| | - Agnès Perrin-Guyomard
- French Agency for Food, Environmental and Occupational Health & Safety, Fougères Laboratory, 10B rue Claude Bourgelat, Javené CS 40608 35306 Fougères Cedex, France
| | - Marisa Haenni
- French Agency for Food, Environmental and Occupational Health & Safety - Lyon University, Lyon Laboratory, 31, avenue Tony Garnier 69394 Lyon Cedex 07, France
| | | | - Hege H Divon
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway
| | | | - Sophie A Granier
- French Agency for Food, Environmental and Occupational Health & Safety, Fougères Laboratory, 10B rue Claude Bourgelat, Javené CS 40608 35306 Fougères Cedex, France
| | - Annette Hammerum
- Statens Serums Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Jette Sejer Kjeldgaard
- Technical University of Denmark, DTU Fødevareinstituttet, Kemitorvet, Bygning 202, DK-2800 Kgs Lyngby, Denmark
| | - Natalie Pauly
- German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Luke Randall
- Animal and Plant Health Agency, Woodham Ln, Addlestone KT15 3NB, United Kingdom
| | - Muna F Anjum
- Animal and Plant Health Agency, Woodham Ln, Addlestone KT15 3NB, United Kingdom
| | - Aleksandra Smialowska
- National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100 PUŁAWY, Poland
| | - Alessia Franco
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", via Appia Nuova, 1411 - 00178 Roma, Italy
| | - Kees Veldman
- Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB Lelystad, the Netherlands
| | | | | |
Collapse
|
19
|
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
| |
Collapse
|
20
|
Anjum MF, Schmitt H, Börjesson S, Berendonk TU. The potential of using E. coli as an indicator for the surveillance of antimicrobial resistance (AMR) in the environment. Curr Opin Microbiol 2021; 64:152-158. [PMID: 34739920 DOI: 10.1016/j.mib.2021.09.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
To understand the dynamics of antimicrobial resistance (AMR), in a One-Health perspective, surveillance play an important role. Monitoring systems already exist in the human health and livestock sectors, but there are no environmental monitoring programs. Therefore there is an urgent need to initiate environmental AMR monitoring programs nationally and globally, which will complement existing systems in different sectors. However, environmental programs should not only identify anthropogenic influences and levels of AMR, but they should also allow for identification of transmissions to and from human and animal populations. In the current review we therefore propose using antimicrobial resistant Escherichia coli as indicators for monitoring occurrence and levels of AMR in the environment, including wildlife.
Collapse
Affiliation(s)
- Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Heike Schmitt
- Centre for Zoonoses and Environmental Microbiology - Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA, Bilthoven, The Netherlands
| | - Stefan Börjesson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), 751 89, Uppsala, Sweden.
| | - Thomas U Berendonk
- Institute for Hydrobiology, Technische Universität Dresden, 01217, Dresden, Germany.
| | | |
Collapse
|
21
|
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.
Collapse
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
| | | |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2021; 75:3491-3500. [PMID: 32780112 PMCID: PMC7662176 DOI: 10.1093/jac/dkaa345] [Citation(s) in RCA: 1285] [Impact Index Per Article: 428.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/16/2022] Open
Abstract
Objectives WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results Genotype–phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype–phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
Collapse
Affiliation(s)
- Valeria Bortolaia
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Rolf S Kaas
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | | | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Vincent Cattoir
- Rennes University Hospital, Department of Clinical Microbiology, Rennes, France.,National Reference Center for Antimicrobial Resistance (lab Enterococci), Rennes, France.,University of Rennes 1, INSERM U1230, Rennes, France
| | - Alain Philippon
- Faculty of Medicine Paris Descartes, Bacteriology, Paris, France
| | - Rosa L Allesoe
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Ana Rita Rebelo
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Alfred Ferrer Florensa
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Linda Fagelhauer
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.,Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Bernd Neumann
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Guido Werner
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Jennifer K Bender
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Minh Nguyen
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Jasmine Coppens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Muna F Anjum
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | - Isabelle Kempf
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | | | | | | | - Ana Amaro
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Lurdes Clemente
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Joël Mossong
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Serge Losch
- Laboratoire de Médecine Vétérinaire de l'Etat, Veterinary Services Administration, Dudelange, Luxembourg
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Ole Lund
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| |
Collapse
|
25
|
Duggett N, Ellington MJ, Hopkins KL, Ellaby N, Randall L, Lemma F, Teale C, Anjum MF. Detection in livestock of the human pandemic Escherichia coli ST131 fimH30(R) clone carrying blaCTX-M-27. J Antimicrob Chemother 2021; 76:263-265. [PMID: 33068401 DOI: 10.1093/jac/dkaa407] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Nicholas Duggett
