Tuberculosis (TB) is one of India’s foremost public health problems. As per World Health Organisation (WHO) estimates, India has the highest burden of TB in the world. In 2021, the country witnessed a 19% upsurge in TB cases over the previous year. Despite having an aggressive TB control programme in place, drug resistance has led to the country witnessing a sharp increase in the number of cases over the last decade.

By recent estimates, 75% of drug-resistant TB (DR-TB) cases remain undiagnosed, with such patients actively transmitting the disease. Diagnosing DR-TB at an early stage is a major challenge, as it can take up to three months to detect it using existing approaches. This is where genome sequencing comes in, as it enables early and accurate diagnosis of such diseases and helps cut the costs of diagnosis and therapy.

HaystackAnalytics, a MedTech startup based out of Mumbai, is leveraging genomics for simplified analytics that doctors can use for better clinical outcomes.

Also Read| Keeping a silent disease in check

Through its Intel Startup Program, Intel collaborated with HaystackAnalytics to create the first edge computing device (αBox) for genomics-based Drug Susceptibility Testing (DST) for TB. Compared to traditional diagnostic techniques, it reduces testing time by up to 80%, cuts patient costs by up to 50% and does away with the need for molecular diagnostic labs to update infrastructure or reskill staff. Moreover, while current methods use 11 different tests to detect resistance to 13 drugs over a few months, genomics can provide a drug resistance profile for 18 antibiotics through one test in 10-15 days. Significantly, the αBox reduces the time needed for the analysis of the whole genome, which currently takes a few days, to less than 15 minutes.

A comprehensive one-test solution, the automated αBox is loaded with ΩTB Software, which provides antibiotic profiling for suspected DR-TB cases within 15 minutes. Ω-Suite is a genomic data analysis, inferencing, and clinical report generation platform intended to enable rapid and comprehensive clinical decisions, while substantially reducing the risk of mis-diagnosis. Moreover, the platform will also be able to use the genomic data to pre-empt disease outbreaks.

“At Intel, we are continuously working on technological innovations for the betterment of humanity. Through the Intel Startup Program, we help deep-tech startups with access to relevant technology platforms, mentoring and ecosystem connect for developing and scaling innovative solutions in key areas of healthcare, retail, industry 4.0, etc. HaystackAnalytics is one such startup. Through its innovation, it is boosting the fight against communicable diseases like tuberculosis. Their plug-and-play genome sequencing solution built on Intel platform allows diagnostic labs to deliver technology-centric diagnosis for general patient consumption at scale. It also promises a faster turnaround time for genomic analytics, at a significantly lower cost,” said Nivruti Rai, country head, Intel India and VP, Intel Foundry Services.

On the development of genome sequencing, she said, “About 20 years back, the first reference human genome was sequenced by using automated machines the size of phone booths. Today, it can be done with a small form factor device. Alongside the advancements in computing and storage, the cost of genome sequencing has come down rapidly and today it can be done for less than $100, as against a few million dollars in the early 2000s.”

Conventionally, the process of genome sequencing is long, taking anything from 72 hours to as long as 30 days. Co-developed with Intel, HaystackAnalytics’ unique computing hardware has brought the processing time down to less than 36 hours and has made the genomics data available to users. Powered by Intel Vtune Analyser (software toolkit) and Intel-optimised genomic software packages, it has yielded a 25% performance improvement and enabled genomic analysis on an Intel Core processor, thus reducing the capex cost by 50%.

Anirvan Chatterjee, co-founder & CEO, HaystackAnalytics, said, “Intel has taken a leap in computing technology for genomics and been a gamechanger in the field. Their expertise in core memory and computing optimisation, specifically for handling genomic data processing algorithms, has enabled us to develop the genomic analysis software and reduce the overall processing time by 80%. We have leveraged the Intel Startup Program to create a revolutionary new test, ΩID, with which we are able to take the entire genome sequencing workflow to hospital premises and provide a single test for all bacterial and fungal infections, along with detection of antimicrobial resistance. The αBox, in conjunction with Oxford Nanopore Sequencing and Haystack’s custom kit and software deployment, ΩID, is a culture-free test for diagnosing sepsis in less than 12 hours.”

Promising future

As per World Health Organisation (WHO) estimates, India has the highest burden of TB in the world
In 2021, the country witnessed a 19% upsurge in TB cases over the previous year
By recent estimates, 75% of drug-resistant TB (DR-TB) cases remain undiagnosed and such patients actively transmit the disease
Intel collaborated with HaystackAnalytics to create the first edge computing device (αBox) for genomics-based Drug Susceptibility Testing (DST) for TB, which cuts testing time by up to 80% and patient costs by up to 50%