Research Article
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Published Online: 1 March 2018

Incorporating Whole-Genome Sequencing into Public Health Surveillance: Lessons from Prospective Sequencing of Salmonella Typhimurium in Australia

Publication: Foodborne Pathogens and Disease
Volume 15, Issue Number 3

Abstract

In Australia, the incidence of Salmonella Typhimurium has increased dramatically over the past decade. Whole-genome sequencing (WGS) is transforming public health microbiology, but poses challenges for surveillance. To compare WGS-based approaches with conventional typing for Salmonella surveillance, we performed concurrent WGS and multilocus variable-number tandem-repeat analysis (MLVA) of Salmonella Typhimurium isolates from the Australian Capital Territory (ACT) for a period of 5 months. We exchanged data via a central shared virtual machine and performed comparative genomic analyses. Epidemiological evidence was integrated with WGS-derived data to identify related isolates and sources of infection, and we compared WGS data for surveillance with findings from MLVA typing. We found that WGS data combined with epidemiological data linked an additional 9% of isolates to at least one other isolate in the study in contrast to MLVA and epidemiological data, and 19% more isolates than epidemiological data alone. Analysis of risk factors showed that in one WGS-defined cluster, human cases had higher odds of purchasing a single egg brand. While WGS was more sensitive and specific than conventional typing methods, we identified barriers to uptake of genomic surveillance around complexity of reporting of WGS results, timeliness, acceptability, and stability. In conclusion, WGS offers higher resolution of Salmonella Typhimurium laboratory surveillance than existing methods and can provide further evidence on sources of infection in case and outbreak investigations for public health action. However, there are several challenges that need to be addressed for effective implementation of genomic surveillance in Australia.

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cover image Foodborne Pathogens and Disease
Foodborne Pathogens and Disease
Volume 15Issue Number 3March 2018
Pages: 161 - 167
PubMed: 29336594

History

Published in print: March 2018
Published online: 1 March 2018
Published ahead of print: 16 January 2018

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Laura Ford
National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University, Canberra, Australia.
OzFoodNet, Health Protection Service, Population Health Protection and Prevention, ACT Health, Canberra, Australia.
Glen P. Carter
Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Qinning Wang
Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West—Institute of Clinical Pathology and Medical Research, Sydney, Australia.
Torsten Seemann
Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Vitali Sintchenko
Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West—Institute of Clinical Pathology and Medical Research, Sydney, Australia.
Centre for Infectious Diseases and Microbiology—Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.
Kathryn Glass
National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University, Canberra, Australia.
Deborah A. Williamson
Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Peter Howard
Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West—Institute of Clinical Pathology and Medical Research, Sydney, Australia.
Mary Valcanis
Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Cristina Fabiola Sotomayor Castillo
Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West—Institute of Clinical Pathology and Medical Research, Sydney, Australia.
Centre for Infectious Diseases and Microbiology—Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.
Sydney Medical School—Westmead, The University of Sydney, Sydney, Australia.
Instituto de Salud Publica, Facultad de Medicina, Universidad Austral de Chile, Valdivia, Chile.
Michelle Sait
Centre for Infectious Diseases and Microbiology—Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.
Benjamin P. Howden
Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Infectious Diseases Department, Austin Health, Heidelberg, Australia.
Martyn D. Kirk
National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University, Canberra, Australia.

Notes

Address correspondence to:Laura Ford, MCHAMNational Centre for Epidemiology and Population HealthResearch School of Population HealthThe Australian National UniversityCanberra ACT 2601Australia
E-mail: [email protected]

Disclosure Statement

No competing financial interests exist.

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