Genomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15, and OXA-232

• DOI: 10.1016/j.cmi.2018.11.004
• Publication Date: 2018-11-22T19:02:57Z
• Authors: P. Espinal; E. Nucleo; M. Caltagirone; V. Mattioni March...; M.R. Fernandes; V. Biscaro; R. Rigoli; A. Carattoli; R. Migliavacca; L. Villa
• Keywords: clone (Java method); Multilocus sequence typing

Genomic characterization of the internationally spread sequence type (ST) 16 carbapenem-resistant Klebsiella pneumoniae.The complete genomes of three carbapenem producing ST16 K. pneumoniae from Italian patients were analysed by single-nucleotide polymorphism-based phylogeny, core genome multilocus sequence typing, resistance, plasmid, and virulence content and compared with ten genomes of ST16 strains isolated in other countries. Plasmids carrying blaNDM-1 or blaOXA-232 carbapenemase genes were assembled and sequences were analysed.The internationally spread ST16 K. pneumoniae clone showed variability in terms of distribution of NDM-1 and OXA-232 type carbapenemases. In some ST16 strains, up to six plasmids can be simultaneously present in the same cell, including ColE-like plasmids carrying blaOXA-232 and IncF plasmids carrying blaNDM-1. The differences observed in plasmid, resistance, and virulence content and core genome suggested that there is not a unique, highly conserved ST16 clone, but instead different variants of this lineage circulate worldwide.The ST16 K. pneumoniae clone has spread worldwide and may become a high-risk clone.