“Recent advances in molecular biology and bioinformatics allow complete genome sequencing of pathogens that can provide accurate genetic information, leading to a better understanding of the epidemiological landscape of infectious diseases, transforming how laboratories diagnose and further characterize the pathogens"
We use Next Generation Sequencing (NGS) instruments (Illumina MiSeq & iSeq100 and Oxford Nanopore Minion) and high-performance computers for genome sequencing and analysis of pathogen genome sequences. NGS has been established as an important tool in microbiology research for analysis of small genomes, including bacteria, viruses, and other microbes. Microbial NGS, including whole-genome sequencing (WGS) and targeted resequencing, enables mapping and de novo assembly of novel organisms, completing genomes of known organisms, and comparing genomes across samples.
The complexity of workflows and interpretation of results and the high costs of instrumentation for DNA library preparation and sequencing of whole genomes and of the computational power required for data processing, transfer, storage, and analysis have been barriers to building an affordable sequencing environment. Our goal is to develop an easier-to-use, less expensive way for smaller laboratories using only a bench-top liquid handler robot, small-scale genome sequencing platforms, and a laptop computer to produce accurate and complete genome sequences of emerging infectious diseases in a timely manner. The process would provide pathogen identification, virulence information, drug resistance profiling, and epidemiological data.
The iSeq 100 provides a cost-effective and easy-to-use platform for clinical and public health laboratories to sequence bacterial isolates for a wide range of potential applications. The iSeq100 is capable of running WGS and targeted NGS library preparations with comparable accuracy to the MiSeq. The iSeq100 has reduced sequencing workflow hands-on time and is able to deliver sequencing results in <24 hours. More info: Illumina iSeq100
Complete bacterial, fungal, and viral (DNA or RNA) genomes with long-read nanopore sequencing. Identify and characterise microbes from environmental or single organism samples, with rapid methods for pathogen detection — whether at the bench or in the field. Accompanied, if required, with antimicrobial resistance profiling. Sequence full-length transcripts using direct RNA or cDNA methods for accurate gene expression and transcript isoform analysis. More info: Oxford Nanopore Minion.
We use a variety of phylogenetic analysis approaches to better understand the emergence, evolution, and transmission history of pathogens originated from wildlife. It enables us to investigate the underlying ecologic and epidemiologic processes associated with evolution and spread of pathogens by performing comparative phylodynamic analyses using whole-genome sequences and metadata.
Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viral phylogenies. Many viruses, especially RNA viruses, rapidly accumulate genetic variation because of short generation times and high mutation rates. Patterns of viral genetic variation are therefore heavily influenced by how quickly transmission occurs and by which entities transmit to one another. Viral phylogenies can therefore be used to investigate important epidemiological, immunological, and evolutionary processes, such as epidemic spread, spatio-temporal dynamics including metapopulation dynamics, zoonotic transmission, tissue tropism, and antigenic drift. The quantitative investigation of these processes through the consideration of viral phylogenies is the central aim of viral phylodynamics. More info: Wikipedia