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Clinical Laboratories and Pathology Groups

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Clinical Laboratories and Pathology Groups

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Global Consortium of Scientists Develop New Whole Genome Sequencing Method That Brings Costs Down to $10 per Genome

At that reduced cost, clinical laboratories in developing countries with no access to WGS could have it as a critical tool in their fight against the spread of deadly bacteria and viruses

New research into a low-cost way to sequence bacterial genomes—for as little as $10—is predicted to give public health authorities in low- and middle-income countries (LMICs) a new tool with which to more quickly identify and control disease outbreaks.

This new approach offers an alternative to more expensive Whole genome sequencing (WGS) methodologies, which clinical laboratories in developed countries typically use to identify and track outbreaks of infectious diseases. And with SARS-CoV-2 variants resulting in increased COVID-19 infections, the ability to perform low-cost, rapid, and accurate WGS is becoming increasingly important.

But for many developing countries that need it the most, the cost of WGS has kept this critical technology out of reach.

Now, a global consortium of scientists has successfully established an efficient and inexpensive pipeline for the worldwide collection and sequencing of bacterial genomes. The large-scale sequencing method could potentially provide researchers in LIMCs with tools to sequence large numbers of bacterial and viral pathogens. This discovery also could strengthen research collaborations and help tackle future pandemics.

The team of scientists, led by researchers at the Earlham Institute and the University of Liverpool, both located in the UK, are confident their technology can be made accessible to clinical laboratories in LMICs around the globe.

The researchers published their findings in the journal Gen Biology, titled, “An Accessible, Efficient and Global Approach for the Large-Scale Sequencing of Bacterial Genomes.”

Neil Hall, PhD
“It has been 26 years since the first bacterial genome was sequenced, and it is now possible to sequence bacterial isolates at scale,” Neil Hall, PhD (above), director of the Earlham Institute and one of the authors of the study, told Genetic Engineering and Biotechnology News. “However, access to this game-changing technology for scientists in low- and middle-income countries has remained restricted. The need to ‘democratize’ the field of pathogen genomic analysis prompted us to develop a new strategy to sequence thousands of bacterial isolates with collaborators based in many economically challenged countries.” (Photo copyright: Earlham Institute.)

Streamlining Collection and Sequencing

The international team of scientists aimed their innovative WGS approach at streamlining the collection and sequencing of bacterial isolates (variants). The researchers collected more than 10,400 clinical and environmental bacterial isolates from several LMICs in less than a year. They optimized their sample logistics pipeline by transporting the bacterial isolates as thermolysates from other countries to the UK. Those isolates were sequenced using a low cost, low input automated method for rapid WGS. They then performed the gene library construction and DNA sequencing analysis for a total reagent cost of less than $10 per genome.

The scientists focused their research on Salmonella enterica, a pathogen that causes infections and deadly diseases in human populations. Non-typhoidal Salmonella (NTS) have been associated with enterocolitis, a zoonotic disease in humans linked to industrial food production.

Because the disease is common in humans, there have been more genome sequences generated for Salmonella than any other type of germ.

“In recent years, new lineages of NTS serovars Typhimurium and Enteritidis have been recognized as common causes of invasive bloodstream infections (iNTS disease), responsible for about 77,000 deaths per year worldwide,” the researchers wrote in their Gen Biology paper. “Approximately 80% of deaths due to iNTS disease occurs in sub-Saharan Africa, where iNTS disease has become endemic.”

Increasing Access to Genomics Technologies in Developing Countries

The research consortium 10,000 Salmonella Genomes Project (10KSG) led the large-scale WGS initiative. The alliance involves contributors from 25 institutions in 16 countries and was designed to generate information relevant to the epidemiology, drug resistance, and virulence factors of Salmonella using WGS techniques.

“One of the most significant challenges facing public health researchers in LMICs is access to state-of-the-art technology, Jay Hinton, PhD, Professor of Microbial Pathogenesis at the University of Liverpool and one of the paper’s authors, told Technology Networks. “For a combination of logistical and economic reasons, the regions associated with the greatest burden of severe bacterial disease have not benefited from widespread availability of WGS. The 10,000 Salmonella genomes project was designed to begin to address this inequality.”

The authors noted in their study that the costs associated with sequencing have remained high mostly due to sample transportation and library construction and the fact that there are only a few centers in the world that have the ability to handle large-scale bacterial genome projects.

“Limited funding resources led us to design a genomic approach that ensured accurate sample tracking and captured comprehensive metadata for individual bacterial isolates, while keeping costs to a minimum for the Consortium,” Hall told Genetic Engineering and Biotechnology News(GEN). “The pipeline streamlined the large-scale collection and sequencing of samples from LMICs.”

“The number of publicly available sequenced Salmonella genomes reached 350,000 in 2021 and are available from several online repositories,” he added. “However, limited genome-based surveillance of Salmonella infections has been done in LMICs, and the existing dataset did not accurately represent the Salmonella pathogens that are currently causing disease across the world.”

The $10 cost is designed to help healthcare systems in developing countries identify the specific genetic composition of infectious diseases. That’s the necessary first step for developing a diagnostic test that enables physicians to make an accurate diagnosis and initiate appropriate therapy.

“The adoption of large-scale genome sequencing and analysis of bacterial pathogens will be an enormous asset to public health and surveillance in LMI countries,” molecular microbiologist Blanca Perez Sepulveda, PhD, told GEN. Sepulveda is a postdoctoral Researcher at the University of Liverpool and one of the authors of the study.

Improvement in next-generation sequencing technology has reduced costs, shortened turnaround time (TAT), and improved accuracy of whole genome sequencing. Once this low-cost method for collecting and transporting bacterial sequences becomes widely available, clinical laboratories in developing countries may be able to adopt it for genome analysis of different strains and variants of bacteria and viruses.

JP Schlingman

Related Information:

Scientists Develop $10 Per Genome Approach for Large-scale Bacterial Sequencing

An Accessible, Efficient and Global Approach for the Large-scale Sequencing of Bacterial Genomes

Affordable Genome Sequencing to Help Tackle Global Epidemics