Mumbai fish harbour high levels of antibiotic-resistant bacteria

  • Fish from Mumbai’s markets harbour high levels of bacteria that are resistant to multiple antibiotics and could pose a threat to humans.
  • They are capable of transferring their resistant genes to other bacteria, such as those in our gut.
  • Extra hygiene should be exercised when handling fish to avoid contamination of cooking utensils and fresh foods.

Every day, millions of litres of untreated and partially treated sewage, as well as waste from industry and agriculture, finds its way to our seas and oceans. These effluents carry residues of everything we use, from pesticides to pharmaceuticals to heavy metals. The pollutants exert selective pressure on marine microbes, including those that can cause disease. Microbes that have the genes to ward off these substances, such as antibiotics, thrive.

Now, researchers have detected high levels of bacteria resistant to multiple antibiotics in five species of fish from Mumbai’s retail markets. While previous studies have reported the presence of antibiotic-resistant bacteria lurking in poultry, vegetables, and seafood around India, this study goes a step further. It shows that these bacteria can share their resistant genes with other bacteria.

“We did expect the presence of antibiotic-resistant bacteria, but not in such high amounts and such high multiple antibiotic resistance,” said senior author Archana Rath, head and assistant professor at the Department of Biotechnology at the University of Mumbai. These resistant bacteria can enter the human gut through the food chain, warns Rath, which can “potentially lead to increased antibiotic resistance in humans.”

A mixture of salty and brackish water fishes such as prawns, sting ray ‘Waghole’ and mullet fish ‘Shevto’ being sold in local fish markets. Photo by Onkar Naik.

Funded by the Board of Research in Nuclear Sciences of the Department of Atomic Energy, the study aims to highlight the importance of “good sanitary practices in fish handling and processing” as well as wise use of antibiotics to raise fish in fish farms.

First author Onkar Naik, a doctoral fellow, and Rath collected five commonly consumed species of fish from different markets across Mumbai. Along with their collaborators Ravindranath Shashidhar and Jayant Bandekar of the Food Technology Division, and Devashish Rath of the Molecular Biology Division from the Bhabha Atomic Research Centre in Mumbai, they identified the bacterial diversity in the fish using next-generation high-throughput sequencing as well as culturing.

Bacteria were isolated and grown in the presence of 13 different antibiotics to see how susceptible they were. Six of the highly resistant isolates were chosen for use in mating experiments to see if they were capable of transferring their resistant genes to a lab strain of Escherichia coli, a species that is also commonly found in our gut.

High levels of antibiotic-resistant bacteria were found in the fish, some of which belonged to genera that are known to cause opportunistic infections in fish under favourable conditions such as Providencia, Staphylococcus, Klebsiella, Enterobacter, Shewanella, Vibrio, and Photobacterium. Upon consumption, some of the genera can also cause infections in humans, particularly in immune-compromised and older individuals.

Fish auction at Mumbai’s Sassoon Docks. Photo by Max Pixel.

These disease-causing bacteria were found to be resistant to multiple antibiotics—trimethoprim, kanamycin, doxycycline, ciprofloxacin, cefotaxime, and rifampicin—that are commonly used in treating human infections. All of the bacteria isolated were resistant to two or more antibiotics, while 86 percent showed resistance to three or more antibiotics.

The spread of resistance

Antibiotic resistance genes are often located on plasmids—tiny fragments of DNA carried by bacteria—that are easily shared with fellow bacteria through a mating process known as conjugation, in which plasmids are transferred from one bacterium to another. Sometimes, multiple resistance genes are found together on the same plasmid.

Indeed, many resistance genes were found on a single plasmid, and what’s concerning is that the bacteria isolated from the fish rapidly transferred their plasmids to a lab strain of E.coli.

If we consume food contaminated with disease-causing bacteria that are resistant to multiple antibiotics, they can transfer their resistant genes via plasmids to our gut bacteria. Over time, we can become resistant to antibiotics. And if we have an infection, we might have fewer treatment options, “which is of grave concern,” adds Rath.

Left: Lady fish or ‘Nogli’, Elops saurus. Right: Sardinella longiceps or ‘Tarli’. Photo by Onkar Naik.

Rath’s team suggested several factors that could be responsible for the high levels of bacteria and antibiotic resistance seen in the fish. First, disposal of domestic, industrial, and agricultural waste creates a reservoir of resistant bacteria in the sea. Second, contamination can occur through improper handling of the fish, which includes the ice and containers housing the fish during transport as well as through dirty hands. And third, many of the antibiotics tested are widely used in fish farms and food animals. Residues of these antibiotics often end up in the sea.

Sumanth Gandra, a resident scholar specialising in infectious diseases from New Delhi’s Center For Disease Dynamics, Economics & Policy, also believes that “contamination of seawater with inadequately treated domestic sewage and by open defecation along the coast could be the potential reasons.” He also points out that testing of the water from the fish containers in the markets would help to confirm the source of contamination.

Iddya Karunasagar, senior director from Niite University in Mangaluru, and formerly a senior officer at the Food and Agriculture Organization of the United Nations, also suspects that the fish could be subject to handling contamination. Retail fish, he explains, are washed and transferred to different storage containers as they make their way from the sea to the table. They can pick up bacteria anywhere along the way.

Left: the widely consumed Indian mackerel, or ‘Bangda’ fish (Rastrelliger kanagurta). Right: Otolithus argenteus, ‘Dhodk’ or ‘Dhomi’. Photos by Onkar Naik.

Resisting the spread of resistant bacteria

“Poor sanitation,” says Gandra, “plays a major role in the spread of antibiotic-resistant bacteria.” Lack of waste treatment facilities means large amounts of untreated sewage ends up contaminating water bodies such as rivers, lakes, and the sea. Research should focus on “developing novel technologies to remove antibiotic-resistant bacteria and resistance genes from sewage treatment plants,” he suggests.

“We need to be aware that antimicrobial resistance occurs naturally in the absence of antibiotic use,” says Karunasagar, “What antimicrobial use is doing is to select resistant bugs and facilitate their proliferation. So we need to focus more on antimicrobial use.”

Karunasagar stresses the need to “minimise misuse and abuse of antimicrobial agents.” The authors agree and suggest formulation of policies to restrict the overuse and misuse of antibiotics to prevent the spread of resistant bacteria in food animals.

These solutions will take time. Meanwhile, Mumbaikars – actually anyone eating seafood – need to exercise extra care and hygiene when cleaning and handling seafood such as fish, to avoid cross-contaminating kitchen utensils and counter-tops.

“If we use the same cutting board for fish as well as vegetables or salads without proper washing of the board, then the microbes from fish can get transferred to vegetables or salads, much of which might be consumed raw,” cautions Rath.

False trevally or ‘Saundala’ (Lactarius lactarius) ready to be cooked after cleaning and marination. Photo by Onkar Naik.


Naik, O.A., Shashidhar, R., Rath, D., Bandekar, J.R., Rath, A. (2017). Characterization of multiple antibiotic resistance of culturable microorganisms and metagenomic analysis of total microbial diversity of marine fish sold in retail shops in Mumbai, India. Environmental Science and Pollution Research.

Banner image: Boys return with a catch of Sardinella longiceps, or Tarli. Picture from PxHere [CC].

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