Experts from Newcastle University, UK, and the Indian Institute of Technology in Delhi (IIT-Delhi), sampled water and sediments at seven sites along the Upper Ganges River, in the foothills of the Himalayas.
They found that in May and June, when hundreds of thousands of visitors travel to Rishikesh and Haridwar to visit sacred sites, levels of resistance genes that lead to "superbugs" were found to be about 60 times greater than other times of the year.
"The specific resistance gene we studied, called blaNDM-1, causes extreme multi-resistance in many bacteria, therefore we must understand how this gene spreads in the environment," said Professor David Graham, an environmental engineer based at Newcastle University.
"If we can stem the spread of such antibiotic resistant genes locally - possibly through improved sanitation and waste treatment - we have a better chance of limiting their spread on larger scales, creating global solutions by solving local problems," said Graham.
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Monitoring levels of other contaminants in the water, the team showed that overloading of waste treatment facilities was likely to blame and that in many cases, untreated sewage was going straight into the river where the pilgrims bathe.
"The bugs and their genes are carried in people's guts. If untreated wastes get into the water supply, resistance potential in the wastes can pass to the next person and spiralling increases in resistance can occur," said Graham.
Of particular concern is NDM-1, which is a protein that confers resistance in a range of bacteria. NDM-1 was first identified in New Delhi and coded by the resistant gene blaNDM-1, researchers said.
Until recently, strains that carry blaNDM-1 were only found in clinical settings, but in 2008, blaNDM-1 positive strains were found in surface waters in Delhi. Since then, blaNDM-1 has been found elsewhere in the world, including new variants, they said.
The study was published in the journal Environmental Science and Technology.