학술논문
Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing.
Document Type
Academic Journal
Author
Yokoyama M; Department of Global Health and Infectious Diseases, Brighton and Sussex Medical School, Brighton, United Kingdom.; Peto L; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.; Budgell EP; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.; Jones N; Department of Infection, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.; Sheridan E; Department of Microbiology, University Hospitals Dorset, Bournemouth, United Kingdom.; Liu J; Department of Microbiology, Royal United Hospitals Bath, Bath, United Kingdom.; Walker AS; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.; Stoesser N; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.; Department of Infection, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.; Gweon HS; School of Biological Sciences, University of Reading, Whiteknights, Reading, United Kingdom.; UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, United Kingdom.; Llewelyn MJ; Department of Global Health and Infectious Diseases, Brighton and Sussex Medical School, Brighton, United Kingdom.
Source
Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
Subject
Language
English
Abstract
Antimicrobial resistance (AMR) is a threat to global public health. However, unsatisfactory approaches to directly measuring the AMR burden carried by individuals has hampered efforts to assess interventions aimed at reducing selection for AMR. Metagenomics can provide accurate detection and quantification of AMR genes within an individual person's faecal flora (their gut "resistome"). Using this approach, we aimed to test the hypothesis that differences in antimicrobial use across different hospitals in the United Kingdom will result in observable differences in the resistome of individual patients. Three National Health Service acute Hospital Trusts with markedly different antibiotic use and Clostridioides difficile infection rates collected faecal samples from anonymous patients which were discarded after C. difficile testing over a period of 9 to 15 months. Metagenomic DNA was extracted from these samples and sequenced using an Illumina NovaSeq 6000 platform. The resulting sequencing reads were analysed for taxonomic composition and for the presence of AMR genes. Among 683 faecal metagenomes we found huge variation between individuals in terms of taxonomic diversity (Shannon Index range 0.10-3.99) and carriage of AMR genes (Median 1.50 genes/cell/sample overall). We found no statistically significant differences in diversity (median Shannon index 2.16 (IQR 1.71-2.56), 2.15 (IQR 1.62-2.50) and 2.26 (IQR 1.55-2.51)) or carriage of AMR genes (median 1.37 genes/cell/sample (IQR 0.70-3.24), 1.70 (IQR 0.70-4.52) and 1.43 (IQR 0.55-3.71)) at the three trusts respectively. This was also the case across the sample collection period within the trusts. While we have not demonstrated differences over place or time using metagenomic sequencing of faecal discards, other sampling frameworks may be more suitable to determine whether organisational level differences in antibiotic use are associated with individual-level differences in burden of AMR carriage.
Competing Interests: We have edited as follows complying with your requirements: ASW is an NIHR Senior Investigator. ASW and MJL were supported by the NIHR Biomedical Research Centre, Oxford during the duration of the research. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
(Copyright: © 2023 Yokoyama et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Competing Interests: We have edited as follows complying with your requirements: ASW is an NIHR Senior Investigator. ASW and MJL were supported by the NIHR Biomedical Research Centre, Oxford during the duration of the research. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
(Copyright: © 2023 Yokoyama et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)