Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time

Authors

  • Alexandra Sofia Simões * This author contributed equally Laboratory of Molecular Microbiology of Human Pathogens. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras.
  • Tiago Touret * This author contributed equally Laboratory of Molecular Microbiology of Human Pathogens. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras.
  • Nuno Alexandre Faria Laboratory of Bacterial Evolution and Molecular Epidemiology. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras.
  • Susana Peres Ladeiro Unidade de Genoma. Instituto Gulbenkian da Ciência. Oeiras.
  • João Costa Unidade de Genoma. Instituto Gulbenkian da Ciência. Oeiras.
  • Soraia Bispo Grupo Coordenador Local do Programa de Prevenção e Controlo de Infeções e de Resistência aos Antimicrobianos. Hospital Beatriz Ângelo. Loures.
  • Mónica Serrano Laboratory of Microbial Development. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras.
  • Carlos Palos Grupo Coordenador Local do Programa de Prevenção e Controlo de Infeções e de Resistência aos Antimicrobianos. Hospital Beatriz Ângelo. Loures.
  • Maria Miragaia Laboratory of Bacterial Evolution and Molecular Epidemiology. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras.
  • Ricardo Bastos Leite Unidade de Genoma. Instituto Gulbenkian da Ciência. Oeiras.
  • Raquel Sá-Leão Laboratory of Molecular Microbiology of Human Pathogens. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras.

DOI:

https://doi.org/10.20344/amp.15174

Keywords:

Carbapenem-Resistant Enterobacteriaceae/genetics, Gene-Environment Interaction, Infection Control, Klebsiella Infections, Klebsiella pneumoniae/genetics, Whole Genome Sequencing

Abstract

Introduction: Healthcare associated infections due to carbapenem-resistant Klebsiella pneumoniae (CRKP) are a major concern in Portuguese hospitals. Whole genome sequencing (WGS) can improve infection control, but this practice is not routinely used by hospital clinical laboratories in Portugal. We simulated the investigation of a CRKP outbreak based on WGS, with the aim of determining, in the minimum possible time, genetic relatedness between CRKP clinical and environmental isolates.
Material and Methods: Ten CRKP clinical isolates routinely obtained in the hospital laboratory were used. Forty environmental samples - from sinks and sink drains of ward rooms - were collected. Environmental samples were plated on selective media and presumptive CRKP colonies were isolated. Total DNA was extracted from all putative CRKP isolates and sequenced. Clonal relatedness was determined by multi-locus sequence typing and core genome single nucleotide polymorphism analysis; the presence of carbapenemase genes was evaluated.
Results: Clinical isolates were characterized in 48 hours: eight strains were confirmed as CRKP, of which six were of ST13 and carried blaKPC-3. Environmental samples results were obtained in six days: eight CRKP were isolated from which five were of ST13 and carried blaKPC-3. Clinical and environmental ST13 isolates were highly related: ten (of 11) isolates differed from each other in < 0.001% of 2 172 367 core nucleotides.
Discussion: WGS can be used as a high-resolution effective tool to investigate healthcare associated infections and track routes of dissemination in real-time.
Conclusion: In Portugal, routine use of WGS to improve infection control could thrive through collaborative initiatives between hospitals and research institutes.

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Published

2022-01-03

How to Cite

1.
Simões AS, Touret T, Faria NA, Peres Ladeiro S, Costa J, Bispo S, Serrano M, Palos C, Miragaia M, Bastos Leite R, Sá-Leão R. Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time. Acta Med Port [Internet]. 2022 Jan. 3 [cited 2022 Dec. 7];35(1):36-41. Available from: https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174

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