Characterization of an NDM-19-producing Klebsiella pneumoniae strain harboring 2 resistance plasmids from China

Abstract

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a major cause of nosocomial infections and posed challenges on clinical treatments. The main objective of this study was to determinate the genetic characteristics of the NDM-19-producing CRKP strain SCM96. From 2015 to 2017, 18 CRKP strains were recovered from sputum samples of patients in respiratory medicine in 6 hospitals from 5 provinces and cities in China. Polymerase chain reaction results for carbapenem resistance genes detection showed strain SCM96 carried bla_NDM-19. Three types of transconjugants harboring different plasmids were selected by conjugation experiment. The Whole Genome Sequencing (WGS) was performed using the PacBio RS platform. The genome size of SCM96 was 5,579,775 bp and composed of chromosomal DNA (5,398,745 bp) and 2 plasmids, IncFII type plasmid pSCM96-1 (134,869 bp) and IncX3 type plasmid pSCM96-2 (46,161 bp). SCM96 belonged to ST15 and K28. In addition to the 4 antibiotic resistance genes located in the chromosome, pSCM96-1 carried a complex resistance region containing 17 resistance genes and several mobile genetic elements (MGEs) like △Tn6029, In4-like integron, and Tn3, and pSCM96-2 had only 1 bla_NDM-19 gene. As far as we know, this was the first description of bla_NDM-19 in K. pneumoniae. Up to 22 antibiotic resistance genes, several important MGEs, and transferable plasmids might increase the possibility of co-spreading of bla_NDM-19 with other resistance genes.

Keywords: CRKP; Plasmid; WGS; bla(NDM-19).