The Rockefeller Foundation-Alliance for Pathogen Surveillance Innovations, RF-APSI-India’s Bangalore cluster conducted its first hands-on workshop, with a rigorous 3-day module (Sept 16-18, 2024), including hands-on molecular biology techniques for pathogen surveillance and AMR detection from wastewater samples and clinical samples.
The participants were selected through open call and after screening about 150 applications, we found our team of 15 best warriors and ambassadors to carry forth this training. The selected candidates were actively working as microbiologists, health technicians or research fields related to public health surveillance. The workshop was organized by Tata Institute for Genetics and Society (TIGS), National Centre for Biological Sciences (NCBS), with mentors from both the institutes and ARTPARK, Bangalore.
The day 1 started off with welcome notes from Dr. Rakesh Mishra, Director, TIGS and Prof. LS Shashidhara, Director, NCBS, motivating the selected candidates to take forth the tools and techniques and implement in their respective practices and institutes.
Dr. Sufia Sadaf, Program Manager, Outreach set the context of the workshop after distribution of the workshop materials and protocol handbooks. The module started off with the first lecture by Dr. Shivranjani C Moharir, Senior Scientist TIGS, covering the relevance and strategies used for environmental surveillance for pathogens and pathogen-traits, such as antimicrobial resistance (AMR). The next-detailed lecture was by Dr. Mansi Malik, Scientist, TIGS on Surveillance of pathogens from clinical samples using molecular approaches, the importance of serosurveillance and pathogen variants to understand the disease mechanisms followed by group discussions and Q & A sessions.
Preparations for the first day of hands-on experiments started off with wastewater sample collection and demonstration by the volunteers from TIGS team and short-talks and demonstration by Ms. Sreelekshmi RS on wastewater sample collection and air-surveillance sample collection techniques, lab visits to see the lab settings for running the experiments and the molecular biology facilities.
Day 2: The candidates were divided into 4 groups, 2 for wastewater surveillance and 2 groups for clinical sample surveillance. Through teamwork, resource sharing and hard-work, both the teams set out for nucleic acid extraction for setting up qPCRS (for AMR) and RT-PCRS for viral pathogens using a mix-of commercially available kits and TIGS-in-house developed kit (DENCHIK) by Dr. Malik’s group, which allows the diagnosis of viral pathogens causing dengue, the serotypes and chikungunya viral detection. The two teams worked in parallel and during the latter part of the day, the teams were swapped to allow training them with techniques for both wastewater and clinical surveillance.
Day 3: The final day module was designed for genomic sequencing and data interpretation to understand the role of next-generation sequencing (NGS), metagenomics for detailed pathogen studies, epidemiological interpretation from evolving gene components etc., especially in the context of AMR and SARS-CoV-2. Dr. Awadhesh Pandit, Facility In-charge, NGS facility, NCBS offered a detailed lecture, followed by a visit to the NGS facility where the participants were given detailed demonstration on the inner-workings of the NGS. This was followed by a lecture by Dr. Bhaskar Rajakumar, Program Director, Health Initiatives, ARTPARK, Bangalore on Data modeling and dashboard integration for public health surveillance, and chose the modelling strategies for Dengue, a field that ARTPARK has actively been part since several years.
After a visit to the Biosafety labs 2, BSL2 and demonstrations by the facility personnels, three final modules on Bioinformatics, with a mix of demonstration and interactive sessions were offered, covering techniques to analyze data for wastewater-based epidemiology, WBE AMR and disease trends, by Mr. Manas Kumar and Ms. Anamika Shukla, TIGS and Ms. Samruddhi Walaskar, covering bioinformatics analysis modules for clinical surveillance, dengue and AMR surveillance.
These sessions were followed by detailed discussions and resource sharing.
The final evening was set-aside for detailed group-quiz, rapid-quiz and fun show-and-tell Pictionary, related to the entire 3-day program, and details related to the hands-on experiments, NGS and bioinformatics! The enthusiastic participation from the entire team of volunteers, mentors, organizers and participants made this workshop a true success!
We will design more workshops in the coming months and are happy to incorporate the valuable suggestions and feedback provided to us by the participants.
We would like to acknowledge Ms. Saniya Mehraj, Ms. Sreelekshmi RS, Ms. Priyanka Bhavsar, Ms. Ritika Majji, Ms. Samruddhi Walaskar, Mr. Manas Kumar, Ms. Anamika Shukla, Ms. Priyadarshini Mohapatra, Ms. Prajakta Jathar and Mr. Antony Selvakumar A, Ms. Chaitra and Mr. Akshay Tharali, the campus hospitality, lab support, reception and security team for their untiring efforts and their help throughout this workshop.
Dr. Sufia Sadaf,
RF-APSI
Dr. Shivranjani C Moharir,
Senior Scientist,
TIGS
and
Dr. Mansi Malik,
Scientist,
TIGS