Laura Ford1, Kathryn Glass1, Deborah A Williamson2, Vitali Sintchenko3,4, Jennifer M B Robson5, Emily Lancsar1, Russell Stafford6, Martyn D Kirk1. 1. Research School of Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia. 2. The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia. 3. Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead, New South Wales, Australia. 4. Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, NSW Health Pathology, Sydney, New South Wales, Australia. 5. Sullivan Nicolaides Pathology, Brisbane, Queensland, Australia. 6. Queensland Department of Health, Herston, Queensland, Australia.
Abstract
BACKGROUND: While whole genome sequencing (WGS) may be more expensive than traditional testing and polymerase chain reaction (PCR), simple cost comparisons ignore the potential for WGS to reduce the societal costs of non-typhoidal Salmonella enterica through public health action to prevent illness. METHODS: We determined how many cases the use of WGS data would need to prevent to be cost-equal to serotyping and MLVA, or culture independent testing based on PCR in Australia. We then examined the costs and cost-savings of current typing methods compared with WGS in outbreak scenarios. RESULTS: A median of 275 (90% CrI -55-775) or 1.9% (90% CrI -0.4%-5.4%) of notified serotyped Salmonella cases would need to be prevented for WGS to be cost-equal to current typing methods and 1,550 (90% CrI 820-2,725) or 9.6% of all notified Salmonella cases would need to be prevented to be cost-equal to PCR. WGS is likely to result in cost savings in prolonged outbreaks, where data can support earlier public health action. CONCLUSIONS: Despite currently having a higher cost per isolate, routine WGS of Salmonella was no more expensive than existing typing methods or PCR where >2% of illness was averted.
BACKGROUND: While whole genome sequencing (WGS) may be more expensive than traditional testing and polymerase chain reaction (PCR), simple cost comparisons ignore the potential for WGS to reduce the societal costs of non-typhoidal Salmonella enterica through public health action to prevent illness. METHODS: We determined how many cases the use of WGS data would need to prevent to be cost-equal to serotyping and MLVA, or culture independent testing based on PCR in Australia. We then examined the costs and cost-savings of current typing methods compared with WGS in outbreak scenarios. RESULTS: A median of 275 (90% CrI -55-775) or 1.9% (90% CrI -0.4%-5.4%) of notified serotyped Salmonella cases would need to be prevented for WGS to be cost-equal to current typing methods and 1,550 (90% CrI 820-2,725) or 9.6% of all notified Salmonella cases would need to be prevented to be cost-equal to PCR. WGS is likely to result in cost savings in prolonged outbreaks, where data can support earlier public health action. CONCLUSIONS: Despite currently having a higher cost per isolate, routine WGS of Salmonella was no more expensive than existing typing methods or PCR where >2% of illness was averted.
Authors: Laura Ford; Qinning Wang; Russell Stafford; Kelly-Anne Ressler; Sophie Norton; Craig Shadbolt; Kirsty Hope; Neil Franklin; Radomir Krsteski; Adrienne Carswell; Glen P Carter; Torsten Seemann; Peter Howard; Mary Valcanis; Cristina Fabiola Sotomayor Castillo; John Bates; Kathryn Glass; Deborah A Williamson; Vitali Sintchenko; Benjamin P Howden; Martyn D Kirk Journal: Foodborne Pathog Dis Date: 2018-03-20 Impact factor: 3.171
Authors: T Inns; P M Ashton; S Herrera-Leon; J Lighthill; S Foulkes; T Jombart; Y Rehman; A Fox; T Dallman; E DE Pinna; L Browning; J E Coia; O Edeghere; R Vivancos Journal: Epidemiol Infect Date: 2016-10-26 Impact factor: 4.434
Authors: Rebecca L Bell; Karen G Jarvis; Andrea R Ottesen; Melinda A McFarland; Eric W Brown Journal: Microb Biotechnol Date: 2016-04-04 Impact factor: 5.813