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, UK
| | | | - Katie L Hopkins
- National Infection Service, Public Health England, London NW9 5EQ, UK
| | - Nicholas Ellaby
- National Infection Service, Public Health England, London NW9 5EQ, UK
| | - Luke Randall
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, UK
| | - Fabrizio Lemma
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, UK
| | - Christopher Teale
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, UK
| |
Collapse
|
26
|
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
| |
Collapse
|
27
|
De Lucia A, Card RM, Duggett N, Smith RP, Davies R, Cawthraw SA, Anjum MF, Rambaldi M, Ostanello F, Martelli F. Reduction in antimicrobial resistance prevalence in Escherichia coli from a pig farm following withdrawal of group antimicrobial treatment. Vet Microbiol 2021; 258:109125. [PMID: 34033985 DOI: 10.1016/j.vetmic.2021.109125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/23/2020] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
An important element in the control of antimicrobial resistance (AMR) is reduction in antimicrobial usage. In the veterinary sector individual antimicrobial treatment of livestock, rather than the use of group treatment, can help achieve this goal. The aim of this study was to investigate how cessation of group antimicrobial treatment impacted the prevalence of AMR in commensal Escherichia coli in pigs at one farm over an 11-month period. Minimum inhibitory concentrations of eight antimicrobials were determined for 259 E. coli isolates collected during the study. A significant reduction in the prevalence of multidrug resistance and a significant increase in the proportion of full susceptibility to the panel of nine antimicrobials tested was seen after 11 months. Whole genome sequencing of 48 multidrug resistant isolates revealed E. coli clones that persisted across multiple visits and provided evidence for the presence of plasmids harbouring AMR genes shared across multiple E. coli lineages. E. coli were also isolated from on-farm environmental samples. Whole genome sequencing of one multidrug resistant isolate obtained from cleaning tools showed it was clonal to pig-derived E. coli that persisted on the farm for 11 months. In this study we provide evidence that withdrawal of group antimicrobial use leads to significant reductions in key indicators for AMR prevalence and the importance of the farm environment as a reservoir of resistant bacteria. These findings support policy makers and producers in the implementation of measures to control AMR and reduce antimicrobial use.
Collapse
Affiliation(s)
- A De Lucia
- Dipartimento di Scienze Mediche Veterinarie Università di Bologna, Italy; Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - R M Card
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - N Duggett
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - R P Smith
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - R Davies
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - S A Cawthraw
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - M F Anjum
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - M Rambaldi
- Dipartimento di Scienze Mediche Veterinarie Università di Bologna, Italy.
| | - F Ostanello
- Dipartimento di Scienze Mediche Veterinarie Università di Bologna, Italy.
| | - F Martelli
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Mesa Varona O, Chaintarli K, Muller-Pebody B, Anjum MF, Eckmanns T, Norström M, Boone I, Tenhagen BA. Monitoring Antimicrobial Resistance and Drug Usage in the Human and Livestock Sector and Foodborne Antimicrobial Resistance in Six European Countries. Infect Drug Resist 2020; 13:957-993. [PMID: 32308439 PMCID: PMC7140725 DOI: 10.2147/idr.s237038] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/26/2020] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Antimicrobial resistance (AMR), associated with antimicrobial use (AMU), is a major public concern. Surveillance and monitoring systems are essential to assess and control the trends in AMU and AMR. However, differences in the surveillance and monitoring systems between countries and sectors make comparisons challenging. The purpose of this article is to describe all surveillance and monitoring systems for AMU and AMR in the human and livestock sectors, as well as national surveillance and monitoring systems for AMR in food, in six European countries (Spain, Germany, France, the Netherlands, the United Kingdom and Norway) as a baseline for developing suggestions to overcome current limitations in comparing AMU and AMR data. METHODS A literature search in 2018 was performed to identify relevant peer-reviewed articles and national and European grey reports as well as AMU/AMR databases. RESULTS Comparison of AMU and AMR systems across the six countries showed a lack of standardization and harmonization with different AMU data sources (prescription vs sales data) and units of AMU and AMR being used. The AMR data varied by sample type (clinical/non-clinical), laboratory method (disk diffusion, microdilution, and VITEK, among others), data type, ie quantitative (minimum inhibition concentration (MIC) in mg/L/inhibition zone (IZ) in mm) vs qualitative data (susceptible-intermediate-resistant (SIR)), the standards used (EUCAST/CLSI among others), and/or the evaluation criteria adopted (epidemiological or clinical). DISCUSSION A One Health approach for AMU and AMR requires harmonization in various aspects between human, animal and food systems at national and international levels. Additionally, some overlap between systems of AMU and AMR has been encountered. Efforts should be made to improve standardization and harmonization and allow more meaningful analyses of AMR and AMU surveillance data under a One Health approach.
