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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » Research » Research Project #428810

Research Project: Genomics and Metagenomics of Antimicrobial-resistance in the Poultry Production Ecosystem

Location: Produce Safety and Microbiology Research

Project Number: 2030-42000-051-005-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 29, 2015
End Date: Sep 30, 2018

Identification of antibiotic resistance genes in the poultry production system through complete genomic and metagenomic DNA sequencing. 2. Characterize the fitness and virulence of Campylobacter jejuni and Campylobacter coli strains analyzed in Objective 1.

Campylobacter strains isolated from conventionally-grown and antibiotic-free chickens and turkeys will be selected for complete genome sequencing, with an emphasis on the identification of antibiotic resistance genes and other genes linked to antibiotic resistance [(The USDA, Agricultural Research Service (ARS)]. Samples (litter, fecal samples, insects) will be obtained from poultry farms. Total genomic DNA will be isolated from these samples and used to construct metagenomic libraries [(Kansas State University (KSU)]. These libraries will be tested on antibiotic-amended agar for the presence of cloned antibiotic resistance genes (KSU). Positive clones will be sequenced by PCR (KSU) or Illumina next-gen sequencing (PSM). Campylobacter strains (from among those selected above for complete genomic sequencing) will be tested for survival in potential insect vectors (e.g. houseflies and darkling beetles; KSU). Strains with different fitness potentials will be analyzed genomically to identify chromosomal markers associated with this enhanced/reduced fitness (ARS).