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Bartlett H, Zanella M, Kaori B, Sabei L, Araujo MS, de Paula TM, Zanella AJ, Holmes MA, Wood JLN, Balmford A. Trade-offs in the externalities of pig production are not inevitable. Nat Food 2024; 5:312-322. [PMID: 38605128 PMCID: PMC11045459 DOI: 10.1038/s43016-024-00921-2] [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] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 01/10/2024] [Indexed: 04/13/2024]
Abstract
Farming externalities are believed to co-vary negatively, yet trade-offs have rarely been quantified systematically. Here we present data from UK and Brazilian pig production systems representative of most commercial systems across the world ranging from 'intensive' indoor systems through to extensive free range, Organic and woodland systems to explore co-variation among four major externality costs. We found that no specific farming type was consistently associated with good performance across all domains. Generally, systems with low land use have low greenhouse gas emissions but high antimicrobial use and poor animal welfare, and vice versa. Some individual systems performed well in all domains but were not exclusive to any particular type of farming system. Our findings suggest that trade-offs may be avoidable if mitigation focuses on lowering impacts within system types rather than simply changing types of farming.
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Affiliation(s)
- Harriet Bartlett
- Department of Zoology, University of Cambridge, Cambridge, UK.
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
- Smith School of Enterprise and Environment, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
| | - Márcia Zanella
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Beatriz Kaori
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Leandro Sabei
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Michelle S Araujo
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Tauana Maria de Paula
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Adroaldo J Zanella
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - James L N Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andrew Balmford
- Department of Zoology, University of Cambridge, Cambridge, UK
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Coll F, Gouliouris T, Blane B, Yeats CA, Raven KE, Ludden C, Khokhar FA, Wilson HJ, Roberts LW, Harrison EM, Horner CS, Le TH, Nguyen TH, Nguyen VT, Brown NM, Holmes MA, Parkhill J, Estee Török M, Peacock SJ. Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data. Lancet Microbe 2024; 5:e151-e163. [PMID: 38219758 DOI: 10.1016/s2666-5247(23)00297-5] [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: 02/01/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND DNA sequencing could become an alternative to in vitro antibiotic susceptibility testing (AST) methods for determining antibiotic resistance by detecting genetic determinants associated with decreased antibiotic susceptibility. Here, we aimed to assess and improve the accuracy of antibiotic resistance determination from Enterococcus faecium genomes for diagnosis and surveillance purposes. METHODS In this retrospective diagnostic accuracy study, we first conducted a literature search in PubMed on Jan 14, 2021, to compile a catalogue of genes and mutations predictive of antibiotic resistance in E faecium. We then evaluated the diagnostic accuracy of this database to determine susceptibility to 12 different, clinically relevant antibiotics using a diverse population of 4382 E faecium isolates with available whole-genome sequences and in vitro culture-based AST phenotypes. Isolates were obtained from various sources in 11 countries worldwide between 2000 and 2018. We included isolates tested with broth microdilution, Vitek 2, and disc diffusion, and antibiotics with at least 50 susceptible and 50 resistant isolates. Phenotypic resistance was derived from raw minimum inhibitory concentrations and measured inhibition diameters, and harmonised primarily using the breakpoints set by the European Committee on Antimicrobial Susceptibility Testing. A bioinformatics pipeline was developed to process raw sequencing reads, identify antibiotic resistance genetic determinants, and report genotypic resistance. We used our curated database, as well as ResFinder, AMRFinderPlus, and LRE-Finder, to assess the accuracy of genotypic predictions against phenotypic resistance. FINDINGS We curated a catalogue of 228 genetic markers involved in resistance to 12 antibiotics in E faecium. Very accurate genotypic predictions were obtained for ampicillin (sensitivity 99·7% [95% CI 99·5-99·9] and specificity 97·9% [95·8-99·0]), ciprofloxacin (98·0% [96·4-98·9] and 98·8% [95·9-99·7]), vancomycin (98·8% [98·3-99·2] and 98·8% [98·0-99·3]), and linezolid resistance (after re-testing false negatives: 100·0% [90·8-100·0] and 98·3% [97·8-98·7]). High sensitivity was obtained for tetracycline (99·5% [99·1-99·7]), teicoplanin (98·9% [98·4-99·3]), and high-level resistance to aminoglycosides (97·7% [96·6-98·4] for streptomycin and 96·8% [95·8-97·5] for gentamicin), although at lower specificity (60-90%). Sensitivity was expectedly low for daptomycin (73·6% [65·1-80·6]) and tigecycline (38·3% [27·1-51·0]), for which the genetic basis of resistance is not fully characterised. Compared with other antibiotic resistance databases and bioinformatic tools, our curated database was similarly accurate at detecting resistance to ciprofloxacin and linezolid and high-level resistance to streptomycin and gentamicin, but had better sensitivity for detecting resistance to ampicillin, tigecycline, daptomycin, and quinupristin-dalfopristin, and better specificity for ampicillin, vancomycin, teicoplanin, and tetracycline resistance. In a validation dataset of 382 isolates, similar or improved diagnostic accuracies were also achieved. INTERPRETATION To our knowledge, this work represents the largest published evaluation to date of the accuracy of antibiotic susceptibility predictions from E faecium genomes. The results and resources will facilitate the adoption of whole-genome sequencing as a tool for the diagnosis and surveillance of antimicrobial resistance in E faecium. A complete characterisation of the genetic basis of resistance to last-line antibiotics, and the mechanisms mediating antibiotic resistance silencing, are needed to close the remaining sensitivity and specificity gaps in genotypic predictions. FUNDING Wellcome Trust, UK Department of Health, British Society for Antimicrobial Chemotherapy, Academy of Medical Sciences and the Health Foundation, Medical Research Council Newton Fund, Vietnamese Ministry of Science and Technology, and European Society of Clinical Microbiology and Infectious Disease.
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Affiliation(s)
- Francesc Coll
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Theodore Gouliouris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Corin A Yeats
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kathy E Raven
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Fahad A Khokhar
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Hayley J Wilson
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Leah W Roberts
- Department of Medicine, University of Cambridge, Cambridge, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ewan M Harrison
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Thi Hoi Le
- National Hospital for Tropical Diseases, Hanoi, Viet Nam; Hanoi Medical University, Hanoi, Viet Nam
| | - Thi Hoa Nguyen
- National Hospital for Tropical Diseases, Hanoi, Viet Nam; Department of Microbiology and National Tuberculosis Reference Laboratory, National Lung Hospital, Hanoi, Viet Nam
| | - Vu Trung Nguyen
- National Hospital for Tropical Diseases, Hanoi, Viet Nam; Hanoi Medical University, Hanoi, Viet Nam
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; British Society for Antimicrobial Chemotherapy, Birmingham, UK; UK Health Security Agency, Cambridge, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Mili Estee Török
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sharon J Peacock
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
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3
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Ba X, Guo Y, Moran RA, Doughty EL, Liu B, Yao L, Li J, He N, Shen S, Li Y, van Schaik W, McNally A, Holmes MA, Zhuo C. Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone. Nat Commun 2024; 15:494. [PMID: 38216585 PMCID: PMC10786849 DOI: 10.1038/s41467-023-43854-3] [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: 05/10/2023] [Accepted: 11/22/2023] [Indexed: 01/14/2024] Open
Abstract
Carbapenem-resistant Escherichia coli (CREC) ST410 has recently emerged as a major global health problem. Here, we report a shift in CREC prevalence in Chinese hospitals between 2017 and 2021 with ST410 becoming the most commonly isolated sequence type. Genomic analysis identifies a hypervirulent CREC ST410 clone, B5/H24RxC, which caused two separate outbreaks in a children's hospital. It may have emerged from the previously characterised B4/H24RxC in 2006 and has been isolated in ten other countries from 2015 to 2021. Compared with B4/H24RxC, B5/H24RxC lacks the blaOXA-181-bearing X3 plasmid, but carries a F-type plasmid containing blaNDM-5. Most of B5/H24RxC also carry a high pathogenicity island and a novel O-antigen gene cluster. We find that B5/H24RxC grew faster in vitro and is more virulent in vivo. The identification of this newly emerged but already globally disseminated hypervirulent CREC clone, highlights the ongoing evolution of ST410 towards increased resistance and virulence.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yingyi Guo
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Emma L Doughty
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Baomo Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Likang Yao
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiahui Li
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Nanhao He
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Yang Li
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
| | - Chao Zhuo
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Ba X, Raisen CL, Restif O, Cavaco LM, Vingsbo Lundberg C, Lee JYH, Howden BP, Bartels MD, Strommenger B, Harrison EM, Larsen AR, Holmes MA, Larsen J. Cryptic susceptibility to penicillin/β-lactamase inhibitor combinations in emerging multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages. Nat Commun 2023; 14:6479. [PMID: 37838722 PMCID: PMC10576800 DOI: 10.1038/s41467-023-42245-y] [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: 04/04/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023] Open
Abstract
Global spread of multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages underscores the need for new therapeutic strategies. Here we show that many S. epidermidis isolates belonging to these lineages display cryptic susceptibility to penicillin/β-lactamase inhibitor combinations under in vitro conditions, despite carrying the methicillin resistance gene mecA. Using a mouse thigh model of S. epidermidis infection, we demonstrate that single-dose treatment with amoxicillin/clavulanic acid significantly reduces methicillin-resistant S. epidermidis loads without leading to detectable resistance development. On the other hand, we also show that methicillin-resistant S. epidermidis is capable of developing increased resistance to amoxicillin/clavulanic acid during long-term in vitro exposure to these drugs. These findings suggest that penicillin/β-lactamase inhibitor combinations could be a promising therapeutic candidate for treatment of a high proportion of methicillin-resistant S. epidermidis infections, although the in vivo risk of resistance development needs to be further addressed before they can be incorporated into clinical trials.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Claire L Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lina Maria Cavaco
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Jean Y H Lee
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mette D Bartels
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Birgit Strommenger
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark.
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5
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Tams KW, Larsen I, Hansen JE, Spiegelhauer H, Strøm-Hansen AD, Rasmussen S, Ingham AC, Kalmar L, Kean IRL, Angen Ø, Holmes MA, Pedersen K, Jelsbak L, Folkesson A, Larsen AR, Strube ML. The effects of antibiotic use on the dynamics of the microbiome and resistome in pigs. Anim Microbiome 2023; 5:39. [PMID: 37605221 PMCID: PMC10440943 DOI: 10.1186/s42523-023-00258-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/25/2023] [Indexed: 08/23/2023] Open
Abstract
Antibiotics are widely used in pig farming across the world which has led to concerns about the potential impact on human health through the selection of antibiotic resistant pathogenic bacteria. This worry has resulted in the development of a production scheme known as pigs Raised Without Antibiotics (RWA), in which pigs are produced in commercial farms, but are ear-tagged as RWA until slaughter unless they receive treatment, thus allowing the farmer to sell the pigs either as premium priced RWA or as conventional meat. Development of antibiotic resistance in pig farming has been studied in national surveys of antibiotic usage and resistance, as well as in experimental studies of groups of pigs, but not in individual pigs followed longitudinally in a commercial pig farm. In this study, a cohort of RWA designated pigs were sampled at 10 time points from birth until slaughter along with pen-mates treated with antibiotics at the same farm. From these samples, the microbiome, determined using 16S sequencing, and the resistome, as determined using qPCR for 82 resistance genes, was investigated, allowing us to examine the difference between RWA pigs and antibiotic treated pigs. We furthermore included 176 additional pigs from six different RWA farms which were sampled at the slaughterhouse as an endpoint to substantiate the cohort as well as for evaluation of intra-farm variability. The results showed a clear effect of age in both the microbiome and resistome composition from early life up until slaughter. As a function of antibiotic treatment, however, we observed a small but significant divergence between treated and untreated animals in their microbiome composition immediately following treatment, which disappeared before 8 weeks of age. The effect on the resistome was evident and an effect of treatment could still be detected at week 8. In animals sampled at the slaughterhouse, we observed no difference in the microbiome or the resistome as a result of treatment status but did see a strong effect of farm origin. Network analysis of co-occurrence of microbiome and resistome data suggested that some resistance genes may be transferred through mobile genetic elements, so we used Hi-C metagenomics on a subset of samples to investigate this. We conclude that antibiotic treatment has a differential effect on the microbiome vs. the resistome and that although resistance gene load is increased by antibiotic treatment load, this effect disappears before slaughter. More studies are needed to elucidate the optimal way to rear pigs without antibiotics.
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Affiliation(s)
- Katrine Wegener Tams
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Inge Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Julie Elvekjær Hansen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Henrik Spiegelhauer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | | | - Sophia Rasmussen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Lajos Kalmar
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Øystein Angen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Karl Pedersen
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, 751 89, Uppsala, Sweden
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anders Folkesson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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6
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Matuszewska M, Dabrowska A, Murray GGR, Kett SM, Vick AJA, Banister SC, Pantoja Munoz L, Cunningham P, Welch JJ, Holmes MA, Weinert LA. Absence of Staphylococcus aureus in Wild Populations of Fish Supports a Spillover Hypothesis. Microbiol Spectr 2023; 11:e0485822. [PMID: 37341608 PMCID: PMC10434045 DOI: 10.1128/spectrum.04858-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 11/29/2022] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Staphylococcus aureus is a human commensal and opportunistic pathogen that also infects other animals. In humans and livestock, where S. aureus is most studied, strains are specialized for different host species. Recent studies have also found S. aureus in diverse wild animals. However, it remains unclear whether these isolates are also specialized for their hosts or whether their presence is due to repeated spillovers from source populations. This study focuses on S. aureus in fish, testing the spillover hypothesis in two ways. First, we examined 12 S. aureus isolates obtained from the internal and external organs of a farmed fish. While all isolates were from clonal complex 45, genomic diversity indicates repeated acquisition. The presence of a φSa3 prophage containing human immune evasion genes suggests that the source was originally human. Second, we tested for S. aureus in wild fish that were isolated from likely sources. In particular, we sampled 123 brown trout and their environment at 16 sites in the remote Scottish Highlands with variable levels of exposure to humans, birds, and livestock. This screen found no S. aureus infection in any of the wild populations or their environment. Together, these results support that the presence of S. aureus in fish and aquaculture is due to spillover from humans rather than specialization. Given the trends of increasing fish consumption, a better understanding of the dynamics of S. aureus spillover in aquaculture will mitigate future risks to fish and human health. IMPORTANCE Staphylococcus aureus is a human and livestock commensal but also an important pathogen responsible for high human mortality rates and economic losses in farming. Recent studies show that S. aureus is common in wild animals, including fish. However, we do not know whether these animals are part of the normal host range of S. aureus or whether infection is due to repeated spillover events from true S. aureus hosts. Answering this question has implications for public health and conservation. We find support for the spillover hypothesis by combining genome sequencing of S. aureus isolates from farmed fish and screens for S. aureus in isolated wild populations. The results imply that fish are unlikely to be a source of novel emergent S. aureus strains but highlight the prominence of the spillover of antibiotic-resistant bacteria from humans and livestock. This may affect both future fish disease potential and the risk of human food poisoning.