Collapse
Affiliation(s)
- Octavio Mesa Varona
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Katerina Chaintarli
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, Surrey, UK
| | - Berit Muller-Pebody
- Healthcare-Associated Infections & Antimicrobial Resistance Division, National Infection Service, Public Health England (PHE), London, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, Surrey, UK
| | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch Institute (RKI), Berlin, Germany
| | - Madelaine Norström
- Department of Analysis and Diagnostics, Section of Epidemiology, Norwegian Veterinary Institute (NVI), Oslo, Norway
| | - Ides Boone
- Department for Infectious Disease Epidemiology, Robert Koch Institute (RKI), Berlin, Germany
| | - Bernd-Alois Tenhagen
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
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 ).
Collapse
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.
| |
Collapse
|
35
|
Anjum MF, Marco-Jimenez F, Duncan D, Marín C, Smith RP, Evans SJ. Livestock-Associated Methicillin-Resistant Staphylococcus aureus From Animals and Animal Products in the UK. Front Microbiol 2019; 10:2136. [PMID: 31572341 PMCID: PMC6751287 DOI: 10.3389/fmicb.2019.02136] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 08/30/2019] [Indexed: 01/08/2023] Open
Abstract
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an emerging problem in many parts of the world. Although animal-adapted LA-MRSA has been known for many years, recent reports suggest a possible increasing trend in the zoonotic transmission of LA-MRSA in Europe. Since its emergence in the early 2000's, several investigations have indicated that persons in prolonged, repeated contact with affected livestock are at a higher risk of becoming colonized with LA-MRSA. LA-MRSA monitoring in livestock is voluntary under current EU legislation, and not all member states, including the UK, participate. UK LA-MRSA isolates have been detected through scanning surveillance, where samples are submitted from clinically diseased livestock for diagnostic investigation, and research studies. Surveys conducted on retail beef, pig and poultry meat on sale in the UK have also detected LA-MRSA. Taken together these results suggest that LA-MRSA is present in the UK, possibly at low prevalence level, as suggested by available evidence. In this review, we examine the data available from UK livestock and animal products, and make recommendations for future. We also review the findings from whole genome sequencing (WGS) of the possible lineage of some UK livestock isolates.
Collapse
Affiliation(s)
- Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Francisco Marco-Jimenez
- Instituto de Ciencia y Tecnología Animal, Universitat Politècnica de València, Valencia, Spain
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Daisy Duncan
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Clara Marín
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- Departamento de Producción Animal, Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, CEU Universities, Valencia, Spain
| | - Richard P. Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Sarah J. Evans
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Kirchner M, Sayers E, Cawthraw S, Duggett N, Gosling R, Jenkins C, Dallman TJ, Mueller-Doblies D, Anjum MF. A sensitive method for the recovery of Escherichia coli serogroup O55 including Shiga toxin-producing variants for potential use in outbreaks. J Appl Microbiol 2019; 127:889-896. [PMID: 31183950 PMCID: PMC6852171 DOI: 10.1111/jam.14345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/16/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022]
Abstract
AIM Shiga toxin-producing Escherichia coli (STEC) cause bloody diarrhoea, kidney failure and occasionally death. However, identifying the source of infection caused by STEC other than serogroup O157 is hampered by the availability of sensitive methods for detecting these pathogens. In this study, we developed novel tools for detecting E. coli O55 that is potentially associated with human outbreaks. METHODS AND RESULTS Overall specificity of immuno-magnetic separation (IMS) beads coated with anti-O55 serum was good with exception of cross-reactivity with E. coli O22 and O23, which was eliminated using an O55-specific PCR. Limit of detection for E. coli O55 using O55-IMS beads in spiked cattle faeces was on average 50 CFU per ml (range 1-90), and improved to <10 CFU per ml using the O55-specific PCR, following IMS on samples enriched for 2 h with E. coli O55. Application of these tools to test cattle faeces collected on-farm allowed the isolation of O55:H19, which through whole genome sequencing was compared to STEC O55:H7 human outbreak strains. CONCLUSION These tools provide a sensitive method which could be used to screen samples for STEC O55, whether environmental or human clinical. SIGNIFICANCE AND IMPACT OF THE STUDY Several human outbreaks reported in England were caused by STEC O55:H7. Tools developed here could assist in identification of the environmental source for these isolates, which has not yet been established.
