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Background  The emergence and spread of multidrug‐resistant organisms (MDRO) present a threat to human and animal health.    Objectives  To assess acquisition, prevalence of and risk factors for MDRO carriage in dogs and cats presented to veterinary clinics or practices in Switzerland.    Animals  Privately owned dogs (n = 183) and cats (n = 88) presented to 4 veterinary hospitals and 1 practice.    Methods  Prospective, longitudinal, observational study. Oronasal and rectal swabs were collected at presentation and 69% of animals were sampled again at discharge. Methicillin‐resistant (MR) staphylococci and macrococci, cephalosporinase‐, and carbapenemase‐producing (CP) Enterobacterales were isolated. Genetic relatedness of isolates was assessed by repetitive sequence‐based polymerase chain reaction and multilocus sequence typing. Risk factors for MDRO acquisition and carriage were analyzed based on questionnaire‐derived and hospitalization data.    Results  Admission prevalence of MDRO carriage in pets was 15.5% (95% confidence interval [CI], 11.4‐20.4). The discharge prevalence and acquisition rates were 32.1% (95% CI, 25.5‐39.3) and 28.3% (95% CI, 22‐35.4), respectively. Predominant hospital‐acquired isolates were extended spectrum β‐lactamase‐producing  Escherichia coli  (ESBL ‐E coli ; 17.3%) and β‐lactamase‐producing  Klebsiella pneumoniae  (13.7%). At 1 institution, a cluster of 24 highly genetically related CP  (bla  oxa181  and  bla  oxa48 ) was identified. Multivariate analysis identified hospitalization at clinic 1 (odds ratio [OR], 5.1; 95% CI, 1.6‐16.8) and days of hospitalization (OR 3‐5 days, 4.4; 95% CI, 1.8‐10.9; OR > 5 days, 6.2; 95% CI, 1.3‐28.8) as risk factors for MDRO acquisition in dogs.    Conclusions  Veterinary hospitals play an important role in the selection and transmission of MDRO among veterinary patients.

Acquisition and carriage of multidrug‐resistant organisms in dogs and cats presented to small animal practices and clinics in Switzerland