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Affiliation(s)
- Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alicja Dabrowska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Gemma G. R. Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, Evolution and Environment, University College London, London
| | - Steve M. Kett
- Department of Natural Sciences, Middlesex University London, London, United Kingdom
| | - Andy J. A. Vick
- RAL Space (UKRI-STFC), Harwell Campus, Didcot, Oxfordshire, United Kingdom
| | - Sofie C. Banister
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Peter Cunningham
- Wester Ross Fisheries Trust, Harbour Centre, Gairloch, Wester Ross, United Kingdom
| | - John J. Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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7
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Zhou Z, Shuai X, Lin Z, Yu X, Ba X, Holmes MA, Xiao Y, Gu B, Chen H. Association between particulate matter (PM) 2·5 air pollution and clinical antibiotic resistance: a global analysis. Lancet Planet Health 2023; 7:e649-e659. [PMID: 37558346 DOI: 10.1016/s2542-5196(23)00135-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Antibiotic resistance is an increasing global issue, causing millions of deaths worldwide every year. Particulate matter (PM)2·5 has diverse elements of antibiotic resistance that increase its spread after inhalation. However, understanding of the contribution of PM2·5 to global antibiotic resistance is poor. Through univariate and multivariable analysis, we aimed to present the first global estimates of antibiotic resistance and burden of premature deaths attributable to antibiotic resistance resulting from PM2·5 pollution. METHODS For this global analysis, data on multiple potential predictors (ie, air pollution, antibiotic use, sanitation services, economics, health expenditure, population, education, climate, year, and region) were collected in 116 countries from 2000 to 2018 to estimate the effect of PM2·5 on antibiotic resistance via univariate and multivariable analysis. Data were obtained from ResistanceMap, European Centre for Disease Prevention and Control Surveillance Atlas (antimicrobial-resistance sources), and PLISA Health Information Platform for the Americas. Future global aggregate antibiotic resistance and premature mortality trends derived from PM2·5 in different scenarios (eg, 50% reduced antibiotic use or PM2·5 controlled to 5 μg/m3) were projected until 2050. FINDINGS The final dataset included more than 11·5 million tested isolates. Raw antibiotic-resistance data included nine pathogens and 43 types of antibiotic agents. Significant correlations between PM2·5 and antibiotic resistance were consistent globally in most antibiotic-resistant bacteria (R2=0·42-0·76, p<0·0001), and correlations have strengthened over time. Antibiotic resistance derived from PM2·5 caused an estimated 0·48 (95% CI 0·34-0·60) million premature deaths and 18·2 (13·4-23·0) million years of life lost in 2018 worldwide, corresponding to an annual welfare loss of US$395 (290-500) billion due to premature deaths. The 5 μg/m3 target of concentration of PM2·5 in the air quality guidelines set by WHO, if reached in 2050, was estimated to reduce antibiotic resistance by 16·8% (95% CI 15·3-18·3) and avoid 23·4% (21·2-25·6) of premature deaths attributable to antibiotic resistance, equivalent to a saving of $640 (580-671) billion. INTERPRETATION This analysis is the first to describe the association between PM2·5 and clinical antibiotic resistance globally. Results provide new pathways for antibiotic-resistance control from an environmental perspective. FUNDING National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities, Zhejiang University Global Partnership Fund, and China Postdoctoral Science Foundation.
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Affiliation(s)
- Zhenchao Zhou
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xinyi Shuai
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zejun Lin
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xi Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Baojing Gu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
| | - Hong Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, Zhejiang University, Hangzhou, China; Zhejiang International Science and Technology Cooperation Base of Environmental Pollution and Ecological Health, Hangzhou, China.
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Sajeev S, Hamza M, Rajan V, Vijayan A, Sivaraman GK, Shome BR, Holmes MA. Resistance profiles and genotyping of extended-spectrum beta-lactamase (ESBL) -producing and non-ESBL-producing E. coli and Klebsiella from retail market fishes. Infect Genet Evol 2023:105446. [PMID: 37245778 DOI: 10.1016/j.meegid.2023.105446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 04/13/2023] [Accepted: 05/01/2023] [Indexed: 05/30/2023]
Abstract
Studies on antimicrobial resistance (AMR) profiles and epidemiological affirmation for AMR transmission are limited in fisheries and aquaculture settings. Since 2015, based on Global Action Plan on AMR by World Health Organization (WHO) and World Organization for Animal Health (OIE), several initiatives have been under taken to enhance the knowledge, skills and capacity to establish AMR trends through surveillance and strengthening of epidemiological evidence. The focus of this study was to determine the prevalence of antimicrobial resistance (AMR), its resistance profiles and molecular characterization with respect to phylogroups, antimicrobial resistance genes (ARGs), virulence genes (VGs), quaternary ammonium compounds resistance (QAC) genes and plasmid typing in retail market fishes. Pulse field gel electrophoresis (PFGE) to understand the genetic lineage of the two most important Enterobacteriaceae members, E. coli and Klebsiella sp. was performed. 94 fish samples were collected from three different sites viz., Silagrant (S1), Garchuk (S2) and North Guwahati Town Committee (NGTC) Region (S3) in Guwahati, Assam. Out of the 113 microbial isolates from the fish samples, 45 (39.82%) were E. coli; 23 (20.35%) belonged to Klebsiella genus. Among E. coli, 48.88% (n = 22) of the isolates were alerted by the BD Phoenix M50 instrument as ESBL, 15.55% (n = 7) as PCP and 35.55% (n = 16) as non-ESBL. E. coli (39.82%) was the most prevalent pathogen among the Enterobacteriaceae members screened and showed resistance to ampicillin (69%) followed by cefazoline (64%), cefotaxime (49%) and piperacillin (49%). In the present study, 66.66% of E. coli and 30.43% of Klebsiella sp. were categorized as multi drug resistance (MDR) bacteria. CTX-M-gp-1, with CTX-M-15 variant (47%), was the most widely circulating beta-lactamase gene, while other ESBL genes blaTEM (7%), blaSHV (2%) and blaOXA-1-like (2%) were also identified in E. coli. Out of the 23 isolates of Klebsiella, 14(60.86%) were ampicillin (AM)-resistant (11(47.82%) K. oxytoca, 3(13.04%) K. aerogenes), whereas 8(34.78%) isolates of K. oxytoca showed intermediate resistance to AM. All Klebsiella isolates were susceptible to AN, SCP, MEM and TZP, although two K. aerogenes were resistant to imipenem. DHA and LAT genes were detected, respectively, in 7(16%) and 1(2%) of the E. coli strains while a single K. oxytoca (4.34%) isolate carried MOX, DHA and blaCMY-2 genes. The fluoroquinolone resistance genes identified in E. coli included qnrB (71%), qnrS (84%), oqxB (73%) and aac(6)-Ib-cr (27%); however, in Klebsiella, these genes, respectively, had a prevalence of 87%, 26%, 74% and 9%. The E. coli isolates belonged to phylogroup A(47%), B1(33%) and D(14%). All of the 22(100%) ESBL E. coli had chromosome-mediated disinfectant resistance genes viz., ydgE, ydgF, sugE(c), mdfA while 82% of ESBL E. coli had emrE. Among the non-ESBL E. coli isolates, 87% of them showed the presence of ydgE, ydgF and sugE(c) genes, while 78% of the isolates had mdfA and 39% had emrE genes respectively. 59% of the ESBL and 26% of the non-ESBL E. coli had showed the presence of qacEΔ1. The sugE(p) was present in 27% of the ESBL-producing E. coli and in 9% of non-ESBL isolates. Out of the 3 ESBL-producing Klebsiella isolates, 2(66.66%) K. oxytoca isolates were found harboring plasmid-mediated qacEΔ1 gene while one (33.33%) K. oxytoca isolate had sugE(p) gene. IncFI was the most prevalent plasmid type detected in the isolates studied, with A/C (18%), P (14%), X, Y (9% each) and I1-Iγ (14%, 4%). 50% (n = 11) of the ESBL and 17% (n = 4) of the non-ESBL E. coli isolates harboured IncFIB and 45% (n = 10) ESBL and one (4.34%) non-ESBL E. coli isolates harboured IncFIA. Dominance of E. coli over other Enterobacterales and diverse phylogenetic profiles of E. coli and Klebsiella sp. suggests the possibility of contamination and this may be due to compromised hygienic practices along the supply chain and contamination of aquatic ecosystem. Continuous surveillance in domestic markets must be a priority in addressing antimicrobial resistance in fishery settings and to identify any unwarranted epidemic clones of E. coli and Klebsiella that can challenge public health sector.
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Affiliation(s)
- Sudha Sajeev
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India
| | - Muneeb Hamza
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India
| | - Vineeth Rajan
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India
| | - Ardhra Vijayan
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India
| | - Gopalan Krishnan Sivaraman
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India.
| | - Bibek R Shome
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, UK
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Bartlett H, Balmford A, Holmes MA, Wood JLN. Advancing the quantitative characterization of farm animal welfare. Proc Biol Sci 2023; 290:20230120. [PMID: 36946112 PMCID: PMC10031399 DOI: 10.1098/rspb.2023.0120] [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] [Indexed: 03/23/2023] Open
Abstract
Animal welfare is usually excluded from life cycle assessments (LCAs) of farming systems because of limited consensus on how to measure it. Here, we constructed several LCA-compatible animal-welfare metrics and applied them to data we collected from 74 diverse breed-to-finish systems responsible for 5% of UK pig production. Some aspects of metric construction will always be subjective, such as how different aspects of welfare are aggregated, and what determines poor versus good welfare. We tested the sensitivity of individual farm rankings, and rankings of those same farms grouped by label type (memberships of quality-assurance schemes or product labelling), to a broad range of approaches to metric construction. We found farms with the same label types clustered together in rankings regardless of metric choice, and there was broad agreement across metrics on the rankings of individual farms. We found woodland and Organic systems typically perform better than those with no labelling and Red tractor labelling, and that outdoor-bred and outdoor-finished systems perform better than indoor-bred and slatted-finished systems, respectively. We conclude that if our goal is to identify relatively better and worse farming systems for animal welfare, exactly how LCA welfare metrics are constructed may be less important than commonly perceived.
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Affiliation(s)
- Harriet Bartlett
- Department of Zoology, University of Cambridge, Cambridge CB2 1TN, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB2 1TN, UK
| | - Andrew Balmford
- Department of Zoology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB2 1TN, UK
| | - James L N Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB2 1TN, UK
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Ba X, Matuszewska M, Kalmar L, Fan J, Zou G, Corander D, Raisen CL, Li S, Li L, Weinert LA, Tucker AW, Grant AJ, Zhou R, Holmes MA. High-Throughput Mutagenesis Reveals a Role for Antimicrobial Resistance- and Virulence-Associated Mobile Genetic Elements in Staphylococcus aureus Host Adaptation. Microbiol Spectr 2023; 11:e0421322. [PMID: 36815781 PMCID: PMC10101091 DOI: 10.1128/spectrum.04213-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex 398 (CC398) is the dominant livestock-associated (LA) MRSA lineage in European livestock and an increasing cause of difficult-to-treat human disease. LA-CC398 MRSA evolved from a diverse human-associated methicillin-sensitive population, and this transition from humans to livestock was associated with three mobile genetic elements (MGEs). In this study, we apply transposon-directed insertion site sequencing (TraDIS), a high-throughput transposon mutagenesis approach, to investigate genetic signatures that contribute to LA-CC398 causing disease in humans. We identified 26 genes associated with LA-CC398 survival in human blood and 47 genes in porcine blood. We carried out phylogenetic reconstruction on 1,180 CC398 isolates to investigate the genetic context of all identified genes. We found that all genes associated with survival in human blood were part of the CC398 core genome, while 2/47 genes essential for survival in porcine blood were located on MGEs. Gene SAPIG0966 was located on the previously identified Tn916 transposon carrying a tetracycline resistance gene, which has been shown to be stably inherited within LA-CC398. Gene SAPIG1525 was carried on a phage element, which in part, matched phiSa2wa_st1, a previously identified bacteriophage carrying the Panton-Valentine leucocidin (PVL) virulence factor. Gene deletion mutants constructed in two LA-CC398 strains confirmed that the SAPIG0966 carrying Tn916 and SAPIG1525 were important for CC398 survival in porcine blood. Our study shows that MGEs that carry antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for host adaptation. IMPORTANCE CC398 is the dominant type of methicillin-resistant Staphylococcus aureus (MRSA) in European livestock and a growing cause of human infections. Previous studies have suggested MRSA CC398 evolved from human-associated methicillin-sensitive Staphylococcus aureus and is capable of rapidly readapting to human hosts while maintaining antibiotic resistance. Using high-throughput transposon mutagenesis, our study identified 26 and 47 genes important for MRSA CC398 survival in human and porcine blood, respectively. Two of the genes important for MRSA CC398 survival in porcine blood were located on mobile genetic elements (MGEs) carrying resistance or virulence genes. Our study shows that these MGEs carrying antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for blood infection and host adaptation.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lajos Kalmar
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jingyan Fan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University College of Veterinary Medicine, Wuhan, China
| | - Geng Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University College of Veterinary Medicine, Wuhan, China
| | - Desirée Corander
- Department of Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Claire L. Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Shaowen Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University College of Veterinary Medicine, Wuhan, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University College of Veterinary Medicine, Wuhan, China
- Cooperative Innovation Centre of Sustainable Pig Production, Wuhan, China
- International Research Centre for Animal Diseases (MOST), Wuhan, China
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alexander W. Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Andrew J. Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University College of Veterinary Medicine, Wuhan, China
- Cooperative Innovation Centre of Sustainable Pig Production, Wuhan, China
- International Research Centre for Animal Diseases (MOST), Wuhan, China
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Zhou Z, Shuai X, Lin Z, Meng L, Ba X, Holmes MA, Chen H. Short-term inhalation exposure evaluations of airborne antibiotic resistance genes in environments. J Environ Sci (China) 2022; 122:62-71. [PMID: 35717091 DOI: 10.1016/j.jes.2021.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 08/27/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance is a sword of Damocles that hangs over humans. In regards to airborne antibiotic resistance genes (AARGs), critical knowledge gaps still exist in the identification of hotspots and quantification of exposure levels in different environments. Here, we have studied the profiles of AARGs, mobile genetic elements (MGEs) and bacterial communities in various atmospheric environments by high throughput qPCR and 16S rRNA gene sequencing. We propose a new AARGs exposure dose calculation that uses short-term inhalation (STI). Swine farms and hospitals were high-risk areas where AARGs standardised abundance was more abundant than suburbs and urban areas. Additionally, resistance gene abundance in swine farm worker sputum was higher than that in healthy individuals in other environments. The correlation between AARGs with MGEs and bacteria was strong in suburbs but weak in livestock farms and hospitals. STI exposure analysis revealed that occupational intake of AARGs (via PM10) in swine farms and hospitals were 110 and 29 times higher than in suburbs, were 1.5 × 104, 5.6 × 104 and 5.1 × 102 copies, i.e., 61.9%, 75.1% and 10.7% of the overall daily inhalation intake, respectively. Our study comprehensively compares environmental differences in AARGs to identify high-risk areas, and forwardly proposes the STI exposure dose of AARGs to guide risk assessment.
