UC Davis

The challenge of new legislation and growing consumer interest in the prudent use of antimicrobials in the dairy industry has spurred research into the state of antimicrobial resistance (AMR) in cattle within the State of California. In addition, the rapid adoption of next generation sequencing has allowed new perspectives into the causes and potential treatments of common diseases of cattle that often require antimicrobial treatment. The data presented in this dissertation focus on three common ailments of cattle: salmonellosis, mastitis, and metritis. Chapter one details the prevalence of extended-spectrum β-lactamase (ESBL) genes, AmpC-type β-lactamase (ACBL) genes, and plasmid-mediated quinolone resistance (PMQR) genes in Salmonella isolated from bovine fecal samples at a Veterinary Medical Teaching Hospital microbiology laboratory that were detected using a single, novel multiplex qPCR that was developed. Chapter two uses 16s rRNA sequencing to evaluate the effects of dry cow antimicrobial therapy (used to prevent mastitis) on the udder milk microbiota by comparing the microbial populations in milk at dry-off (DRY) (~60 days before calving) and post-partum (FRESH) (4-11 days after calving) from cows receiving intramammary antibiotic infusion prior to dry-off (IMT) and cows that did not receive treatment (CTL). Chapter three presents a large cross-sectional study designed to evaluate factors affecting recovery and AMR in intrauterine E. coli. In total, 307 cows with and without metritis, from which a single E. coli was randomly selected (n = 162), were sampled from 25 farms throughout California. All intrauterine E. coli were resistant to ampicillin, with an AMR prevalence of 30.2% and 33.9% observed for chlortetracycline and oxytetracycline, respectively. Only 8.6% of isolates were resistant to ceftiofur, one of the most common drugs used to treat metritic cows on the farms sampled. Lastly, chapter four reveals the microbial ecology and diversity of the microbiota present within the uterus of post-partum dairy cows with and without metritis using shotgun metagenomics, only the second study to do so, on a subset of the sample population analyzed in chapter three. In general, the uterine microbiota from cows with and without metritis were highly diverse, with the top 12 most abundant genera only accounting for roughly 10% of mean relative abundance. The results presented here highlight the need for better clinical testing data used for interpretation of phenotypic antimicrobial susceptibility testing within large animal veterinary medicine and showcase the potential of 16s rRNA and shotgun sequencing to analyze the endogenous and pathogenic bacteria present within the bovine mammary and uterine microbiomes.