title: Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities.
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.
authors.affiliation: Public Health Services, Ministry of Health, Jerusalem, Israel. giladko@post.bgu.ac.il.|Surveillance and Pathogenomics Israeli Centre of Excellence (SPICE), National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva, Israel. giladko@post.bgu.ac.il.
authors.forename: Jacob
authors.initials: J
authors.lastname: Moran-Gilad
authors.affiliation: Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia. vitali.sintchenko@sydney.edu.au.|Centre for Infectious Diseases and Microbiology - Public Health, Institute of Clinical Pathology and Medical Research - Pathology West, Westmead Hospital, Sydney, Australia. vitali.sintchenko@sydney.edu.au.
authors.forename: Vitali
authors.initials: V
authors.lastname: Sintchenko
authors.affiliation: 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. suska@food.dtu.dk.
authors.forename: Susanne Karlsmose
authors.initials: SK
authors.lastname: Pedersen
authors.affiliation: Bacteriology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA. william.wolfgang@health.ny.gov.
authors.forename: William J
authors.initials: WJ
authors.lastname: Wolfgang
authors.affiliation: Biostatistics Branch, US Food and Drug Administration, College Park, Maryland, USA. James.Pettengill@fda.hhs.gov.
authors.forename: James
authors.initials: J
authors.lastname: Pettengill
authors.affiliation: Biostatistics Branch, US Food and Drug Administration, College Park, Maryland, USA. Errol.Strain@fda.hhs.gov.
authors.forename: Errol
authors.initials: E
authors.lastname: Strain
authors.affiliation: 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. rshe@food.dtu.dk.
authors.forename: Rene S
authors.initials: RS
authors.lastname: Hendriksen
mesh_terms: D019295:Computational Biology; D004269:DNA, Bacterial / Q000032:analysis*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D059021:Laboratory Proficiency Testing; D012015:Reference Standards; D011795:Surveys and Questionnaires
chemical_list: D004269:DNA, Bacterial