HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.
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Authors
Hadjirin, Nazreen
Lay, Elizabeth M
Bateman, Michael
Stevens, Mark P
Publication Date
2022-03Journal Title
PLoS Genet
ISSN
1553-7390
Publisher
Public Library of Science (PLoS)
Volume
18
Issue
3
Language
eng
Type
Article
This Version
VoR
Metadata
Show full item recordCitation
Kalmar, L., Gupta, S., Kean, I., Ba, X., Hadjirin, N., Lay, E. M., de Vries, S. P., et al. (2022). HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.. PLoS Genet, 18 (3) https://doi.org/10.1371/journal.pgen.1009776
Abstract
Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.
Sponsorship
Medical Research Council (MR/N002660/1)
Identifiers
35286304, PMC8947609
External DOI: https://doi.org/10.1371/journal.pgen.1009776
This record's URL: https://www.repository.cam.ac.uk/handle/1810/336144
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