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United States Department of Agriculture

Agricultural Research Service

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Research Project: Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Location: Bacterial Epidemiology & Antimicrobial Resistance Research

Project Number: 6040-32000-009-01-T
Project Type: Trust Fund Cooperative Agreement

Start Date: Mar 1, 2014
End Date: Aug 30, 2016

1. Screen isolates of Salmonella serovars most often associated with meat products and human infection for resistance to antimicrobials, sanitizers, and biocides used as interventions in meat and poultry production. 2. Compare the genome sequences of resistant isolates to susceptible isolates to identify resistance mechanisms. Also determine if these biocide resistance mechanisms are linked to antibiotic resistance or virulence genes, or if they are found in outbreak strains. 3. Determine which genetic elements encoding the resistance could be used as markers to identify biocide-resistant strains of Salmonella.

We will select isolates from our NARMS (National Antimicrobial Resistance Monitoring System) collection of over 50,000 Salmonella isolated from beef, chicken, swine, and turkeys. We will assay ten randomly chosen isolates of each of the top ten serovars collected from that animal source. From each animal source, we will also randomly pick ten isolates each of the top 10 serovars isolated from human infections. All of these isolates [(4 animals X top 10 serovars X 10 isolates) + (4 animals X top 10 human serovars x 10 isolates = 800 isolates)] will be assayed for resistance to 14 different sanitizer chemicals, using a broth-dilution method. The results from all isolates will be compared to minimum inhibitory concentrations (MIC) of a susceptible Salmonella Typhimurium LT2 control. Isolates will also be assayed for resistance to the standard NARMS antimicrobials to detect any correlations between intervention resistance and antibiotic resistance. The results will be reported to American Meat Institute Foundation (deliverable 1) and released by publication. Twenty-four representative isolates with increased resistance will be selected for genome sequencing using our in-house Roche 454 instrument. The sequences will be loaded into databases for access by other industry researchers (deliverable 2). For each resistant serovar genome sequenced, a sensitive genome will be downloaded from public databases for comparison. For any serovars that do not have a sensitive isolate in the database, a sensitive isolate will be selected from our analyzed collection (estimate ~12 isolates) and sequenced for comparison. Bioinformatics genome comparisons will be used to mine the resistant isolates’ genomes for mechanisms of resistance (e.g. genes encoding transport systems, single nucleotide polymorphisms [SNPS], etc.)that lead to resistance. Genomes will also be analyzed to determine if the resistances to interventions are linked to antimicrobial resistance or virulence genes. Any linkage of resistance to interventions to antimicrobial resistance or virulence would be an important finding. These sequences will be further evaluated for use as markers indicative of especially virulent, resistant, or outbreak strains. These markers will also be evaluated for the development of detection assays that could be used on-farm or in-processing plants to divert or treat animals carrying resistant bacteria. The analysis of these genomes and any markers will be reported to American Meat Institute Foundation and released to the scientific community via publication after any patentable products have been investigated by AMI and ARS (deliverable 3).

Last Modified: 10/16/2017
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