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Affiliation(s)
- Zhenchao Zhou
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 9DA , UK
| | - Xinyi Shuai
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zejun Lin
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lingxuan Meng
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 9DA , UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 9DA , UK
| | - Hong Chen
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Huber C, Wolf SA, Ziebuhr W, Holmes MA, Assmann J, Lübke-Becker A, Thürmer A, Semmler T, Brombach J, Bethe A, Bischoff M, Wieler LH, Epping L, Walther B. How to survive pig farming: Mechanism of SCC mec element deletion and metabolic stress adaptation in livestock-associated MRSA. Front Microbiol 2022; 13:969961. [PMID: 36504815 PMCID: PMC9728531 DOI: 10.3389/fmicb.2022.969961] [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: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
Previous research on methicillin susceptible Staphylococcus aureus (MSSA) belonging to livestock-associated (LA-) sequence type (ST) 398, isolated from pigs and their local surroundings, indicated that differences between these MSSA and their methicillin resistant predecessors (MRSA) are often limited to the absence of the staphylococcal cassette chromosome mec (SCCmec) and few single nucleotide polymorphisms. So far, our understanding on how LA-MRSA endure the environmental conditions associated with pig-farming as well as the putative impact of this particular environment on the mobilisation of SCCmec elements is limited. Thus, we performed in-depth genomic and transcriptomic analyses using the LA-MRSA ST398 strain IMT38951 and its methicillin susceptible descendant. We identified a mosaic-structured SCCmec region including a putative replicative SCCmecVc which is absent from the MSSA chromosome through homologous recombination. Based on our data, such events occur between short repetitive sequences identified within and adjacent to two distinct alleles of the large cassette recombinase genes C (ccrC). We further evaluated the global transcriptomic response of MRSA ST398 to particular pig-farm associated conditions, i.e., contact with host proteins (porcine serum) and a high ammonia concentration. Differential expression of global regulators involved in stress response control were identified, i.e., ammonia-induced alternative sigma factor B-depending activation of genes for the alkaline shock protein 23, the heat shock response and the accessory gene regulator (agr)-controlled transcription of virulence factors. Exposure to serum transiently induced the transcription of distinct virulence factor encoding genes. Transcription of genes reported for mediating the loss of methicillin resistance, especially ccrC, was not significantly different compared to the unchallenged controls. We concluded that, from an evolutionary perspective, bacteria may save energy by incidentally dismissing a fully replicative SCCmec element in contrast to the induction of ccr genes on a population scale. Since the genomic SCCmec integration site is a hot-spot of recombination, occasional losses of elements of 16 kb size may restore capacities for the uptake of foreign genetic material. Subsequent spread of resistance, on the other hand, might depend on the autonomous replication machinery of the deleted SCCmec elements that probably enhance chances for reintegration of SCCmec into susceptible genomes by mere multiplication.
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Affiliation(s)
- Charlotte Huber
- Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, Berlin, Germany
| | - Silver A. Wolf
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Wilma Ziebuhr
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Julia Assmann
- Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Andrea Thürmer
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Julian Brombach
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Lothar H. Wieler
- Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, Berlin, Germany,*Correspondence: Birgit Walther,
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Sajeev S, Hamza M, Sivaraman GK, Ghatak S, Ojha R, Mendem SK, Murugesan D, Raisen C, Shome BR, Holmes MA. Genomic insights of beta-lactamase producing Klebsiella quasipneumoniae subsp. similipneumoniae belonging to sequence type 1699 from retail market fish, India. Arch Microbiol 2022; 204:454. [PMID: 35781844 DOI: 10.1007/s00203-022-03071-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/12/2021] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022]
Abstract
Klebsiella quasipneumoniae is a recently described species and often misidentified as Klebsiella pneumoniae. Here, we report the genomic characterization of Klebsiella quasipneumoniae subsp. similipneumoniae (India238 strain) isolated from fish. The annotated genome acknowledged the presence of blaCTX-M-15, blaOKP-B-1, fosA5, oqxAB and virulence genes. The strain with ST1699 and serotypes KL52 and OL103 also harboured insertion sequences (ISs): ISKpn26 and ISEc9. Three complete phage genomes were identified in contigs 1 and 6 of the bacterial genome, enhancing the prospects of genome manipulation. The study highlights the pitfall of conventional microbiological identification methods to distinguish K. pneumoniae and K. quasipneumoniae. This is the first Indian study documenting the incidence of extended-spectrum beta-lactamase (ESBL)-producing K. quasipneumoniae subsp. similipneumoniae from a non-clinical environment, equipped with virulomes and associated mobile genetic elements. Given that fish can act as a potential vector for transmission of antimicrobial resistance genes, our findings have paramount importance on human health.
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Affiliation(s)
- Sudha Sajeev
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, Kerala, India
| | - Muneeb Hamza
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, Kerala, India
| | - Gopalan Krishnan Sivaraman
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, Kerala, India.
| | - Sandeep Ghatak
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, India.
| | - Rakshit Ojha
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Suresh Kumar Mendem
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Devi Murugesan
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Claire Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Bibek R Shome
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Ba X, Raisen CL, Zhou ZC, Harrison EM, Peacock SJ, Holmes MA. Simultaneously screening for methicillin-resistant Staphylococcus aureus and its susceptibility to potentiated penicillins. J Med Microbiol 2022; 71. [PMID: 35867942 DOI: 10.1099/jmm.0.001562] [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] [Indexed: 11/18/2022] Open
Abstract
Introduction. We recently revealed that a significant proportion of clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates are susceptible to pencillins and clavulanic acid (potentiated penicillins), including widely available combinations such as co-amoxiclav. These isolates also showed increased susceptibility to oxacillin on Iso-Sensitest Agar (ISA).Hypothesis/Gap Statement. The increased susceptibility to oxacillin displayed on ISA by these MRSA isolates may be used to distinguish them from the resistant ones.Aim. We aimed to develop a method to simultaneously screen a S. aureus clinical isolate for its susceptibility to methicillin and potentiated penicillins.Methodology. A double-disc diffusion method using 10 µg cefoxitin and 1 µg oxacillin discs on ISA was developed and tested against a panel of 120 whole genome-sequenced MRSA isolates. The sensitivity of the method was compared with that of previously published genotypic and phenotypic methods. In addition, double-disc diffusion was performed for all isolates on Müller-Hinton agar (MHA) following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) protocol.Results. All isolates (120/120) were reconfirmed to be phenotypically MRSA, as indicated by the result of cefoxitin disc diffusion testing. All isolates (40/40) that had a pencillins and clavulanic acid (Pen-Clav)-resistant genotype were not inhibited by oxacillin, while 77/80 (96.3 %) isolates that had a Pen-Clav-susceptible genotype were inhibited by oxacillin on ISA. The results also showed that the EUCAST method using MHA correctly identified all isolates as MRSA but failed to distinguish the Pen-Clav-susceptible isolates from the Pen-Clav-resistant isolates.Conclusions. This double-disc diffusion method using ISA could be used to accurately screen for clinical MRSA isolates and determine their susceptibility to Pen-Clav simultaneously, rapidly identifying MRSA infections that might be suitable for treatment with potentiated penicillins.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Claire L Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Zhen-Chao Zhou
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Institute of Environmental Technology College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Ewan M Harrison
- Wellcome Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Matuszewska M, Murray GGR, Ba X, Wood R, Holmes MA, Weinert LA. Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA. eLife 2022; 11:74819. [PMID: 35762208 PMCID: PMC9239682 DOI: 10.7554/elife.74819] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 10/18/2021] [Accepted: 05/23/2022] [Indexed: 01/11/2023] Open
Abstract
Mobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here, we fully characterise the evolutionary dynamics of these MGEs using a collection of 1180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline, and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398 have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised. Antibiotic-resistant infections are a growing threat to human health. In 2019, these hard-to-treat infections resulted in 4.95 million deaths making them the third leading cause of death that year. Excessive use of antibiotics in humans is likely driving the emergence of drug-resistant bacteria. But there is a concern that use of antibiotics on livestock farms is also contributing. A type of bacteria traced back to livestock is a growing cause of human infections that do not respond to treatment with the antibiotic methicillin in Europe. It is called livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA). Bacteria can share genes that make them drug resistant or more deadly. These genes are often carried on mobile genetic elements that promote their movement from one bacterial cell to another. The most common type of LA-MRSA in Europe is clonal-complex 398 (CC398). It has two mobile genetic elements carrying antibiotic-resistance genes, but generally lacks a mobile genetic element that helps the bacterium escape the human immune system. Learning more about how LA-MRSA acquired these genetic changes may help scientists develop better strategies to protect the public. Matuszewska, Murray et al. analyzed the genomes of more than 1,000 samples of CC398 collected from humans, pigs and 13 other animal species in 28 countries over 27 years. They used this data to reconstruct the bacteria’s evolutionary history. Matuszewska, Murray et al. show that two mobile elements containing antibiotic resistance genes in CC398 were gained decades ago. One is more than 50 years old and was likely acquired around the time antibiotic use in livestock became common. While most CC398 in livestock do not have a mobile element that helps LA-MRSA evade the human immune system, they often gain it when they infect humans. This leads to highly drug-resistant human MRSA infections. The results of this study suggest that LA-MRSA is a serious threat to human health. The resistance of this bacterium has persisted for decades, spreading across different livestock species and different countries. These drug-resistant bacteria in livestock readily infect humans. Current efforts to reduce antibiotic use in farms may take decades to mitigate these risks. Additionally, the ban on zinc-oxide use on livestock in the European Union (coming into force June 2022) may not help reduce LA-MRSA, because the genes conferring resistance to bacteria and zinc treatment are not always linked.
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Affiliation(s)
- Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Rhiannon Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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16
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Bartlett H, Holmes MA, Petrovan SO, Williams DR, Wood JLN, Balmford A. Understanding the relative risks of zoonosis emergence under contrasting approaches to meeting livestock product demand. R Soc Open Sci 2022; 9:211573. [PMID: 35754996 PMCID: PMC9214290 DOI: 10.1098/rsos.211573] [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] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/30/2022] [Indexed: 05/03/2023]
Abstract
It has been argued that intensive livestock farming increases the risk of pandemics of zoonotic origin because of long-distance livestock movements, high livestock densities, poor animal health and welfare, low disease resistance and low genetic diversity. However, data on many of these factors are limited, and analyses to date typically ignore how land use affects emerging infectious disease (EID) risks, and how these risks might vary across systems with different yields (production per unit area). Extensive, lower yielding practices typically involve larger livestock populations, poorer biosecurity, more workers and more area under farming, resulting in different, but not necessarily lower, EID risks than higher yielding systems producing the same amount of food. To move this discussion forward, we review the evidence for each of the factors that potentially link livestock production practices to EID risk. We explore how each factor might vary with yield and consider how overall risks might differ across a mix of production systems chosen to reflect in broad terms the current livestock sector at a global level and in hypothetical low- and high-yield systems matched by overall level of production. We identify significant knowledge gaps for all potential risk factors and argue these shortfalls in understanding mean we cannot currently determine whether lower or higher yielding systems would better limit the risk of future pandemics.
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Affiliation(s)
- Harriet Bartlett
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Silviu O. Petrovan
- Department of Zoology, University of Cambridge, Cambridge, UK
- BioRISC (Biosecurity Research Initiative at St Catharine's), St Catharine's College, Cambridge, UK
| | - David R. Williams
- Sustainability Research Institute, School of Earth and Environment, University of Leeds, Leeds, UK
| | - James L. N. Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andrew Balmford
- Department of Zoology, University of Cambridge, Cambridge, UK
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17
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Eltholth M, Govindaraj G, Das B, Shanabhoga MB, Swamy HM, Thomas A, Cole J, Shome BR, Holmes MA, Moran D. Factors Influencing Antibiotic Prescribing Behavior and Understanding of Antimicrobial Resistance Among Veterinarians in Assam, India. Front Vet Sci 2022; 9:864813. [PMID: 35558894 PMCID: PMC9087579 DOI: 10.3389/fvets.2022.864813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
This study investigates factors influencing veterinarians' antibiotic prescribing behaviors and their understanding of antimicrobial resistance (AMR). The study used a telephone survey of 50 veterinarians conducted in five districts in Assam state, India. The survey sought information on the most prevalent animal diseases, veterinarians' awareness of potential preventive measures, including factors determining antimicrobial prescribing; the types of antimicrobials used for different health conditions in different species, and possible options to reduce antimicrobial use (AMU). The majority (86%) of respondents worked for the government, 98% reported having no written policy for the use of veterinary health products, and 58% have no on-site diagnostic facilities. Ceftriaxone, Enrofloxacin, and Oxytetracycline were the antibiotics (ABX) most frequently prescribed, by 76, 68, and 54% of veterinarians, respectively. These ABX were prescribed mainly for respiratory health problems and mastitis in cattle, and gastrointestinal infections in buffaloes, sheep, goat, and pigs. Severity of clinical symptoms, economic status of the livestock owner, and withdrawal period for ABX were ranked as very important factors for giving ABX. Less than two thirds (64%) were aware of the government ban for Colistin and only 2% were aware of a national plan for AMR. This study highlighted that ABX prescription is mostly based on tentative diagnosis given the lack of diagnostic facilities in most veterinary clinics. There is a need to enhance veterinary healthcare and to improve communication between policy makers and field veterinarians and, importantly, a need to disseminate clear prescribing guidelines on prudent AMU.
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Affiliation(s)
- Mahmoud Eltholth
- Global Academy of Agriculture and Food Security, The Royal (Dick) School of Veterinary Studies and the Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Hygiene and Preventive Medicine Department, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Shaikh, Egypt
- *Correspondence: Mahmoud Eltholth
| | - Gurrappanaidu Govindaraj
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI) Ramagondanahalli, Bangalore, India
| | - Banani Das
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI) Ramagondanahalli, Bangalore, India
| | - M. B. Shanabhoga
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI) Ramagondanahalli, Bangalore, India
| | - H. M. Swamy
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI) Ramagondanahalli, Bangalore, India
| | - Abin Thomas
- Global Academy of Agriculture and Food Security, The Royal (Dick) School of Veterinary Studies and the Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jennifer Cole
- Department of Health Studies, Royal Holloway, University of London, Egham, United Kingdom
| | - Bibek R. Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI) Ramagondanahalli, Bangalore, India
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Dominic Moran
- Global Academy of Agriculture and Food Security, The Royal (Dick) School of Veterinary Studies and the Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
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18
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Alves L, de Novais FJ, da Silva AN, Araujo MS, Bernardino T, Osowski GV, Zanella R, Lee Settles M, Holmes MA, Fukumasu H, Ruiz VLDA, Zanella AJ. Vaginal Microbiota Diversity in Response to Lipopolysaccharide in Gilts Housed Under Three Housing Systems. Front Genet 2022; 13:836962. [PMID: 35464863 PMCID: PMC9024362 DOI: 10.3389/fgene.2022.836962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/04/2022] [Indexed: 12/13/2022] Open
Abstract
The United Kingdom and European Union have banned crates for pregnant sows. However, animals are kept in a restrictive environment for up to four weeks after mating, leading to stress and different responses of the animals’ immune system. Here, we used vaginal flushing of gilts to investigate whether housing systems or an experimental inflammatory challenge with lipopolysaccharide (LPS) can modify the gilt vaginal microbiome. Alpha-diversity indices showed differences in the microbiota of gilts housed under different systems (q = 0.04). Shannon alpha-diversity richness was higher in gilts group-housed in pens than in gilts housed in crates (q = 0.035), but not higher than in other groups. The relative abundance of the operational taxonomic unit (OTU) (q < 0.05) revealed specific differences in housing systems before a LPS or saline (SAL control) challenge. We found different abundances in taxa of Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria in gilts housed in the different systems before challenge. After the LPS challenge, significant differences were detected in the relative abundance of OTUs (q < 0.05) for the LPS-challenged group compared with SAL animals for each housing system. The phylum Staphylococcus showed higher abundance among the LPS-challenged gilts than in SAL-challenged animals. Furthermore, Enterobacter was more abundant in the LPS-challenged gilts housed in crates than in SAL-challenged gilts housed in crates. Streptococcus suis, Conchiformibius, Globicatella and Actinobacillus were more abundant in LPS-challenged gilts in indoor group housing than in SAL gilts in the same housing system. Gilts kept outdoors did not show changes in vaginal microbiota after an LPS challenge. Gilts housed in crates showed clinical signs of urogenital infection, whereas gilts housed outdoors and in indoor group housing did not. The relationship between environment, immune response, and microbiota suggested that animals in a poor environments experience difficulties responding to a challenge and their vaginal microbiota is altered as a consequence, with decreased richness of normal vaginal microbiota, and increased opportunistic bacteria. Welfare indicators measured by gilts’ responses to housing systems however, do not fully explain mechanisms associated with the unique signature in vaginal microbiota encountered in the different housing systems.
