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

Whole-genome sequence analyses revealed the presence ofbla NDM-1 (n = 31),bla GES-5 (n = 8),bla OXA-232 (n = 1), orbla NDM-5 (n = 1) in extensively drug-resistant and pandrug-resistantEnterobacteriaceae organisms isolated from in-patients in 10 private hospitals (2012 to 2013) in Durban, South Africa. Two novel NDM-1-encoding plasmids fromKlebsiella pneumoniae were circularized 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 thebla 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 inK. pneumoniae (n = 7) only, whereas p18-43_01 was tracked toK. pneumoniae (n = 4),Klebsiella michiganensis (n = 1),Serratia marcescens (n = 11),Enterobacter spp. (n = 7), andCitrobacter freundii (n = 1), revealing horizontal spread of thisbla NDM-1 -bearing plasmid structure. Global phylogeny showed clustering of theK. pneumoniae (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 carriedbla GES-5 andaacA4 within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detectedbla OXA-232 carried by pPKPN4 inK. pneumoniae (ST14) andbla NDM-5 contained by a pNDM-MGR194-like genetic structure inEscherichia coli (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of carbapenem-resistantEnterobacteriaceae in Durban, South Africa.