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 blaCTX-M gene,
whilst 41/42(97%) contained blaTEM, 36/42(86%) contained blaOXA and 35/42(83%) harboured blaSHV
genes. Other resistance genes found included blaLEN, aac(6′)-lb-cr, qnrA, qnrB, qnrS, oqxAB, aad, aph,
dfr, sul1, sul2, fosA, and cat genes. Fluoroquinolone and colistin resistance-conferring mutations in
parC, gyrAB, pmrAB, phoPQ and kpnEF were identified. The blaLEN 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 blaCTX-M-15 and blaTEM-1 genes were bracketed by
Tn3 transposons, ISEc9, 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
Part of this work was presented at the International Society for Infectious Diseases (ISID) Congress, Buenos Aires, Argentina, 2018 (Abstract #1732) and the American Society of Microbiology (ASM) congress, Atlanta, USA 2018 (Abstract #5351).
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