[HTML][HTML] Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools

AL Cooper, A Low, A Wong, S Tamber, BW Blais… - BMC microbiology, 2024 - Springer
Background Although the spread of antimicrobial resistance (AMR) through food and its
production poses a significant concern, there is limited research on the prevalence of AMR …

[HTML][HTML] Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods

JA Shay, LSE Haniford, A Cooper, CD Carrillo… - Environmental …, 2023 - Springer
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 …

On the Utility of Genomics-Based Methods for Surveillance of Antimicrobial-Resistant Bacteria in the Food Production Continuum

A Cooper - 2021 - repository.library.carleton.ca
Overuse of antimicrobials in medicine and agriculture are believed to be drivers of the
spread of AMR among pathogenic bacteria. Antimicrobial use in agriculture and food …

[HTML][HTML] Detection of antimicrobial resistance genes in the milk production environment: Impact of host DNA and sequencing depth

S Rubiola, F Chiesa, A Dalmasso, P Di Ciccio… - Frontiers in …, 2020 - frontiersin.org
Over the past decades, antimicrobial resistance (AMR) has been recognized as one of the
most serious threats to public health. Although originally considered a problem to human …

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

A Flint, A Cooper, M Rao, K Weedmark… - Frontiers in …, 2023 - frontiersin.org
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 …

Risk assessment of antimicrobial resistance along the food chain through culture‐independent methodologies

Host institution: Department of Food Hygiene and … - Efsa …, 2018 - Wiley Online Library
Antimicrobial resistance (AMR) represents a major challenge for Public Health and the
scientific community, and requires immediate and drastic solutions. Acquired resistance to …

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

SJ Bloomfield, AL Zomer, J O'grady, GL Kay, J Wain… - Food …, 2023 - Elsevier
Food products carry bacteria unless specifically sterilised. These bacteria can be
pathogenic, commensal or associated with food spoilage, and may also be resistant to …

[HTML][HTML] Analysis of Antimicrobial Resistance in Bacterial Pathogens Recovered from Food and Human Sources: Insights from 639,087 Bacterial Whole-Genome …

AL Cooper, A Wong, S Tamber, BW Blais, CD Carrillo - Microorganisms, 2024 - mdpi.com
Understanding the role of foods in the emergence and spread of antimicrobial resistance
necessitates the initial documentation of antibiotic resistance genes within bacterial species …

[HTML][HTML] Integrating whole-genome sequencing data into quantitative risk assessment of foodborne antimicrobial resistance: a review of opportunities and challenges

L Collineau, P Boerlin, CA Carson… - Frontiers in …, 2019 - frontiersin.org
Whole-genome sequencing (WGS) will soon replace traditional phenotypic methods for
routine testing of foodborne antimicrobial resistance (AMR). WGS is expected to improve …

Antibiotic resistance genes across a wide variety of metagenomes

D Fitzpatrick, F Walsh - FEMS microbiology ecology, 2016 - academic.oup.com
The distribution of potential clinically relevant antibiotic resistance (AR) genes across soil,
water, animal, plant and human microbiomes is not well understood. We aimed to …