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Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts.
McCallum, Gregory E; Rossiter, Amanda E; Quraishi, Mohammed Nabil; Iqbal, Tariq H; Kuehne, Sarah A; van Schaik, Willem.
Afiliação
  • McCallum GE; Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
  • Rossiter AE; Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
  • Quraishi MN; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.
  • Iqbal TH; Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
  • Kuehne SA; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.
  • van Schaik W; Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
Microb Genom ; 9(6)2023 06.
Article em En | MEDLINE | ID: mdl-37272920
The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are located on plasmids. Metagenomic chromosome conformation capture approaches (meta3C and Hi-C) have recently been developed to link bacterial genes to phylogenetic markers, thus potentially allowing the assignment of ARGs to their hosts on a microbiome-wide scale. Here, we generated a meta3C dataset of a human stool sample and used previously published meta3C and Hi-C datasets to investigate bacterial hosts of ARGs in the human gut microbiome. Sequence reads mapping to repetitive elements were found to cause problematic noise in, and may importantly skew interpretation of, meta3C and Hi-C data. We provide a strategy to improve the signal-to-noise ratio by discarding reads that map to insertion sequence elements and to the end of contigs. We also show the importance of using spike-in controls to quantify whether the cross-linking step in meta3C and Hi-C protocols has been successful. After filtering to remove artefactual links, 87 ARGs were assigned to their bacterial hosts across all datasets, including 27 ARGs in the meta3C dataset we generated. We show that commensal gut bacteria are an important reservoir for ARGs, with genes coding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Genes Bacterianos / Antibacterianos Limite: Humans Idioma: En Ano de publicação: 2023 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Genes Bacterianos / Antibacterianos Limite: Humans Idioma: En Ano de publicação: 2023 Tipo de documento: Article