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Surveillance of carbapenem-resistant organisms using next-generation sequencing

The genomic data generated from next-generation sequencing (NGS) provides nucleotide-level resolution of bacterial genomes which is critical for disease surveillance and the implementation of prevention strategies to interrupt the spread of antimicrobial resistance (AMR) bacteria. Infection with AMR...

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Autores principales: Gali, Katelin V., St. Jacques, Rachael M., Daniels, Cheyanne I. D., O'Rourke, Allison, Turner, Lauren
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225708/
https://www.ncbi.nlm.nih.gov/pubmed/37255756
http://dx.doi.org/10.3389/fpubh.2023.1184045
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author Gali, Katelin V.
St. Jacques, Rachael M.
Daniels, Cheyanne I. D.
O'Rourke, Allison
Turner, Lauren
author_facet Gali, Katelin V.
St. Jacques, Rachael M.
Daniels, Cheyanne I. D.
O'Rourke, Allison
Turner, Lauren
author_sort Gali, Katelin V.
collection PubMed
description The genomic data generated from next-generation sequencing (NGS) provides nucleotide-level resolution of bacterial genomes which is critical for disease surveillance and the implementation of prevention strategies to interrupt the spread of antimicrobial resistance (AMR) bacteria. Infection with AMR bacteria, including Gram-negative Carbapenem-Resistant Organisms (CRO), may be acute and recurrent—once they have colonized a patient, they are notoriously difficult to eradicate. Through phylogenetic tools that assess the single nucleotide polymorphisms (SNPs) within a pathogen genome dataset, public health scientists can estimate the genetic identity between isolates. This information is used as an epidemiologic proxy of a putative outbreak. Pathogens with minimal to no differences in SNPs are likely to be the same strain attributable to a common source or transmission between cases. These genomic comparisons enhance public health response by prompting targeted intervention and infection control measures. This methodology overview demonstrates the utility of phenotypic and molecular assays, antimicrobial susceptibility testing (AST), NGS, publicly available genomics databases, and open-source bioinformatics pipelines for a tiered workflow to detect resistance genes and potential clusters of illness. These methods, when used in combination, facilitate a genomic surveillance workflow for detecting potential AMR bacterial outbreaks to inform epidemiologic investigations. Use of this workflow helps to target and focus epidemiologic resources to the cases with the highest likelihood of being related.
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spelling pubmed-102257082023-05-30 Surveillance of carbapenem-resistant organisms using next-generation sequencing Gali, Katelin V. St. Jacques, Rachael M. Daniels, Cheyanne I. D. O'Rourke, Allison Turner, Lauren Front Public Health Public Health The genomic data generated from next-generation sequencing (NGS) provides nucleotide-level resolution of bacterial genomes which is critical for disease surveillance and the implementation of prevention strategies to interrupt the spread of antimicrobial resistance (AMR) bacteria. Infection with AMR bacteria, including Gram-negative Carbapenem-Resistant Organisms (CRO), may be acute and recurrent—once they have colonized a patient, they are notoriously difficult to eradicate. Through phylogenetic tools that assess the single nucleotide polymorphisms (SNPs) within a pathogen genome dataset, public health scientists can estimate the genetic identity between isolates. This information is used as an epidemiologic proxy of a putative outbreak. Pathogens with minimal to no differences in SNPs are likely to be the same strain attributable to a common source or transmission between cases. These genomic comparisons enhance public health response by prompting targeted intervention and infection control measures. This methodology overview demonstrates the utility of phenotypic and molecular assays, antimicrobial susceptibility testing (AST), NGS, publicly available genomics databases, and open-source bioinformatics pipelines for a tiered workflow to detect resistance genes and potential clusters of illness. These methods, when used in combination, facilitate a genomic surveillance workflow for detecting potential AMR bacterial outbreaks to inform epidemiologic investigations. Use of this workflow helps to target and focus epidemiologic resources to the cases with the highest likelihood of being related. Frontiers Media S.A. 2023-05-15 /pmc/articles/PMC10225708/ /pubmed/37255756 http://dx.doi.org/10.3389/fpubh.2023.1184045 Text en Copyright © 2023 Gali, St. Jacques, Daniels, O'Rourke and Turner. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Public Health
Gali, Katelin V.
St. Jacques, Rachael M.
Daniels, Cheyanne I. D.
O'Rourke, Allison
Turner, Lauren
Surveillance of carbapenem-resistant organisms using next-generation sequencing
title Surveillance of carbapenem-resistant organisms using next-generation sequencing
title_full Surveillance of carbapenem-resistant organisms using next-generation sequencing
title_fullStr Surveillance of carbapenem-resistant organisms using next-generation sequencing
title_full_unstemmed Surveillance of carbapenem-resistant organisms using next-generation sequencing
title_short Surveillance of carbapenem-resistant organisms using next-generation sequencing
title_sort surveillance of carbapenem-resistant organisms using next-generation sequencing
topic Public Health
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225708/
https://www.ncbi.nlm.nih.gov/pubmed/37255756
http://dx.doi.org/10.3389/fpubh.2023.1184045
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