scholarly journals Peer Review #2 of "Identification of Salmonella for public health surveillance using whole genome sequencing (v0.1)"

2016 ◽  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Peer Review ◽  
Genome Sequencing ◽  
Public Health Surveillance ◽  
Health Surveillance ◽  
Whole Genome

scholarly journals Identification and typing of Salmonella for public health surveillance using whole genome sequencing

2015 ◽  
Author(s):  
Philip M Ashton ◽  
Satheesh Nair ◽  
Tansy Peters ◽  
Janet Bale ◽  
David G Powell ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Public Health Surveillance ◽  
Health Surveillance ◽  
Current Data ◽  
Whole Genome ◽  
Mlst Database ◽  
Typing Method ◽  
Process Error

In April 2015, Public Health England implemented whole genome sequencing (WGS) as a routine typing tool for public health surveillance of Salmonella, adopting a multilocus sequence typing (MLST) approach as a replacement for traditional serotyping. The WGS derived sequence type (ST) was compared to the phenotypic serotype for 6887 isolates of S. enterica subspecies I, and of these, 6616 (96%) were concordant. Of the 4% (n=271) of isolates of subspecies I exhibiting a mismatch, 119 were due to a process error in the laboratory, 26 were likely caused by the serotype designation in the MLST database being incorrect and 126 occurred when two different serovars belonged to the same ST. The population structure of S. enterica subspecies II-IV differs markedly from that of subspecies I and, based on current data, defining the serovar from the clonal complex may be less appropriate for the classification of this group. Novel sequence types that were not present in the MLST database were identified in 8.6% of the total number of samples tested (including S. enterica subspecies I-IV and S. bongori) and these 654 isolates belonged to 326 novel STs. For S. enterica subspecies I, WGS MLST derived serotyping is a high throughput, accurate, robust, reliable typing method, well suited to routine public health surveillance. The combined output of ST and serovar supports the maintenance of traditional serovar nomenclature while providing additional insight on the true phylogenetic relationship between isolates.

scholarly journals Whole Genome Sequencing for Public Health Surveillance of Shiga Toxin-Producing Escherichia coli Other than Serogroup O157

2016 ◽  
Vol 7 ◽  
Author(s):  
Marie A. Chattaway ◽  
Timothy J. Dallman ◽  
Amy Gentle ◽  
Michael J. Wright ◽  
Sophie E. Long ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Shiga Toxin ◽  
Public Health Surveillance ◽  
Health Surveillance ◽  
Whole Genome

scholarly journals An implementation science approach to evaluating pathogen whole genome sequencing in public health

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Angeline S. Ferdinand ◽  
Margaret Kelaher ◽  
Courtney R. Lane ◽  
Anders Gonçalves da Silva ◽  
Norelle L. Sherry ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Public Health Surveillance ◽  
Public Health Practice ◽  
Health Surveillance ◽  
Health Impacts ◽  
Whole Genome ◽  
Health Departments ◽  
Health Practice

Abstract Background Pathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control systems worldwide and has the potential to make significant contributions to infectious disease surveillance, outbreak investigation and infection prevention and control. However, to date, there are limited data regarding (i) the optimal models for integration of genomic data into epidemiological investigations and (ii) how to quantify and evaluate public health impacts resulting from genomic epidemiological investigations. Methods We developed the Pathogen Genomics in Public HeAlth Surveillance Evaluation (PG-PHASE) Framework to guide examination of the use of WGS in public health surveillance and disease control. We illustrate the use of this framework with three pathogens as case studies: Listeria monocytogenes, Mycobacterium tuberculosis and SARS-CoV-2. Results The framework utilises an adaptable whole-of-system approach towards understanding how interconnected elements in the public health application of pathogen genomics contribute to public health processes and outcomes. The three phases of the PG-PHASE Framework are designed to support understanding of WGS laboratory processes, analysis, reporting and data sharing, and how genomic data are utilised in public health practice across all stages, from the decision to send an isolate or sample for sequencing to the use of sequence data in public health surveillance, investigation and decision-making. Importantly, the phases can be used separately or in conjunction, depending on the need of the evaluator. Subsequent to conducting evaluation underpinned by the framework, avenues may be developed for strategic investment or interventions to improve utilisation of whole genome sequencing. Conclusions Comprehensive evaluation is critical to support health departments, public health laboratories and other stakeholders to successfully incorporate microbial genomics into public health practice. The PG-PHASE Framework aims to assist public health laboratories, health departments and authorities who are either considering transitioning to whole genome sequencing or intending to assess the integration of WGS in public health practice, including the capacity to detect and respond to outbreaks and associated costs, challenges and facilitators in the utilisation of microbial genomics and public health impacts.

