Foods

Study reveals low use of whole genome sequencing outside of U.S. and Europe

One-third of survey respondents in low and middle-income international locations don’t use entire genome sequencing, in accordance with a examine.

Solely 8 % reported utilizing WGS in a routine, real-time means, highlighting minimal uptake of the know-how for foodborne illness surveillance exterior america, Canada, and Europe.

The primary obstacles for implementation have been lack of funding, gaps in experience, and coaching, particularly for knowledge evaluation and interpretation, in accordance with the examine printed within the journal Foodborne Pathogens and Illness.

PulseNet Worldwide (PNI) did the examine to establish challenges international locations have been dealing with regarding WGS. The group consists of nationwide, regional, and sub-regional labs and laboratory networks in 88 international locations that observe foodborne illness globally.

Sequencing stats
Forty-one establishments from 33 of 54 international locations in Africa, Asia-Pacific, Latin America, the Caribbean and the Center East accomplished the survey in early 2020. Two-thirds of respondents have been nationwide reference laboratories, together with these from nationwide public well being, agriculture, and meals security authorities.

One in 5 use WGS for outbreak investigations after they’re recognized by different means and 28 % use it for analysis and pilot research solely.

Of the labs that should not have WGS carried out, 40 % outsource sequencing to a different establishment, however they’ve plans to take up WGS in-house throughout or after 2022.

Twenty % of labs don’t use WGS for foodborne illness surveillance, though sequencing is carried out onsite for different functions. The vast majority of labs that use WGS for investigations after an outbreak or for pilot research do sequencing at their very own establishment.

In 2019, solely 5 % of labs sequenced greater than 1,000 isolates. Though 66 % sequenced 0 to 100 isolates that 12 months, the remaining labs sequenced between 100 and 1,000 isolates. The vast majority of testing was carried out on key foodborne pathogens similar to Salmonella, E. coli, Shigella, Vibrio, Campylobacter and Listeria.

Knowledge evaluation points
The capability for producing sequences is mostly larger than that for analyzing or decoding the information. Capability for computation and bioinformatics was discovered to be typically low.

Forty-four % of respondents mentioned their laboratories’ capability and experience to make the most of, develop, optimize, and troubleshoot bioinformatics evaluation protocols for WGS knowledge was little or none.

The vast majority of labs should not have established tips for decoding WGS knowledge such because the variety of allele or SNP variations for outbreak detection.

Finish-user information for efficient use of WGS knowledge is low. Solely a 3rd of labs mentioned the extent of data and talent to make use of WGS knowledge for public well being decision-making was good or wonderful.

Dissemination of WGS outcomes is basically by way of conventional strategies, and knowledge sharing is restricted. Conventional methods, together with excel spreadsheets, exhausting copies together with fax, and in-person or by phone dominated over trendy strategies similar to laboratory info administration methods and inner web sites.

Greater than half of labs don’t alternate sequence knowledge with exterior companions inside their nation and solely half of respondents make their sequencing knowledge publicly accessible generally.

Half of labs consider that PNI ought to give attention to coaching, particularly in WGS knowledge evaluation, and that gaining access to globally standardized and validated evaluation instruments and pipelines are key to progress towards worldwide foodborne illness surveillance utilizing WGS.

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