Collapse
Affiliation(s)
- M Kirchner
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - E Sayers
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK.,University of East Anglia/Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - S Cawthraw
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - N Duggett
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - R Gosling
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | | | - D Mueller-Doblies
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - M F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| |
Collapse
|
38
|
Velasova M, Smith RP, Lemma F, Horton RA, Duggett NA, Evans J, Tongue SC, Anjum MF, Randall LP. Detection of extended-spectrum β-lactam, AmpC and carbapenem resistance in Enterobacteriaceae in beef cattle in Great Britain in 2015. J Appl Microbiol 2019; 126:1081-1095. [PMID: 30693606 DOI: 10.1111/jam.14211] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 09/25/2018] [Revised: 01/02/2019] [Accepted: 01/21/2019] [Indexed: 02/06/2023]
Abstract
AIMS This study investigated the occurrence and genetic diversity of Enterobacteriaceae with extended-spectrum β-lactamase (ESBL)-, AmpC- and carbapenemase-mediated resistance in British beef cattle, and related risk factors. METHODS AND RESULTS Faecal samples (n = 776) were obtained from farms in England and Wales (n = 20) and Scotland (n = 20) in 2015. Isolates from selective agars were identified by MALDI ToF mass spectrometry. Selected isolates were characterized by multiplex PCR (blaCTX -M, blaOXA , blaSHV and blaTEM genes), whole-genome sequencing (WGS), minimum inhibitory concentrations and pulsed-field gel electrophoresis. None of the faecal samples yielded carbapenem-resistant Escherichia coli. Ten (25%) of the farms tested positive for ESBL-producing CTX-M Enterobacteriaceae, 15 (37·5%) of the farms were positive for AmpC phenotype E. coli and none were positive for carbapenem-resistant E. coli. WGS showed a total of 30 different resistance genes associated with E. coli, Citrobacter and Serratia from ESBL agars, and colocation of resistance genes with blaCTX -M1 . Buying bulls and bringing in fattening cattle from another farm were identified as significant risk factors for positive samples harbouring CTX-M Enterobacteriaceae or AmpC phenotype E. coli respectively. CONCLUSIONS Beef cattle on a proportion of farms in GB carry ESBL-producing Enterobacteriaceae. Factors, such as operating as a closed herd, may have an important role in reducing introduction and transmission of resistant Enterobacteriaceae. The results indicate management factors may play an important role in impacting ESBL prevalence. In particular, further study would be valuable to understand the impact of maintaining a closed herd on reducing the introduction of resistant Enterobacteriaceae. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study showing the presence of ESBL-producing Enterobacteriaceae in British beef cattle.
