Amoebic meningoencephalitis | Conflated cases

It’s an infection that has been documented in India since the 1970s. The first case of amoebic meningoencephalitis (AME) in two Indian children was reported by Pan et al. in 1971, and thereafter, several cases were reported from various parts of India. But AME has suddenly been making huge national and even international headlines because Kerala has now made it a serious business to aggressively test and treat all cases of AME, most of which may have otherwise been bracketed under the head of acute encephalitis (AES) syndrome with unknown etiologies.

This strategy has had a huge downside, too. In a State where every health-related issue assumes huge political dimensions and comes under intense public scrutiny, Kerala’s health officials are now having a hard time explaining to the public at large why there has been a sudden surge in AME cases, which are still considered to be rare.

The first case of AME was documented in the State in 2016, and till 2023, cases were sporadic and fatality was total. In 2024, AME cases suddenly surged to 39, but with just eight fatalities. This year so far, there have been 71 cases of AME — 24 cases diagnosed in September alone — and 19 deaths.

Misleading headlines

Significantly, of the 110 cases of AME reported in Kerala in 2024 and 2025, only 11 were due to Naegleria fowleri, the “brain-eating” amoeba, which causes primary amoebic meningoencephalitis (PAM), which has a fatality rate of 99%. Almost all of the remaining were cases of encephalitis caused by Acanthamoeba, another free-living amoeba.

Thus, media headlines that Kerala is battling “brain-eating” amoeba are misleading.

Acanthamoeba, is a ubiquitous pathogen which is widely distributed in the environment in waterbodies, wells, overhead storage tanks, swimming pools and even treated tap water. It has been isolated from dust samples in dialysis units, air-conditioning and ventilation in hospitals. Acanthamoeba is so ubiquitous that 80% of the human population has natural IgG antibodies against it.

There have also been documented cases wherein the colonisation of nasal mucosa by Acanthamoeba, without active infection, has been reported in immunocompetent individuals. It is in individuals with immunocompromising conditions, ranging from alcoholism and diabetes to cancer, that Acanthamoeba emerges as a huge health risk.

While the commonest mode of exposure to this pathogen in the general population could be through waterbodies and nasal irrigation using tap/untreated water, in immunocompromised individuals, Acanthamoeba can also enter through skin wounds and reach the brain through the bloodstream.

Clinicians treating AME cases in Kerala clarify that the majority of the patients are indeed immunocompromised individuals, such as renal patients on dialysis or cancer patients. They stress that the people are not up against a universal public health risk. Avoiding unclean waterbodies and risky habits such as nasal irrigation should protect the majority from amoebic infections.

In the case of infection by N.fowleri, usually there is a clear epidemiological link to waterbodies, or nasal irrigation and dramatic presentation of central nervous system infection in patients within a short incubation period of 5-14 days. However, in the case of encephalitis caused by Acanthamoeba, it is difficult to establish a clear epidemiological link as the source is often unknown and the incubation period could range from weeks to months.

The confounding epidemiology of the disease is thus posing diagnostic challenges to clinicians, while making it harder for the health experts to dispel the public’s conviction that they were up against a new public health threat.

In India, not more than 25-30% of AES cases have a known etiology. But there have been many research studies from within the country in recent years, which point to the fact that central nervous system infections caused by Free-Living Amoebae (FLA) could be underdiagnosed because of a lack of awareness/clinical suspicion.

In Kerala, after the Nipah outbreak of 2023, in all cases of Acute Encephalitis Syndrome (AES) which are negative for viral diseases, the CSF samples are tested for amoeba, resulting in a surge in AME cases in the last two years. This aggressive testing strategy has been saving many lives in the State. Early diagnosis followed by intensive management has helped Kerala bring down the mortality of AME to 24.5%, something that the clinicians are very proud of.

N. fowleri has a mortality rate of 99% but of its 11 cases of AME due to N.fowleri, the State managed to save six.

Adopting a public health approach rooted in the One Health principle, a massive chlorination exercise has been launched across Kerala to clean its waterbodies. In a State which has 55,000 ponds and 55 lakh wells, this is a task which may not sound practical, but reducing water contamination in all waterbodies is important to reduce amoebic density.

Last heard, the ICMR and other research institutions are stepping in to help Kerala analyse the epidemiological data and explore the routes in which amoebic infections are acquired.