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Antibiotic-resistant  Escherichia coli  is a common occurrence in food, clinical, community and environmental settings worldwide. The resistome, mobilome, virulome and phylogenomics of 20 multidrug resistant (MDR) clinical  E. coli  isolates collected in 2013 from Pretoria, South Africa, were characterised. The isolates were all extended-spectrum β-lactamase producers, harbouring CTX-M (n = 16; 80%), TEM-1B (n = 10; 50%) and OXA (n = 12, 60%) β-lactamases alongside genes mediating resistance to fluoroquinolones, aminoglycosides, tetracyclines etc. Most resistance determinants were found on contigs containing IncF plasmid replicons and bracketed by composite transposons (Tn3), diverse ISs and class 1 integrons (In13, In54, In369, and In467). Gene cassettes such as  bla  OXA,   dfrA5-psp-aadA2-cmlA1a-aadA1-qac  and  estX3-psp-aadA2-cmlA1a-aadA1a-qac  were encompassed by Tn 3  and ISs; several isolates had same or highly similar genomic antibiotic resistance islands. ST131 (n = 10), ST617 (n = 2) and singletons of ST10, ST73, ST95, ST410, ST648, ST665, ST744 and ST998 clones were phylogenetically related to clinical (human and animal) strains from Egypt, Kenya, Niger, Nigeria, Tanzania, and UK. A rich repertoire of virulence genes, including  iss, gad and iha  were identified. MDR  E. coli  harbouring chromosomal and plasmid-borne resistance genes in same and multiple clones exist in South Africa, which is very worrying for clinical epidemiology and infectious diseases management.

The Resistome, Mobilome, Virulome and Phylogenomics of Multidrug-Resistant Escherichia coli Clinical Isolates from Pretoria, South Africa