Pathogenomics and Evolutionary Epidemiology of Multi-Drug Resistant Clinical Klebsiella pneumoniae Isolated from Pretoria, South Africa

Antibiotic-resistant Klebsiella pneumoniae is increasingly being implicated in invasive infections worldwide with high mortalities. Forty-two multidrug resistant (MDR) K. pneumoniae isolates were collected over a 4-month period. Antimicrobial susceptibility was determined using Microscan. The evolutionary epidemiology, resistome, virulome and mobilome of the isolates were characterised using whole-genome sequencing and bioinformatics analysis. All isolates contained the bla CTX-M gene, whilst 41/42(97%) contained bla TEM , 36/42(86%) contained bla OXA and 35/42(83%) harboured bla SHV genes. Other resistance genes found included bla LEN , aac(6 ′ )-lb-cr , qnr A, qnr B, qnr S, oqx AB, aad , aph , dfr , sul 1, sul 2, fos A, and cat genes. Fluoroquinolone and colistin resistance-conferring mutations in par C, gyr AB, pmr AB, pho PQ and kpn EF were identified. The bla LEN gene, rarely described worldwide, was identified in four isolates. The isolates comprised diverse sequence types, the most common being ST152 in 7/42(17%) isolates; clone-specific O and K capsule types were identified. Diverse virulence genes that were not clone-specific were identified in all but one isolate. IncF, IncH and IncI plasmid replicons and two novel integrons were present. The bla CTX-M-15 and bla TEM-1 genes were bracketed by Tn3 transposons, IS Ec9 , a resolvase and IS91 insertion sequence. There were 20 gene cassettes in 14 different cassette arrays, with the dfrA and aadA gene cassettes being the most frequent. Phylogenetic analysis demonstrated that the isolates were evolutionarily associated with strains from both South Africa and abroad. These findings depict the rich resistome, mobilome and virulome repertoire in clinical K. pneumoniae strains, which are mainly transmitted by clonal, multiclonal and horizontal means in South Africa.