Collapse
Affiliation(s)
- M Velasova
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - R P Smith
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - F Lemma
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - R A Horton
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - N A Duggett
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - J Evans
- SRUC (Inverness Campus), Edinburgh, UK
| | | | - M F Anjum
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - L P Randall
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| |
Collapse
|
39
|
Figueiredo R, Card RM, Nunez-Garcia J, Mendonça N, da Silva GJ, Anjum MF. Multidrug-Resistant Salmonella enterica Isolated from Food Animal and Foodstuff May Also Be Less Susceptible to Heavy Metals. Foodborne Pathog Dis 2018; 16:166-172. [PMID: 30480469 DOI: 10.1089/fpd.2017.2418] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica is a foodborne pathogen showing increasing multidrug resistance (MDR). We characterized the antimicrobial resistance (AMR) genotype using microarrays in a panel of 105 nontyphoidal S. enterica isolated from food animals and foodstuff. Nineteen isolates were chosen on the basis of their MDR and virulence for determination of heavy metal susceptibilities and screened by polymerase chain reaction for heavy metal resistance genes. Whole-genome sequencing (WGS) was performed on three isolates carrying clinically important AMR genes and the cdtB toxin gene to detect other heavy metal resistance mechanisms, and conjugation assays were performed to evaluate transfer of AMR/toxin genes with heavy metal resistance genes. AMR genotyping results showed isolates harbored between 1 and 12 mobile AMR genes, with 58% being classified as MDR. The tested subset of isolates showed reduced susceptibility to zinc (78%), copper (68%), silver (63%), arsenic (47%), and tellurite (26%); phenotypes that could be attributed to zitB (n = 32%), pcoA/pcoD (n = 32%), tcrB (n = 16%), arsB (n = 16%), silA/silE (n = 42%), and terF (n = 26%) genes. WGS confirmed the presence of other heavy metal resistance genes such as copA, cusA, and czcD. Isolates often harbored multiple heavy metal resistance genes. Two strains (Sal25 and Sal368) were able to conjugate with Escherichia coli J53 at a relatively high frequency (∼10-4 colony-forming units per recipient). Transformants selected in the presence of copper harbored either an IncHI2 (J53/Sal25 transconjugant) or IncF (J53/Sal368 transconjugant) plasmid with decreased susceptibilities to tellurite, zinc, copper, cobalt, arsenic, lead, mercury, and silver. blaCTX-M-1 and mcr-1 genes were also transferred to one transconjugant, and tet(M) and blaTEM-1 genes to the other. This work shows the presence of a diversity of AMR genes in this zoonotic pathogen, and suggests that heavy metals may contribute to selection of clinically important ones through the food chain, such as the plasmid-mediated colistin resistance gene mcr-1.
Collapse
Affiliation(s)
- Rui Figueiredo
- 1 Department of Microbiology, Faculty of Pharmacy, University of Coimbra , Coimbra, Portugal .,2 Center for Neuroscience and Cell Biology, Laboratory of Microbiology, University of Coimbra , Coimbra, Portugal .,3 Department of Bacteriology, Animal and Plant Health and Agency , Surrey, United Kingdom
| | - Roderick M Card
- 3 Department of Bacteriology, Animal and Plant Health and Agency , Surrey, United Kingdom
| | - Javier Nunez-Garcia
- 3 Department of Bacteriology, Animal and Plant Health and Agency , Surrey, United Kingdom
| | - Nuno Mendonça
- 1 Department of Microbiology, Faculty of Pharmacy, University of Coimbra , Coimbra, Portugal .,2 Center for Neuroscience and Cell Biology, Laboratory of Microbiology, University of Coimbra , Coimbra, Portugal
| | - Gabriela Jorge da Silva
- 1 Department of Microbiology, Faculty of Pharmacy, University of Coimbra , Coimbra, Portugal .,2 Center for Neuroscience and Cell Biology, Laboratory of Microbiology, University of Coimbra , Coimbra, Portugal
| | - Muna F Anjum
- 3 Department of Bacteriology, Animal and Plant Health and Agency , Surrey, United Kingdom
| |
Collapse
|
40
|
Duggett NA, Randall LP, Horton RA, Lemma F, Kirchner M, Nunez-Garcia J, Brena C, Williamson SM, Teale C, Anjum MF. Molecular epidemiology of isolates with multiple mcr plasmids from a pig farm in Great Britain: the effects of colistin withdrawal in the short and long term. J Antimicrob Chemother 2018; 73:3025-3033. [DOI: 10.1093/jac/dky292] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/25/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Nicholas A Duggett
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, UK
| | - Luke P Randall
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, UK
| | - Robert A Horton
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, UK
| | - Fabrizio Lemma
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, UK
| | - Miranda Kirchner
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, UK
| | | | - Camilla Brena
- Animal and Plant Health Agency (Thirsk), West House, Station Road, Thirsk, North Yorkshire, UK
| | - Susanna M Williamson
- Animal and Plant Health Agency (Bury St Edmunds), Rougham Hill, Bury St Edmunds, Suffolk, UK
| | - Christopher Teale
- Animal and Plant Health Agency (Shrewsbury), Kendal Road, Shrewsbury, UK
| | - Muna F Anjum
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, UK
| |
Collapse
|
41
|
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
|
42
|
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
| | | |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
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.
