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. 2019 Nov 21:7:317.
doi: 10.3389/fpubh.2019.00317. eCollection 2019.

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

Marie Anne Chattaway  1 , Timothy J Dallman  1 , Lesley Larkin  2 , Satheesh Nair  1 , Jacquelyn McCormick  2 , Amy Mikhail  2 , Hassan Hartman  1 , Gauri Godbole  1 , David Powell  1 , Martin Day  1 , Robert Smith  3 , Kathie Grant  1
Affiliations

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

Marie Anne Chattaway et al. Front Public Health. .

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.

Keywords: SNP typing; Salmonella; WGS; genomic typing; molecular epidemiology.

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Figures

Figure 1
Figure 1
Flow Chart of Service Provision and information workflows between PHE and external organizations for Salmonella reference microbiology and surveillance. NHS, National Health Service; FW&E, Food, Water and Environmental; PHE, Public Health England; GBRU, Gastrointestinal Bacteria Reference Unit; WGSDU, Whole Genome Sequencing Delivery Unit; LIMS, Laboratory Information Management System; GDW, Gastro Data Warehouse; SGSS, Second Generation Surveillance System; NCBI, National Center for Biotechnology Information; SRA, Short Read Archive; GI, Gastrointestinal; FS, Field Services; HPT, Health Protection Team; EPIS, Epidemic Intelligence Information System; RASFF, Rapid Alert System for Food and Feed; EHO, Environmental Health Officers; FSA, Food Standards Agency; APHA, Animal and Plant Health Agency; ECDC, European Center for Disease Prevention and Control; EFSA, European Food Safety Authority; DEFRA, Department for Environment, Food and Rural Affairs. Databases/Platforms include GDW, LIMS, EPIS, RASFF, and Enterobase.
Figure 2
Figure 2
Population structure of 16,854 Salmonella isolated from humans and submitted to PHE from local and regional hospital laboratories in England and Wales between April 2016 and March 2018.
Figure 3
Figure 3
Overview of Salmonella reports and methodology for serovar identification, April 2016–March 2018.
See this image and copyright information in PMC

References

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    1. England PH. The Health Protection (Notification) Regulations 2010. Public Health England, The Stationery Office Limited; (2010). p. 659.
    1. Wales PH. The Health Protection (Notification) (Wales) Regulations 2010. Public Health England, The Stationery Office Limited; (2010). p. 1546.

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