Between 2016 and 2022, Kerala reported only eight cases of amoebic meningoencephalitis. But in 2023, the numbers surged: 36 infections and nine deaths. At present, 10 patients are undergoing treatment.
Published Sep 12, 2025 | 7:00 AM ⚊ Updated Sep 12, 2025 | 7:00 AM
Visual concept of deadly brain-eating amoeba infection.
Synopsis: Kerala has reported six deaths and ten active cases from a rare but deadly brain infection caused by a “brain-eating” amoeba. Experts link the surge to climate change, poor sanitation, and cultural practices that expose people to contaminated freshwater. Despite improved vigilance and preventive measures, treatment remains limited, and experts stress that only coordinated management of water safety across local governments, health departments, and communities can minimise exposure.
When 47-year-old Shaji from Chelambra in Malappuram fell ill, it seemed at first to be a simple case of fever and headache. He was rushed to Kozhikode Medical College Hospital, but within days, on Thursday, 11 September, he was dead.
His was the sixth death in Kerala in just one month from a rare but deadly brain infection: amoebic meningoencephalitis.
A nine-year-old girl from Thamarassery, a three-month-old infant from Omassery, 52-year-old Ramla from Malappuram, Ratheesh from Sulthan Bathery, and Shobhana from Thiruvali all died before him.
Shobhana was admitted on 6 September and remained unconscious for days before succumbing.
At present, 10 patients are undergoing treatment – seven at Kozhikode Medical College Hospital and three children at the Institute of Maternal and Child Health. One of them is in critical condition, fighting for life against an infection that kills 97 percent of its victims worldwide.
The illness begins with what appears to be a routine fever and headache but progresses rapidly. By the time doctors recognise what is happening, it is often too late.
The cause is Naegleria fowleri, a microscopic organism more widely known as the “brain-eating amoeba.” This free-living amoeba thrives in warm freshwater – lakes, ponds, rivers, and even contaminated soil.
The pathway of infection is alarmingly simple. Contaminated water enters through the nose, the amoeba travels upward to the brain, and death usually follows.
“At the base of the skull lies a bone called the ethmoid bone, which has a perforated section known as the cribriform plate. Just above it is the olfactory bulb – the part of the brain that allows us to smell,” Dr TS Anish, Nodal Officer at Kerala One Health Centre for Nipah Research and Resilience, Kozhikode, told South First.
“For example, when you smell a rose, aromatic compounds pass through the cribriform plate directly to your brain. The amoeba uses the same pathway.”
Between 2016 and 2022, Kerala reported only eight cases of amoebic meningoencephalitis. But in 2023, the numbers surged: 36 infections and nine deaths.
The first death in 2024 was that of a five-year-old girl. Until then, every known case in India had proved fatal, reinforcing the sense that the pattern was unbreakable.
“This is a rare infection. It’s not common like herpes, TB encephalitis, bacterial meningitis, or even fungal infections. If you look at the order, you’ll see bacterial cases first, then viral, then TB, then fungal – and only after that does this infection appear,” said Dr Sudhir Kumar, neurologist at Apollo Hospitals, Hyderabad, speaking to South First.
“Twenty-one years ago, I would see maybe one case a year, and that trend has continued. We never see clusters, mainly because the infection is waterborne.”
The current outbreak, however, marks something new for Kerala: clusters of cases in a disease long known for its rarity.
So why is this happening now? Experts point to climate change.
“In our tropical climate, the baseline temperature may have risen by 1–2°C over the past few decades. As a result, surface water temperatures have also gone up,” explained Dr TS Anish.
“Pathogenic amoebas such as Naegleria fowleri and others are thermophilic – they thrive at higher temperatures, especially close to 40°C. Climate change keeps them in their most active stage, known as the trophozoite form. In this stage, they feed, multiply, and can infect humans.”
