Antimicrobial Resistance and Molecular Epidemiology of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Klebsiella Species in Dairy Farms

Extended-spectrum beta-lactamase (ESBL)-producing-E. coli and -Klebsiella species present major global health threats. However, there is limited information on the status and genomic epidemiology of these bacteria in the United States conventional dairy cattle farms that frequently use beta-lactam antibiotics. This dissertation is aimed to determine the prevalence, antimicrobial resistance, spread mechanisms, and public health implication of ESBL-E. coli and -Klebsiella spp. using microbiological and molecular tools. A total of 605 samples (rectal feces, bulk tank milk (BTM), manure, water, and feed) were tested. From these, 241 ESBL-E. coli and 59 ESBL-Klebsiella spp. were detected. The prevalence of fecal ESBL-E. coli and -Klebsiella spp. were 47.5% (n=508) and 7.2 % (n=508), respectively. Most E. coli isolates (94.4%, n=241) were multidrug-resistant (MDR), whereas only 19% (n=57) ESBL-Klebsiella spp. were MDR. Six families of beta-lactamase (bla) genes, along with several other resistance genes (ARGs), were detected in both E. coli and Klebsiella spp. The bla_CTX-M and bla_TEM were the most frequent in E. coli, whereas bla_SHV and bla_CTX-M were dominant in ESBL-Klebsiella spp. A 47 distinct sequence types (STs), 13 unknown, and 4 novel STs of ESBL-E. coli and 15 distinct STs, and 10 unknown STs of ESBL-K. pneumoniae were identified. High-risk E. coli clones accounted for 28% (n=67) of the identified STs. Both ESBL-E. coli and -K. pneumoniae STs were clustered within farms, suggesting animal-to-animal transmission. Evidence of horizontal spread of bla genes via plasmid was also observed. ESBL-E. coli and -Klebsiella spp. were detected in 24.2% and 6.1 % of BTM, respectively. About 41% of dairy farms had ESBL-E. coli in their BTM. All ESBL-E. coli isolates from BTM were MDR and co-carried the bla_CTX-M, other ARGs, and several virulence genes. Isolates with matching STs and resistance patterns were detected in BTM, and fecal samples collected from the same farm. Four ESBL-E. coli STs obtained from BTM were high-risk pandemic clones. MDR ESBL-E. coli, including high risk-clones, and ESBL-Klebsiella spp. were widespread in dairy farms and BTM. These findings indicate that dairy cattle can serve as a reservoir for zoonotic ESBL-E. coli and -K. pneumoniae