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Affiliation(s)
- Luana Alves
- Department of Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil
| | - Francisco José de Novais
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Arthur Nery da Silva
- Department of Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil
| | - Michelle Silva Araujo
- Department of Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil
| | - Thiago Bernardino
- Department of Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil.,Graduation Program in One Health, University of Santo Amaro, São Paulo, Brazil
| | - Germana Vizzotto Osowski
- Department of Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil
| | - Ricardo Zanella
- Faculty of Agronomy and Veterinary Medicine, University of Passo Fundo, Passo Fundo, Brazil
| | - Matthew Lee Settles
- Director of Bioinformatics Core, UC Davis Genome Center, Davis, CA, United States
| | - Mark A Holmes
- Department of Veterinary Medicine, School of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Heidge Fukumasu
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Vera Letticie de Azevedo Ruiz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Adroaldo José Zanella
- Department of Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil
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19
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Zou G, Matuszewska M, Jia M, Zhou J, Ba X, Duan J, Zhang C, Zhao J, Tao M, Fan J, Zhang X, Jin W, Cui T, Zeng X, Jia M, Qian X, Huang C, Zhuo W, Yao Z, Zhang L, Li S, Li L, Huang Q, Wu B, Chen H, Tucker AW, Grant AJ, Holmes MA, Zhou R. A Survey of Chinese Pig Farms and Human Healthcare Isolates Reveals Separate Human and Animal Methicillin-Resistant Staphylococcus aureus Populations. Adv Sci (Weinh) 2022; 9:e2103388. [PMID: 34894204 PMCID: PMC8811834 DOI: 10.1002/advs.202103388] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/10/2021] [Indexed: 06/14/2023]
Abstract
There has been increasing concern that the overuse of antibiotics in livestock farming is contributing to the burden of antimicrobial resistance in people. Farmed animals in Europe and North America, particularly pigs, provide a reservoir for livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA ST398 lineage) found in people. This study is designed to investigate the contribution of MRSA from Chinese pig farms to human infection. A collection of 483 MRSA are isolated from 55 farms and 4 hospitals in central China, a high pig farming density area. CC9 MRSA accounts for 97.2% of all farm isolates, but is not present in hospital isolates. ST398 isolates are found on farms and hospitals, but none of them formed part of the "LA-MRSA ST398 lineage" present in Europe and North America. The hospital ST398 MRSA isolate form a clade that is clearly separate from the farm ST398 isolates. Despite the presence of high levels of MRSA found on Chinese pig farms, the authors find no evidence of them spilling over to the human population. Nevertheless, the ST398 MRSA obtained from hospitals appear to be part of a widely distributed lineage in China. The new animal-adapted ST398 lineage that has emerged in China is of concern.
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Affiliation(s)
- Geng Zou
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Marta Matuszewska
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB3 0ESUK
| | - Ming Jia
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Jianwei Zhou
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Xiaoliang Ba
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB3 0ESUK
| | - Juan Duan
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | | | - Jian Zhao
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Meng Tao
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Jingyan Fan
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | | | | | | | | | - Min Jia
- Wuhan First HospitalWuhan430014China
| | | | - Chao Huang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Wenxiao Zhuo
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Zhiming Yao
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Lijun Zhang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Shaowen Li
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Lu Li
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
- Cooperative Innovation Center of Sustainable Pig ProductionWuhan430070China
- International Research Center for Animal Diseases (MOST)Wuhan430070China
| | - Qi Huang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
- Cooperative Innovation Center of Sustainable Pig ProductionWuhan430070China
- International Research Center for Animal Diseases (MOST)Wuhan430070China
| | - Bin Wu
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
- Cooperative Innovation Center of Sustainable Pig ProductionWuhan430070China
- International Research Center for Animal Diseases (MOST)Wuhan430070China
| | - Huanchun Chen
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
- Cooperative Innovation Center of Sustainable Pig ProductionWuhan430070China
- International Research Center for Animal Diseases (MOST)Wuhan430070China
| | | | - Andrew J. Grant
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB3 0ESUK
| | - Mark A. Holmes
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB3 0ESUK
| | - Rui Zhou
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
- Cooperative Innovation Center of Sustainable Pig ProductionWuhan430070China
- International Research Center for Animal Diseases (MOST)Wuhan430070China
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20
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Larsen J, Raisen CL, Ba X, Sadgrove NJ, Padilla-González GF, Simmonds MSJ, Loncaric I, Kerschner H, Apfalter P, Hartl R, Deplano A, Vandendriessche S, Černá Bolfíková B, Hulva P, Arendrup MC, Hare RK, Barnadas C, Stegger M, Sieber RN, Skov RL, Petersen A, Angen Ø, Rasmussen SL, Espinosa-Gongora C, Aarestrup FM, Lindholm LJ, Nykäsenoja SM, Laurent F, Becker K, Walther B, Kehrenberg C, Cuny C, Layer F, Werner G, Witte W, Stamm I, Moroni P, Jørgensen HJ, de Lencastre H, Cercenado E, García-Garrote F, Börjesson S, Hæggman S, Perreten V, Teale CJ, Waller AS, Pichon B, Curran MD, Ellington MJ, Welch JJ, Peacock SJ, Seilly DJ, Morgan FJE, Parkhill J, Hadjirin NF, Lindsay JA, Holden MTG, Edwards GF, Foster G, Paterson GK, Didelot X, Holmes MA, Harrison EM, Larsen AR. Emergence of methicillin resistance predates the clinical use of antibiotics. Nature 2022; 602:135-141. [PMID: 34987223 PMCID: PMC8810379 DOI: 10.1038/s41586-021-04265-w] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [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: 05/12/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022]
Abstract
The discovery of antibiotics more than 80 years ago has led to considerable improvements in human and animal health. Although antibiotic resistance in environmental bacteria is ancient, resistance in human pathogens is thought to be a modern phenomenon that is driven by the clinical use of antibiotics1. Here we show that particular lineages of methicillin-resistant Staphylococcus aureus-a notorious human pathogen-appeared in European hedgehogs in the pre-antibiotic era. Subsequently, these lineages spread within the local hedgehog populations and between hedgehogs and secondary hosts, including livestock and humans. We also demonstrate that the hedgehog dermatophyte Trichophyton erinacei produces two β-lactam antibiotics that provide a natural selective environment in which methicillin-resistant S. aureus isolates have an advantage over susceptible isolates. Together, these results suggest that methicillin resistance emerged in the pre-antibiotic era as a co-evolutionary adaptation of S. aureus to the colonization of dermatophyte-infected hedgehogs. The evolution of clinically relevant antibiotic-resistance genes in wild animals and the connectivity of natural, agricultural and human ecosystems demonstrate that the use of a One Health approach is critical for our understanding and management of antibiotic resistance, which is one of the biggest threats to global health, food security and development.
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Affiliation(s)
- Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark.
| | - Claire L Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | | | | | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Ariane Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
| | - Stien Vandendriessche
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
- Laboratory for Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Hulva
- Department of Zoology, Charles University, Prague, Czech Republic
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Maiken C Arendrup
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus K Hare
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Céline Barnadas
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Marc Stegger
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Robert L Skov
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Petersen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Øystein Angen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sophie L Rasmussen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Wildlife Conservation Research Unit (WildCRU), Department of Zoology, University of Oxford, Tubney, UK
| | - Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Laura J Lindholm
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Frederic Laurent
- Bacteriology Department and French National Reference Center for Staphylococci, Hospices Civils de Lyon, University of Lyon, Lyon, France
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Birgit Walther
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, Berlin, Germany
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus-Liebig University Giessen, Giessen, Germany
| | - Christiane Cuny
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Franziska Layer
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Wolfgang Witte
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | | | - Paolo Moroni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
- Quality Milk Production Services, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA
| | | | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB NOVA, Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Emilia Cercenado
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Fernando García-Garrote
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
- Servicio de Microbiología, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - Stefan Börjesson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Sara Hæggman
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | - Andrew S Waller
- Animal Health Trust, Newmarket, UK
- Intervacc AB, Stockholm, Stockholm, Sweden
- Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bruno Pichon
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Matthew J Ellington
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - David J Seilly
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Fiona J E Morgan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nazreen F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jodi A Lindsay
- Institute of Infection and Immunity, St George's, University of London, London, UK
| | | | - Giles F Edwards
- Scottish MRSA Reference Laboratory, NHS Greater Glasgow and Clyde, Stobhill Hospital, Glasgow, UK
| | | | - Gavin K Paterson
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Warwick, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Anders R Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
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21
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Crestani C, Forde TL, Lycett SJ, Holmes MA, Fasth C, Persson-Waller K, Zadoks RN. The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps? Microb Genom 2021; 7. [PMID: 34486971 PMCID: PMC8715428 DOI: 10.1099/mgen.0.000648] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Group B Streptococcus (GBS; Streptococcus agalactiae) is a major neonatal and opportunistic bacterial pathogen of humans and an important cause of mastitis in dairy cattle with significant impacts on food security. Following the introduction of mastitis control programmes in the 1950s, GBS was nearly eradicated from the dairy industry in northern Europe, followed by re-emergence in the 21st century. Here, we sought to explain this re-emergence based on short and long read sequencing of historical (1953–1978; n=44) and contemporary (1997–2012; n=76) bovine GBS isolates. Our data show that a globally distributed bovine-associated lineage of GBS was commonly detected among historical isolates but never among contemporary isolates. By contrast, tetracycline resistance, which is present in all major GBS clones adapted to humans, was commonly and uniquely detected in contemporary bovine isolates. These observations provide evidence for strain replacement and suggest a human origin of newly emerged strains. Three novel GBS plasmids were identified, including two showing >98 % sequence similarity with plasmids from Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis, which co-exist with GBS in the human oropharynx. Our findings support introduction of GBS into the dairy population due to human-to-cattle jumps on multiple occasions and demonstrate that reverse zoonotic transmission can erase successes of animal disease control campaigns.
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Affiliation(s)
- Chiara Crestani
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Campus, Glasgow G61 1QH, UK
| | - Taya L Forde
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Campus, Glasgow G61 1QH, UK
| | - Samantha J Lycett
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge CB3 0ES, UK
| | - Charlotta Fasth
- National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden
| | | | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Campus, Glasgow G61 1QH, UK.,Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK.,School of Veterinary Science, University of Sydney, Werombi Road, Camden, NSW 2570, Australia
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22
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Crisci MA, Chen LX, Devoto AE, Borges AL, Bordin N, Sachdeva R, Tett A, Sharrar AM, Segata N, Debenedetti F, Bailey M, Burt R, Wood RM, Rowden LJ, Corsini PM, van Winden S, Holmes MA, Lei S, Banfield JF, Santini JM. Closely related Lak megaphages replicate in the microbiomes of diverse animals. iScience 2021; 24:102875. [PMID: 34386733 PMCID: PMC8346664 DOI: 10.1016/j.isci.2021.102875] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/18/2021] [Accepted: 07/14/2021] [Indexed: 02/01/2023] Open
Abstract
Lak phages with alternatively coded ∼540 kbp genomes were recently reported to replicate in Prevotella in microbiomes of humans that consume a non-Western diet, baboons, and pigs. Here, we explore Lak phage diversity and broader distribution using diagnostic polymerase chain reaction and genome-resolved metagenomics. Lak phages were detected in 13 animal types, including reptiles, and are particularly prevalent in pigs. Tracking Lak through the pig gastrointestinal tract revealed significant enrichment in the hindgut compared to the foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. An anomalously large (∼660 kbp) complete genome reconstructed for the most deeply branched Lak from a horse microbiome is also alternatively coded. From the Lak genomes, we identified proteins associated with specific animal species; notably, most have no functional predictions. The presence of closely related Lak phages in diverse animals indicates facile distribution coupled to host-specific adaptation.
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Affiliation(s)
- Marco A. Crisci
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Audra E. Devoto
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Adair L. Borges
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Nicola Bordin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Rohan Sachdeva
- Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
| | - Allison M. Sharrar
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Mick Bailey
- Bristol Veterinary School, University of Bristol, Langford, Bristol, UK
| | - Rachel Burt
- Bristol Veterinary School, University of Bristol, Langford, Bristol, UK
| | - Rhiannon M. Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Paula M. Corsini
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Shufei Lei
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
- The University of Melbourne, Melbourne, VIC, Australia
| | - Joanne M. Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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23
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Chen Y, Sun L, Ba X, Jiang S, Zhuang H, Zhu F, Wang H, Lan P, Shi Q, Wang Z, Chen Y, Shi K, Ji S, Jiang Y, Holmes MA, Yu Y. Epidemiology, evolution and cryptic susceptibility of methicillin-resistant Staphylococcus aureus in China: a whole-genome-based survey. Clin Microbiol Infect 2021; 28:85-92. [PMID: 34022399 DOI: 10.1016/j.cmi.2021.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 12/16/2020] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 01/19/2023]
Abstract
OBJECTIVES The aim of this study was to investigate the genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in China to identify predominant lineages and their associations with clinical data and antimicrobial resistance profiles. METHODS We performed a national prevalence study of patients with S. aureus infections in 22 tertiary hospitals in China from 2015 to 2017. Clinical data from patients and the antimicrobial phenotypes were collected for each isolate. Genome sequencing was performed on a proportion of isolates and a phylogenetic analysis was undertaken. Genotypic and phenotypic β-lactam susceptibilities were compared. RESULTS A total of 1900 patients with S. aureus infections were included, of which 40% involved MRSA. Community-associated MRSA (CA-MRSA) infections were 24% of the total isolates. Genomic data showed that more than three-quarters of the MRSA were from three dominant lineages CC239 (25%, 116/471), CC5 (21%, 96/471) and CC59 (33%, 154/471) with CC59 accounting for more than half of the CA-MRSA isolates. Penicillin susceptibility genomic features were observed in 53% (251/470) of MRSA, including almost all of the CC59 (152/154) lineage, and 96% (242/251) of these isolates demonstrated in vitro susceptibility to penicillin or amoxicillin combined with clavulanic acid. Phylogenetic analysis indicated that the CC59 lineage can be divided into six lineages with all Asian CC59 isolates likely arising from an ancestral Mainland China lineage. CONCLUSIONS This study showed a high prevalence of CA-MRSA in China, largely due to the widespread presence of CC59. As almost all isolates in this lineage possess genetic variants leading to increased β-lactam susceptibility, we suggest that to improve antibiotic stewardship combinations of penicillins and β-lactamase inhibitors should be included in the antibiotic susceptibility testing panels used to inform treatment decisions and research undertaken on this combination therapy.
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Affiliation(s)
- Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lu Sun
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Shengnan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hemu Zhuang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Feiteng Zhu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiping Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Peng Lan
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiucheng Shi
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Centre for Child Health, Zhejiang, China
| | - Zhengan Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiyi Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Keren Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shujuan Ji
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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24
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Anderson T, Beever L, Hall J, Moores A, Llanos C, Adams R, Meakin L, Coppola M, Bowlt-Blacklock K, Holmes MA, Barnes D. Outcome following surgery to treat septic peritonitis in 95 cats in the United Kingdom. J Small Anim Pract 2021; 62:744-749. [PMID: 33999425 DOI: 10.1111/jsap.13346] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To review the cause, management and outcome in cats with septic peritonitis within the United Kingdom (2008 to 2018) and to identify if previously identified prognostic factors were associated with survival in this population. MATERIALS AND METHODS Clinical records from 10 referral hospitals in United Kingdom were reviewed. Data collected included signalment, clinicopathological data and management techniques. Serum albumin, glucose, lactate and ionised calcium concentration; presence of intraoperative hypotension and correct empirical antibiosis were analysed via logistic regression for association with survival. RESULTS Ninety-five cats were included. The overall survival rate was 66%. Lethargy (89%) and anorexia (75%) were the most common clinical signs, with abdominal pain and vomiting in 44% and 27% of cases, respectively. Gastro-intestinal leakage was the most common source of contamination. The presence of an abdominal mass on clinical examination was not strongly predictive of the presence of neoplasia on histology and did not confer a worse prognosis. Cats presenting with dehiscence of a previous enterotomy/enterectomy did not have a worse prognosis than those presenting with other aetologies. Intraoperative hypotension (adjusted odds ratio 0.173, 95% confidence intervals 0.034 to 0.866, P=0.033) was associated with non-survival. Cats that survived beyond 1 day postoperatively had an improved likelihood of survival (87.5%). All cats that survived beyond 6 days were successfully discharged. CLINICAL SIGNIFICANCE This study describes the largest group of cats with septic peritonitis with an overall survival rate of 66%. The presence of an abdominal mass on clinical examination or having dehiscence of a previous gastrointestinal surgery did not confer a worse prognosis.
