Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities

BMC Infectious Diseases

Correspondence

William J Wolfgang¹  Errol Strain²  James Pettengill²  Jacob Moran-Gilad³  Vitali Sintchenko⁴  Rene S Hendriksen⁵  Susanne Karlsmose Pedersen⁵ 

[1] Bacteriology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA;Biostatistics Branch, US Food and Drug Administration, College Park, Maryland, USA;Public Health Services, Ministry of Health, Jerusalem, Israel;Surveillance and Pathogenomics Israeli Centre of Excellence (SPICE), National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva, Israel;Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia;Centre for Infectious Diseases and Microbiology – Public Health, Institute of Clinical Pathology and Medical Research – Pathology West, Westmead Hospital, Sydney, Australia;Technical University of Denmark, National Food Institute, Research Group of Microbial Genomics and Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, ground floor, DK - 2800, Kongens Lyngby, Denmark;

关键词: Proficiency;    Bioinformatics;    Next-generation sequencing;    Survey;    End-users;    Public health;    Microbiology;    Standards;   

DOI  :  10.1186/s12879-015-0902-3

 received in 2014-11-13, accepted in 2015-03-13,  发布年份 2015

来源: Springer

【 摘 要 】

The advent of next-generation sequencing (NGS) has revolutionised public health microbiology. Given the potential impact of NGS, it is paramount to ensure standardisation of ‘wet’ laboratory and bioinformatic protocols and promote comparability of methods employed by different laboratories and their outputs. Therefore, one of the ambitious goals of the Global Microbial Identifier (GMI) initiative (http://www.globalmicrobialidentifier.org/) has been to establish a mechanism for inter-laboratory NGS proficiency testing (PT). This report presents findings from the survey recently conducted by Working Group 4 among GMI members in order to ascertain NGS end-use requirements and attitudes towards NGS PT. The survey identified the high professional diversity of laboratories engaged in NGS-based public health projects and the wide range of capabilities within institutions, at a notable range of costs. The priority pathogens reported by respondents reflected the key drivers for NGS use (high burden disease and ‘high profile’ pathogens). The performance of and participation in PT was perceived as important by most respondents. The wide range of sequencing and bioinformatics practices reported by end-users highlights the importance of standardisation and harmonisation of NGS in public health and underpins the use of PT as a means to assuring quality. The findings of this survey will guide the design of the GMI PT program in relation to the spectrum of pathogens included, testing frequency and volume as well as technical requirements. The PT program for external quality assurance will evolve and inform the introduction of NGS into clinical and public health microbiology practice in the post-genomic era.

【 授权许可】

Unknown   
© Moran-Gilad et al.; licensee BioMed Central. 2015. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.