One-third of survey respondents in low and middle-income countries do not use whole genome sequencing, according to a study.
Only 8 percent reported using WGS in a routine, real-time way, highlighting minimal uptake of the technology for foodborne disease surveillance outside the United States, Canada, and Europe.
The main barriers for implementation were lack of funding, gaps in expertise, and training, especially for data analysis and interpretation, according to the study published in the journal Foodborne Pathogens and Disease.
PulseNet International (PNI) did the study to identify challenges countries were facing concerning WGS. The group consists of national, regional, and sub-regional labs and laboratory networks in 88 countries that track foodborne disease globally.
Sequencing stats
Forty-one institutions from 33 of 54 countries in Africa, Asia-Pacific, Latin America, the Caribbean and the Middle East completed the survey in early 2020. Two-thirds of respondents were national reference laboratories, including those from national public health, agriculture, and food safety authorities.
One in five use WGS for outbreak investigations after they are identified by other means and 28 percent use it for research and pilot studies only.
Of the labs that do not have WGS implemented, 40 percent outsource sequencing to another institution, but they have plans to take up WGS in-house during or after 2022.
Twenty percent of labs do not use WGS for foodborne disease surveillance, although sequencing is performed onsite for other purposes. The majority of labs that use WGS for investigations after an outbreak or for pilot studies do sequencing at their own institution.
In 2019, only 5 percent of labs sequenced more than 1,000 isolates. Although 66 percent sequenced 0 to 100 isolates that year, the remaining labs sequenced between 100 and 1,000 isolates. The majority of testing was performed on key foodborne pathogens such as Salmonella, E. coli, Shigella, Vibrio, Campylobacter and Listeria.
Data analysis issues
The capacity for generating sequences is generally higher than that for analyzing or interpreting the data. Capacity for computation and bioinformatics was found to be generally low.
Forty-four percent of respondents said their laboratories’ capacity and expertise to utilize, develop, optimize, and troubleshoot bioinformatics analysis protocols for WGS data was little or none.
The majority of labs do not have established guidelines for interpreting WGS data such as the number of allele or SNP differences for outbreak detection.
End-user knowledge for effective use of WGS data is low. Only a third of labs said the level of knowledge and ability to use WGS data for public health decision-making was good or excellent.
Dissemination of WGS results is largely through traditional methods, and data sharing is limited. Traditional ways, including excel spreadsheets, hard copies including fax, and in-person or by telephone dominated over modern methods such as laboratory information management systems and internal websites.
More than half of labs do not exchange sequence data with external partners within their country and only half of respondents make their sequencing data publicly available sometimes.
Half of labs believe that PNI should focus on training, especially in WGS data analysis, and that having access to globally standardized and validated analysis tools and pipelines are key to progress toward worldwide foodborne disease surveillance using WGS.
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