By the end of September, Kerala recorded 21 deaths of people with amoebic encephalitis this year. Sixty-seven others diagnosed with the infection have mostly recovered, while a few remain under treatment. This translates to a mortality rate of 24%, significantly lower than the global average of 90% for the disease.
The rare and fatal infection -- caused by free living amoeba -- began to surface in unusually high numbers in Kerala last year. A disease, with an average of 3.7 cases reported a year across the world until early 2023, was found in 36 people in Kerala in 2024. Most cases were traced to contact with contaminated water carrying free-living amoeba. Guidelines were released and testing became rampant. Early diagnosis and treatment helped bring down the mortality rate considerably. By the end of the year, 27 of the 36 patients had recovered.
“My son had gone for a bath in a pond in Navaikulam around the time of Onam last year. When he developed a fever the next day I was concerned. I had read in the newspaper about the amoebic infection and we took him to the nearby Primary Health Centre. They recommended that we take him to the Medical College. We did when his fever didn’t subside and he began having trouble with his vision. They took his [cerebrospinal] fluid for testing and it was confirmed that he had the infection. But within 10 to 15 days of the treatment, he began showing improvement. After 36 days he was discharged,” says Noushad, an electrician in Thiruvananthapuram.
Noushad’s son could be saved because of timely intervention. He was 17 at the time.
Unlike COVID-19, amoebic meningoencephalitis can be more fatal for children and young adults, since the cribriform plate, connecting the nose to the brain, is more porous in younger people. The amoeba enters the body through the nose, and infection occurs when it can further travel to the brain from the nose.
“There are a lot of microorganisms in our body. If we study a nose we will get so many varieties of them. But they attack when the person is less immune,” says Dr Shameer VK, Assistant Professor of General Medicine at the Kozhikode Medical College.
Doctors and other experts have repeatedly recommended caution in pouring water into the nose, or coming in contact with contaminated ponds, pools and wells.
“A lot of the problem is related to water quality. But we are also advising change in behaviour – avoiding rinsing of the nose among other practises,” says Dr Anish TS, Professor of Community Medicine, Kozhikode Medical College.
Treatment strategies
Kerala's experience of dealing with another deadly virus called the Nipah had prepared the medical experts to be ready with a testing strategy that they had also employed during the outbreak of COVID-19.
Doctors began to proactively test every case of meningoencephalitis for amoeba. This is a job for microbiologists, who will look for amoeba in a sample of the cerebrospinal fluid taken from the patient. Once the amoeba is spotted, the treatment would begin. However, doctors did not wait for the PCR results that would confirm the type of amoeba behind the infection, since it would take a few more days, by which time the condition of the patient could worsen. The recovery was heavily dependent on timely diagnosis and treatment.
There are two kinds of amoebic meningoencephalitis.
Primary Amoebic Meningoencephalitis or PAM is caused by a brain-eating amoeba called Naegleria Fowleri, known to infect only one in 26 lakh people exposed to it. PAM has a mortality rate of 97% across the world.
The second type of the infection is the Granulomatous Amoebic Encephalitis (GME), caused by several types of amoeba, including acanthamoeba which is more common in Kerala. GME progresses slowly but can be deadly if left untreated. This year, most of the infections in Kerala were caused by acanthamoeba, which has a lower mortality rate (worldwide, the average mortality rate of PAM and GME together is nearly 90%).
It is in this context that Kerala’s numbers become significant, both in terms of the number of infections, as well as the recoveries.
Kerala has reported 30 deaths due to amoebic meningoencephalitis since May 2024. As of September 30, the total number of diagnosed cases in the state had reached 124.
More than three-fourths of the patients have survived this otherwise fatal infection, bringing the mortality rate down to 25% in Kerala compared to the global average of 89%.
Cases in Kerala should be placed in a larger context when it is a disease so rare that it is hardly tested for, let alone diagnosed. Until early 2023, only an average of 3.7 cases were reported worldwide every year. The more fatal type of the disease, PAM, was diagnosed only in 488 people between 1962 and 2023, across the globe.
