The application of genomics is reducing the number of people who become ill from foodborne infections, according to Public Health England.

PHE made the comments in a paper on the transition to use of whole genome sequencing (WGS).

“The introduction of routine WGS has improved national and local surveillance, increased the number of outbreaks being detected and has led to outbreaks being detected earlier than previously possible,” the agency said in the paper.

“WGS analysis provides information on the potential source and/or potential geographical location of the source as well as improving monitoring of the effectiveness of control and preventative measures. Implementation of WGS has refined outbreak investigations by providing more robust case definitions enabling cases to be ruled in or out of outbreaks more accurately.”

PHE has implemented WGS techniques since 2012. Past methods included PCR, serotyping and phage typing followed by molecular typing methods such as PFGE, MLVA or fAFLP.

The change has resulted in less consumable and equipment costs for multiple laboratory workflows, reducing the lab footprint and staffing costs by 17 percent. At PHE Colindale a centralized WGS service provides a service for pathogens including E. coli, Shigella, Listeria, Campylobacter, Staphylococcus aureus, Salmonella and Mycobacteria.

Services have migrated to using WGS for pathogen typing, surveillance and outbreak investigation. The Gastrointestinal Bacteria Reference Unit (GBRU) lab provides testing of bacteria that cause gastrointestinal illnesses associated with foodborne transmission and direct contact with animals and their environments.

WGS can provide a more comprehensive set of microbiological information than multiple traditional lab processes and higher resolution information than conventional genotyping tests, which analyze a limited portion of the genome.

“This minimizes the need for laboratories to maintain the broad array of equipment, reagents and expertise to perform and analyze the numerous different phenotypic and genotypic assays needed to undertake surveillance of a diverse range of organisms,” said the PHE paper.

In England, WGS has replaced at least 10 different validated processes for different bacteria. Before WGS, most samples containing live organisms would be handled between seven to nine times and after implementation, all samples require handling twice.

Salmonella was switched first for a number of reasons, including transitioning to WGS presented the biggest improvements in lab safety and simplifying workflows. Routine serotyping stopped in April 2015. Approximately 10,000 Salmonella isolates are received by the GBRU per year.

Serotyping of Salmonella bacteria takes about 20 days and requires antibodies raised in animals. The WGS services take five days from sample submission to final report.

“WGS-based methods have vastly improved the identification and classification of Salmonella subspecies and serovars and identification of clusters during outbreaks,” PHE reported.

Within the reference lab, WGS has been expanded to investigate all E. coli, Shigella, Salmonella, Listeria and Campylobacter samples. More than 100,000 bacterial and viral genomes have been sequenced since the service launch in 2014. That’s about 600 to 700 bacterial samples per week.

Once organisms have been grown in culture media, all sample processing is done in a microbiological safety cabinet. Pathogens are made safe by heat inactivation and automated DNA extraction occurs in a second lab.

Information about samples is collected via a laboratory information management system (LIMS).

Specialized bioinformatics staff are needed to develop bioinformatics pipelines and analyze data, as well as people with expertise in computing and software development.

PHE’s paper reported future developments include long-read sequencing technologies such as the MinION nanopore sequencer having an impact on infectious disease management due to portability and speed.

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