A large-scale bacterial sequencing method for only $10 per genome

A global consortium of scientists led by the Earlham Institute and the University of Liverpool has developed an efficient, inexpensive method for large-scale bacterial genome sequencing that can enable researchers in low- and middle-income countries (LMICs) An inexpensive and available method of sequencing bacterial pathogens—each genome costs less than $10
.

This group of scientists believes that at a time when global coronavirus genome monitoring is receiving attention, the ability of countries to contribute through low-cost and rapid whole-genome sequencing (WGS) has become increasingly important
.

"It has been 26 years since the first bacterial genome was sequenced, and bacterial isolates can now be sequenced on a large scale," said Dr.
Neil Hall, director of the Earlham Institute
.

The team published a paper entitled " An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes " in the " Genome Biology " magazine .

The author said that in the past ten years, WGS has completely changed our understanding of microbial diseases
.

The authors continue to say that the need for sequencing the human genome has reduced the cost of sequencing reagents to less than $1,000 per sample
.

This large-scale genome sequencing project is led by the Global 10,000 Salmonella Genome Research Consortium (10KSG), focusing on the study of Salmonella enterica, a pathogen of global significance that can cause infections and fatal diseases
.

The author pointed out that non-typhoid Salmonella (NTS) has been widely associated with human enterocolitis, a zoonotic disease associated with the industrialization of food production
.

The authors continue to write in their report: "In recent years, the new lineage of NTS serotype typhoid fever and enteritis has been recognized as a common cause of invasive bloodstream infections (iNTS diseases), causing approximately 77,000 deaths worldwide each year
.

The goal of 10KSG is to make genomic data more accessible to low- and middle-income countries
.

Hall commented: “By 2021, the number of publicly available sequenced Salmonella genomes will reach 350,000, which can be obtained from several online repositories
.
However, there are limited genome-based studies of Salmonella infections in low- and middle-income countries.
Surveillance, the existing data set cannot accurately represent the Salmonella pathogens that are currently causing diseases around the world
.
” The co-author of the study, Dr.
Jay Hinton, professor of microbial pathogenesis at the University of Liverpool, further pointed out: “Public health researchers in low- and middle-income countries face One of the most important challenges of the company is to obtain the most advanced technology
.
Due to a combination of logistical and economic reasons, the areas associated with the greatest burden of severe bacterial diseases have not benefited from the widespread provision of WGS.
The
10,000 Salmonella Genome Project is to begin to address this.
Kind of inequality
.
"

The newly reported method aims to simplify large-scale bacterial collection and genome sequencing.
Researchers have collected genetic material from more than 10,400 clinical and environmental bacterial isolates from low- and middle-income countries in less than a year
.
In fact, the members of 10KSG provided 10,419 isolates from 51 low- and middle-income countries and regions, covering 7 bacterial genera: Acinetobacter, Enterobacter, Klebsiella, Pseudomonas The genera of Monas, Shigella and Staphylococcus coordinated the collection of samples and the transportation of materials to be sequenced in the UK
.

The sample logistics pipeline developed by the Liwupu University team uses the heat-inactivated bacterial isolate as a "pyrolysate" to ship to the UK under environmental conditions around the world, and then uses the unique Lite protocol at the Ullham Institute in the United States Perform low-cost sequencing
.
Low-input automated method for rapid genome sequencing
.
The researchers said: "A key aspect of our approach is to involve multilingual researchers in communications with collaborators to maximize clear and continuous communication via e-mail
.
"

In general, the construction of gene libraries and the completion of DNA sequencing bioinformatics analysis, the total reagent cost for each genome is less than US$10 (approximately £7.
50)
.
The co-author of the research report and a postdoctoral researcher at the University of Liverpool, Dr.
Blanca Perez Sepulveda (Blanca Perez Sepulveda) led the global sample collection, optimization and analysis work.
She added: “Using large-scale genome sequencing and Bacterial pathogen analysis will provide huge assets for public health and surveillance in low- and middle-income countries
.
Here, we have established an efficient and relatively inexpensive pipeline for collecting and sequencing bacterial genomes on a global scale
.
"

The author writes: "We have established an efficient and relatively inexpensive pipeline to collect and sequence bacterial genomes on a global scale
.
Our new method allows the transportation of large numbers of bacterial pathogens and whole genome sequencing through the combined use of thermal lysis solution and DNA.
Extraction and sequencing, and use the innovative LITE pipeline for library construction
.
Through global research cooperation, we evaluated this method and the model organism Salmonella enterica, and produced 6117 high-quality Salmonella genomes, which have been used in many Published research
.
"

Dr.
Darren Heavens, a postdoctoral scientist at the Ereham Institute, developed a whole-genome sequencing pipeline.
He further pointed out: “We believe it is necessary to simplify and expand the genome monitoring of Salmonella from Africa and other parts of the world, including human invasive diseases and gastrointestinal diseases.
Inflammation-related isolates, and extend to bacteria from animals and the environment
.
Our pipeline is a cost-effective and powerful tool that can obtain bacterial genome data from LMI countries, so that the epidemiology, epidemiology, Resistance and virulence factors
.
"

As the author explains, “Our research project is a relatively inexpensive and powerful tool for generating bacterial genome data from LMI countries, allowing investigations of the epidemiology, resistance and virulence factors of isolates.
.
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…In the future, this method will facilitate rapid, low-cost, and collaborative genome sequencing of bacterial pathogens
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Our coordinated approach demonstrates the value of true global cooperation and may help future investigations of international epidemics or pandemics
.
"

The bioinformatics analysis pipeline and the obtained genomic data are publicly available at https://github.
com/apredeus/10k_genomes and the EMBL European Nucleotide Archive (ENA).
The project numbers are PRJEB35182 and PRJEB47910, and serve as the scientific community’s Data resources
.