2025 story
The doctors point out that most of the cases reported this year are not the more fatal PAM, but GAE, caused by acanthamoeba, which can take a long time to manifest symptoms. In two years, only 11 cases of PAM have been diagnosed in the state. The other kind of amoebic infection has a longer incubation period, and so it can be hard to trace the source. It is also more likely to affect people with comorbidities.
About 25 to 26 cases of adults with amoebic meningoencephalitis were diagnosed at the Kozhikode Medical College this year. Six of the patients died, most likely, due to existing conditions – heart problem, liver disease and so on, which would in turn make them less tolerant to the cocktail of medicines used for the amoebic infection, says Dr Shameer. But they too get counted among amoebic deaths. On the other hand, there are recovery stories that surprised the doctors.
One of them is a person aged around 30, who was diagnosed with PAM and had an abscess in his brain. “He had come with the usual symptoms of fever and severe headache and all. But the brain abscess - accumulating puss – made it even more dangerous. Repeated tests were turning positive. Medicine was injected directly to the spinal cord, and not through IV. One month later he began to show improvement, but it took further time for the cerebrospinal fluid to be clear of the amoeba. He recovered after three months and we discharged him only a week ago,” says Dr Shameer.
One of the most celebrated recoveries in the state was reported earlier this month, when a student with PAM as well as a fungal infection (caused by the fungus aspergillus flavus) survived both conditions. After four months of treatment at the Thiruvananthapuram Medical College, the student from Kollam was discharged fully healthy.
"The student was 17 years old, whose left side was paralysed after the amoebic infection. He was in a comatose state. It was a complicated case that needed two neuro surgeries," says Dr Aravind Reghukumar, Head of Community Medicine at the Thiruvananthapuram Medical College.
After the fungus was discovered during the second surgery, the course of medication was revised, stated Health Minister Veena George, noting that this was the first time a person with the two conditions could be saved.
Dr Aravind was also in charge when Thiruvananthapuram reported a success story last year, after 10 patients with amoebic meningoencephalitis survived the disease. Among the treatment strategies was snowball sampling, that would study common histories of patients with a rare disease. In Thiruvananthapuram, they found a common high-risk factor for several people who were infected from the same pond.
What changed this year
Medical strategies changed as more cases of GME began to be diagnosed. There seemed little point to trying to trace the source when the amoeba might have entered the body weeks or months ago. “It was illogical. More than the environmental factors, it became important to study the host factors - such as, why one particular person got infected when several others might have bathed with the same well water,” Dr Aravind says.
Testing strategy has also drastically changed. All cases of meningoencephalitis are tested for amoeba, and this, the doctors say, is the reason for the ‘surge’ in cases. This is in line with the strategy adopted for combating Nipah virus in 2018, when testing was maximised. “It can mean that there were always more cases before and we had just not diagnosed them before because we never tested for it. But then, it is also a fact that water pollution has increased and climate change has led to warmer waters, favourable for free-living amoeba. Warmer temperatures increase the bacterial load which becomes food for the amoeba,” says Dr Anish.
Facilities improved with PCR testing now happening in Thiruvananthapuram (as opposed to distant Chandigarh before). However, you need genome sequencing to zero in on the exact type and subtype of amoeba, and the ICMR (Indian Council of Medical Research) has agreed to take this up now, says Dr Shameer.
Another crucial factor is the ability to spot the amoeba itself, he points out. This happens in microbiology when a human looks at the fluid sample through a microscope. “If they are not trained for it, or used to it, they may find it difficult. This is not like having a machine to detect a virus,” Dr Shameer adds. With the increased testing happening in Kerala, microbiologists have become more equipped to identify the presence of amoeba.
A modification was also made in the guidelines issued by the Health Department, requiring wells also to be chlorinated along with swimming pools. No easy task considering there are about 65 lakh wells in the state, in addition to regularly keeping 51000 ponds clean. But it is vital, the doctors stress, that water quality be improved, and effects of global warming tackled.