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Affiliation(s)
- T Anderson
- Surgery Department, Dick White Referrals, Six Mile Bottom, Cambridgeshire, CB8 0UH, UK
| | - L Beever
- Department of Clinical Sciences and Services, The Royal Veterinary College, Hertfordshire, AL9 7TA, UK
| | - J Hall
- Surgery Department, Wear Referrals, Bradbury, Stockton-on-Tees, TS21 2ES, UK.,Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Edinburgh, EH25 9RG, UK
| | - A Moores
- Surgery Department, Anderson Moores Veterinary Specialists, Winchester, Hampshire, SO21 2LL, UK
| | - C Llanos
- Surgery Department, Willows Referral Service, Solihull, West Midlands, B90 4NH, UK
| | - R Adams
- Surgery Department, Northern Ireland Veterinary Specialists, Hillsborough, Co. Down, NI, BT26 6 PB, UK.,Surgery Department, Davies Veterinary Specialists, Higham Gobion, Hitchin, SG5 3HR, UK
| | - L Meakin
- Surgery Department, Langford Vets, Langford, BS40 5DU, UK
| | - M Coppola
- Surgery Department, University of Glasgow, Glasgow, G61 1QH, UK
| | - K Bowlt-Blacklock
- Surgery Department, Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - M A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - D Barnes
- Surgery Department, Dick White Referrals, Six Mile Bottom, Cambridgeshire, CB8 0UH, UK
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25
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Gómez P, Ruiz-Ripa L, Fernández-Fernández R, Gharsa H, Ben Slama K, Höfle U, Zarazaga M, Holmes MA, Torres C. Genomic Analysis of Staphylococcus aureus of the Lineage CC130, Including mecC-Carrying MRSA and MSSA Isolates Recovered of Animal, Human, and Environmental Origins. Front Microbiol 2021; 12:655994. [PMID: 33841383 PMCID: PMC8027229 DOI: 10.3389/fmicb.2021.655994] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/03/2021] [Indexed: 02/02/2023] Open
Abstract
Most methicillin resistant Staphylococcus aureus (MRSA) isolates harboring mecC gene belong to clonal complex CC130. This lineage has traditionally been regarded as animal-associated as it lacks the human specific immune evasion cluster (IEC), and has been recovered from a broad range of animal hosts. Nevertheless, sporadic mecC-MRSA human infections have been reported, with evidence of zoonotic transmission in some cases. The objective of this study was to investigate the whole-genome sequences of 18 S. aureus CC130 isolates [13 methicillin-resistant (mecC-MRSA) and five methicillin-susceptible (MSSA)] from different sequences types, obtained from a variety of host species and origins (human, livestock, wild birds and mammals, and water), and from different geographic locations, in order to identify characteristic markers and genomic features. Antibiotic resistance genes found among MRSA-CC130 were those associated with the SSCmecXI element. Most MRSA-CC130 strains carried a similar virulence gene profile. Additionally, six MRSA-CC130 possessed scn-sak and one MSSA-ST130 had lukMF'. The MSSA-ST700 strains were most divergent in their resistance and virulence genes. The pan-genome analysis showed that 29 genes were present solely in MRSA-CC130 (associated with SCCmecXI) and 21 among MSSA-CC130 isolates (associated with phages). The SCCmecXI, PBP3, GdpP, and AcrB were identical at the amino acid level in all strains, but some differences were found in PBP1, PBP2, PBP4, and YjbH proteins. An examination of the host markers showed that the 3' region of the bacteriophage φ3 was nearly identical to the reference sequence. Truncated hlb gene was also found in scn-negative strains (two of them carrying sak-type gene). The dtlB gene of wild rabbit isolates included novel mutations. The vwbp gene was found in the three MSSA-ST700 strains from small ruminants and in one MSSA-ST130 from a red deer; these strains also carried a scn-type gene, different from the human and equine variants. Finally, a phylogenetic analysis showed that the three MSSA-ST700 strains and the two MSSA-ST130 strains cluster separately from the remaining MRSA-CC130 strains with the etD2 gene as marker for the main lineage. The presence of the human IEC cluster in some mecC-MRSA-CC130 strains suggests that these isolates may have had a human origin.
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Affiliation(s)
- Paula Gómez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Laura Ruiz-Ripa
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Rosa Fernández-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Haythem Gharsa
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Ursula Höfle
- Health and Biotechnology SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
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26
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Cui C, Ba X, Holmes MA. Prevalence and characterization of mecC MRSA in bovine bulk tank milk in Great Britain, 2017-18. JAC Antimicrob Resist 2021; 3:dlaa125. [PMID: 34223074 PMCID: PMC8210137 DOI: 10.1093/jacamr/dlaa125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/03/2020] [Accepted: 12/15/2020] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES To evaluate the current prevalence status of mecC MRSA among dairy farms in England and Wales 5 years after a previous survey conducted in 2011-12. METHODS A convenience sample of 697 dairy farms in England and Wales was used for the study, conducted in 2017-18, testing bulk tank milk samples for the presence of mecC MRSA using high salt broth enrichment and chromogenic MRSA agar selection. All putative MRSA isolates were screened by PCR for the presence of mecA and mecC genes and subjected to antimicrobial susceptibility testing using both the disc diffusion method and VITEK® 2. MRSA isolates were also sequenced for genomic characterization. RESULTS mecC MRSA were detected on 4 out of 697 dairy farms in England and Wales (prevalence 0.57%, 95% CI 0.16%-1.46%). Three of the mecC isolates were ST425 and one was ST4652 (in the CC130 lineage). Two mecA MRSA were also isolated: one ST5 and one ST398. CONCLUSIONS These results indicate that there has been a substantial reduction in the prevalence of mecC MRSA in England and Wales with a 72% reduction (2.15% to 0.57%) compared with a previous study. While the levels of mecA MRSA remain very low the continued presence of ST398, a livestock-associated MRSA, suggests that this lineage is established in the UK.
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Affiliation(s)
- Cheng Cui
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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27
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Ba X, Kalmar L, Hadjirin NF, Kerschner H, Apfalter P, Morgan FJ, Paterson GK, Girvan SL, Zhou R, Harrison EM, Holmes MA. Truncation of GdpP mediates β-lactam resistance in clinical isolates of Staphylococcus aureus. J Antimicrob Chemother 2021; 74:1182-1191. [PMID: 30759229 DOI: 10.1093/jac/dkz013] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES High-level β-lactam resistance in MRSA is mediated in the majority of strains by a mecA or mecC gene. In this study, we identified 10 mec gene-negative MRSA human isolates from Austria and 11 bovine isolates from the UK showing high levels of β-lactam resistance and sought to understand the molecular basis of the resistance observed. METHODS Different antimicrobial resistance testing methods (disc diffusion, Etest and VITEK® 2) were used to establish the β-lactam resistance profiles for the isolates and the isolates were further investigated by WGS. RESULTS A number of mutations (including novel ones) in PBPs, AcrB, YjbH and the pbp4 promoter were identified in the resistant isolates, but not in closely related susceptible isolates. Importantly, a truncation in the cyclic diadenosine monophosphate phosphodiesterase enzyme, GdpP, was identified in 7 of the 10 Austrian isolates and 10 of the 11 UK isolates. Complementation of four representative isolates with an intact copy of the gdpP gene restored susceptibility to penicillins and abolished the growth defects caused by the truncation. CONCLUSIONS This study reports naturally occurring inactivation of GdpP protein in Staphylococcus aureus of both human origin and animal origin, and demonstrates clinical relevance to a previously reported association between this truncation and increased β-lactam resistance and impaired bacterial growth in laboratory-generated mutants. It also highlights possible limitations of genomic determination of antibiotic susceptibility based on single gene presence or absence when choosing the appropriate antimicrobial treatment for patients.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lajos Kalmar
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nazreen F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Heidrun Kerschner
- National Reference Centre for Antibiotic Resistance and Nosocomial Infections, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Petra Apfalter
- National Reference Centre for Antibiotic Resistance and Nosocomial Infections, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Fiona J Morgan
- Department of Physics, University of Cambridge, Cambridge, UK
| | - Gavin K Paterson
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Samantha L Girvan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology and International Research Centre for Animal Disease (Ministry of Science & Technology), College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ewan M Harrison
- Wellcome Sanger Institute, Hinxton, UK.,Department of Medicine, University of Cambridge, Cambridge, UK.,Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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MacFadyen AC, Harrison EM, Drigo I, Parkhill J, Holmes MA, Paterson GK. A mecC allotype, mecC3, in the CoNS Staphylococcus caeli, encoded within a variant SCCmecC. J Antimicrob Chemother 2020; 74:547-552. [PMID: 30590583 DOI: 10.1093/jac/dky502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/07/2018] [Accepted: 11/07/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Methicillin resistance in staphylococci is conferred by an alternative PBP (PBP2a/2') with low affinity for most β-lactam antibiotics. PBP2a is encoded by mecA, which is carried on a mobile genetic element known as SCCmec. A variant of mecA, mecC, was described in 2011 and has been found in Staphylococcus aureus from humans and a wide range of animal species as well as a small number of other staphylococcal species from animals. OBJECTIVES We characterized a novel mecC allotype, mecC3, encoded by an environmental isolate of Staphylococcus caeli cultured from air sampling of a commercial rabbit holding. METHODS The S. caeli isolate 82BT was collected in Italy in 2013 and genome sequenced using MiSeq technology. This allowed the assembly and comparative genomic study of the novel SCCmec region encoding mecC3. RESULTS The study isolate encodes a novel mecA allotype, mecC3, with 92% nucleotide identity to mecC. mecC3 is encoded within a novel SCCmec element distinct from those previously associated with mecC, including a ccrAB pairing (ccrA5B3) not previously linked to mecC. CONCLUSIONS This is the first description of the novel mecC allotype mecC3, the first isolation of a mecC-positive Staphylococcus in Italy and the first report of mecC in S. caeli. Furthermore, the SCCmec element described here is highly dissimilar to the archetypal SCCmec XI encoding mecC in S. aureus and to elements encoding mecC in other staphylococci. Our report highlights the diversity of mecC allotypes and the diverse staphylococcal species, ecological settings and genomic context in which mecC may be found.
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Affiliation(s)
- A C MacFadyen
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - E M Harrison
- The Wellcome Trust Sanger Institute, Wellcome Trust, Genome Campus, Hinxton, UK
| | - I Drigo
- Istituto Zooprofilattico Sperimentale delle Venezie, via dell'Università 10, Legnaro, PD, Italy
| | - J Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust, Genome Campus, Hinxton, UK
| | - M A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - G K Paterson
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK
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Gómez P, Aspiroz C, Hadjirin NF, Benito D, Zarazaga M, Torres C, Holmes MA. Simultaneous Nasal Carriage by Methicillin-Resistant and Methicillin Susceptible Staphylococcus aureus of Lineage ST398 in a Live Pig Transporter. Pathogens 2020; 9:E401. [PMID: 32455801 PMCID: PMC7281718 DOI: 10.3390/pathogens9050401] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST)398 is a livestock associated (LA) lineage with zoonotic potential, especially in humans with live pig contact. The objective of this study was to characterize two S. aureus strains of lineage ST398 (one methicillin-resistant (MRSA), one methicillin-susceptible (MSSA)) isolated from the same nasal sample of a patient admitted in the Intensive-Care Unit of a Spanish Hospital, and with previous occupational exposure to live pigs, by whole-genome-sequencing (WGS). The sample was obtained during routine surveillance for MRSA colonization. Purified genomic DNA was sequenced using Illumina HiSeq 2000 and processed using conventional bioinformatics software. The two isolates recovered were both S. aureus t011/ST398 and showed similar resistance-phenotypes, other than methicillin susceptibility. The possession of antibiotic resistance genes was the same, except for the mecA-gene located in SCCmecV in the MRSA isolate. The MSSA isolate harbored remnants of a SCCmec following the deletion of 17342bp from a recombination between two putative primases. Both isolates belonged to the livestock-associated clade as defined by three canonical single-nucleotide-polymorphisms, and neither possessed the human immune evasion cluster genes, chp, scn, or sak. The core genome alignment showed a similarity of 99.6%, and both isolates harbored the same mobile genetic elements. The two nasal ST398 isolates recovered from the patient with previous occupational exposure to pigs appeared to have a livestock origin and could represent different evolutionary steps of animal-human interface lineage. The MSSA strain was formed as a result of the loss of the mecA gene from the livestock-associated-MRSA lineage.
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Affiliation(s)
- Paula Gómez
- Area of Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (P.G.); (D.B.); (M.Z.)
| | - Carmen Aspiroz
- Department of Microbiology, Hospital Royo Villanova, 50015 Zaragoza, Spain;
| | - Nazreen F. Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (N.F.H.); (M.A.H.)
| | - Daniel Benito
- Area of Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (P.G.); (D.B.); (M.Z.)
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (P.G.); (D.B.); (M.Z.)
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (P.G.); (D.B.); (M.Z.)
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (N.F.H.); (M.A.H.)
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Egyir B, Hadjirin NF, Gupta S, Owusu F, Agbodzi B, Adogla-Bessa T, Addo KK, Stegger M, Larsen AR, Holmes MA. Whole-genome sequence profiling of antibiotic-resistant Staphylococcus aureus isolates from livestock and farm attendants in Ghana. J Glob Antimicrob Resist 2020; 22:527-532. [PMID: 32439567 DOI: 10.1016/j.jgar.2020.03.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/25/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Epidemic methicillin-resistant Staphylococcus aureus (MRSA) clones have been described in Ghana, but so far, no typical livestock-associated MRSA isolates (CC398) have been found. In this study we provide baseline information on antimicrobial resistance, population structure, and virulence gene content of S. aureus isolates from livestock and farm attendants. METHODS Nasal samples were collected from cattle, pigs, goats, sheep, and farm attendants from three farms. Staphylococcus aureus was identified by matrix-assisted laser desorption/ionisation time-of-flight and antimicrobial susceptibility testing was performed using VITEK II (Biomerieux, Marcy l'Etoile, France) and interpreted according to EUCAST guidelines. Whole-genome sequencing was performed using the Illumina, San Diego, CA, USA MiSeq Platform. RESULTS In total, 401 nasal swab samples were obtained from 57 farm attendants, 208 pigs, 30 goats, 26 sheep, and 80 cattle. The S. aureus isolates (n = 25) recovered (farm attendants: n = 10; pigs: n = 8; and goats: n = 7) were frequently resistant to penicillin (68%), tetracycline (44%), and ciprofloxacin (32%); two human isolates were MRSA. Twelve isolates (48%) were multidrug resistant (MDR) (>3 classes). Genome sequencing of the isolates revealed ST152-t355, ST9-t1430, and ST133-t8662 as dominant clones among farm attendants, pigs, and goats, respectively. The two MRSA isolates detected belonged to ST8-t334 and ST152-t355. The scn and sak genes associated with human-adaption were detected in 10 isolates; 9 from humans and 1 from a goat. Typing results provided evidence of a single potential transmission event (t861, PVL-, scn+). CONCLUSION No MRSA was detected among livestock, perhaps because of low intensive farming; however, the relatively high prevalence of MDR isolates may be a result of inappropriate antibiotic usage in Ghanaian livestock production.
