Foodborne diseases are an important food safety issue worldwide. Early detection and identification of the cause are important guarantees for the prevention and control. With the development of next-generation sequencing (NGS) technology, molecular typing techniques based on whole genome sequencing (WGS) has shown great application value and development potential in the investigation of foodborne disease clustering cases and outbreak source investigation.
The promotion and use of WGS technology needs to solve the transmission, storage, fast calculation and accurate comparison of huge genomic data, and requires a mature and easy-to-use bioinformatics analysis process and standardized interpretation system. In response to the above problems, CD Genomics has built comprehensive genome-wide data storage engine and transferring systems, which greatly reduced clients’ WGS data analysis, calculation and usage threshold. On the basis, a genome-wide characteristic gene map recognition algorithm based on WGS original and post-splicing data was also established. Through the mutual correction, the accuracy of genome-wide characteristic gene analysis was significantly improved, and the resolution was established. Highly reproducible whole genome multi-site sequence typing (wgMLST) and core genomic multi-site sequence typing (cgMLST) standardization method, combined with epidemiological information, CD Genomics constructed a traceability analysis knowledge base and realized rapid analysis, comparison and sharing of WGS data among various laboratories.
The scientist team also studied and integrated the characteristic gene data in public databases such as NCBI, CARD, ResFinder, and VFDB, and developed automated analysis function modules, such as virulence factors, drug resistance genes, and serum molecular typing of common food-borne pathogens.
“It will help many laboratories conduct basic research on the genetic and variability of food-borne microbes, pathogenic and drug resistance mechanisms, and strain evolution. So far, our system has been successfully applied in the investigation of incidents such as cross-province traceability of Salmonella enteritidis and inter-provincial tracking of Listeria monocytogenes in frozen drinks. Our WGS solutions have provided technical support for the rapid investigation and accurate traceability of foodborne disease outbreaks internationally,” said by a scientist of the company.
The advantages of microbial whole genome sequencing in clinical practice
Whole genome sequencing has been a routine tool for clinical microbiology. It can reduce diagnostic time and improve control and treatment. It describes and improves our understanding of microbial evolution, outbreaks and transmission events. The conventional procedures for whole genome sequencing often include multiple cultivation and incubation steps followed by species identification, susceptibility testing and typing, which may take several weeks. A number of other approaches (such as PCR based methods) are cheap and rapid, but limited in the sensitivity. Although whole genome sequencing is still too expensive, the price and turnaround time will most likely fall in terms of the competition among sequencing platforms.
About CD Genomics
With decades of experience in the fields of genome sequencing, CD Genomics is devoted to providing the accurate and affordable microbial whole genome sequencing service. The company combines both Illumina (short reads) and PacBio (long reads) platforms for microbial re-sequencing and complete genome de novo sequencing. Its strong expertise is enhanced by flexible sequencing strategies and professional bioinformatics pipelines.