Webinar on WGS of bacterial pathogens

UTAR Centre for Research on Communicable Diseases (CRCD), in collaboration with Centre for Corporate and Community Development (CCCD), organised a webinar titled “Whole genome sequencing of bacterial pathogens: Its potential and limitations” on 7 December 2020. 

The webinar was conducted via Zoom. It was moderated by Asst Prof Dr Saw Seow Hoon from UTAR Faculty of Science and delivered by Prof Dr Yeo Chew Chieng from Universiti Sultan Zainal Abidin (UniSZA) Medical Campus in Kuala Terengganu.

In his talk, Prof Yeo first gave a brief introduction on milestones in genome sequencing and assembly. “In 1995, the first complete genome of a free-living microorganism was published in Science. Sequenced using the Sanger dideoxy method, this is what we now called ‘First generation’ sequencing technology, It is expensive, cumbersome and time-consuming.” He then explained the two waves of sequencing technology innovation in the 21st century—the second-generation (routinely termed as NGS) and the third-generation sequencing (TGS). In order to provide participants with a better understanding, Prof Yeo gave an idea of the differences between the second and the third generation sequencing technologies. He further explained the third generation sequencing technologies, focusing on PacBio systems and Oxford Nanopore Sequencing. 

Moreover, he talked about the use of whole genome sequencing (WGS) in clinical microbiology. “The early applications of WGS in clinical microbiology and public health is to elucidate and interrupt transmission pathways in nosocomial outbreaks such as for Acinetobacter baumannii, Staphylococcus aureus, and Klebsiella pneumonia. WGS analyses always were conducted from cultured isolates,” he said, adding that WGS provides large amounts of information regarding species, strain type, antibiotic resistance, virulence and other information needed for an outbreak and case management. 

Furthermore, he talked about metagenome sequencing, explaining that NGS and TGS can be applied directly to clinical specimens—sequencing the DNA or RNA extracted from patients sample by shotgun metagenome sequencing. He also shared some drawbacks of the metagenomics NGS approach in clinical microbiology, as well as the analysis about WGS of Acinetobacter baumannii from Terengganu. He mentioned that the biggest challenge in introducing NGS in clinical microbiology laboratory was the data analyses. He also highlighted that dedicated and well-trained staff are required to ensure successful implementation of WGS in routine clinical microbiology. Besides, he also presented a simple cost analysis for Illumina sequencing and nanopore sequencing, as well as discussed the current WGS issues. 

“Sequencing technology, bioinformatics and informatics infrastructure are all rapidly evolving. The focus in these recent years is nanopore sequencing. The role of WGS and metagenome sequencing in clinical microbiology will increase in the coming years. This will transform clinical microbiology into a genome-powered and personalised diagnostic area,” he said. The talk then ended with a Q&A session.

A timeline presented by Prof Yeo illustrating milestones in genome assembly

 

Prof Yeo presenting the differences between the second and the third generation sequencing technologies

Prof Yeo sharing some platforms for WGS

Prof Yeo presenting the typical WGS workflow in a clinical or a public health laboratory