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Affiliation(s)
- Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana.
| | - Nazreen F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Srishti Gupta
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Felicia Owusu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Bright Agbodzi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Tsatsu Adogla-Bessa
- Livestock and Poultry Research Centre Institute of Agricultural and Consumer Sciences, University of Ghana, Legon, Accra, Ghana
| | - Kennedy Kwasi Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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McDougall S, Clausen L, Ha HJ, Gibson I, Bryan M, Hadjirin N, Lay E, Raisen C, Ba X, Restif O, Parkhill J, Holmes MA. Mechanisms of β-lactam resistance of Streptococcus uberis isolated from bovine mastitis cases. Vet Microbiol 2020; 242:108592. [PMID: 32122596 DOI: 10.1016/j.vetmic.2020.108592] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 05/23/2019] [Revised: 01/12/2020] [Accepted: 01/21/2020] [Indexed: 11/24/2022]
Abstract
A number of veterinary clinical pathology laboratories in New Zealand have been reporting emergence of increased minimum in inhibitory concentrations for β-lactams in the common clinical bovine mastitis pathogen Streptococcus uberis. The objective of this study was to determine the genetic basis of this increase in MIC for β-lactams amongst S. uberis. Illumina sequencing and determination of oxacillin MIC was performed on 265 clinical isolates. Published sequences of the five penicillin binding proteins pbp1a, pbp1b, pbp2a, pbp2b, and pbp2x were used to identify, extract and align these sequences from the study isolates. Amino acid substitutions resulting from single nucleotide polymorphisms (SNP) within these genes were analysed for associations with elevated (≥ 0.5 mg/L) oxacillin MIC together with a genome wide association study. The population structure of the study isolates was approximated using a phylogenetic tree generated from an alignment of the core genome. A total of 53 % of isolates had MIC ≥ 0.5 mg/L for oxacillin. A total of 101 substitutions within the five pbp were identified, of which 11 were statistically associated with an MIC ≥ 0.5 mg/L. All 140 isolates which exhibited an increased β-lactam MIC had SNPs leading to pbp2x E381K and Q554E substitutions. The phylogenetic tree indicated that the genotype and phenotype associated with the increased MIC for oxacillin were present in several different lineages suggesting that acquisition of this increased β-lactam MIC had occurred in multiple geographically distinct regions. Reanalysis of the data from the intervention studies from which the isolates were originally drawn found a tendency for the pbp2x E381K substitution to be associated with lower cure rates. It is concluded that there is geographically and genetically widespread presence of pbp substitutions associated with reduced susceptibility to β-lactam antimicrobials. Additionally, presence of pbp substitutions tended to be associated with poorer cure rate outcomes following antimicrobial therapy for clinical mastitis.
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Affiliation(s)
| | | | - Hye-Jeong Ha
- Animal Health Laboratory, Ministry for Primary Industry, Upper Hutt, New Zealand
| | - Isobel Gibson
- New Zealand Veterinary Pathology, Hamilton, New Zealand
| | | | - Nazreen Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Elizabeth Lay
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Claire Raisen
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK; Wellcome Sanger Institute, Hinxton, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
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Kepiro IE, Marzuoli I, Hammond K, Ba X, Lewis H, Shaw M, Gunnoo SB, De Santis E, Łapińska U, Pagliara S, Holmes MA, Lorenz CD, Hoogenboom BW, Fraternali F, Ryadnov MG. Engineering Chirally Blind Protein Pseudocapsids into Antibacterial Persisters. ACS Nano 2020; 14:1609-1622. [PMID: 31794180 DOI: 10.1021/acsnano.9b06814] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antimicrobial resistance stimulates the search for antimicrobial forms that may be less subject to acquired resistance. Here we report a conceptual design of protein pseudocapsids exhibiting a broad spectrum of antimicrobial activities. Unlike conventional antibiotics, these agents are effective against phenotypic bacterial variants, while clearing "superbugs" in vivo without toxicity. The design adopts an icosahedral architecture that is polymorphic in size, but not in shape, and that is available in both l and d epimeric forms. Using a combination of nanoscale and single-cell imaging we demonstrate that such pseudocapsids inflict rapid and irreparable damage to bacterial cells. In phospholipid membranes they rapidly convert into nanopores, which remain confined to the binding positions of individual pseudocapsids. This mechanism ensures precisely delivered influxes of high antimicrobial doses, rendering the design a versatile platform for engineering structurally diverse and functionally persistent antimicrobial agents.
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Affiliation(s)
- Ibolya E Kepiro
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Irene Marzuoli
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Randall Centre for Cell and Molecular Biophysics , King's College London , London , SE1 1UL , U.K
| | - Katharine Hammond
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Department of Physics and Astronomy , University College London , London , WC1E 6BT , U.K
- London Centre for Nanotechnology , University College London , London , WC1H 0AH , U.K
| | - Xiaoliang Ba
- Department of Veterinary Medicine , University of Cambridge , Cambridge , CB3 0ES , U.K
| | - Helen Lewis
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Michael Shaw
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Department of Computer Science , University College London , London , WC1 6BT , U.K
| | - Smita B Gunnoo
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Emiliana De Santis
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Urszula Łapińska
- Living Systems Institute , University of Exeter , Exeter , EX4 4QD , U.K
| | - Stefano Pagliara
- Living Systems Institute , University of Exeter , Exeter , EX4 4QD , U.K
| | - Mark A Holmes
- Department of Veterinary Medicine , University of Cambridge , Cambridge , CB3 0ES , U.K
| | - Christian D Lorenz
- Department of Physics , King's College London , Strand Lane , London , WC2R 2LS , U.K
| | - Bart W Hoogenboom
- Department of Physics and Astronomy , University College London , London , WC1E 6BT , U.K
- London Centre for Nanotechnology , University College London , London , WC1H 0AH , U.K
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics , King's College London , London , SE1 1UL , U.K
| | - Maxim G Ryadnov
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Department of Physics , King's College London , Strand Lane , London , WC2R 2LS , U.K
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Monforte Monteiro SR, Rossmeisl JH, Russell J, Holmes MA, Wessmann A, Morris J, Dobson JM, Vanhaesebrouck AE. Effect of radiotherapy on freedom from seizures in dogs with brain tumors. J Vet Intern Med 2020; 34:821-827. [PMID: 32032456 PMCID: PMC7096644 DOI: 10.1111/jvim.15695] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/20/2019] [Indexed: 11/28/2022] Open
Abstract
Background Seizures are a common presenting sign in dogs with brain tumors. Hypothesis/Objectives To investigate the effect of radiotherapy on freedom from brain tumor‐associated seizures and survival time in dogs. Animals Thirty‐two client‐owned dogs with brain tumor‐associated seizures; 18 received medical treatment and radiotherapy, 14 received medical treatment alone. Methods Multicenter retrospective study. Baseline characteristics (seizure semiology, magnetic resonance imaging [MRI] characteristics, and treatment) and duration of seizure freedom were recorded for the 2 treatment groups. Duration of seizure freedom between groups was compared (log‐rank test) using Cox's proportional hazard analysis, with baseline characteristics entered as covariates. Results The duration of seizure freedom and survival time were significantly longer in the radiotherapy group (P < .001), with a mean of 24 months (95% confidence interval [CI], 14.3‐33.8) versus 1.7 months in the control group (95% CI, 0.5‐2.9) and a mean of 34.6 months (95% CI: 25.2‐44.1) versus 6.2 months in the control group (95% CI, 2.6‐9.7) respectively. Baseline characteristics were not associated with duration of seizure freedom after the start of treatment. In the radiotherapy group, 5 dogs were euthanized during the study period because of causes other than seizures. In the control group, recurrence of seizures was observed before death in all dogs. Conclusions and Clinical Importance A longer period of seizure freedom and longer survival time was observed in dogs with brain tumors after radiotherapy compared to medical treatment only. The pathophysiological mechanisms of epileptogenesis and the effect of radiation therapy on seizure control are unclear to date. Further prospective studies are needed.
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Affiliation(s)
| | - John H Rossmeisl
- The Department of Veterinary Sciences, Virginia Maryland College of Veterinary Medicine, Blacksburg, Virginia
| | - Jason Russell
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee
| | - Mark A Holmes
- The Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Jo Morris
- The School of Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Jane M Dobson
- The Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - An E Vanhaesebrouck
- The Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Matuszewska M, Murray GGR, Harrison EM, Holmes MA, Weinert LA. The Evolutionary Genomics of Host Specificity in Staphylococcus aureus. Trends Microbiol 2020; 28:465-477. [PMID: 31948727 DOI: 10.1016/j.tim.2019.12.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/18/2019] [Accepted: 12/09/2019] [Indexed: 12/31/2022]
Abstract
Staphylococcus aureus is an important human bacterial pathogen that has a cosmopolitan host range, including livestock, companion and wild animal species. Genomic and epidemiological studies show that S. aureus has jumped between host species many times over its evolutionary history. These jumps have involved the dynamic gain and loss of host-specific adaptive genes, usually located on mobile genetic elements. The same functional elements are often consistently gained in jumps into a particular species. Further sampling of diverse animal species is likely to uncover an even broader host range and greater genetic diversity of S. aureus than is already known, and understanding S. aureus host specificity in these hosts will mitigate the risks of emergent human and livestock strains.
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Affiliation(s)
- Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Ewan M Harrison
- Wellcome Sanger Institute, University of Cambridge, Cambridge, CB10 1SA, UK; Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK; Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
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Kronbichler A, Blane B, Holmes MA, Wagner J, Parkhill J, Peacock SJ, Jayne DRW, Harrison EM. Nasal carriage of Staphylococcus pseudintermedius in patients with granulomatosis with polyangiitis. Rheumatology (Oxford) 2020; 58:548-550. [PMID: 30412252 PMCID: PMC6381761 DOI: 10.1093/rheumatology/key317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2018] [Indexed: 11/25/2022] Open
Affiliation(s)
- Andreas Kronbichler
- Vasculitis and Lupus Clinic, Addenbrooke's Hospital, Cambridge, UK.,Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Beth Blane
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Josef Wagner
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - David R W Jayne
- Vasculitis and Lupus Clinic, Addenbrooke's Hospital, Cambridge, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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Wagner J, Harrison EM, Martinez Del Pero M, Blane B, Mayer G, Leierer J, Gopaluni S, Holmes MA, Parkhill J, Peacock SJ, Jayne DRW, Kronbichler A. The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study. Microbiome 2019; 7:137. [PMID: 31640771 PMCID: PMC6806544 DOI: 10.1186/s40168-019-0753-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 09/24/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Ear, nose and throat involvement in granulomatosis with polyangiitis (GPA) is frequently the initial disease manifestation. Previous investigations have observed a higher prevalence of Staphylococcus aureus in patients with GPA, and chronic nasal carriage has been linked with an increased risk of disease relapse. In this cross-sectional study, we investigated changes in the nasal microbiota including a detailed analysis of Staphylococcus spp. by shotgun metagenomics in patients with active and inactive granulomatosis with polyangiitis (GPA). Shotgun metagenomic sequence data were also used to identify protein-encoding genes within the SEED database, and the abundance of proteins then correlated with the presence of bacterial species on an annotated heatmap. RESULTS The presence of S. aureus in the nose as assessed by culture was more frequently detected in patients with active GPA (66.7%) compared with inactive GPA (34.1%). Beta diversity analysis of nasal microbiota by bacterial 16S rRNA profiling revealed a different composition between GPA patients and healthy controls (P = 0.039). Beta diversity analysis of shotgun metagenomic sequence data for Staphylococcus spp. revealed a different composition between active GPA patients and healthy controls and disease controls (P = 0.0007 and P = 0.0023, respectively), and between healthy controls and inactive GPA patients and household controls (P = 0.0168 and P = 0.0168, respectively). Patients with active GPA had a higher abundance of S. aureus, mirroring the culture data, while healthy controls had a higher abundance of S. epidermidis. Staphylococcus pseudintermedius, generally assumed to be a pathogen of cats and dogs, showed an abundance of 13% among the Staphylococcus spp. in our cohort. During long-term follow-up of patients with inactive GPA at baseline, a higher S. aureus abundance was not associated with an increased relapse risk. Functional analyses identified ten SEED protein subsystems that differed between the groups. Most significant associations were related to chorismate synthesis and involved in the vitamin B12 pathway. CONCLUSION Our data revealed a distinct dysbiosis of the nasal microbiota in GPA patients compared with disease and healthy controls. Metagenomic sequencing demonstrated that this dysbiosis in active GPA patients is manifested by increased abundance of S. aureus and a depletion of S. epidermidis, further demonstrating the antagonist relationships between these species. SEED functional protein subsystem analysis identified an association between the unique bacterial nasal microbiota clusters seen mainly in GPA patients and an elevated abundance of genes associated with chorismate synthesis and vitamin B12 pathways. Further studies are required to further elucidate the relationship between the biosynthesis genes and the associated bacterial species.
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Affiliation(s)
- Josef Wagner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Ewan M. Harrison
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, CB1 8RN UK
| | | | - Beth Blane
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Gert Mayer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Johannes Leierer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Seerapani Gopaluni
- Vasculitis and Lupus Clinic, Box 57, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Sharon J. Peacock
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK
| | - David R. W. Jayne
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Vasculitis and Lupus Clinic, Box 57, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
- Vasculitis and Lupus Clinic, Box 57, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
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MacFadyen AC, Harrison EM, Ellington MJ, Parkhill J, Holmes MA, Paterson GK. A highly conserved mecC-encoding SCCmec type XI in a bovine isolate of methicillin-resistant Staphylococcus xylosus. J Antimicrob Chemother 2019; 73:3516-3518. [PMID: 30165441 DOI: 10.1093/jac/dky333] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- A C MacFadyen
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - E M Harrison
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - M J Ellington
- Public Health England, National Infection Service, Level 6 Addenbrookes Hospital, Cambridge, UK
| | - J Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - M A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - G K Paterson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK
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Harrison EM, Ba X, Coll F, Blane B, Restif O, Carvell H, Köser CU, Jamrozy D, Reuter S, Lovering A, Gleadall N, Bellis KL, Uhlemann AC, Lowy FD, Massey RC, Grilo IR, Sobral R, Larsen J, Rhod Larsen A, Vingsbo Lundberg C, Parkhill J, Paterson GK, Holden MTG, Peacock SJ, Holmes MA. Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus. Nat Microbiol 2019; 4:1680-1691. [PMID: 31235959 PMCID: PMC7611363 DOI: 10.1038/s41564-019-0471-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/26/2019] [Indexed: 01/04/2023]
Abstract
Antibiotic resistance in bacterial pathogens threatens the future of modern medicine. One such resistant pathogen is methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to nearly all β-lactam antibiotics, limiting treatment options. Here, we show that a significant proportion of MRSA isolates from different lineages, including the epidemic USA300 lineage, are susceptible to penicillins when used in combination with β-lactamase inhibitors such as clavulanic acid. Susceptibility is mediated by a combination of two different mutations in the mecA promoter region that lowers mecA-encoded penicillin-binding protein 2a (PBP2a) expression, and in the majority of isolates by either one of two substitutions in PBP2a (E246G or M122I) that increase the affinity of PBP2a for penicillin in the presence of clavulanic acid. Treatment of S. aureus infections in wax moth and mouse models shows that penicillin/β-lactamase inhibitor susceptibility can be exploited as an effective therapeutic choice for 'susceptible' MRSA infection. Finally, we show that isolates with the PBP2a E246G substitution have a growth advantage in the presence of penicillin but the absence of clavulanic acid, which suggests that penicillin/β-lactamase susceptibility is an example of collateral sensitivity (resistance to one antibiotic increases sensitivity to another). Our findings suggest that widely available and currently disregarded antibiotics could be effective in a significant proportion of MRSA infections.
