India's Leadership in AMR Genomics Through Nanopore Technology

Saransh Chaudhary, President of Global Critical Care and CEO of Venus Medicine Research Centre at Venus Remedies Ltd, spans over 10 years of experience in drug development, R&D, and global critical care. He led the Phase 3 trials of Elores and established India’s first organ-on-a-chip lab. Saransh’s expertise spans finance, corporate strategy, and antimicrobial resistance. He has also pioneered initiatives like the PLEA trust and driven innovations in drug discovery.

This article delivers an in-depth analysis of India’s escalating antimicrobial resistance (AMR) crisis, highlighting the gaps in current surveillance systems and exploring how Nanopore sequencing can revolutionize real-time detection and management of resistant pathogens.

The prevalence of Antimicrobial resistance (AMR) has proliferated to an alarming extent globally, with India being at the brink of this crisis. According to a recent study published in The Lancet eClinical Medicine, Indian patients face extremely high colonialization by multidrug-resistant organisms (MDROs) within hospital settings.

Despite different studies published over time stating extended-spectrum beta-lactamase (ESBL) producing E. coli and Klebsiella, carbapenem-resistant Gram-negatives and other priority pathogens as most responsible agents for India’s AMR burden, the country faces a widening gap between the growing complexity of resistance patterns and the preparedness of healthcare infrastructure to detect, monitor, and manage them.

The Surveillance Gap and Its Consequences

Traditionally, many low and middle income countries (LMICs), including India have been relying on patchy laboratory frameworks and delayed reporting while allowing resistant strains to spread silently across hospitals, farms, and communities. The outcome is a growing disconnect between real-world antibiotic practices and the timely insights required to steer stewardship, preserve last-resort drugs, and avert potential outbreaks.

While the conventional diagnostic and surveillance tools, centralized reference labs and batched sequencing are some of the potent systems deployed to monitor AMR within LMICs, they are often slow and capital-intensive. Moreover, high patient loads and limited infrastructure, especially in rural settings, have translated into missed opportunities to contain hospital outbreaks, target hotspot districts and align with national policy guidelines such as National Action Plan (NAP) within time.

As a result, incremental improvements to legacy systems are no longer enough. India needs to move towards more disruptive technologies, such as nanopore sequencing that moves genomics from the periphery of surveillance to its front line.​

How Nanopore Can Be Disruptive in India’s Fight Against AMR

Unlike traditional sequencing technologies that are restricted to well-equipped labs and long turnaround times, Nanopore reads DNA and RNA in real time by measuring ionic current changes as nucleic acids move through nanoscale pores. For India specifically, Nanopore could be a compelling technology to combat AMR due to its practicality.

The technology works directly from complex clinical or environmental samples with minimal preparation, collapsing turnaround times from days to hours, and in some targeted workflows, to mere minutes. More importantly, its long-read capability exposes the full architecture of resistance: the pathogen, the resistance genes, and the mobile elements that help those genes jump across species and settings. For public health teams, that means a level of real-time, high-resolution intelligence that India’s fragmented surveillance ecosystem has simply never had.

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Another benefit is its portability. A device like Oxford Nanopore’s MinION can sit in the palm of your hand, plug into an ordinary laptop, and function reliably in district labs or field environments. Its portability and simple USB connectivity enable real-time DNA and RNA sequencing outside traditional, specialized laboratories giving frontline teams the ability to conduct rapid, on-site genomic analysis. With rapid metagenomic workflows capable of identifying pathogens and predefined AMR genes within the first 10–60 minutes of a run, Oxford Nanopore is transforming both bedside diagnostics and outbreak intelligence.

This democratizes genomic surveillance, extending it beyond elite institutions to primary health centres, rural hospitals and outbreak sites where AMR is quietly spreading. However, real-world implementation will still require sustained efforts in capacity building, training, and reliable supply chains to enable consistent field-level use.

In a country as large, diverse, and infrastructure-constrained as India, such technology has the potential to be a true paradigm shift in AMR surveillance, stewardship, and the broader fight against this silent epidemic. However, translating this potential into routine, nationwide practice will require phased implementation and operational readiness to support consistent use across varied healthcare settings.

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India’s Strategic Push: From Pilot to Pipeline

India is moving decisively from pilots to pipelines in establishing this technology. BRIC-NIBMG, a key national genomics institution under the Biotechnology Research and Innovation Council, has entered into formal collaboration with Oxford Nanopore to establish a Centre of Excellence that will anchor new sequencing workflows across priority public health domains.

As part of this effort, BRIC-NIBMG will integrate nanopore sequencing into AMR surveillance within a broader One Health agenda, linking human, animal, and environmental data and building training programmes in biomedical genomics and data science. These pipelines are designed not just for tertiary centres but to inform networks spanning hospitals, reference labs, agriculture and livestock systems, food safety monitoring, and environmental reservoirs such as wastewater.  

If India succeeds in embedding nanopore-based AMR genomics into routine surveillance, it will generate a scalable playbook spanning governance, procurement, training, and data use that other LMICs can adapt in fight against AMR.