The seasonal pattern is consistent. Cases emerge in late February, rise through the monsoon months, and decline by October or November when cooler weather sets in. Year after year, the cycle repeats.
“Normally, these amoebas can also exist in two other forms: a flagellated form, where they don’t multiply, and a cyst form, which is dormant when food or conditions are unfavourable. But warmer water prevents them from shifting to those dormant or less active stages, keeping them infectious for longer,” Dr Anish added.
The impact of warmer waters goes beyond the amoeba itself. Rising temperatures suppress natural predators, increase cyanobacteria that serve as food for amoebas, and drive more people to seek relief in ponds and other water bodies.
“And finally, when the weather is hotter, people are more likely to bathe or swim in ponds, pools, or other stagnant water bodies, increasing the risk of exposure,” said Dr Anish.
Complicating the picture is inadequate water sanitation.
Dr Shubin Chenayil, District Surveillance Officer with Malappuram’s health department, has been tracking the cases closely.
“Out of 17 cases reported, 4 are children and the remaining 13 are adults. Only 3 of them have a history of bathing in ponds or rivers. The rest used well water, borewell water, or piped water supply. But knowingly or unknowingly, water may have entered through the nostrils – that might be the cause of infection,” Dr Shubin told South First.
His team has been systematically testing water sources.
“We are finding the presence of amoeba in water in almost all these cases. We are also testing the quality of water from wells. And what are the findings? In most of these cases, amoeba is detected. But not all are Naegleria fowleri – the deadly one. Some are other amoebas which are more treatable and not as fatal,” he added.
Dr TS Anish explained the cycle of contamination:
“In Kerala, all reported cases so far have been linked to natural water sources, not swimming pools. These rivers often get contaminated with sewage waste or effluents from nearby poultry farms. Water contamination increases the biomass, especially coliform bacteria, which serve as food for amoebas. So pollution provides a favourable environment for their growth.”
He pointed to the risks of cultural practices as well.
“It is especially dangerous during ritual practices where water is poured into the nostrils – whether at Sabarimala in Kerala, the Ganges in North India, or during certain religious practices among Muslims,” he said.
“This is behavioural practices. In some cases, water enters the nostrils through ritual practices – such as nasal irrigation or pouring holy water into the nose. These cultural habits can also increase the risk of infection.”
His advice is clear: “Avoid letting untreated water enter your nose – that is the most important precaution. Use only chlorinated or boiled and cooled water for any practice involving the nostrils.”
There is also a connection with animal waste.
“I don’t completely agree with the view that this amoeba originates in animals and then comes to humans. It is actually a free-living organism, present in water and soil in varying quantities everywhere,” Dr Anish added.
“However, there is a connection with animals. Animal waste—cow dung and similar by-products—provides a rich substrate for coliform bacteria, and these bacteria are food for amoebas.”
While the surge in cases has caused alarm, there is at least one positive takeaway: the rise in numbers reflects greater vigilance rather than a sudden increase in disease occurrence.
“Since 2023, more cases are being reported because doctors have become very cautious. Now, in any suspected case of acute encephalitis syndrome or meningitis, doctors in Kerala routinely send cerebrospinal fluid samples for wet microscopy to check for the presence of amoebas. This improved vigilance has significantly increased the detection rate,” explained Dr TS Anish.
Dr Shubin Chenayil agrees. “All the AES cases, we are subjecting to CSF microscopy. Even if there is no initial microscopy, we are still detecting the cases,” he said.
But despite medical advances, treatment options remain severely limited.
“Treatment protocols have not changed much. To develop new treatments, you need randomised controlled trials. But when the whole country reports fewer than 10 cases a year, how can you do a trial? That’s one of the reasons we still don’t have an effective treatment, even though the infection has been known for over 30 years,” explained Dr Sudhir Kumar.
Drawing parallels with other diseases, he added: “Some diseases, like rabies, have thousands of cases but still no cure. Others, like HIV, eventually saw effective antivirals developed. But here, given the extremely low numbers, I don’t expect major treatment breakthroughs in the future.”
