Brain-eating amoeba kills more than rabies & influenza in Kerala this year

There's been a change in Kerala's usual communicable disease killers in 2025. Amoebic meningoencephalitis caused more deaths than flu (influenza) and rabies in the state in 2025. The health department figures showed that the number of cases leapfrogged in 2025; from 39 cases in 2024 to 200; a rise of over 400 per cent. Correspondingly, the deaths due to brain-eating amoeba have gone up from 9 to 47 between 2024 and 2025.

The fatality due to Amoebic Meningoencephalitis in 2025 is higher than influenza (43) and rabies (28) in Kerala. Data furnished in response to Onmanorama's RTI query showed that, of the 161 cases reported in 2025 till November, PCR investigations returned negative/indeterminate results in 79 cases, of which 16 were fatal.

The ubiquitous free-living amoebae (FLA); Acanthamoeba, found in soil, water and dust accounted for 61 cases causing 14 deaths. Naegleria fowleri was identified as the causative organism in only 8 cases, 4 of which were fatal. While exposure to unchlorinated water has been considered as a major reason for the disease, figures state that the number of cases with swimming/diving history was only 18.

Almost all the age-groups were affected by the disease in Kerala with people aged between 30-44 reporting highest incidence of 39 cases followed by those in the age-group 45-59 (38 cases). A total of 33 cases were confirmed among children in 2025.

Following the spurt in number of cases in 2025, Kerala had to revise the guidelines. It was directed that a history of nasal exposure to fresh water in the 14 days before symptom onset should be asked of any patient who presents with symptoms of acute meningitis. In patients with clinical and CSF (cerebrospinal fluid) picture suggestive of bacterial meningitis who are not responding to antibiotics or are rapidly deteriorating, doctors were directed to consider PAM (Primary Amoebic Meningoencephalitis) even in the absence of exposure to fresh water.

Infectious disease experts associated with the management of Amoebic Meningoencephalitis said that Kerala amped up testing, and reporting strategy was revised which naturally resulted in increased detection of cases. "Our PCR-diagnosis has improved significantly. We are also on the look-out for cases where Acanthamoeba and some other FLA can act as Trojan horse.

Amoeba consumes algae and fungus which survive inside the pathogen and when it enters human brain, the immune system takes on the amoeba. Fungus and algae can manifest in some cases and cause co-infection. Our drugs partly address such consequence. We have revised our guideline to consider this aspect as well," said an infectious disease expert.

Dr Anish T S, Professor, community medicine, said that the amoeba situation in Kerala is bit complicated. "When we say that Acanthamoeba caused the highest percentage of cases, the question arises whether these are precisely confirmed one or suspected. There is a chance of false positivity, considering Acanthamoeba is found almost everywhere. We are picking cases because they give us the treatment options.

Even the lesser proportion of cases due to Naegleria fowleri is unacceptable, because it affects mostly children and the fatality rate is high. It's a high-priority group. As for Acanthamoeba, people with immunocompromised conditions are more vulnerable. Those with a history of head injuries, rare conditions like CSF rhinorrhea (leakage of CSF through the nose) should use a mask and avoid exposure to water," said Dr Anish.

A recent article published by Nazia Nagi in the Lancet on Kerala's strategy against the disease also echoes this point of misdiagnosis. It notes that clinical diagnosis of Amoebic meningoencephalitis is challenging due to its non-specific presentation and resemblance to other CNS infections. Routine culture methods do not detect these pathogens, making rapid microscopic examination of cerebrospinal fluid essential for identification; however, poor clinical familiarity with the organisms often contributes to missed diagnosis, the article notes.

Dr Sumeeta Khurana, Department of Medical Parasitology, PG Institute of Medical Education & Research, Chandigarh, observes in her article on the disease outbreak in Kerala that the recent rise in cases is possibly due to a combination of heightened clinical suspicion and early diagnostic workup for FLA. Kerala used to send samples to Chandigarh before the in-house facility was set up in the state public health lab.

According to Khurana, the environmental sources or hotspots of infection of some of these patients, when tested, also demonstrate the same organism, thereby proving the causality. "Recently, the  Kerala State government has started chlorination of wells. It is, however, important to mention that Kerala’s geographical landscape comprises 40 per cent water, and it is next to impossible to treat each pond or well in the State, and this may also lead to killing of fish in ponds, which is a source of livelihood," Khurana says in the article.