Collapse
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
| |
Collapse
|
45
|
Randall LP, Horton RA, Lemma F, Martelli F, Duggett NAD, Smith RP, Kirchner MJ, Ellis RJ, Rogers JP, Williamson SM, Simons RRL, Brena CM, Evans SJ, Anjum MF, Teale CJ. Longitudinal study on the occurrence in pigs of colistin-resistant Escherichia coli carrying mcr-1 following the cessation of use of colistin. J Appl Microbiol 2018; 125:596-608. [PMID: 29741287 DOI: 10.1111/jam.13907] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/09/2018] [Accepted: 04/12/2018] [Indexed: 11/27/2022]
Abstract
AIMS In 2015, colistin-resistant Escherichia coli and Salmonella with the mcr-1 gene were isolated from a pig farm in Great Britain. Pigs were subsequently monitored over a ~20-month period for the occurrence of mcr-1-mediated colistin resistance and the risk of mcr-1 E. coli entering the food chain was assessed. METHODS AND RESULTS Pig faeces and slurry were cultured for colistin-resistant E. coli and Salmonella, tested for the mcr-1 gene by PCR and selected isolates were further analysed. Seventy-eight per cent of faecal samples (n = 275) from pigs yielded mcr-1 E. coli after selective culture, but in positive samples only 0·2-1·3% of the total E. coli carried mcr-1. Twenty months after the initial sampling, faecal samples (n = 59) were negative for E. coli carrying mcr-1. CONCLUSIONS The risk to public health from porcine E. coli carrying mcr-1 was assessed as very low. Twenty months after cessation of colistin use, E. coli carrying mcr-1 was not detected in pig faeces on a farm where it was previously present. SIGNIFICANCE AND IMPACT OF THE STUDY The results suggest that cessation of colistin use may help over time to reduce or possibly eliminate mcr-1 E. coli on pig farms where it occurs.
Collapse
Affiliation(s)
- L P Randall
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - R A Horton
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - F Lemma
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - F Martelli
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - N A D Duggett
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - R P Smith
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - M J Kirchner
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - R J Ellis
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - J P Rogers
- Animal and Plant Health Agency (Bury St Edmunds), Bury St Edmunds, Suffolk, UK
| | - S M Williamson
- Animal and Plant Health Agency (Bury St Edmunds), Bury St Edmunds, Suffolk, UK
| | - R R L Simons
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - C M Brena
- Animal and Plant Health Agency (Thirsk), Thirsk, North Yorkshire, UK
| | - S J Evans
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - M F Anjum
- Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, Surrey, UK
| | - C J Teale
- Animal and Plant Health Agency (Shrewsbury), Shrewsbury, UK
| |
Collapse
|
46
|
Leekitcharoenphon P, Garcia‐Graells C, Botteldoorn N, Dierick K, Kempf I, Olkkola S, Rossi M, Nykäsenoja S, Malorny B, Stingl K, Battisti A, Franco A, Mossong J, Veldman K, Mevius D, Wasyl D, Wieczorek K, Osek J, Clemente L, Lacatus A, Nicorescu I, García MA, Escobar CDF, Ferrer MD, Ugarte‐Ruiz M, Anjum MF, Teale C, Ågren J, Hendriksen RS, Aarestrup FM. Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP). ACTA ACUST UNITED AC 2018. [DOI: 10.2903/sp.efsa.2018.en-1398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pimlapas Leekitcharoenphon
- National Food Institute Technical University of Denmark WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics European Union Reference Laboratory for Antimicrobial Resistance Denmark
| | | | - Nadine Botteldoorn
- Institut Scientifique Santé Publique (WIV‐ISP) Faculty of Veterinary University of Zaragoza
| | - Katelijne Dierick
- Institut Scientifique Santé Publique (WIV‐ISP) Faculty of Veterinary University of Zaragoza
| | | | - Satu Olkkola
- Microbiology Research Unit Finnish Food Safety Authority Evira Finland
| | - Mirko Rossi
- Microbiology Research Unit Finnish Food Safety Authority Evira Finland
| | - Suvi Nykäsenoja
- Microbiology Research Unit Finnish Food Safety Authority Evira Finland
| | | | - Kerstin Stingl
- NRL for the Analysis and Testing of Zoonoses (Salmonella)
| | - Antonio Battisti
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana Italy
| | - Alessia Franco
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana Italy
| | | | - Kees Veldman
- Central Veterinary Institute (CVI) part of Wageningen UR The Netherlands
| | - Dik Mevius
- Central Veterinary Institute (CVI) part of Wageningen UR The Netherlands
| | | | | | - Jacek Osek
- National Veterinary Research Institute Poland
| | - Lurdes Clemente
- INIAV ‐ National Institute for Agrarian and Veterinary Research Microbiology and Mycology Laboratory Portugal
| | - Angela Lacatus
- Institute for Hygiene and Veterinary Public Health Romania
| | | | | | | | | | - María Ugarte‐Ruiz
- VISAVET Health Surveillance Centre Universidad Complutense Madrid Spain
| | | | | | | | - Rene S. Hendriksen
- National Food Institute Technical University of Denmark WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics European Union Reference Laboratory for Antimicrobial Resistance Denmark
| | - Frank M. Aarestrup
- National Food Institute Technical University of Denmark WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics European Union Reference Laboratory for Antimicrobial Resistance Denmark
| |
Collapse
|
47
|
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.
