TY - JOUR
T1 - Using whole genome sequencing to investigate a mock-outbreak of carbapenem-resistant klebsiella pneumoniae in real-time
AU - Simões, Alexandra Sofia
AU - Touret, Tiago
AU - Faria, Nuno Alexandre
AU - Ladeiro, Susana Peres
AU - Costa, João
AU - Bispo, Soraia
AU - Serrano, Mónica
AU - Palos, Carlos
AU - Miragaia, Maria
AU - Leite, Ricardo Bastos
AU - Sá-Leão, Raquel
N1 - Funding Information:
Fundação para a Ciência e a Tecnologia (FCT) project UID/DTP/04567/2016. This work was financially supported by projects LISBOA-01-0145-FEDER (Microbiologia Molecular, Estrutural e Celular, funded by FEDER through COMPETE2020 – Programa Operacional Competitividade e Internacionalização) and LISBOA-01-0145-FEDER-016417 [ONEIDA co-funded by Fundos Europeus Estruturais e de Investimento, Programa Operacional Regional Lisboa 2020 and Fundação para a Ciência e a Tecnologia (FCT)].
Publisher Copyright:
Copyright © Ordem dos Médicos 2021
PY - 2022/1/3
Y1 - 2022/1/3
N2 - 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.
AB - 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.
KW - Carbapenem-Resistant Enterobacteriaceae/genetics
KW - Gene-Environment Interaction
KW - Infection Control
KW - Klebsiella Infections
KW - Klebsiella pneumoniae/genetics
KW - Whole Genome Sequencing
UR - http://www.scopus.com/inward/record.url?scp=85120618655&partnerID=8YFLogxK
U2 - 10.20344/amp.15174
DO - 10.20344/amp.15174
M3 - Article
C2 - 34755594
AN - SCOPUS:85120618655
SN - 0870-399X
VL - 35
SP - 36
EP - 41
JO - Acta Médica Portuguesa
JF - Acta Médica Portuguesa
IS - 1
ER -