Molecular epidemiology of Antibiotic-Resistant Escherichia coli from companion animals attending veterinary practices in Durban, KwaZulu-Natal, South Africa.

Abstract

Background: Companion animals are globally documented to harbour antibiotic-resistant E. coli.This study aimed to investigate the molecular epidemiology of antibiotic-resistant E. coli from companion animals presenting at veterinary practices in Durban, KwaZulu-Natal, South Africa.Methods: E. coli were isolated on selective media from rectal swabs sampled from dogs and cats attending veterinary practices in Durban, KwaZulu-Natal, South Africa. All isolates were confirmed using real-time polymerase chain reaction (PCR) of the uidA gene. Antibiotic susceptibility testing was done against 20 antibiotics using the Kirby-Bauer disk diffusion method. Selected antibioticresistance genes (ARGs) that confer resistance to third-generation cephalosporins (blaTEM, blaSHV, and blaCTX-M), tetracycline (tetA, and tetB), and tigecycline (tetX/X2, tetX3, and tetX4), were detected using conventional PCR. PCR amplicons were confirmed by DNA sequencing and bioinformatics analysis. Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) was carried out to determine the clonality of E. coli (101) isolates that showed resistance to at least one antibiotic. Results: A total of 330 E. coli isolates from dogs (234) and cats (96) formed the study sample. Overall resistance was high in tetracycline (24.2%), ampicillin (18.8%), trimethoprimsulfamethoxazole (14%), cephalexin (11.2%) and nalidixic acid (9.7%). Whilst lower resistance was observed in amikacin (0.3%), ceftazidime (0.3%), and piperacillin-tazobactam (0.6%). Thirdgeneration cephalosporin-resistant E. coli retrieved from cats (26%) was more prevalent compared to dogs (9.8%). E. coli from dogs (2.1%) and cats (2%) were resistant to forth-generational cephalosporins. E. coli (3%) retrieved from dogs was resistant to tigecycline, which is regarded as a medically important antimicrobial (MIA) in human medicine. No resistance was observed against carbapenems. Thirty-five (10.6%) E. coli were multidrug-resistant (MDR) and exhibited twenty-two different phenotypic patterns. Amongst the E. coli that were not susceptible to third-generation cephalosporin, and tetracycline, it was observed that the blaCTX-M-15 (8%), and tetA (24%) were the most prevalent resistance genes. Thirty-one (9.3%) isolates were non-susceptible to third-generation cephalosporins and had the corresponding extended-spectrum beta-lactamase (ESBL) genes. The blaCTX-M-15 type gene was prevalent in all 25 E. coli isolates that tested positive for the blaCTX-M. The blaTEM-1 (17) was the second most prevalent β-lactamase gene. A total of 80/330 (24%) isolates were phenotypically not susceptible to tetracycline and carried either one, or both of tetA and tetB resistance genes. Only one tetracycline-resistant E. coli isolate did not harbour either tetA, or tetB genes. The blaSHV, tetX/X2, tetX3, and tetX4 were not detected in all the isolates. Using a 75% similarity cut-off, forty-eight clusters with isolates from both dogs and cats were identified. The xv ERIC-PCR types depicted a variety of clust...