Bio-surveillance of Antimicrobial Resistance (AMR) and COVID-19 prevalence in Chennai: A MetaSUB approach using metagenomic

In this project, we propose to establish a bio-surveillance paradigm through longitudinal sampling from Chennai city zones that transition from a COVID-19 Red zone to a Green zone. This will be done by niche modelling to infer variation in environmental viral/antimicrobial resistance (AMR) load within Chennai city using metagenomics data on bacterial, fungal and viral communities and their interplay.

We are a group of researchers from IIT Madras led by Drs Karthik Raman and Himanshu Sinha working in collaboration with the Christopher Mason laboratory at Weill Cornell Medical School, New York, USA. This effort arose from the initial research outcomes generated by the Gates Foundation project called MetaSUB to investigate Antimicrobial Resistance in subways and transit systems in New York. The consortium holds robust data which shall be accessed to build early warning/forecasting systems. This dataset holds data such as time, geographic information represented by GPS, metagenomic Next Generation Sequence data, type of treatment plants, site location, and country/continent.

This will help in developing surveillance systems based on DNA and RNA metagenomics data for the city of Chennai. With COVID19 as one of the microbes being sampled, data from this analysis can help in COVID19 surveillance and prediction tool for public health.

We utilise such datasets to compare between MetaSUB partner labs around the world starting with sister cities such as Denver, USA; New York, US; London UK, Tokyo, Japan and Rio De Janeiro, Brazil. Notwithstanding the Chennai metro terminus is adjacent to the Koyambedu vegetable market cluster, COVID-19 outbreak occurred in 2020.