Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak analysis

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Whole-genome sequencing of bacterial pathogens : the future of nosocomial outbreak analysis. / Quainoo, Scott; Coolen, Jordy P. M.; van Hijum, Sacha A. F. T.; Huynen, Martijn A.; Melchers, Willem J. G.; van Schaik, Willem; Wertheim, Heiman F. L.

In: Clinical Microbiology Reviews, Vol. 30, No. 4, 10.2017, p. 1015-1063.

Research output: Contribution to journalArticlepeer-review

Harvard

Quainoo, S, Coolen, JPM, van Hijum, SAFT, Huynen, MA, Melchers, WJG, van Schaik, W & Wertheim, HFL 2017, 'Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak analysis', Clinical Microbiology Reviews, vol. 30, no. 4, pp. 1015-1063. https://doi.org/10.1128/CMR.00016-17

APA

Quainoo, S., Coolen, J. P. M., van Hijum, S. A. F. T., Huynen, M. A., Melchers, W. J. G., van Schaik, W., & Wertheim, H. F. L. (2017). Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak analysis. Clinical Microbiology Reviews, 30(4), 1015-1063. https://doi.org/10.1128/CMR.00016-17

Vancouver

Author

Quainoo, Scott ; Coolen, Jordy P. M. ; van Hijum, Sacha A. F. T. ; Huynen, Martijn A. ; Melchers, Willem J. G. ; van Schaik, Willem ; Wertheim, Heiman F. L. / Whole-genome sequencing of bacterial pathogens : the future of nosocomial outbreak analysis. In: Clinical Microbiology Reviews. 2017 ; Vol. 30, No. 4. pp. 1015-1063.

Bibtex

@article{b1cb1e8ea82b473cb15a6adf526903b3,
title = "Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak analysis",
abstract = "Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.",
keywords = "whole-genome sequencing, bioinformatics , intensive care units, next-generation sequencing, nosocomial infections, outbreak analysis, outbreak management, pathogen surveillance, point of care",
author = "Scott Quainoo and Coolen, {Jordy P. M.} and {van Hijum}, {Sacha A. F. T.} and Huynen, {Martijn A.} and Melchers, {Willem J. G.} and {van Schaik}, Willem and Wertheim, {Heiman F. L.}",
note = "Copyright {\textcopyright} 2017 American Society for Microbiology.",
year = "2017",
month = oct,
doi = "10.1128/CMR.00016-17",
language = "English",
volume = "30",
pages = "1015--1063",
journal = "Clinical Microbiology Reviews",
issn = "0893-8512",
publisher = "American Society for Microbiology",
number = "4",

}

RIS

TY - JOUR

T1 - Whole-genome sequencing of bacterial pathogens

T2 - the future of nosocomial outbreak analysis

AU - Quainoo, Scott

AU - Coolen, Jordy P. M.

AU - van Hijum, Sacha A. F. T.

AU - Huynen, Martijn A.

AU - Melchers, Willem J. G.

AU - van Schaik, Willem

AU - Wertheim, Heiman F. L.

N1 - Copyright © 2017 American Society for Microbiology.

PY - 2017/10

Y1 - 2017/10

N2 - Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.

AB - Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.

KW - whole-genome sequencing

KW - bioinformatics

KW - intensive care units

KW - next-generation sequencing

KW - nosocomial infections

KW - outbreak analysis

KW - outbreak management

KW - pathogen surveillance

KW - point of care

UR - https://cmr.asm.org/content/31/1/e00082-17

U2 - 10.1128/CMR.00016-17

DO - 10.1128/CMR.00016-17

M3 - Article

C2 - 28855266

VL - 30

SP - 1015

EP - 1063

JO - Clinical Microbiology Reviews

JF - Clinical Microbiology Reviews

SN - 0893-8512

IS - 4

ER -