Targeted metagenomics using bait-capture to detect antibiotic resistance genes in retail meat and seafood

Annika Flint; Ashley Cooper; Mary Rao; Kelly Weedmark; Catherine Carrillo; Sandeep Tamber

doi:10.3389/fmicb.2023.1188872

Targeted metagenomics using bait-capture to detect antibiotic resistance genes in retail meat and seafood

Front Microbiol. 2023 Jul 13:14:1188872. doi: 10.3389/fmicb.2023.1188872. eCollection 2023.

Authors

Annika Flint¹, Ashley Cooper², Mary Rao¹, Kelly Weedmark¹, Catherine Carrillo², Sandeep Tamber¹

Affiliations

¹ Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada.
² Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.

Abstract

Metagenomics analysis of foods has the potential to provide comprehensive data on the presence and prevalence of antimicrobial resistance (AMR) genes in the microbiome of foods. However, AMR genes are generally present in low abundance compared to other bacterial genes in the food microbiome and consequently require multiple rounds of in-depth sequencing for detection. Here, a metagenomics approach, using bait-capture probes targeting antimicrobial resistance and plasmid genes, is used to characterize the resistome and plasmidome of retail beef, chicken, oyster, shrimp, and veal enrichment cultures (n = 15). Compared to total shotgun metagenomics, bait-capture required approximately 40-fold fewer sequence reads to detect twice the number of AMR gene classes, AMR gene families, and plasmid genes across all sample types. For the detection of critically important extended spectrum beta-lactamase (ESBL) genes the bait capture method had a higher overall positivity rate (44%) compared to shotgun metagenomics (26%), and a culture-based method (29%). Overall, the results support the use of bait-capture for the identification of low abundance genes such as AMR genes from food samples.

Keywords: antimicrobial resistance; beef; chicken; gene detection; oysters; resistome; shrimp; veal.