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