Antimicrobial resistance is a widely recognized concern in companion animal medicine. Fecal, oral and aural culture swabs were obtained from 77 dogs and 32 cats at the time of routine spay/neuter surgery. Each swab was processed utilizing sequential selective media broths (MacConkey + cephalothin followed by MacConkey + cephalothin + ceftiofur) followed by MacConkey agar plating. Colonies phenotypically and morphologically consistent with E. coli or K. pneumoniae were positively identified to species level with PCR, and a multiplex PCR protocol was utilized for identification of extended spectrum betalactamase (ESBL) genes. Numerous ESBL genes, including those from the ACC, CIT, CTM, EBC, FOX, OXA, TEM and VIM families, were detected. Kirby Bauer antimicrobial susceptibility testing was performed on all isolates. Multidrug resistance was common in E. coli isolates as indicated by high resistance rates for tetracycline (76.8%), trimethoprim sulfamethoxazole (78.6%), enrofloxacin (37.5%), gentamicin (30.4%), and chloramphenicol (32.1%). No isolates were resistant to imipenem. Resistance to cefpodoxime was detected in 100% of E. coli and K. pneumoniae isolates. Escherichia coli and K. pneumoniae with confirmed ESBL characteristics were detected in 39% and 11.7% of dogs, and in 28.1% and 25% of cats, respectively. In total, an ESBL-producing E. coli and/or K. pneumoniae was detected in 53.2% of dogs and cats presenting for routine surgery. This alarmingly high prevalence of ESBL-producing E. coli and K. pneumoniae in apparently healthy dogs and cats suggests that there is an urgent need for improved antibiotic stewardship guidelines and compliance in the veterinary community.