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Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing.

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Title: Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing.
Authors: Yokoyama, Maho, Peto, Leon, Budgell, Eric P., Jones, Nicola, Sheridan, Elizabeth, Liu, Jane, Walker, A. Sarah, Stoesser, Nicole, Gweon, Hyun S., Llewelyn, Martin J.
Source: PLoS ONE; 3/16/2023, Vol. 18 Issue 3, p1-10, 10p
Subject Terms: SHOTGUN sequencing, MICROBIAL diversity, DRUG resistance in microorganisms, METAGENOMICS, CLOSTRIDIOIDES difficile, INDIVIDUAL differences
Geographic Terms: UNITED Kingdom
Company/Entity: GREAT Britain. National Health Service
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. [ABSTRACT FROM AUTHOR]
Copyright of PLoS ONE is the property of Public Library of Science and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Complementary Index
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  Data: Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing.
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  Data: <searchLink fieldCode="AR" term="%22Yokoyama%2C+Maho%22">Yokoyama, Maho</searchLink><br /><searchLink fieldCode="AR" term="%22Peto%2C+Leon%22">Peto, Leon</searchLink><br /><searchLink fieldCode="AR" term="%22Budgell%2C+Eric+P%2E%22">Budgell, Eric P.</searchLink><br /><searchLink fieldCode="AR" term="%22Jones%2C+Nicola%22">Jones, Nicola</searchLink><br /><searchLink fieldCode="AR" term="%22Sheridan%2C+Elizabeth%22">Sheridan, Elizabeth</searchLink><br /><searchLink fieldCode="AR" term="%22Liu%2C+Jane%22">Liu, Jane</searchLink><br /><searchLink fieldCode="AR" term="%22Walker%2C+A%2E+Sarah%22">Walker, A. Sarah</searchLink><br /><searchLink fieldCode="AR" term="%22Stoesser%2C+Nicole%22">Stoesser, Nicole</searchLink><br /><searchLink fieldCode="AR" term="%22Gweon%2C+Hyun+S%2E%22">Gweon, Hyun S.</searchLink><br /><searchLink fieldCode="AR" term="%22Llewelyn%2C+Martin+J%2E%22">Llewelyn, Martin J.</searchLink>
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  Data: PLoS ONE; 3/16/2023, Vol. 18 Issue 3, p1-10, 10p
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  Data: <searchLink fieldCode="DE" term="%22SHOTGUN+sequencing%22">SHOTGUN sequencing</searchLink><br /><searchLink fieldCode="DE" term="%22MICROBIAL+diversity%22">MICROBIAL diversity</searchLink><br /><searchLink fieldCode="DE" term="%22DRUG+resistance+in+microorganisms%22">DRUG resistance in microorganisms</searchLink><br /><searchLink fieldCode="DE" term="%22METAGENOMICS%22">METAGENOMICS</searchLink><br /><searchLink fieldCode="DE" term="%22CLOSTRIDIOIDES+difficile%22">CLOSTRIDIOIDES difficile</searchLink><br /><searchLink fieldCode="DE" term="%22INDIVIDUAL+differences%22">INDIVIDUAL differences</searchLink>
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– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: 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. [ABSTRACT FROM AUTHOR]
– Name: Abstract
  Label:
  Group: Ab
  Data: <i>Copyright of PLoS ONE is the property of Public Library of Science and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1371/journal.pone.0282584
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        Text: English
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              Text: 3/16/2023
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