Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods
Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods
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- dc.contributor.author
- Shay, Julie A.
- Haniford, Laura S. E.
- Cooper, Ashley
- Carrillo, Catherine D.
- Blais, Burton W.
- Lau, Calvin Ho-Fung
- dc.date.accepted
- 2023-03-15
- dc.date.accessioned
- 2023-10-26T21:50:18Z
- dc.date.available
- 2023-10-26T21:50:18Z
- dc.date.issued
- 2023-03-29
- dc.date.submitted
- 2022-10-05
- dc.description.abstract - en
- Background With the escalating risk of antimicrobial resistance (AMR), there are limited analytical options available that can comprehensively assess the burden of AMR carried by clinical/environmental samples. Food can be a potential source of AMR bacteria for humans, but its significance in driving the clinical spread of AMR remains unclear, largely due to the lack of holistic-yet-sensitive tools for surveillance and evaluation. Metagenomics is a culture-independent approach well suited for uncovering genetic determinants of defined microbial traits, such as AMR, present within unknown bacterial communities. Despite its popularity, the conventional approach of non-selectively sequencing a sample’s metagenome (namely, shotgun-metagenomics) has several technical drawbacks that lead to uncertainty about its effectiveness for AMR assessment; for instance, the low discovery rate of resistance-associated genes due to their naturally small genomic footprint within the vast metagenome. Here, we describe the development of a targeted resistome sequencing method and demonstrate its application in the characterization of the AMR gene profile of bacteria associated with several retail foods. Result A targeted-metagenomic sequencing workflow using a customized bait-capture system targeting over 4,000 referenced AMR genes and 263 plasmid replicon sequences was validated against both mock and sample-derived bacterial community preparations. Compared to shotgun-metagenomics, the targeted method consistently provided for improved recovery of resistance gene targets with a much-improved target detection efficiency (> 300-fold). Targeted resistome analyses conducted on 36 retail-acquired food samples (fresh sprouts, n = 10; ground meat, n = 26) and their corresponding bacterial enrichment cultures (n = 36) reveals in-depth features regarding the identity and diversity of AMR genes, most of which were otherwise undetected by the whole-metagenome shotgun sequencing method. Furthermore, our findings suggest that foodborne Gammaproteobacteria could be the major reservoir of food-associated AMR genetic determinants, and that the resistome structure of the selected high-risk food commodities are, to a large extent, dictated by microbiome composition. Conclusions For metagenomic sequencing-based surveillance of AMR, the target-capture method presented herein represents a more sensitive and efficient approach to evaluate the resistome profile of complex food or environmental samples. This study also further implicates retail foods as carriers of diverse resistance-conferring genes indicating a potential impact on the dissemination of AMR.
- dc.identifier.citation
- Shay, J. A., Haniford, L. S., Cooper, A., Carrillo, C. D., Blais, B. W., & Lau, C. H.-F. (2023). Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in Retail Foods. Environmental Microbiome, 18(1). https://doi.org/10.1186/s40793-023-00482-0
- dc.identifier.doi
- https://doi.org/10.1186/s40793-023-00482-0
- dc.identifier.issn
- 2524-6372
- dc.identifier.uri
- https://open-science.canada.ca/handle/123456789/1239
- dc.language.iso
- en
- dc.publisher
- Springer Nature
- dc.rights - en
- Creative Commons Attribution 4.0 International (CC BY 4.0)
- dc.rights - fr
- Creative Commons Attribution 4.0 International (CC BY 4.0)
- dc.rights.openaccesslevel - en
- Gold
- dc.rights.openaccesslevel - fr
- Or
- dc.rights.uri - en
- https://creativecommons.org/licenses/by/4.0/
- dc.rights.uri - fr
- https://creativecommons.org/licenses/by/4.0/deed.fr
- dc.subject - en
- Science and technology
- dc.subject - fr
- Sciences et technologie
- dc.subject.en - en
- Science and technology
- dc.subject.fr - fr
- Sciences et technologie
- dc.title - en
- Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods
- dc.type - en
- Accepted manuscript
- dc.type - fr
- Manuscrit accepté
- local.acceptedmanuscript.articlenum
- 25 (2023)
- local.article.journaltitle
- Environmental Microbiome
- local.article.journalvolume
- 18
- local.peerreview - en
- Yes
- local.peerreview - fr
- Oui
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