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Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK

A multidrug-resistant strain of Klebsiella pneumoniae (Kp) sequence type (ST) 1788, an otherwise uncommon ST worldwide, was isolated from 65 patients at 11 hospitals and 11 general practices across South and West Wales, UK, between February 2019 and November 2021. A collection of 97 Kp ST1788 isolat...

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Autores principales: Mentasti, Massimo, David, Sophia, Turton, Jane, Morgan, Mari, Turner, Luke, Westlake, Joseph, Jenkins, Jonathan, Williams, Catie, Rey, Sara, Watkins, Joanne, Daniel, Victoria, Mitchell, Shanine, Forbes, Gavin, Wootton, Mandy, Jones, Lim
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10569728/
https://www.ncbi.nlm.nih.gov/pubmed/37668148
http://dx.doi.org/10.1099/mgen.0.001104
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author Mentasti, Massimo
David, Sophia
Turton, Jane
Morgan, Mari
Turner, Luke
Westlake, Joseph
Jenkins, Jonathan
Williams, Catie
Rey, Sara
Watkins, Joanne
Daniel, Victoria
Mitchell, Shanine
Forbes, Gavin
Wootton, Mandy
Jones, Lim
author_facet Mentasti, Massimo
David, Sophia
Turton, Jane
Morgan, Mari
Turner, Luke
Westlake, Joseph
Jenkins, Jonathan
Williams, Catie
Rey, Sara
Watkins, Joanne
Daniel, Victoria
Mitchell, Shanine
Forbes, Gavin
Wootton, Mandy
Jones, Lim
author_sort Mentasti, Massimo
collection PubMed
description A multidrug-resistant strain of Klebsiella pneumoniae (Kp) sequence type (ST) 1788, an otherwise uncommon ST worldwide, was isolated from 65 patients at 11 hospitals and 11 general practices across South and West Wales, UK, between February 2019 and November 2021. A collection of 97 Kp ST1788 isolates (including 94 from Wales) was analysed to investigate the diversity and spread across Wales and to identify molecular marker(s) to aid development of a strain-specific real-time PCR. Whole genome sequencing (WGS) was performed with Illumina technology and the data were used to perform phylogenetic analyses. Pan-genome analysis of further Kp genome collections was used to identify an ST1788-specific gene target; a real-time PCR was then validated against a panel of 314 strains and 218 broth-enriched screening samples. Low genomic diversity was demonstrated amongst the 94 isolates from Wales. Evidence of spread within and across healthcare facilities was found. A yersiniabactin locus and the KL2 capsular locus were identified in 85/94 (90.4 %) and 94/94 (100 %) genomes respectively; bla (SHV-232), bla (TEM-1), bla (CTX-M-15) and bla (OXA-1) were simultaneously carried by 86/94 (91.5 %) isolates; 4/94 (4.3 %) isolates also carried bla (OXA-48) carbapenemase. Aminoglycoside and fluoroquinolone resistance markers were found in 94/94 (100 %) and 86/94 (91.5 %) isolates respectively. The ST1788-specific real-time PCR was 100 % sensitive and specific. Our analyses demonstrated recent clonal expansion and spread of Kp ST1788 in the community and across healthcare facilities in South and West Wales with isolates carrying well-defined antimicrobial resistance and virulence markers. An ST1788-specific marker was also identified, enabling rapid and reliable preliminary characterization of isolates by real-time PCR. This study confirms the utility of WGS in investigating novel strains and in aiding proactive implementation of molecular tools to assist infection control specialists.
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spelling pubmed-105697282023-10-13 Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK Mentasti, Massimo David, Sophia Turton, Jane Morgan, Mari Turner, Luke Westlake, Joseph Jenkins, Jonathan Williams, Catie Rey, Sara Watkins, Joanne Daniel, Victoria Mitchell, Shanine Forbes, Gavin Wootton, Mandy Jones, Lim Microb Genom Research Articles A multidrug-resistant strain of Klebsiella pneumoniae (Kp) sequence type (ST) 1788, an otherwise uncommon ST worldwide, was isolated from 65 patients at 11 hospitals and 11 general practices across South and West Wales, UK, between February 2019 and November 2021. A collection of 97 Kp ST1788 isolates (including 94 from Wales) was analysed to investigate the diversity and spread across Wales and to identify molecular marker(s) to aid development of a strain-specific real-time PCR. Whole genome sequencing (WGS) was performed with Illumina technology and the data were used to perform phylogenetic analyses. Pan-genome analysis of further Kp genome collections was used to identify an ST1788-specific gene target; a real-time PCR was then validated against a panel of 314 strains and 218 broth-enriched screening samples. Low genomic diversity was demonstrated amongst the 94 isolates from Wales. Evidence of spread within and across healthcare facilities was found. A yersiniabactin locus and the KL2 capsular locus were identified in 85/94 (90.4 %) and 94/94 (100 %) genomes respectively; bla (SHV-232), bla (TEM-1), bla (CTX-M-15) and bla (OXA-1) were simultaneously carried by 86/94 (91.5 %) isolates; 4/94 (4.3 %) isolates also carried bla (OXA-48) carbapenemase. Aminoglycoside and fluoroquinolone resistance markers were found in 94/94 (100 %) and 86/94 (91.5 %) isolates respectively. The ST1788-specific real-time PCR was 100 % sensitive and specific. Our analyses demonstrated recent clonal expansion and spread of Kp ST1788 in the community and across healthcare facilities in South and West Wales with isolates carrying well-defined antimicrobial resistance and virulence markers. An ST1788-specific marker was also identified, enabling rapid and reliable preliminary characterization of isolates by real-time PCR. This study confirms the utility of WGS in investigating novel strains and in aiding proactive implementation of molecular tools to assist infection control specialists. Microbiology Society 2023-09-05 /pmc/articles/PMC10569728/ /pubmed/37668148 http://dx.doi.org/10.1099/mgen.0.001104 Text en © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License.
spellingShingle Research Articles
Mentasti, Massimo
David, Sophia
Turton, Jane
Morgan, Mari
Turner, Luke
Westlake, Joseph
Jenkins, Jonathan
Williams, Catie
Rey, Sara
Watkins, Joanne
Daniel, Victoria
Mitchell, Shanine
Forbes, Gavin
Wootton, Mandy
Jones, Lim
Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK
title Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK
title_full Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK
title_fullStr Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK
title_full_unstemmed Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK
title_short Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK
title_sort clonal expansion and rapid characterization of klebsiella pneumoniae st1788, an otherwise uncommon strain spreading in wales, uk
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10569728/
https://www.ncbi.nlm.nih.gov/pubmed/37668148
http://dx.doi.org/10.1099/mgen.0.001104
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