Scientists from the Translational Health Science and Technology Institute (THSTI), Faridabad, have developed an affordable way to check for antimicrobial resistance in sewage.
In their study, detailed in a paper published in Nature Communications on December 29, the scientists analysed sewage samples from 381 sites in Assam, Haryana, Jharkhand, Uttar Pradesh, Uttarakhand, and West Bengal, looking for antibiotic residues, microbial diversity, and resistance genes.
Urban sewage in India is known to be a hotspot and reservoir for antimicrobial resistance (AMR), which the team was able to confirm. But equally importantly, the findings validated the scientific test, or assay, the team developed for the purpose, which the team said was affordable without sacrificing efficiency, and thus a solution suitable for use in low- and middle-income countries.
‘See with your naked eye’
“The workflow to perform the dipstick assay is straightforward,” Deepjyoti Paul, a research scientist at THSTI and the study’s first author, said.
The approach is similar to a rapid diagnostic test, in this case to detect the resistance genes, i.e. those that confer microbes with the ability to resist certain drugs, in environmental sources. Scientists first collect sewage samples and process them to isolate the genetic material, then they amplify the quantities of those genes, e.g. using the PCR method, so that they’re easier to detect.
Then, the amplified genetic material and a detection reagent are added to a dipstick. If the AMR genes are present in the sample, they will bind to the dipstick and produce a band of a visible colour, and thus a clear visual readout.
“The beauty of the dipstick assay is that you can see bands with your naked eye and understand if the sample has a resistance gene or not,” Dr. Paul said.
Snapshot of antibiotic use
Antibiotics that once worked may become ineffective in treating infections as bacteria develop defenses against one or multiple types of the drugs. As a result, treating resistant pathogens becomes more difficult, reducing the number of treatment options available. AMR pathogens can cause life-threatening infections and create complications following surgery and organ transplantation.
Sewage is a complex environment that offers a snapshot of antibiotic usage and provides an early warning system for resistance development. Samples from sewage can capture upstream signals from communities, hospitals, animal farms, and industries. If certain antibiotics or resistance genes are prevalent at a particular location, it can be a sign that medical intervention may be required at the sources upstream. In fact, sewage sampling is considered an ethically acceptable and economically feasible approach to check for AMR in a population.
Likewise, for a nation as populous and geographically vast as India, affordable, time-efficient, and scalable testing technology is critical to curb the spread of AMR. A key feature of the dipstick assay is its affordability, with a unit cost of just around Rs 400-550 — far lower than alternatives like shotgun sequencing, whose cost can exceed Rs 9,000.
Each dipstick can also recognise 16 different resistance genes from a given sample and deliver results within two hours. In case new resistance genes are discovered anywhere in the world, researchers can also upgrade the dipstick in just three days.
“The dipstick based assay that we developed can easily be adopted in very minimal-resource settings,” THSTI professor and the study’s corresponding author Bhabatosh Das said.
Where there is smoke
While techniques like shotgun sequencing can provide a comprehensive picture of resistance genes, they are not feasible to use for routine testing and surveillance. According to the authors, the dipstick assay can fill this gap by performing rapid large-scale surveillance to potentially flag a location in the sewage system for deeper investigation and intervention, by researchers, healthcare workers, and the government.
The approach also builds on an earlier proof of concept developed in 2017 by researchers in Japan, to detect carbapenemase genes in stool specimens. Dr. Das’s lab adapted the dipstick assay approach for other applications, including to detect microbiota associated with preterm births and to identify and differentiate SARS-CoV-2 variants.
But while the dipstick assay offers rapid insights, experts urged careful interpretation of its results at this stage.
“A gene doesn’t make you unwell,” David Graham, an antimicrobial resistance expert and retired professor at Durham University who now advises the United Nations, said. “A gene just tells you the possibility of an organism being there that might make you unwell.” As he put it: “Genes are like smoke: where there is smoke, there is often fire.”
Because resistance to antibiotics can be a result of different genes or even sets of genes in different countries, he emphasised the need for a deeper understanding of the context.
Cheaper, faster, scalable
Culturing resistant pathogens and studying them at genomic, transcriptomic, and metagenomic levels could eventually develop a comprehensive understanding of the genetics of resistance. That information would provide crucial context to help researchers select genetic signatures that reliably indicate resistant pathogens.
“Our goal is to ultimately be able to track pathogens using genetics,” Dr Graham said, “because it is cheaper, faster and can be done at mass scales”.
Thus, the dipstick assay can be useful in local settings where the context and circumstances of resistance are exceptionally well understood.
“Finding a gene is probably two or three biological steps away from finding something that is resistant, [such as] a viable organism or in worst case a viable pathogen,” he added.
For now, the dipstick assay is best positioned as an early warning tool for AMR risk in and around Indian cities. Sewage-based surveillance using dipsticks could help identify localities in which wastewater treatment is inadequate or where antibiotic use might be high, allowing public health authorities to intervene upstream.
The approach could also help assess whether pharmaceutical effluent treatment plants actually reduce the spread of resistance. Such utilities offer a crucial advantage in monitoring public health threats in a country which has become a global hotspot for AMR.
Edries Yousaf Hajam is a freelance science journalist.
Published – February 04, 2026 05:30 am IST
