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Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain

1
Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-033 Lisboa, Portugal
2
Laboratory of Microbiology Research in Environmental Health (EnviHealthMicro Lab), Institute of Environmental Health (ISAMB), Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal
3
Institute of Preventive Medicine and Public Health (IMP&SP), Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal
4
Department of Microbiology and Immunology, Faculty of Pharmacy, Universidade de Lisboa, 1649-033 Lisboa, Portugal
5
Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
6
Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
7
Serviço de Patologia Clínica, Centro Hospitalar de Trás-os-Montes e Alto Douro, 5000-508 Vila Real, Portugal
8
Laboratory Medical Microbiology, Department of Veterinary Sciences, CITAB-Centre for the Research and Technology Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
9
Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, 2829-511 Monte da Caparica, Portugal
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Microorganisms 2020, 8(12), 1986; https://doi.org/10.3390/microorganisms8121986
Received: 17 October 2020 / Revised: 9 December 2020 / Accepted: 10 December 2020 / Published: 13 December 2020
(This article belongs to the Special Issue Virulence and Resistance of Klebsiella pneumoniae)
The evolutionary epidemiology, resistome, virulome and mobilome of thirty-one multidrug resistant Klebsiella pneumoniae clinical isolates from the northern Vila Real region of Portugal were characterized using whole-genome sequencing and bioinformatic analysis. The genomic population structure was dominated by two main sequence types (STs): ST147 (n = 17; 54.8%) and ST15 (n = 6; 19.4%) comprising four distinct genomic clusters. Two main carbapenemase coding genes were detected (blaKPC-3 and blaOXA-48) along with additional extended-spectrum β-lactamase coding loci (blaCTX-M-15, blaSHV-12, blaSHV-27, and blaSHV-187). Moreover, whole genome sequencing enabled the identification of one Klebsiella variicola KPC-3 producer isolate previously misidentified as K. pneumoniae, which in addition to the blaKPC-3 carbapenemase gene, bore the chromosomal broad spectrum β-lactamase blaLEN-2 coding gene, oqxAB and fosA resistance loci. The blaKPC-3 genes were located in a Tn4401b transposon (K. variicolan = 1; K. pneumoniaen = 2) and Tn4401d isoform (K. pneumoniaen = 28). Overall, our work describes the first report of a blaKPC-3 producing K. variicola, as well as the detection of this species during infection control measures in surveillance cultures from infected patients. It also highlights the importance of additional control measures to overcome the clonal dissemination of carbapenemase producing clones. View Full-Text
Keywords: Klebsiella pneumoniae; Klebsiella variicola; KPC-3; OXA-48; Gram-negative; molecular epidemiology; carbapenemase; whole-genome sequencing; Enterobacteriaceae; Portugal Klebsiella pneumoniae; Klebsiella variicola; KPC-3; OXA-48; Gram-negative; molecular epidemiology; carbapenemase; whole-genome sequencing; Enterobacteriaceae; Portugal
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MDPI and ACS Style

Perdigão, J.; Caneiras, C.; Elias, R.; Modesto, A.; Spadar, A.; Phelan, J.; Campino, S.; Clark, T.G.; Costa, E.; Saavedra, M.J.; Duarte, A. Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain. Microorganisms 2020, 8, 1986. https://doi.org/10.3390/microorganisms8121986

AMA Style

Perdigão J, Caneiras C, Elias R, Modesto A, Spadar A, Phelan J, Campino S, Clark TG, Costa E, Saavedra MJ, Duarte A. Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain. Microorganisms. 2020; 8(12):1986. https://doi.org/10.3390/microorganisms8121986

Chicago/Turabian Style

Perdigão, João, Cátia Caneiras, Rita Elias, Ana Modesto, Anton Spadar, Jody Phelan, Susana Campino, Taane G. Clark, Eliana Costa, Maria J. Saavedra, and Aida Duarte. 2020. "Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain" Microorganisms 8, no. 12: 1986. https://doi.org/10.3390/microorganisms8121986

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