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

Detalhes bibliográficos
Autor(a) principal: Simões, Alexandra Sofia
Data de Publicação: 2022
Outros Autores: Touret, Tiago, Faria, Nuno Alexandre, Peres Ladeiro, Susana, Costa, João, Bispo, Soraia, Serrano, Mónica, Palos, Carlos, Miragaia, Maria, Bastos Leite, Ricardo, Sá-Leão, Raquel
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174
Resumo: 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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spelling Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-TimeSequenciação Total do Genoma Como Ferramenta Para Investigar em Tempo Real um Simulacro de Surto por Klebsiella pneumoniae Resistente aos CarbapenemosCarbapenem-Resistant Enterobacteriaceae/geneticsGene-Environment InteractionInfection ControlKlebsiella InfectionsKlebsiella pneumoniae/geneticsWhole Genome SequencingControle de InfecçõesEnterobacteriáceas Resistentes a Carbapenémicos/genéticaInfecções por KlebsiellaInteração Gene-AmbienteKlebsiella pneumoniae/genéticaSequenciamento Completo do GenomaIntroduction: 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.Introdução: As infeções associadas aos cuidados de saúde por Klebsiella pneumoniae resistente aos carbapenemos (CRKP) são uma preocupação nos hospitais portugueses. A sequenciação total do genoma [whole genome sequencing (WGS)] pode ajudar no controlo de infecção, mas esta prática não é comummente utilizada nos laboratórios clínicos hospitalares em Portugal. O objetivo deste estudo foi simular a investigação de um surto causado por CRKP, utilizando WGS. Pretendia-se testar a utilização desta técnica e determinar, no menor tempo possível, relações genéticas entre estirpes.Material e Métodos: Foram analisados dez isolados clínicos de CRKP. Foram obtidas quarenta amostras ambientais que foram inoculadas em meio seletivo para isolamento de colónias sugestivas de CRKP e depois sequenciado o DNA total dos isolados presumptivamente identificados como CRKP A relação clonal entre as estirpes foi determinada por multi-locus sequence typing e análise de single nucleotide polymorphisms no genoma core. Foi determinada a presença de genes de carbapenemases.Resultados: Os isolados clínicos foram caraterizados em 48 horas: oito isolados foram confirmados como CRKP. A maioria pertencia ao ST13 (n = 6) e possuía o gene blaKPC-3. As amostras ambientais foram caraterizadas em seis dias: foram isoladas oito CRKP, das quais cinco eram ST13 e continham o gene blaKPC-3. Os isolados ST13 clínicos e ambientais eram muito semelhantes entre si: dez dos 11 isolados diferiam entre si em menos de 0,001% dos 2 172 367 nucleótidos core analisados.Discussão: A sequenciação total do genoma pode ser usada como uma ferramenta útil para investigar infecções nosocomiais e rastrear cadeias de disseminação em tempo real.Conclusão: Em Portugal, o uso desta técnica em controlo de infecção pode ser implementado através de colaborações entre hospitais e institutos de investigação.Ordem dos Médicos2022-01-03info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfapplication/pdfapplication/vnd.openxmlformats-officedocument.presentationml.presentationapplication/vnd.openxmlformats-officedocument.presentationml.presentationapplication/pdfapplication/pdfapplication/pdfhttps://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174oai:ojs.www.actamedicaportuguesa.com:article/15174Acta Médica Portuguesa; Vol. 35 No. 1 (2022): January; 36-41Acta Médica Portuguesa; Vol. 35 N.º 1 (2022): Janeiro; 36-411646-07580870-399Xreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAPenghttps://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/6482https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/6483https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/13010https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/13011https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/13034https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/13035https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/13419Direitos de Autor (c) 2021 Acta Médica Portuguesainfo:eu-repo/semantics/openAccessSimões, Alexandra SofiaTouret, TiagoFaria, Nuno AlexandrePeres Ladeiro, SusanaCosta, JoãoBispo, SoraiaSerrano, MónicaPalos, CarlosMiragaia, MariaBastos Leite, RicardoSá-Leão, Raquel2022-12-20T11:07:26Zoai:ojs.www.actamedicaportuguesa.com:article/15174Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T16:20:37.256040Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time
