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Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines

BACKGROUND: Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied. METHODS: A retrospective sequencing survey was performed on carbapenem-, ex...

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Autores principales: Carlos, Celia C, Masim, Melissa Ana L, Lagrada, Marietta L, Gayeta, June M, Macaranas, Polle Krystle V, Sia, Sonia B, Facun, Maria Adelina M, Palarca, Janziel Fiel C, Olorosa, Agnettah M, Cueno, Gicell Anne C, Abrudan, Monica, Abudahab, Khalil, Argimón, Silvia, Kekre, Mihir, Underwood, Anthony, Stelling, John, Aanensen, David M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8634409/
https://www.ncbi.nlm.nih.gov/pubmed/34850834
http://dx.doi.org/10.1093/cid/ciab776
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author Carlos, Celia C
Masim, Melissa Ana L
Lagrada, Marietta L
Gayeta, June M
Macaranas, Polle Krystle V
Sia, Sonia B
Facun, Maria Adelina M
Palarca, Janziel Fiel C
Olorosa, Agnettah M
Cueno, Gicell Anne C
Abrudan, Monica
Abudahab, Khalil
Argimón, Silvia
Kekre, Mihir
Underwood, Anthony
Stelling, John
Aanensen, David M
author_facet Carlos, Celia C
Masim, Melissa Ana L
Lagrada, Marietta L
Gayeta, June M
Macaranas, Polle Krystle V
Sia, Sonia B
Facun, Maria Adelina M
Palarca, Janziel Fiel C
Olorosa, Agnettah M
Cueno, Gicell Anne C
Abrudan, Monica
Abudahab, Khalil
Argimón, Silvia
Kekre, Mihir
Underwood, Anthony
Stelling, John
Aanensen, David M
author_sort Carlos, Celia C
collection PubMed
description BACKGROUND: Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied. METHODS: A retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Known AMR mechanisms were identified. Potential outbreaks were investigated by detecting clusters from epidemiologic, phenotypic, and genome-derived data. RESULTS: Prevalent AMR mechanisms detected include bla(CTX-M-15) (76.8%) and bla(NDM-1) (37.5%). An epidemic IncFII(Yp) plasmid carrying bla(NDM-1) was also detected in 46 isolates from 6 sentinel sites and 14 different sequence types (STs). This plasmid was also identified as the main vehicle of carbapenem resistance in 2 previously unrecognized local outbreaks of ST348 and ST283 at 2 different sentinel sites. A third local outbreak of ST397 was also identified but without the IncFII(Yp) plasmid. Isolates in each outbreak site showed identical STs and K- and O-loci, and similar resistance profiles and AMR genes. All outbreak isolates were collected from blood of children aged < 1 year. CONCLUSION: WGS provided a better understanding of the epidemiology of multidrug resistant Klebsiella in the Philippines, which was not possible with only phenotypic and epidemiologic data. The identification of 3 previously unrecognized Klebsiella outbreaks highlights the utility of WGS in outbreak detection, as well as its importance in public health and in implementing infection control programs.
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spelling pubmed-86344092021-12-01 Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines Carlos, Celia C Masim, Melissa Ana L Lagrada, Marietta L Gayeta, June M Macaranas, Polle Krystle V Sia, Sonia B Facun, Maria Adelina M Palarca, Janziel Fiel C Olorosa, Agnettah M Cueno, Gicell Anne C Abrudan, Monica Abudahab, Khalil Argimón, Silvia Kekre, Mihir Underwood, Anthony Stelling, John Aanensen, David M Clin Infect Dis Supplement Articles BACKGROUND: Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied. METHODS: A retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Known AMR mechanisms were identified. Potential outbreaks were investigated by detecting clusters from epidemiologic, phenotypic, and genome-derived data. RESULTS: Prevalent AMR mechanisms detected include bla(CTX-M-15) (76.8%) and bla(NDM-1) (37.5%). An epidemic IncFII(Yp) plasmid carrying bla(NDM-1) was also detected in 46 isolates from 6 sentinel sites and 14 different sequence types (STs). This plasmid was also identified as the main vehicle of carbapenem resistance in 2 previously unrecognized local outbreaks of ST348 and ST283 at 2 different sentinel sites. A third local outbreak of ST397 was also identified but without the IncFII(Yp) plasmid. Isolates in each outbreak site showed identical STs and K- and O-loci, and similar resistance profiles and AMR genes. All outbreak isolates were collected from blood of children aged < 1 year. CONCLUSION: WGS provided a better understanding of the epidemiology of multidrug resistant Klebsiella in the Philippines, which was not possible with only phenotypic and epidemiologic data. The identification of 3 previously unrecognized Klebsiella outbreaks highlights the utility of WGS in outbreak detection, as well as its importance in public health and in implementing infection control programs. Oxford University Press 2021-11-25 /pmc/articles/PMC8634409/ /pubmed/34850834 http://dx.doi.org/10.1093/cid/ciab776 Text en © The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Supplement Articles
Carlos, Celia C
Masim, Melissa Ana L
Lagrada, Marietta L
Gayeta, June M
Macaranas, Polle Krystle V
Sia, Sonia B
Facun, Maria Adelina M
Palarca, Janziel Fiel C
Olorosa, Agnettah M
Cueno, Gicell Anne C
Abrudan, Monica
Abudahab, Khalil
Argimón, Silvia
Kekre, Mihir
Underwood, Anthony
Stelling, John
Aanensen, David M
Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines
title Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines
title_full Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines
title_fullStr Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines
title_full_unstemmed Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines
title_short Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines
title_sort genome sequencing identifies previously unrecognized klebsiella pneumoniae outbreaks in neonatal intensive care units in the philippines
topic Supplement Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8634409/
https://www.ncbi.nlm.nih.gov/pubmed/34850834
http://dx.doi.org/10.1093/cid/ciab776
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