Abstract
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.
Highlights
Public Health England’s (PHE) Gastrointestinal Bacterial Reference Unit (GBRU) receives approximately 10,000 presumptive Salmonella isolates each year from diagnostic microbiology laboratories, private laboratories and food, water and environmental laboratories for confirmation of identity and typing
Frontline diagnostic laboratories report the isolation of Salmonella spp to PHE via the Second Generation Surveillance System (SGSS), a database that stores and manages data on laboratory isolates and results, and is the preferred method for capturing routine laboratory surveillance data on all infectious diseases and antimicrobial resistance from laboratories across England [25]
This data is used for the monitoring of the overall number of Salmonella isolated at frontline laboratories and the number of isolates referred to GBRU
Summary
Public Health England’s (PHE) Gastrointestinal Bacterial Reference Unit (GBRU) receives approximately 10,000 presumptive Salmonella isolates each year from diagnostic microbiology laboratories, private laboratories and food, water and environmental laboratories for confirmation of identity and typing. The reporting of Salmonella isolated from human clinical diagnostic samples in public health laboratories is mandatory under national legislation [4, 5]. Prior to the introduction of WGS, presumptive Salmonella isolates were identified and characterized using a variety of methods including assaying biochemical properties [6], real-time PCR [7], phenotypic microarrays (Omnilog), and serology [8, 9]. When the option of using a Whole Genome Sequencing (WGS) approach to streamline laboratory processes, reduce processing time, improve the fine typing discriminatory power for surveillance and outbreak detection in real-time became available, PHE utilized the opportunity to assess its potential in a public health setting
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