Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics

Bloomfield, Samuel J., Zomer, Aldert L., O'Grady, Justin, Kay, Gemma L., Wain, John, Janecko, Nicol, Palau, Raphaëlle and Mather, Alison E. (2023) Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics. Food Microbiology, 110. ISSN 0740-0020

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Abstract

Food products carry bacteria unless specifically sterilised. These bacteria can be pathogenic, commensal or associated with food spoilage, and may also be resistant to antimicrobials. Current methods for detecting bacteria on food rely on culturing for specific bacteria, a time-consuming process, or 16S rRNA metabarcoding that can identify different taxa but not their genetic content. Directly sequencing metagenomes of food is inefficient as its own DNA vastly outnumbers the bacterial DNA present. We optimised host DNA depletion enabling efficient sequencing of food microbiota, thereby increasing the proportion of non-host DNA sequenced 13-fold (mean; range: 1.3–40-fold) compared to untreated samples. The method performed best on chicken, pork and leafy green samples which had high mean prokaryotic read proportions post-depletion (0.64, 0.74 and 0.74, respectively), with lower mean prokaryotic read proportions in salmon (0.50) and prawn samples (0.19). We show that bacterial compositions and concentrations of antimicrobial resistance (AMR) genes differed by food type, and that salmon metagenomes were influenced by the production/harvesting method. The approach described in this study is an efficient and effective method of identifying and quantifying the predominant bacteria and AMR genes on food.

Item Type:	Article
Additional Information:	Funding information: This project was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain) and Food Standards Agency (FSA) project FS101185 through an FSA Fellowship to AEM.
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Related URLs:	https://linkinghub.elsevier.com/retrieve...
Depositing User:	LivePure Connector
Date Deposited:	18 Oct 2022 10:32
Last Modified:	06 Jun 2024 15:20
URI:	https://ueaeprints.uea.ac.uk/id/eprint/89143
DOI:	10.1016/j.fm.2022.104162

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