Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis
Scott Quainoo,Jordy P. M. Coolen,Sacha A. F. T. van Hijum,Martijn A. Huynen,Willem J. G. Melchers,Willem van Schaik,Heiman F. L. Wertheim +6 more
TLDR
This review assesses the feasibility of whole-genome sequencing (WGS) technologies and bioinformatics analysis tools for nosocomial outbreak analyses, and presents a real-world example of the implementation of WGS for antimicrobial resistance 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.read more
Citations
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SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
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Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix
TL;DR: FastTree as mentioned in this paper uses sequence profiles of internal nodes in the tree to implement neighbor-joining and uses heuristics to quickly identify candidate joins, then uses nearest-neighbor interchanges to reduce the length of the tree.
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Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution
TL;DR: This review provides a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species.
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Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present
Ricardo Franco-Duarte,Lucia Černáková,Snehal Kadam,Karishma S. Kaushik,Bahare Salehi,Antonio Bevilacqua,Maria Rosaria Corbo,Hubert Antolak,Katarzyna Dybka-Stępień,Martyna Leszczewicz,Saulo R. Tintino,Veruska Cintia Alexandrino de Souza,Javad Sharifi-Rad,Henrique Douglas Melo Coutinho,Natália Martins,Célia F. Rodrigues +15 more
TL;DR: The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations.
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