Spread of Plasmid-Encoded NDM-1 and GES-5 Carbapenemases among Extensively Drug-Resistant and Pandrug-Resistant Clinical Enterobacteriaceae in Durban, South Africa

Abstract

Whole-genome sequence analyses revealed the presence of <i>bla</i>_NDM-1 (<i>n</i> = 31), <i>bla</i>_GES-5 (<i>n</i> = 8), <i>bla</i>_OXA-232 (<i>n</i> = 1), or <i>bla</i>_NDM-5 (<i>n</i> = 1) in extensively drug-resistant and pandrug-resistant <i>Enterobacteriaceae</i> organisms isolated from in-patients in 10 private hospitals (2012 to 2013) in Durban, South Africa. Two novel NDM-1-encoding plasmids from <i>Klebsiella pneumoniae</i> were circularized by PacBio sequencing. In p19-10_01 [IncFIB(K); 223.434 bp], <i>bla</i>_NDM-1 was part of a Tn<i>1548</i>-like structure (16.276 bp) delineated by IS<i>26</i> The multireplicon plasmid p18-43_01 [IncR_1/IncFIB(pB171)/IncFII(Yp); 212.326 bp] shared an 80-kb region with p19-10_01, not including the <i>bla</i>_NDM-1-containing region. The two plasmids were used as references for tracing NDM-1-encoding plasmids in the other genome assemblies. The p19-10_01 sequence was detected in <i>K. pneumoniae</i> (<i>n</i> = 7) only, whereas p18-43_01 was tracked to <i>K. pneumoniae</i> (<i>n</i> = 4), <i>Klebsiella michiganensis</i> (<i>n</i> = 1), <i>Serratia marcescens</i> (<i>n</i> = 11), <i>Enterobacter</i> spp. (<i>n</i> = 7), and <i>Citrobacter freundii</i> (<i>n</i> = 1), revealing horizontal spread of this <i>bla</i>_NDM-1-bearing plasmid structure. Global phylogeny showed clustering of the <i>K. pneumoniae</i> (18/20) isolates together with closely related carbapenemase-negative ST101 isolates from other geographical origins. The South African isolates were divided into three phylogenetic subbranches, where each group had distinct resistance and replicon profiles, carrying either p19-10_01, p18-10_01, or pCHE-A1 (8,201 bp). The latter plasmid carried <i>bla</i>_GES-5 and <i>aacA4</i> within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detected <i>bla</i>_OXA-232 carried by pPKPN4 in <i>K. pneumoniae</i> (ST14) and <i>bla</i>_NDM-5 contained by a pNDM-MGR194-like genetic structure in <i>Escherichia coli</i> (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of carbapenem-resistant <i>Enterobacteriaceae</i> in Durban, South Africa.