The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales

Frontiers in Public Health

article

Marie Anne Chattaway¹  Martin Day¹  Robert Smith²  Kathie Grant¹  Timothy J. Dallman¹  Lesley Larkin³  Satheesh Nair¹  Jacquelyn McCormick³  Amy Mikhail³  Hassan Hartman¹  Gauri Godbole¹  David Powell¹ 

[1] Gastrointestinal Bacteria Reference Unit, Public Health England, United Kingdom;Public Health Wales, United Kingdom;and Travel Health and IHR Division (T.A.R.G.E.T.), Public Health England, United Kingdom

关键词: WGS;    genomic typing;    molecular epidemiology;    Salmonella;    SNP typing;   

DOI  :  10.3389/fpubh.2019.00317

学科分类：社会科学、人文和艺术（综合）

来源: Frontiers

【 摘 要 】

The use of whole genome sequencing (WGS) as a method for supporting outbreak investigations, studying Salmonella microbial populations and improving understanding of pathogenicity has been well-described ( 1 – 3 ). However, performing WGS on a discrete dataset does not pose the same challenges as implementing WGS as a routine, reference microbiology service for public health surveillance. Challenges include translating WGS data into a useable format for laboratory reporting, clinical case management, Salmonella surveillance, and outbreak investigation as well as meeting the requirement to communicate that information in an understandable and universal language for clinical and public health action. Public Health England have been routinely sequencing all referred presumptive Salmonella isolates since 2014 which has transformed our approach to reference microbiology and surveillance. Here we describe an overview of the integrated methods for cross-disciplinary working, describe the challenges and provide a perspective on how WGS has impacted the laboratory and surveillance processes in England and Wales.

【 授权许可】

CC BY