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 mechani- cal ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understand- ing 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 dis- criminating even highly related lineages of bacteria and revolutionize outbreak anal- ysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early se- quencing 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 ad- vantages 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 out- break analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.

Authors: Scott Quainoo [a], Jordy P. M. Coolen [b], Sacha A. F. T. van Hijum [c,d], Martijn A. Huynen [c], Willem J. G. Melchers [b], Willem van Schaik [e], Heiman F. L. Wertheim [b]
[a] Department of Microbiology, Radboud University, Nijmegen, The Netherlands;
[b] Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands;
[c] Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands;
[d] NIZO, Ede, The Netherlandsd; Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom

klik hier voor volledige artikel, gepubliseerd in Clin Microbiol Rev 30:1015–1063 – 30 aug 2018

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