Collapse
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
| |
Collapse
|
48
|
Sharma M, Kirchner M, Fearnley C, Giles M, Smith L, Brown D, Anjum MF. Real-time PCR for the detection ofLeptospiraspecies in lungworm preparations. Vet Rec 2017; 181:197. [DOI: 10.1136/vr.104063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 06/16/2017] [Accepted: 06/22/2017] [Indexed: 11/04/2022]
|
49
|
Card RM, Cawthraw SA, Nunez-Garcia J, Ellis RJ, Kay G, Pallen MJ, Woodward MJ, Anjum MF. An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli. mBio 2017; 8:e00777-17. [PMID: 28720731 PMCID: PMC5516254 DOI: 10.1128/mbio.00777-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/06/2017] [Indexed: 01/28/2023] Open
Abstract
The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity. Bacterial community profiles obtained by culture-independent methods showed that Salmonella inoculation resulted in no significant changes to bacterial community alpha diversity and beta diversity, whereas administration of cefotaxime caused significant alterations to both measures of diversity, which largely recovered. MDR plasmid transfer from Salmonella to commensal Escherichia coli was demonstrated by PCR and whole-genome sequencing of isolates purified from agar plates containing cefotaxime. Transfer occurred to seven E. coli sequence types at high rates, even in the absence of cefotaxime, with resistant strains isolated within 3 days. Our chemostat system provides a good representation of bacterial interactions, including antibiotic resistance transfer in vivo It can be used as an ethical and relatively inexpensive approach to model dissemination of antibiotic resistance within the gut of any animal or human and refine interventions that mitigate its spread before employing in vivo studies.IMPORTANCE The spread of antimicrobial resistance presents a grave threat to public health and animal health and is affecting our ability to respond to bacterial infections. Transfer of antimicrobial resistance via plasmid exchange is of particular concern as it enables unrelated bacteria to acquire resistance. The gastrointestinal tract is replete with bacteria and provides an environment for plasmid transfer between commensals and pathogens. Here we use the chicken gut microbiota as an exemplar to model the effects of bacterial infection, antibiotic administration, and plasmid transfer. We show that transfer of a multidrug-resistant plasmid from the zoonotic pathogen Salmonella to commensal Escherichia coli occurs at a high rate, even in the absence of antibiotic administration. Our work demonstrates that the in vitro gut model provides a powerful screening tool that can be used to assess and refine interventions that mitigate the spread of antibiotic resistance in the gut before undertaking animal studies.
Collapse
Affiliation(s)
- Roderick M Card
- Department of Bacteriology, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Shaun A Cawthraw
- Department of Bacteriology, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Javier Nunez-Garcia
- Central Sequencing Unit, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Richard J Ellis
- Central Sequencing Unit, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Gemma Kay
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Martin J Woodward
- Food and Nutritional Sciences Department, University of Reading, Whiteknights, Reading, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| |
Collapse
|
50
|
Kirchner M, Lemma F, Randall L, Anjum MF. Loop-mediated isothermal amplification for extended spectrum β-lactamase gene detection in poultry carcase. Vet Rec 2017; 181:119. [PMID: 28512232 DOI: 10.1136/vr.104150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2017] [Indexed: 11/04/2022]
Affiliation(s)
- M Kirchner
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey KT15 3NB, UK
| | - F Lemma
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey KT15 3NB, UK
| | - L Randall
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey KT15 3NB, UK
| | - M F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey KT15 3NB, UK
| |
Collapse
|