Microbial sequencing in Singapore, a journey from the wet lab to the dry lab

As humans, we share our existence with a complex community of microbial partners; fungal, viral and bacterial. At the Genome Institute of Singapore (GIS), I run a platform, the GIS Efficient Rapid Microbial Sequencing (GERMS) platform, which utilizes both wet lab and dry lab tools to genetically characterize these populations and how they impact our lives. The principal goal of the platform is to enable industrial and academic partners to use microbial genomics for a variety of applications. We have used our tools to help medicinal chemists with data mining after rational drug design with Novartis (1), used comparative genomics and transcriptomics to decipher novel gene families that can explain how that fungi can survive on lipids from the skin, and potentially serve as therapeutic targets with P&G (2).

We also collaborate with academics in South East Asia such as the Oxford Clinical Research Unit in Vietnam and Duke-NUS in Singapore to understand microbial causes for the infectious diseases prominent in this part of the world. In August 2016 Zika was simultaneously reported by various sentinel surveillance sites around Singapore and the Ministry of Health (MOH) declared a public health emergency. In an island wide effort involving the MOH, Singaporean hospitals, Duke-NUS, GIS and the National Environmental Agency (NEA), we managed to rapidly sequence, analyze and curb the spread of infection. The outbreak tracking of this pathogen was conducted in both mosquitos and humans (3). Our whole genome sequences were deposited in the NCBI database and doubled the existing whole genome sequences for Zika in the database at the time of publication. In this study we describe how our investigation and control of the Zika outbreak in Singapore, by detailing the effort to contain and control vector mosquito populations by the NEA, which likely contributed to a reduction in disease transmission within weeks of discovery.

The world of genomics and the data mining process is an ever changing and challenging landscape. However, if we stay on top of the innovative wet lab methods and current bioinformatics tools available the power of informing public health through genomics is vast.

References:

1. Exploring the mode of action of bioactive compounds by microfluidic transcriptional profiling in mycobacteria. PLoS One, PMID 23935951.

2. Genus-wide comparative genomics of Malassezia delineates its phylogeny, physiology, and niche adaptation on human skin. PLoS Genetetics, PMID 26539826.
3. Outbreak of Zika in Singapore – a Clinical, Epidemiological, Phylogenetic , and Entomological Account. Lancet Infectious Disease, PMID 28527892