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Genomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15, and OXA-232.
Clin Microbiol Infect 2019; 25(3):385.e1-385.e5CM

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.

Authors+Show Affiliations

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.Clinical-Surgical, Diagnostic and Paediatric Sciences Department, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy.Clinical-Surgical, Diagnostic and Paediatric Sciences Department, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy.Clinical-Surgical, Diagnostic and Paediatric Sciences Department, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy.Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy; Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil.Microbiology Department, Treviso Hospital, Treviso, Italy.Microbiology Department, Treviso Hospital, Treviso, Italy.Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy. Electronic address: alessandra.carattoli@iss.it.Clinical-Surgical, Diagnostic and Paediatric Sciences Department, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy.Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30472424

Citation

Espinal, P, et al. "Genomics of Klebsiella Pneumoniae ST16 Producing NDM-1, CTX-M-15, and OXA-232." Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases, vol. 25, no. 3, 2019, pp. 385.e1-385.e5.
Espinal P, Nucleo E, Caltagirone M, et al. Genomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15, and OXA-232. Clin Microbiol Infect. 2019;25(3):385.e1-385.e5.
Espinal, P., Nucleo, E., Caltagirone, M., Mattioni Marchetti, V., Fernandes, M. R., Biscaro, V., ... Villa, L. (2019). Genomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15, and OXA-232. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases, 25(3), pp. 385.e1-385.e5. doi:10.1016/j.cmi.2018.11.004.
Espinal P, et al. Genomics of Klebsiella Pneumoniae ST16 Producing NDM-1, CTX-M-15, and OXA-232. Clin Microbiol Infect. 2019;25(3):385.e1-385.e5. PubMed PMID: 30472424.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15, and OXA-232. AU - Espinal,P, AU - Nucleo,E, AU - Caltagirone,M, AU - Mattioni Marchetti,V, AU - Fernandes,M R, AU - Biscaro,V, AU - Rigoli,R, AU - Carattoli,A, AU - Migliavacca,R, AU - Villa,L, Y1 - 2018/11/22/ PY - 2018/07/13/received PY - 2018/10/22/revised PY - 2018/11/03/accepted PY - 2018/11/26/pubmed PY - 2019/9/20/medline PY - 2018/11/26/entrez KW - Antimicrobial resistance KW - Carbapenemase KW - Healthcare-associated infections KW - IncF KW - Outbreak SP - 385.e1 EP - 385.e5 JF - Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases JO - Clin. Microbiol. Infect. VL - 25 IS - 3 N2 - 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. SN - 1469-0691 UR - https://www.unboundmedicine.com/medline/citation/30472424/Genomics_of_Klebsiella_pneumoniae_ST16_producing_NDM_1_CTX_M_15_and_OXA_232_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1198-743X(18)30730-4 DB - PRIME DP - Unbound Medicine ER -