Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-015-0902-3) contains supplementary material, which is available to authorized users.
Highlights
The advent of next-generation sequencing (NGS) technologies has revolutionised molecular microbiology by making genome sequences of pathogens of clinical or public health importance, readily available [1]
Recent studies have demonstrated that Single nucleotide polymorphism (SNP) mined from whole genome sequence (WGS) data [5,6,7] as well as gene-by-gene (core genome multi-locus sequence typing (MLST) [8]) comparisons provided far greater resolution for outbreak detection and for microbial strain tracking for a wide range of bacterial pathogens than current gold standards such as pulsed-field gel electrophoresis (PFGE), spoligotyping, and variable number tandem repeat-based typing
Proficiency testing programs that cover both sequencing “wet lab” and analytical “dry lab” steps are urgently required. This is the first review of the current state of play, needs and priorities in relation to the proficiency testing for WGS performed in the field of microbiology
Summary
The advent of next-generation sequencing (NGS) technologies has revolutionised molecular microbiology by making genome sequences of pathogens of clinical or public health importance, readily available [1]. NGS has many advantages over other existing molecular approaches, including throughput, quality, flexibility, scalability and may potentially replace a multitude of assays currently run simultaneously in a diagnostic microbiology laboratory [2,3]. Translation of NGS from research centres to public health and clinical laboratories has already begun. Recent studies have demonstrated that SNPs mined from whole genome sequence (WGS) data [5,6,7] as well as gene-by-gene (core genome multi-locus sequence typing (MLST) [8]) comparisons provided far greater resolution for outbreak detection and for microbial strain tracking for a wide range of bacterial pathogens than current gold standards such as pulsed-field gel electrophoresis (PFGE), spoligotyping, and variable number tandem repeat-based typing.
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