Whole Genome Sequence Analysis Reveals Antimicrobial Resistance Genes, Plasmids and Potentially Unique Sequence Types of Enterotoxigenic Escherichia coli Isolates Causing Colibacillosis in Neonatal and Weaning Piglets of South Africa

Enterotoxigenic Escherichia coli (ETEC) are pathogenic strains of E. coli that cause colibacillosis in animals and humans. The use of antimicrobials for treatment of colibacillosis may be hampered by the increase in antimicrobial resistance. Plasmids are implicated in the dissemination and persistence of antimicrobial resistance between and amongst different bacterial communities. The aim of this study was to determine the sequence types of, assess the antimicrobial resistance profiles and genes confering such resistance and to screen for plasmids in 20 ETEC samples recovered from piglets from the Limpopo and Eastern Cape provinces of South Africa. Out of 20 samples, 12 were further analysed using whole genome sequencing (WGS) to determine the antimicrobial resistance genes and plasmids. Multilocus sequence typing using WGS showed six different sequence types (ST10, ST56, ST101, ST4253, ST4704, ST1830). Plasmid profiling identified 10 plasmids between 1.3kb and >10kb. Six isolates harbored multiple plasmids. Whole genome sequencing identified seven different plasmids originating from Klebsiella pneumoniae, Salmonella enterica, E. coli K-12, β-lactamase CTX-M-15 plasmids, and Incompatibility groups FII and I2. Furthermore, samples carried antimicrobial resistance genes for tetracycline A (tetA), tetracycline B (tetB), gentamycin (aac(6')-Ii) and the MLS class of antimicrobials (msr(C)). Interestingly, ST4704, ST4253 and ST5766 found in this study appear to be unique as they have not been reported elsewere, and may be important in future. Antimicrobial resistance profiling showed samples exhibiting multiple antimicrobial resistance. This study expands our understanding of ETEC affecting pigs in general and South Africa in particular, which would aid in controlling colibacillosis.