The importance of public health genomics for ensuring health security for Australia

Williamson, Deborah A; Kirk, Martyn; Sintchenko, Vitali; Howden, Benjamin P

doi:10.5694/mja2.50063

Cited by 10 publications

(7 citation statements)

References 11 publications

(16 reference statements)

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“…The appeal of WGS data comes from the promise of a single workflow to process all microbial pathogens, and the provision of easily portable data that promote deeper integration of surveillance and investigation efforts across jurisdictions. This promise is leading to a concerted effort to move microbial public health to a primarily genome-based workflow in numerous countries [8–10], including Australia [11].…”

Section: Introductionmentioning

confidence: 99%

Complete microbial genomes for public health in Australia and the Southwest Pacific

et al. 2020

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Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbiology laboratories. In this first step, we present 26 complete high-quality bacterial genomes. Additionally, we describe here a framework for reconstructing complete microbial genomes and highlight some of the challenges and considerations for accurate and reproducible genome reconstruction.

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Section: Introductionmentioning

confidence: 99%

Complete microbial genomes for public health in Australia and the Southwest Pacific

et al. 2020

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“…The appeal of WGS data comes from the promise of a single workflow to process all microbial pathogens that can provide easily portable data that promotes deeper integration of surveillance and investigation efforts across jurisdictions. This promise is leading to a concerted effort to move microbial public health to a primarily genome-based workflow at numerous jurisdictions (8–10), including Australia (11).…”

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confidence: 99%

Complete microbial genomes for public health in Australia and Southwest Pacific

Baines

Silva

Carter

et al. 2019

Preprint

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“…Furthermore, we assumed that WGS data will be received prospectively by the public health departments in a timely and standardized format. The harmonisation of WGS and bioinformatic methods, terminology, and reporting across public health and environmental health laboratories is essential for public health surveillance and outbreak detection nationally [28,29]. The ability to link Salmonella isolates from humans, foods, water, animals, and the environment through standardized WGS data across states, regions, and even globally will be key to using WGS data effectively to prevent cases.…”

Section: Plos Onementioning

confidence: 99%

Cost of whole genome sequencing for non-typhoidal Salmonella enterica

et al. 2021

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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.

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The importance of public health genomics for ensuring health security for Australia

Cited by 10 publications

References 11 publications

Complete microbial genomes for public health in Australia and the Southwest Pacific

Complete microbial genomes for public health in Australia and the Southwest Pacific

Complete microbial genomes for public health in Australia and Southwest Pacific

Cost of whole genome sequencing for non-typhoidal Salmonella enterica

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