cam.issuedOnline	2022-03-14
datacite.contributor.supervisor	editor: Didelot, Xavier
datacite.issupplementedby.url	https://doi.org/10.17863/CAM.80312
dc.contributor.author	Kalmar, Lajos
dc.contributor.author	Gupta, Srishti
dc.contributor.author	Kean, Iain RL
dc.contributor.author	Ba, Xiaoliang
dc.contributor.author	Hadjirin, Nazreen
dc.contributor.author	Lay, Elizabeth M
dc.contributor.author	de Vries, Stefan PW
dc.contributor.author	Bateman, Michael
dc.contributor.author	Bartlet, Harriet
dc.contributor.author	Hernandez-Garcia, Juan
dc.contributor.author	Tucker, Alexander W
dc.contributor.author	Restif, Olivier
dc.contributor.author	Stevens, Mark P
dc.contributor.author	Wood, James LN
dc.contributor.author	Maskell, Duncan J
dc.contributor.author	Grant, Andrew J
dc.contributor.author	Holmes, Mark A
dc.contributor.orcid	Kalmar, Lajos [0000-0003-3691-8350]
dc.contributor.orcid	Gupta, Srishti [0000-0001-6721-1783]
dc.contributor.orcid	Kean, Iain RL [0000-0003-1066-8285]
dc.contributor.orcid	Ba, Xiaoliang [0000-0002-3882-3585]
dc.contributor.orcid	de Vries, Stefan PW [0000-0002-0823-208X]
dc.contributor.orcid	Bartlet, Harriet [0000-0002-7389-8785]
dc.contributor.orcid	Hernandez-Garcia, Juan [0000-0001-5932-9327]
dc.contributor.orcid	Tucker, Alexander W [0000-0003-0062-0843]
dc.contributor.orcid	Restif, Olivier [0000-0001-9158-853X]
dc.contributor.orcid	Wood, James LN [0000-0002-0258-3188]
dc.contributor.orcid	Maskell, Duncan J [0000-0002-5065-653X]
dc.contributor.orcid	Grant, Andrew J [0000-0001-9746-2989]
dc.contributor.orcid	Holmes, Mark A [0000-0002-5454-1625]
dc.date.accessioned	2022-03-31T18:01:50Z
dc.date.available	2022-03-31T18:01:50Z
dc.date.issued	2022-03
dc.date.submitted	2021-08-10
dc.date.updated	2022-03-31T18:01:49Z
dc.description.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.
dc.identifier.doi	10.17863/CAM.83052
dc.identifier.eissn	1553-7404
dc.identifier.issn	1553-7390
dc.identifier.other	pgenetics-d-21-00617
dc.identifier.uri	https://www.repository.cam.ac.uk/handle/1810/335621
dc.language	en
dc.language.iso	eng
dc.publisher	Public Library of Science (PLoS)
dc.publisher.url	http://dx.doi.org/10.1371/journal.pgen.1009776
dc.subject	Animals
dc.subject	Anti-Bacterial Agents
dc.subject	Anti-Infective Agents
dc.subject	Drug Resistance, Bacterial
dc.subject	Metagenomics
dc.subject	Microbiota
dc.subject	Swine
dc.title	HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.
dc.type	Article
dcterms.dateAccepted	2022-02-07
prism.issueIdentifier	3
prism.publicationName	PLoS Genet
prism.volume	18
pubs.funder-project-id	Medical Research Council (MR/N002660/1)
rioxxterms.licenseref.uri	http://creativecommons.org/licenses/by/4.0/
rioxxterms.version	VoR
rioxxterms.versionofrecord	10.1371/journal.pgen.1009776

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.

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