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

P Espinal; E Nucleo; M Caltagirone; V Mattioni Marchetti; M R Fernandes; V Biscaro; R Rigoli; A Carattoli; R Migliavacca; L Villa

doi:10.1016/j.cmi.2018.11.004

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

Clin Microbiol Infect. 2019 Mar;25(3):385.e1-385.e5. doi: 10.1016/j.cmi.2018.11.004. Epub 2018 Nov 22.

Authors

P Espinal¹, E Nucleo², M Caltagirone², V Mattioni Marchetti², M R Fernandes³, V Biscaro⁴, R Rigoli⁴, A Carattoli⁵, R Migliavacca², L Villa⁶

Affiliations

¹ Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy; Servei de Microbiologia Hospital de la Santa Creu i Sant Pau, Institut d'Investigaciò Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain.
² Clinical-Surgical, Diagnostic and Paediatric Sciences Department, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy.
³ Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy; Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil.
⁴ Microbiology Department, Treviso Hospital, Treviso, Italy.
⁵ Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy. Electronic address: alessandra.carattoli@iss.it.
⁶ Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.

PMID: 30472424
DOI: 10.1016/j.cmi.2018.11.004

Abstract

Objectives: Genomic characterization of the internationally spread sequence type (ST) 16 carbapenem-resistant Klebsiella pneumoniae.

Methods: 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 bla_NDM-1 or bla_OXA-232 carbapenemase genes were assembled and sequences were analysed.

Results: 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 bla_OXA-232 and IncF plasmids carrying bla_NDM-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.

Conclusions: The ST16 K. pneumoniae clone has spread worldwide and may become a high-risk clone.

Keywords: Antimicrobial resistance; Carbapenemase; Healthcare-associated infections; IncF; Outbreak.

MeSH terms

Anti-Bacterial Agents / pharmacology*
Bacterial Proteins / genetics
Bacterial Proteins / metabolism*
Carbapenems / pharmacology*
Drug Resistance, Multiple, Bacterial / genetics*
Genetic Variation
Genome, Bacterial / genetics*
Humans
Klebsiella Infections / microbiology
Klebsiella pneumoniae / classification
Klebsiella pneumoniae / genetics*
Klebsiella pneumoniae / isolation & purification
Phylogeny
Plasmids / genetics
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
beta-Lactamases / genetics
beta-Lactamases / metabolism*

Substances

Anti-Bacterial Agents
Bacterial Proteins
Carbapenems
beta-Lactamases