scholarly journals Identification and typing of Salmonella for public health surveillance using whole genome sequencing

2015 ◽  
Author(s):  
Philip M Ashton ◽  
Satheesh Nair ◽  
Tansy Peters ◽  
Janet Bale ◽  
David G Powell ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Public Health Surveillance ◽  
Health Surveillance ◽  
Current Data ◽  
Whole Genome ◽  
Mlst Database ◽  
Typing Method ◽  
Process Error

In April 2015, Public Health England implemented whole genome sequencing (WGS) as a routine typing tool for public health surveillance of Salmonella, adopting a multilocus sequence typing (MLST) approach as a replacement for traditional serotyping. The WGS derived sequence type (ST) was compared to the phenotypic serotype for 6887 isolates of S. enterica subspecies I, and of these, 6616 (96%) were concordant. Of the 4% (n=271) of isolates of subspecies I exhibiting a mismatch, 119 were due to a process error in the laboratory, 26 were likely caused by the serotype designation in the MLST database being incorrect and 126 occurred when two different serovars belonged to the same ST. The population structure of S. enterica subspecies II-IV differs markedly from that of subspecies I and, based on current data, defining the serovar from the clonal complex may be less appropriate for the classification of this group. Novel sequence types that were not present in the MLST database were identified in 8.6% of the total number of samples tested (including S. enterica subspecies I-IV and S. bongori) and these 654 isolates belonged to 326 novel STs. For S. enterica subspecies I, WGS MLST derived serotyping is a high throughput, accurate, robust, reliable typing method, well suited to routine public health surveillance. The combined output of ST and serovar supports the maintenance of traditional serovar nomenclature while providing additional insight on the true phylogenetic relationship between isolates.

scholarly journals The Pathogen Genomics in Public HeAlth Surveillance Evaluation (PG-PHASE) Framework: An Implementation Science Approach to Evaluating Pathogen Whole Genome Sequencing in Public Health

2020 ◽  
Author(s):  
Angeline S Ferdinand ◽  
Margaret Kelaher ◽  
Courtney R Lane ◽  
Anders Gonçalves da Silva ◽  
Norelle Sherry ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Public Health Surveillance ◽  
Public Health Practice ◽  
Health Surveillance ◽  
Health Impacts ◽  
Whole Genome ◽  
Health Departments ◽  
Health Practice

Abstract Background Pathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control systems worldwide and has the potential to make significant contributions to infectious disease surveillance, outbreak investigation and infection prevention and control. However, to date, there are limited data regarding: (i) the optimal models for integration of genomic data into epidemiological investigations, and (ii) how to quantify and evaluate public health impacts resulting from genomic epidemiological investigations. Methods We developed the Pathogen Genomics in Public HeAlth Surveillance Evaluation (PG-PHASE) Framework to guide examination of the use of WGS in public health surveillance and disease control. We illustrate the use of this framework with three pathogens as case studies: Listeria monocytogenes, Mycobacterium tuberculosis and SARS-CoV-2. Results The framework utilises an adaptable whole-of-system approach towards understanding how interconnected elements in the public health application of pathogen genomics contribute to public health processes and outcomes. The three phases of the PG-PHASE Framework are designed to support understanding of WGS laboratory processes, analysis, reporting and data sharing, and how genomic data are utilised in public health practice across all stages, from the decision to send an isolate or sample for sequencing to the use of sequence data in public health surveillance, investigation and decision-making. Importantly, the phases can be used separately or in conjunction, depending on the need of the evaluator. Subsequent to conducting evaluation underpinned by the framework, avenues may be developed for strategic investment or interventions to improve utilisation of whole genome sequencing. Conclusions Comprehensive evaluation is critical to support health departments, public health laboratories and other stakeholders to successfully incorporate microbial genomics into public health practice. The PG-PHASE Framework aims to assist public health laboratories, health departments and authorities who are either considering transitioning to whole genome sequencing or intending to assess the integration of WGS in public health practice, including the capacity to detect and respond to outbreaks and associated costs, challenges and facilitators in the utilisation of microbial genomics and public health impacts.

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

2018 ◽  
Vol 15 (3) ◽  
pp. 161-167 ◽  
Author(s):  
Laura Ford ◽  
Glen P. Carter ◽  
Qinning Wang ◽  
Torsten Seemann ◽  
Vitali Sintchenko ◽  
...  
Keyword(s):  
Public Health ◽  
Salmonella Typhimurium ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Public Health Surveillance ◽  
Health Surveillance ◽  
Whole Genome
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