Sequenciação Total do Genoma Como Ferramenta Para Investigar em Tempo Real um Simulacro de Surto por Klebsiella pneumoniae Resistente aos Carbapenemos
title Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time
spellingShingle Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time
Simões, Alexandra Sofia
Carbapenem-Resistant Enterobacteriaceae/genetics
Gene-Environment Interaction
Infection Control
Klebsiella Infections
Klebsiella pneumoniae/genetics
Whole Genome Sequencing
Controle de Infecções
Enterobacteriáceas Resistentes a Carbapenémicos/genética
Infecções por Klebsiella
Interação Gene-Ambiente
Klebsiella pneumoniae/genética
Sequenciamento Completo do Genoma
title_short Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time
title_full Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time
title_fullStr Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time
title_full_unstemmed Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time
title_sort Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time
author Simões, Alexandra Sofia
author_facet Simões, Alexandra Sofia
Touret, Tiago
Faria, Nuno Alexandre
Peres Ladeiro, Susana
Costa, João
Bispo, Soraia
Serrano, Mónica
Palos, Carlos
Miragaia, Maria
Bastos Leite, Ricardo
Sá-Leão, Raquel
author_role author
author2 Touret, Tiago
Faria, Nuno Alexandre
Peres Ladeiro, Susana
Costa, João
Bispo, Soraia
Serrano, Mónica
Palos, Carlos
Miragaia, Maria
Bastos Leite, Ricardo
Sá-Leão, Raquel
author2_role author
author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Simões, Alexandra Sofia
Touret, Tiago
Faria, Nuno Alexandre
Peres Ladeiro, Susana
Costa, João
Bispo, Soraia
Serrano, Mónica
Palos, Carlos
Miragaia, Maria
Bastos Leite, Ricardo
Sá-Leão, Raquel
dc.subject.por.fl_str_mv Carbapenem-Resistant Enterobacteriaceae/genetics
Gene-Environment Interaction
Infection Control
Klebsiella Infections
Klebsiella pneumoniae/genetics
Whole Genome Sequencing
Controle de Infecções
Enterobacteriáceas Resistentes a Carbapenémicos/genética
Infecções por Klebsiella
Interação Gene-Ambiente
Klebsiella pneumoniae/genética
Sequenciamento Completo do Genoma
topic Carbapenem-Resistant Enterobacteriaceae/genetics
Gene-Environment Interaction
Infection Control
Klebsiella Infections
Klebsiella pneumoniae/genetics
Whole Genome Sequencing
Controle de Infecções
Enterobacteriáceas Resistentes a Carbapenémicos/genética
Infecções por Klebsiella
Interação Gene-Ambiente
Klebsiella pneumoniae/genética
Sequenciamento Completo do Genoma
description 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.
publishDate 2022
dc.date.none.fl_str_mv 2022-01-03
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oai:ojs.www.actamedicaportuguesa.com:article/15174
url https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174
identifier_str_mv oai:ojs.www.actamedicaportuguesa.com:article/15174
dc.language.iso.fl_str_mv eng
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dc.relation.none.fl_str_mv https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174
https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/6482
https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/6483
https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/13010
https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/13011
https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/13034
https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/13035
https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/15174/13419
dc.rights.driver.fl_str_mv Direitos de Autor (c) 2021 Acta Médica Portuguesa
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Direitos de Autor (c) 2021 Acta Médica Portuguesa
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dc.publisher.none.fl_str_mv Ordem dos Médicos
publisher.none.fl_str_mv Ordem dos Médicos
dc.source.none.fl_str_mv Acta Médica Portuguesa; Vol. 35 No. 1 (2022): January; 36-41
Acta Médica Portuguesa; Vol. 35 N.º 1 (2022): Janeiro; 36-41
1646-0758
0870-399X
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