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Clin Microbiol Infect. 2018 Nov 22. pii: S1198-743X(18)30730-4. doi: 10.1016/j.cmi.2018.11.004. [Epub ahead of print]

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

Author information

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.

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 blaNDM-1 or blaOXA-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 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.

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

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

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