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Affiliation(s)
- Ewan M Harrison
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Francesc Coll
- London School of Hygiene and Tropical Medicine, London, UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Henry Carvell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Andrew Lovering
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | | | | | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Franklin D Lowy
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Inês R Grilo
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Rita Sobral
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Gavin K Paterson
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Sharon J Peacock
- Wellcome Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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MacFadyen AC, Leroy S, Harrison EM, Parkhill J, Holmes MA, Paterson GK. Staphylococcus pseudoxylosus sp. nov., isolated from bovine mastitis. Int J Syst Evol Microbiol 2019; 69:2208-2213. [PMID: 31225789 DOI: 10.1099/ijsem.0.003416] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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] [Indexed: 02/02/2023] Open
Abstract
Strain S04009T, a Gram-stain-positive, coagulase-negative staphylococcus, was isolated from bovine mastitis in France. 16S rRNA gene analysis revealed it to be closely related to the coagulase-negative species Staphylococcusxylosus, Staphylococcussaprophyticus, Staphylococcuscaeli and Staphylococcus edaphicus. At the whole-genome level, strain S04009T had an average nucleotide identity value <95 % and an inferred DNA-DNA hybridization value <70 % when compared to these species. Furthermore, phenotypic characteristics distinguished S04009T from those species. From these related species only strain S04009T and S. xylosus are able to ferment xylose and these two can be distinguished by the inability of strain S04009T to express urease activity. Based on the genotypic and phenotypic results, it is proposed that this isolate is a novel species, with the name Staphylococcus pseudoxylosus sp. nov. The type strain is S04009T (=DSM 107950T=CCUG 72763T=NCTC 14184T).
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Affiliation(s)
- A C MacFadyen
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Campus, Midlothian, EH25 9RG, UK
| | - S Leroy
- Université Clermont Auvergne-INRA, MEDIS, 63000 Clermont-Ferrand, France
| | - E M Harrison
- The Wellcome Sanger Institute, Wellcome Trust, Genome Campus, Hinxton, CB10 1SA, UK
| | - J Parkhill
- The Wellcome Sanger Institute, Wellcome Trust, Genome Campus, Hinxton, CB10 1SA, UK
| | - M A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - G K Paterson
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Campus, Midlothian, EH25 9RG, UK
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Seni J, Mshana SE, Msigwa F, Iddi S, Mazigo H, Parkhill J, Holmes MA, Paterson GK. Draft genome sequence of a multidrug-resistant caprine isolate of Staphylococcus cohnii subsp. urealyticus from Tanzania encoding ermB, tet(K), dfrG, fusF and fosD. J Glob Antimicrob Resist 2019; 18:163-165. [PMID: 31323428 DOI: 10.1016/j.jgar.2019.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/05/2019] [Accepted: 07/10/2019] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Coagulase-negative staphylococci such as Staphylococcus cohnii are opportunistic pathogens of humans and animals. A multidrug-resistant isolate of S. cohnii subsp. urealyticus (073AN) was isolated from the nasal cavity of a healthy goat in Tanzania. This study produced and analysed a draft genome sequence of strain 073AN to investigate the genetic basis for antimicrobial resistance in this isolate. METHODS Strain 073AN was sequenced using HiSeq 2000 technology, sequencing reads were assembled using Velvet, and the genome was annotated using Prokka. RESULTS The draft genome of strain 073AN is 2677652bp in size with a GC content of 32.5%. The isolate was resistant to several classes of antimicrobials, which correlated with the presence of known antimicrobial resistance genes. Of particular note, the draft genome sequence of strain 073AN represents the first report of fosD in S. cohnii and the first descriptions of fosD and fusF in Africa. CONCLUSION The draft genome sequence of S. cohnii subsp. urealyticus 073AN released here provides an insight into the antimicrobial resistance determinants found in this species and in Tanzania and offers a valuable resource for further studies on staphylococcal genomics and antimicrobial resistance.
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Affiliation(s)
- Jeremiah Seni
- Department of Microbiology/Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Science, Mwanza, Tanzania
| | - Stephen E Mshana
- Department of Microbiology/Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Science, Mwanza, Tanzania
| | - Felician Msigwa
- Department of Microbiology/Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Science, Mwanza, Tanzania
| | - Shabani Iddi
- Department of Physiology, Weill Bugando School of Medicine, Catholic University of Health and Allied Science, Mwanza, Tanzania
| | - Humphrey Mazigo
- Department of Parasitology and Entomology, Weill Bugando School of Medicine, Catholic University of Health and Allied Science, Mwanza, Tanzania
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Gavin K Paterson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, UK.
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Barkham T, Zadoks RN, Azmai MNA, Baker S, Bich VTN, Chalker V, Chau ML, Dance D, Deepak RN, van Doorn HR, Gutierrez RA, Holmes MA, Huong LNP, Koh TH, Martins E, Mehershahi K, Newton P, Ng LC, Phuoc NN, Sangwichian O, Sawatwong P, Surin U, Tan TY, Tang WY, Thuy NV, Turner P, Vongsouvath M, Zhang D, Whistler T, Chen SL. One hypervirulent clone, sequence type 283, accounts for a large proportion of invasive Streptococcus agalactiae isolated from humans and diseased tilapia in Southeast Asia. PLoS Negl Trop Dis 2019; 13:e0007421. [PMID: 31246981 PMCID: PMC6597049 DOI: 10.1371/journal.pntd.0007421] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022] Open
Abstract
Background In 2015, Singapore had the first and only reported foodborne outbreak of invasive disease caused by the group B Streptococcus (GBS; Streptococcus agalactiae). Disease, predominantly septic arthritis and meningitis, was associated with sequence type (ST)283, acquired from eating raw farmed freshwater fish. Although GBS sepsis is well-described in neonates and older adults with co-morbidities, this outbreak affected non-pregnant and younger adults with fewer co-morbidities, suggesting greater virulence. Before 2015 ST283 had only been reported from twenty humans in Hong Kong and two in France, and from one fish in Thailand. We hypothesised that ST283 was causing region-wide infection in Southeast Asia. Methodology/Principal findings We performed a literature review, whole genome sequencing on 145 GBS isolates collected from six Southeast Asian countries, and phylogenetic analysis on 7,468 GBS sequences including 227 variants of ST283 from humans and animals. Although almost absent outside Asia, ST283 was found in all invasive Asian collections analysed, from 1995 to 2017. It accounted for 29/38 (76%) human isolates in Lao PDR, 102/139 (73%) in Thailand, 4/13 (31%) in Vietnam, and 167/739 (23%) in Singapore. ST283 and its variants were found in 62/62 (100%) tilapia from 14 outbreak sites in Malaysia and Vietnam, in seven fish species in Singapore markets, and a diseased frog in China. Conclusions GBS ST283 is widespread in Southeast Asia, where it accounts for a large proportion of bacteraemic GBS, and causes disease and economic loss in aquaculture. If human ST283 is fishborne, as in the Singapore outbreak, then GBS sepsis in Thailand and Lao PDR is predominantly a foodborne disease. However, whether transmission is from aquaculture to humans, or vice versa, or involves an unidentified reservoir remains unknown. Creation of cross-border collaborations in human and animal health are needed to complete the epidemiological picture. An outbreak due to a bacterium called Streptococccus agalactiae in Singapore in 2015 was caused by a clone called ST283, and was associated with consumption of raw freshwater-fish. It was considered unique as it was the only reported foodborne outbreak of this bacterium. Our new data show that invasive ST283 disease is far from unique. ST283 has been causing disease in humans and farmed fish in SE Asian countries for decades. Reports of ST283 are almost absent outside Asia. We suspect that human ST283 is fishborne in other Asian countries, as it was in Singapore, but we haven’t looked at this yet. We don’t know where ST283 originally came from; it may have been transmitted from humans to fish, or come from another animal. More studies are needed to determine ST283’s geographical extent and burden of disease, as well as its origin, how it is transmitted, and what enables it to be so aggressive. We may then be able to interrupt transmission, to the benefit of fish, farmers, and the general public.
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Affiliation(s)
- Timothy Barkham
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
- * E-mail: (TB); (SLC)
| | - Ruth N. Zadoks
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mohammad Noor Amal Azmai
- Department of Biology, Faculty of Science, and Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, Selangor, Malaysia
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Bich
- Centre for Tropical Medicine, Oxford University Clinical Research Unit, Hanoi, Vietnam
| | | | - Man Ling Chau
- Environmental Health Institute, National Environment Agency, Singapore
- National Centre for Food Science, Singapore Food Agency, Singapore
| | - David Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Ramona A. Gutierrez
- Environmental Health Institute, National Environment Agency, Singapore
- National Centre for Infectious Diseases, Singapore
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Tse Hsien Koh
- Department of Microbiology, Singapore General Hospital, Singapore
| | - Elisabete Martins
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Kurosh Mehershahi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Paul Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, Singapore
| | - Nguyen Ngoc Phuoc
- Faculty of Fisheries, University of Agriculture and Forestry, Hue University, Hue City, Vietnam
| | - Ornuma Sangwichian
- Thailand Ministry of Public Health (MOPH)-US Centers for Disease Control and Prevention Collaboration (TUC), Nonthaburi, Thailand
| | - Pongpun Sawatwong
- Thailand Ministry of Public Health (MOPH)-US Centers for Disease Control and Prevention Collaboration (TUC), Nonthaburi, Thailand
| | - Uraiwan Surin
- Nakhon Phanom General Hospital, Nakhon Phanom Provincial Health Office, Nakhon Phanom, Thailand
| | - Thean Yen Tan
- Department of Laboratory Medicine, Changi General Hospital, Singapore
| | - Wen Ying Tang
- Molecular Biology Laboratory, Tan Tock Seng Hospital, Singapore
| | - Nguyen Vu Thuy
- National Hospital for Obstetrics & Gynaecology, Hanoi, Vietnam
| | - Paul Turner
- Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
| | - Defeng Zhang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, People’s Republic of China
| | - Toni Whistler
- Thailand Ministry of Public Health (MOPH)-US Centers for Disease Control and Prevention Collaboration (TUC), Nonthaburi, Thailand
- Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Swaine L. Chen
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Infectious Diseases Group, Genome Institute of Singapore, Singapore
- * E-mail: (TB); (SLC)
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Loncaric I, Kübber-Heiss A, Posautz A, Ruppitsch W, Lepuschitz S, Schauer B, Feßler AT, Krametter-Frötscher R, Harrison EM, Holmes MA, Künzel F, Szostak MP, Hauschild T, Desvars-Larrive A, Misic D, Rosengarten R, Walzer C, Slickers P, Monecke S, Ehricht R, Schwarz S, Spergser J. Characterization of mecC gene-carrying coagulase-negative Staphylococcus spp. isolated from various animals. Vet Microbiol 2019; 230:138-144. [PMID: 30827379 DOI: 10.1016/j.vetmic.2019.02.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 12/20/2018] [Revised: 02/02/2019] [Accepted: 02/05/2019] [Indexed: 11/30/2022]
Abstract
The presence of the methicillin resistance gene mecC in coagulase-negative Staphylococcus spp. (CoNS) is scarce. The aim of this study was to characterize mecC-positive CoNS isolated from various wild and domestic animals. The presence of the mecC gene was screened in 4299 samples from wild animals and domestic animals. Fifteen coagulase-negative staphylococci, that displayed a cefoxitin-resistant phenotype, were tested mecC-positive by PCR. Antimicrobial susceptibility testing was performed for all isolates. The 15 isolates were genotyped by sequencing of the entire class E mec gene complex (blaZ-mecC-mecR1-mecI), the ccrA and ccrB recombinase genes and other determinants within the type XI SCCmec element. DNA microarray analysis was performed and five selected isolates were additionally whole genome sequenced and analyzed. S. stepanovicii (n = 3), S. caprae (n = 1), S. warneri (n = 1), S. xylosus (n = 1) and S. sciuri (n = 9) were detected. All but the S. sciuri isolates were found to be susceptible to all non-beta lactams. The entire class E mec gene complex was detected in all isolates but ccrA and ccrB genes were not identified in S. stepanovicii and S. xylosus. The genes erm(B) and fexA (n = 4, each) were the most predominant non-beta lactam resistance genes detected in the S. sciuri isolates. Even though the presence of the mecC gene among CoNS is a rare observation, this study further expands our knowledge by showing that the mecC gene, including its allotypes, are present in more staphylococcal species from different animal species than has been previously described.
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Affiliation(s)
- Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria.
| | - Anna Kübber-Heiss
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Annika Posautz
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Bernhard Schauer
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre of Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Ewan M Harrison
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mark A Holmes
- Departement of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Frank Künzel
- Clinical Unit of Internal Medicine Small Animals, University of Veterinary Medicine, Vienna, Austria
| | - Michael P Szostak
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Tomasz Hauschild
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Amélie Desvars-Larrive
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Dusan Misic
- Department for Microbiology, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Renate Rosengarten
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria; Wildlife Health Program, Wildlife Conservation Society, Bronx, NY, USA
| | | | - Stefan Monecke
- InfectoGnostics research campus, Jena, Germany; Leibniz Institute of Photonic Technology (IPHT), Jena, Germany; Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany
| | - Ralf Ehricht
- InfectoGnostics research campus, Jena, Germany; Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre of Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
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Busche T, Hillion M, Van Loi V, Berg D, Walther B, Semmler T, Strommenger B, Witte W, Cuny C, Mellmann A, Holmes MA, Kalinowski J, Adrian L, Bernhardt J, Antelmann H. Comparative Secretome Analyses of Human and Zoonotic Staphylococcus aureus Isolates CC8, CC22, and CC398. Mol Cell Proteomics 2018; 17:2412-2433. [PMID: 30201737 PMCID: PMC6283302 DOI: 10.1074/mcp.ra118.001036] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Indexed: 12/24/2022] Open
Abstract
The proteogenomes and secretomes of dominant human and zoonotic S. aureus lineages CC8, CC22 and CC398 were compared revealing genomic and regulatory differences in the secretion of 869 proteins. In the core secretome, 101 secreted or cell surface anchored virulence factors contribute with 82.4% to total secretome abundance. CC398 isolates showed higher secretion of α- and ß-hemolysins and lower secretion of surface proteins resulting in strong hemolysis and decreased biofilm formation because of lower SigB activity compared to human-specific CC8 and CC22. The spread of methicillin-resistant Staphylococcus aureus (MRSA) in the community, hospitals and in livestock is mediated by highly diverse virulence factors that include secreted toxins, superantigens, enzymes and surface-associated adhesins allowing host adaptation and colonization. Here, we combined proteogenomics, secretome and phenotype analyses to compare the secreted virulence factors in selected S. aureus isolates of the dominant human- and livestock-associated genetic lineages CC8, CC22, and CC398. The proteogenomic comparison revealed 2181 core genes and 1306 accessory genes in 18 S. aureus isolates reflecting the high genome diversity. Using secretome analysis, we identified 869 secreted proteins with 538 commons in eight isolates of CC8, CC22, and CC398. These include 64 predicted extracellular and 37 cell surface proteins that account for 82.4% of total secretome abundance. Among the top 10 most abundantly secreted virulence factors are the major autolysins (Atl, IsaA, Sle1, SAUPAN006375000), lipases and lipoteichoic acid hydrolases (Lip, Geh, LtaS), cytolytic toxins (Hla, Hlb, PSMβ1) and proteases (SspB). The CC398 isolates showed lower secretion of cell wall proteins, but higher secretion of α- and β-hemolysins (Hla, Hlb) which correlated with an increased Agr activity and strong hemolysis. CC398 strains were further characterized by lower biofilm formation and staphyloxanthin levels because of decreased SigB activity. Overall, comparative secretome analyses revealed CC8- or CC22-specific enterotoxin and Spl protease secretion as well as Agr- and SigB-controlled differences in exotoxin and surface protein secretion between human-specific and zoonotic lineages of S. aureus.