Yet Dr Kumar maintained hope for ethical research approaches. “In such a fatal condition, you can tell the family that without treatment the chance of survival is almost nil, but there is a new medicine that may or may not work. This is how new drugs are discovered, even in cancer.”
Kerala, meanwhile, is not waiting for breakthroughs in treatment. The state has launched comprehensive prevention efforts.
“As for preventive measures, we are carrying out chlorination – cleaning wells, then chlorinating them, and doing the same with ponds. With community participation, ponds, rivers, and streams are being cleaned and made safe. Till then, entry into water sources is being restricted,” said Dr Chenayil.
Local self-government bodies are also stepping up. “Local Self Governments (LSGs) are actively engaged in cleaning ponds and streams. They are also providing coordination support by supplying bleaching powder and logistics,” he added.
But challenges remain. Despite repeated advocacy for chlorination, “not more than 25 percent of household wells in Kerala are chlorinated,” admitted Dr Anish.
The scope of the problem is daunting. Recreational facilities such as water theme parks present particular risks. “If these are contaminated, outbreaks could occur. Strong surveillance and strict chlorination protocols for such facilities are essential,” he warned.
Experts say the solution goes beyond medicine. What Kerala needs, they argue, is a comprehensive “One Health” strategy.
“That means integrating animal husbandry, health, education, and other departments at the local level. Kerala’s 2023 Public Health Act empowers local self-government bodies to lead public health committees that bring these sectors together,” said Dr TS Anish.
He sees Kerala’s decentralised governance as a major advantage. “Different states in India have different governance mechanisms. In Kerala, the irrigation department is not very strong, but the local self-governments (LSGs) are highly vibrant. Much of Kerala’s development is attributed to the strength of its local self-government system.”
He argues that local control is key. “It is more feasible for LSGs to look after the safety of water bodies in their own jurisdictions rather than depending on a centralised system like the state irrigation department, which is responsible for 44 rivers and numerous tributaries.”
The evidence points in the same direction. “If we look at recent outbreaks in Kerala, hepatitis A has been concentrated in the northern Malabar districts – the same regions now reporting clusters of amoebic meningoencephalitis. This overlap strongly indicates that water contamination is a key issue.”
Still, experts caution that complete elimination of amoebas is not possible.
“At the same time, we must recognise that amoebas are ubiquitous. You will find them in wells, ponds, and rivers everywhere. So, simply detecting amoebas in water does not prove a direct cause of disease. Instead, we need an umbrella approach: all water bodies should be cleaned, and amoeba density must be kept at the minimum possible level. While complete elimination is impossible, reducing the burden makes water safer,” Dr Anish explained.
Dr Sudhir Kumar added perspective on transmission: “The risk is highest in stagnant, fresh water like ponds, lakes, or poorly maintained swimming pools. It doesn’t occur in seawater, rivers, or flowing streams. Most cases I’ve seen came from ponds or pools where water was trapped.”
He described how contamination spreads: “Some people can carry them without symptoms. When they bathe, they release the organisms into the water. Add to that the fact that pools and ponds often contain urine, faeces, and secretions. The next person who inhales or gets water up the nose may get infected. Still, not everyone exposed will fall sick; immune mechanisms protect many people.”
A health specialist reflected on the wider challenge: “Scarcity of safe drinking water remains one of our biggest challenges. Clean water is a necessity, not a luxury, yet many still depend on unsafe sources. People must practise good drinking habits.”
The healthcare system, too, faces structural pressures. “Unfortunately doctors are often not included in these community forums. The health department alone cannot manage this crisis. With 44 rivers, water is both a boon and a curse for Kerala – it sustains life but also spreads disease if neglected. Only a coordinated effort between government, doctors, and local bodies can make water truly safe,” the health specialist added.
(Edited by Dese Gowda)
