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

Whole-genome sequence analyses revealed the presence of bla_NDM-1 (n=31), bla_GES-5 (n=8), bla_OXA-232 (n=1), or bla_NDM-5 (n=1) in extensively drug-resistant and pandrug-resistant Enterobacteriaceae isolated from in-patients in 10 private hospitals (2012-2013) in Durban, South Africa. Two novel NDM-1 encoding plasmids from Klebsiella pneumoniae were closed by PacBio sequencing. In p19-10_01 (IncFIB(K), 223.434 bp) bla_NDM-1 was part of a Tn1548-like structure (16.276 bp) delineated by IS26. 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 bla_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 K. pneumonia (n=7) only. Whereas p18-43_01 was tracked to K. pneumoniae (n=4), Klebsiella michiganensis (n=1), Serratia marcescens (n=11), Enterobacter spp. (n=7), and Citrobacter freundii (n=1), revealing horizontal spread of this bla_NDM-1-bearing plasmid structure. Global phylogeny showed clustering of the K. pneumoniae (18/20) isolates together with closely related carbapenemase-negative ST101 isolates from other geographical origin. The South African isolates divided into three phylogenetic sub-branches, where each group had distinct resistance and replicon profile, and Fig. carrying either p19-10_01, p18-10_01 or pCHE-A1 (8201 bp). The latter carrying bla_GES-5 and aacA4 within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detected bla_OXA-232 carried by pPKPN4 in K. pneumoniae (ST14) and bla_NDM-5 contained by a pNDM-MGR194-like genetic structure in Escherichia coli (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of CRE in Durban, South Africa.

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