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Affiliation(s)
- Tobias Busche
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany; Center for Biotechnology, Bielefeld University, D-33594 Bielefeld, Germany
| | - Mélanie Hillion
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Vu Van Loi
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany
| | - David Berg
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Birgit Walther
- Robert Koch Institute, Advanced Light and Electron Microscopy, D-13353 Berlin, Germany; Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, D-14153 Berlin, Germany
| | - Torsten Semmler
- Robert Koch Institute, Advanced Light and Electron Microscopy, D-13353 Berlin, Germany
| | | | - Wolfgang Witte
- Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
| | - Christiane Cuny
- Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Münster, D-48149 Münster, Germany
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, D-33594 Bielefeld, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, D-04318 Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, D-13355 Berlin, Germany
| | - Jörg Bernhardt
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany; Institute for Microbiology, University of Greifswald, D-17489 Greifswald, Germany
| | - Haike Antelmann
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany.
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Abstract
OBJECTIVE To investigate whether there are differences in the resting energy expenditure (REE) and body composition of athletes with a spinal cord injury (SCI) compared to active able-bodied controls. DESIGN In this cross sectional study, male athletes with a SCI were compared to active able-bodied controls matched for age, stretch stature and body mass. In addition, the accuracy of standard REE prediction equations in estimating REE was assessed. PARTICIPANTS Seven male wheelchair athletes with a SCI and six matched active able-bodied controls volunteered to participate. OUTCOME MEASURES REE was measured using indirect calorimetry and estimated using population-specific prediction equations. Body composition (lean tissue mass, fat mass and bone mineral content) was measured by dual energy X-ray absorptiometry (DXA). RESULTS While absolute and adjusted REE in the athletes with SCI was lower than controls, this difference was not significant (P = 0.259). When adjusted for lean tissue mass (LTM), REE was significantly higher (P = 0.038) in the athletes with SCI compared to the controls (146 ± 29kJ/kg LTM vs. 125 ± 8kJ/kg LTM). LTM was significantly lower in the athletes with SCI (44.35 ± 6.98 kg) compared to the able-bodied controls (56.02 ± 4.93 kg; P < 0.01). The differences between predicted and measured REE in the athletes with SCI were not statistically significant (except for the Owen equation), however there was no significant correlation between the measures. CONCLUSION This suggests that existing prediction equations used to estimate energy requirements may require modification for athletes with SCI.
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Affiliation(s)
- Fiona E. Pelly
- School of Health and Sport Sciences, University of the Sunshine Coast, Queensland, Australia,Correspondence to: Fiona E. Pelly, School of Health and Sport Sciences, University of the Sunshine Coast, Sippy Downs Drive, Queensland, Australia.
| | | | - Natalie Stuart
- School of Health and Sport Sciences, University of the Sunshine Coast, Queensland, Australia
| | - Mark A. Holmes
- School of Health and Sport Sciences, University of the Sunshine Coast, Queensland, Australia
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45
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Moradigaravand D, Gouliouris T, Ludden C, Reuter S, Jamrozy D, Blane B, Naydenova P, Judge K, H. Aliyu S, F. Hadjirin N, A. Holmes M, Török E, M. Brown N, Parkhill J, Peacock S. Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages. Microb Genom 2018; 4:e000162. [PMID: 29498619 PMCID: PMC5885014 DOI: 10.1099/mgen.0.000162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/09/2018] [Indexed: 01/03/2023] Open
Abstract
There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is contaminated with C. difficile spores. Here, we describe a study that used genome sequencing to compare C. difficile isolated from multiple wastewater treatment plants across the East of England and from patients with clinical disease at a major hospital in the same region. We confirmed that C. difficile from 65 patients were highly diverse and that most cases were not linked to other active cases in the hospital. In total, 186 C. difficile isolates were isolated from effluent water obtained from 18 municipal treatment plants at the point of release into the environment. Whole genome comparisons of clinical and environmental isolates demonstrated highly related populations, and confirmed extensive release of toxigenic C. difficile into surface waters. An analysis based on multilocus sequence types (STs) identified 19 distinct STs in the clinical collection and 38 STs in the wastewater collection, with 13 of 44 STs common to both clinical and wastewater collections. Furthermore, we identified five pairs of highly similar isolates (≤2 SNPs different in the core genome) in clinical and wastewater collections. Strategies to control community acquisition should consider the need for bacterial control of treated wastewater.
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Affiliation(s)
| | | | | | - Sandra Reuter
- University of Freiburg, Freiburg im Breisgau, Germany
| | | | | | | | - Kim Judge
- Wellcome Trust Sanger Institute, Hinxton, UK
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46
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de Vries SPW, Hadjirin NF, Lay EM, Zadoks RN, Peacock SJ, Parkhill J, Grant AJ, McDougall S, Holmes MA. Streptococcus bovimastitidis sp. nov., isolated from a dairy cow with mastitis. Int J Syst Evol Microbiol 2018; 68:21-27. [PMID: 29099353 DOI: 10.1099/ijsem.0.002321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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] [Indexed: 02/15/2024] Open
Abstract
Here we describe a new species of the genus Streptococcus that was isolated from a dairy cow with mastitis in New Zealand. Strain NZ1587T was Gram-positive, coccus-shaped and arranged as chains, catalase and coagulase negative, γ-haemolytic and negative for Lancefield carbohydrates (A-D, F and G). The 16S rRNA sequence did not match sequences in the NCBI 16S rRNA or GreenGenes databases. Taxonomic classification of strain NZ1587T was investigated using 16S rRNA and core genome phylogeny, genome-wide average nucleotide identity (ANI) and predicted DNA-DNA hybridisation (DDH) analyses. Phylogeny based on 16S rRNA was unable to resolve the taxonomic position of strain NZ1587T, however NZ1587T shared 99.4 % identity at the 16S rRNA level with a distinct branch of S. pseudoporcinus. Importantly, core genome phylogeny demonstrated that NZ1587T grouped amongst the 'pyogenic' streptococcal species and formed a distinct branch supported by a 100 % bootstrap value. In addition, average nucleotide identity and inferred DNA-DNA hybridisation analyses showed that NZ1587T represents a novel species. Biochemical profiling using the rapid ID 32 strep identification test enabled differentiation of strain NZ1587T from closely related streptococcal species. In conclusion, strain NZ1587T can be classified as a novel species, and we propose a novel taxon named Streptococcus bovimastitidis sp. nov.; the type strain is NZ1587T. NZ1587T has been deposited in the Culture Collection University of Gothenburg (CCUG 69277T) and the Belgian Co-ordinated Collections of Micro-organisms/LMG (LMG 29747).
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Affiliation(s)
| | - Nazreen F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Elizabeth M Lay
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Sharon J Peacock
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Julian Parkhill
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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47
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Hernandez-Garcia J, Wang J, Restif O, Holmes MA, Mather AE, Weinert LA, Wileman TM, Thomson JR, Langford PR, Wren BW, Rycroft A, Maskell DJ, Tucker AW. Patterns of antimicrobial resistance in Streptococcus suis isolates from pigs with or without streptococcal disease in England between 2009 and 2014. Vet Microbiol 2017; 207:117-124. [PMID: 28757010 PMCID: PMC5548070 DOI: 10.1016/j.vetmic.2017.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [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: 09/28/2016] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 12/25/2022]
Abstract
Antimicrobial resistance in Streptococcus suis, a global zoonotic pathogen of pigs, has been mostly studied only in diseased animals using surveys that have not evaluated changes over time. We compared patterns of resistance between S. suis isolates from clinical cases of disease (CC) and non-clinical case (NCC) pigs in England, collected over two discrete periods, 2009-2011 and 2013-2014. Minimum inhibitory concentrations (MIC) of 17 antimicrobials (nine classes) were determined on 405 S. suis isolates categorised by sampling period and disease association to assess changes in resistance over time and association with disease. First, isolates were characterized as resistant or susceptible using published clinical breakpoints. Second, epidemiological cut-offs (ECOFF) were derived from MIC values, and isolates classified as wild type (WT) below the ECOFF and non-wild type (NWT) above the ECOFF. Finally, isolate subsets were analysed for shifts in MIC distribution. NCC isolates were more resistant than CC isolates to cephalosporins, penams, pleuromutilins, potentiated sulphonamides and tetracyclines in both study periods. Resistance levels among CC isolates increased in 2013-2014 relative to 2009-2011 for antimicrobials including aminoglycosides, cephalosporins, fluoroquinolones, pleuromutilins, potentiated sulphonamides and tetracyclines. The prevalence of isolates categorised as NWT for five or more classes of antimicrobials was greater among NCC than CC isolates for both time periods, and increased with time. This study used standardised methods to identify significant shifts in antimicrobial resistance phenotypes of S. suis isolated from pigs in England, not only over time but also between isolates from known clinical cases or disease-free pigs.
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Affiliation(s)
- Juan Hernandez-Garcia
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Jinhong Wang
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Thomas M Wileman
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Jill R Thomson
- SAC Consulting: Veterinary Services, Bush State, Penicuik, EH26 0QE, Scotland, UK.
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, W2 1 PG, UK.
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Andrew Rycroft
- The Royal Veterinary College, Hawkshead Campus, Hatfield, Hertfordshire, AL9 7TA, UK.
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
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48
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Affiliation(s)
- J. Michael Doster
- North Carolina State University, Department of Nuclear Engineering P.O. Box 7909, Raleigh, North Carolina 27695-7909
| | - Mark A. Holmes
- North Carolina State University, Department of Nuclear Engineering P.O. Box 7909, Raleigh, North Carolina 27695-7909
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49
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Bodey AL, Almond CJ, Holmes MA. Double-blinded randomised placebo-controlled clinical trial of individualised homeopathic treatment of hyperthyroid cats. Vet Rec 2017; 180:377. [PMID: 28077754 DOI: 10.1136/vr.104007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2016] [Indexed: 11/04/2022]
Abstract
Feline hyperthyroidism is a common endocrine disorder in older cats for which homeopathic treatment has been advocated. A double-blinded, placebo-controlled randomised trial was performed to look for evidence of efficacy for the use of individualised homeopathy in the treatment of this disease. Using a case definition of a concentration of the thyroid hormone T4 >66 nmol/l, cats were randomised into two treatment arms. Either a placebo or a homeopathic treatment was given to each cat blindly. After 21 days, the T4 levels, weight (Wt) and heart rate (HR) were compared with pretreatment values. There were no statistically significant differences in the changes seen between the two treatment arms following placebo or homeopathic treatment (T4 P=0.96, Wt P=0.16, HR P=0.36) or between the means of each parameter for either treatment arm before and after placebo or homeopathic treatment (all P values >0.13). In a second phase of the study, patients in both treatment arms were given methimazole treatment for 21 days and T4, Wt and HR determined again. Again there were no statistically significant differences between the groups, but there were statistically significant reductions in T4 (P<0.0001) and HR (P=0.02), and a statistically significant increase in Wt (P=0.004) in both groups compared with their pre-methimazole treatment levels. The results of this study failed to provide any evidence of the efficacy of homeopathic treatment of feline hyperthyroidism.
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Affiliation(s)
- A L Bodey
- The Hyperthyroid Cat Centre, 433 Birch Park, Thorp Arch Estate, Wetherby, Yorkshire, LS23 7FG, UK
| | - C J Almond
- Forrest House Veterinary Ltd, 5 Little Market Place, Masham, Ripon, North Yorkshire, HG4 4DY, UK
| | - M A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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50
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Koop G, Vrieling M, Storisteanu DML, Lok LSC, Monie T, van Wigcheren G, Raisen C, Ba X, Gleadall N, Hadjirin N, Timmerman AJ, Wagenaar JA, Klunder HM, Fitzgerald JR, Zadoks R, Paterson GK, Torres C, Waller AS, Loeffler A, Loncaric I, Hoet AE, Bergström K, De Martino L, Pomba C, de Lencastre H, Ben Slama K, Gharsa H, Richardson EJ, Chilvers ER, de Haas C, van Kessel K, van Strijp JAG, Harrison EM, Holmes MA. Identification of LukPQ, a novel, equid-adapted leukocidin of Staphylococcus aureus. Sci Rep 2017; 7:40660. [PMID: 28106142 PMCID: PMC5247767 DOI: 10.1038/srep40660] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/08/2016] [Indexed: 11/09/2022] Open
Abstract
Bicomponent pore-forming leukocidins are a family of potent toxins secreted by Staphylococcus aureus, which target white blood cells preferentially and consist of an S- and an F-component. The S-component recognizes a receptor on the host cell, enabling high-affinity binding to the cell surface, after which the toxins form a pore that penetrates the cell lipid bilayer. Until now, six different leukocidins have been described, some of which are host and cell specific. Here, we identify and characterise a novel S. aureus leukocidin; LukPQ. LukPQ is encoded on a 45 kb prophage (ΦSaeq1) found in six different clonal lineages, almost exclusively in strains cultured from equids. We show that LukPQ is a potent and specific killer of equine neutrophils and identify equine-CXCRA and CXCR2 as its target receptors. Although the S-component (LukP) is highly similar to the S-component of LukED, the species specificity of LukPQ and LukED differs. By forming non-canonical toxin pairs, we identify that the F-component contributes to the observed host tropism of LukPQ, thereby challenging the current paradigm that leukocidin specificity is driven solely by the S-component.
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Affiliation(s)
- Gerrit Koop
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Manouk Vrieling
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Daniel M. L. Storisteanu
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke’s and Papworth Hospitals, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Laurence S. C. Lok
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke’s and Papworth Hospitals, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Tom Monie
- Medical Research Council Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge CB1 9NL, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Glenn van Wigcheren
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Claire Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Nicholas Gleadall
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Nazreen Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Arjen J. Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
- Central Veterinary Institute of Wageningen UR, 8200 AB Lelystad, The Netherlands
| | - Heleen M. Klunder
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - J. Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, EH25 9RG, Edinburgh, United Kingdom
| | - Ruth Zadoks
- Moredun Research Institute, Bush Loan, Penicuik EH26 0PZ, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Gavin K. Paterson
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom
| | - Carmen Torres
- Área Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, Logroño 26006, Spain
| | - Andrew S. Waller
- Animal Health Trust, Lanwades Park, Kentford, Newmarket CB8 7UU, United Kingdom
| | - Anette Loeffler
- Department of Clinical Sciences and Services, Royal Veterinary College, Hawkshead Lane, Hatfield, North Mymms, Hertfordshire AL9 7TA, United Kingdom
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Armando E. Hoet
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, 1900 Coffey Road, Columbus, OH 43210, USA
- Veterinary Public Health Program, College of Public Health, The Ohio State University, 1900 Coffey Road, Columbus, OH 43210, USA
| | - Karin Bergström
- Department of Animal Health and Antimicrobial Strategies, SVA, SE-751 89 Uppsala, Sweden
| | - Luisa De Martino
- Department of Veterinary Medicine and Animal Production, Infectious Diseases Section, University of Naples “Federico II”, 80137 Naples, Italy
| | - Constança Pomba
- Interdisciplinary Centre of Research in Animal Health, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 LISBOA, Portugal
| | - Hermínia de Lencastre
- Laboratório de Genética Molecular, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY10065, USA
| | - Karim Ben Slama
- Laboratoire de Microorganismes et Biomolécules actives, Département de Biologie, Faculté de Sciences de Tunis, 2092 Tunis, Tunisia
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia
| | - Haythem Gharsa
- Laboratoire de Microorganismes et Biomolécules actives, Département de Biologie, Faculté de Sciences de Tunis, 2092 Tunis, Tunisia
| | - Emily J. Richardson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Edwin R. Chilvers
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke’s and Papworth Hospitals, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Carla de Haas
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Kok van Kessel
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jos A. G. van Strijp
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Ewan M. Harrison
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
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