2020
DOI: 10.1101/2020.03.19.999250
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Abstract: 24The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs); however, in 25 Australia the profile of the gut 'resistome', or ensemble of ARGs, has not been investigated. This 26 study provides a first preliminary mapping of the major bacterial ARGs present in human, domestic 27 dog and wild duck fecal samples collected from south-eastern Victoria, Australia; and evaluates 28 the use of shotgun metagenomics sequencing (SMS) and targeted amplification of ARGs. We 29 analysed SMS data us… Show more

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“…A commonly used single target for profiling bacterial communities is the 16S rRNA gene which possesses both highly conserved regions facilitating the use of universal primers, and hypervariable regions which can be used to discriminate between bacterial taxa 11,12 . Increasingly, targeted ultra-highly multiplexed PCR panels have been developed to enable amplicon-based evaluation of the presence/absence and diversity of specific features of a metagenome associated with a key phenotype, for example AMR gene diversity [13][14][15] , or of a subset of organisms associated with disease, for example respiratory viruses. One example is Illumina AmpliSeq TM which can be used with both Illumina-and community-curated panels (primer pools).…”
Section: Introductionmentioning
confidence: 99%
“…A commonly used single target for profiling bacterial communities is the 16S rRNA gene which possesses both highly conserved regions facilitating the use of universal primers, and hypervariable regions which can be used to discriminate between bacterial taxa 11,12 . Increasingly, targeted ultra-highly multiplexed PCR panels have been developed to enable amplicon-based evaluation of the presence/absence and diversity of specific features of a metagenome associated with a key phenotype, for example AMR gene diversity [13][14][15] , or of a subset of organisms associated with disease, for example respiratory viruses. One example is Illumina AmpliSeq TM which can be used with both Illumina-and community-curated panels (primer pools).…”
Section: Introductionmentioning
confidence: 99%