The outbreak of amoebic meningoencephalitis in Kerala: A wake-up call

Kerala, a South Indian State, has been witnessing a marked rise in suspected/confirmed severe central nervous system (CNS) infections caused by free-living amoebae (FLA) during 2024-2025 with reports indicating a total of 129 cases and 26 deaths as of October 18, 2025¹. Districts like Kollam, Thiruvananthapuram, Kozhikode, and Malappuram are particularly affected. These infections are being increasingly reported and are associated with high mortality. This unusual rise in cases has prompted the State government to rapidly expand testing capacity for early diagnosis and institution of aggressive therapy¹.

Free living amoebae viz. Naegleria fowleri, Acanthamoeba genotypes T1-T23, Balamuthia mandrillaris and various other genera, are ubiquitous organisms that live in fresh or warm brackish water, lakes, ponds, irrigation canals, soil, etc. While all of the above named species cause rare central nervous system infections, Acanthamoeba is also associated with vision-threatening keratitis and disseminated disease. To date, more than 20 genotypes (T1–T23) of Acanthamoeba have been described, of which a subset, notably genotypes T1, T2, T3, T4, T5, T10, T12, and T18, are implicated in human disease. Among these, the T4 genotype is the most commonly isolated from both clinical and environmental samples and is considered the predominant pathogenic genotype worldwide^2-6. N. fowleri, the only pathogenic species of genus Naegleria, causes an acute fulminant meningoencephalitis (Primary amoebic meningoencephalitis, PAM) that is associated with high mortality. Acanthamoeba and Balamuthia lead to subacute to chronic infection (Granulomatous amoebic encephalitis) with relatively better survival. The infections are clinically indistinguishable from bacterial or viral meningitis or encephalitis. Naegleria trophozoites gain entry into the brain mainly through the naso-olfactory route and can affect healthy individuals. Acanthamoeba or Balamuthia infection is primarily acquired through breaks in the skin and spread via a hematogenous route, or via naso-olfactory route or inhalation and mainly affects immune compromised individuals. Therefore, swimming in natural water and nasal irrigation practices are considered risk factors for free-living amoebae infections.

Several contextual factors could possibly explain the surge of free-living amoebae infections in Kerala.

Kerala has an abundant, intricate network of low-lying freshwater and brackish water systems, mainly lakes, ponds, backwaters, etc. The temperature is warm and conducive to the proliferation of free-living amoebae. Intermittent chlorination, open reservoirs and informal water storage increases the risk of free-living amoebae proliferation and subsequent contact with humans in periurban and rural settings. N. fowleri trophozoites especially thrive in warmer water temperatures between 30℃ and 46℃. Global warming has extended the ecological range of these free-living amoebae and is especially reported in unusually hot summers⁷. Moreover, increased droughts and enhanced evaporation reduce water levels creating warm, shallow stagnant pools in which free-living amoebae flourish. Conversely, episodes of extreme rainfall and flooding can facilitate the dispersal of these free-living amoebae into new habitats. Outbreaks have been reported in the USA, Europe and Australia⁸. In India, sporadic cases of free-living amoebae CNS infections are reported from all parts of India, but are increasingly being reported from Kolkata and Kerala, and both these States have similar geography and climate^9-14. In these regions, close human-water interaction is common due to cultural and occupational practices such as recreation, bathing, swimming, religious rituals, irrigation, fishing, etc. Thus, there are multiple opportunities for exposure to the pathogenic free-living amoebae that may increase the risk of infection and disease. Most of the reported cases from Kerala have a history of swimming or nasal irrigation.

It is documented that approx. 30-80 per cent cases of meningoencephalitis remain undiagnosed in developing countries. Kerala is known for its well-developed health infrastructure and was quick to respond to initial cases of Primary amoebic meningoencephalitis (PAM) or Granulomatous amoebic encephalitis^12,13. It promptly improved diagnostic vigilance, built in-state capacity for PCR diagnostics of free-living amoebae, and also sent the samples to referral laboratories outside the State for species-level identification of the pathogen. Most of the samples sent to Postgraduate Institute of Medical Education and Research, Chandigarh, detected Acanthamoeba with a few cases of N. fowleri and even one case of non-fowleri Naegleria^12,13,15. One case of Vermamoeba infection also warrants further investigations and diagnostic scrutiny¹⁶. Thus, the recent rise in cases is possibly due to a combination of genuine increase in cases, heightened clinical suspicion and early diagnostic workup for free-living amoebae¹⁶. Kerala has a responsive public health system and media attention led to more testing and a public warning system through press alerts and risks^1.

The environmental sources or hotspots of infection of some of these patients, when tested also demonstrate the same organism thereby proving the causality. Recently, Kerala State government has started chlorination of wells. It is, however, important to mention that Kerala’s geographical landscape comprises of 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 fishes in ponds which is a source of livelihood.

Curiously, most of the Acanthamoeba meningoencephalitis cases in Kerala are immunocompetent, which is in stark contrast to the global trend^12,17. However, many patients have some comorbid conditions, especially diabetes, hypertension, chronic liver disease, etc., which could be considered as a risk factor and warrant further investigations.

Kerala has been successful in improving the survival outcome of these patients in comparison to global mortality rates of >90 per cent, especially for Primary amoebic meningoencephalitis¹⁸. This may be attributed to early diagnosis and institution of an aggressive antimicrobial therapy with the addition of amphotericin B and miltefosine (used off-label), which has been reported to improve survival in various studies¹⁸.

Many of the reported cases have documented the concomitant isolation of other pathogens from CSF in addition to free-living amoebae viz. Pneumococcus, Mycobacterium tuberculosis and Staphylococcus^15,19. This observation raises the possibility that free-living amoebae may act as a ‘trojan horse’ and harbour pathogens intracellularly and transport these to the CNS²⁰. Moreover, interactions between biofilms, cyanobacteria and free-living amoebae need to be studied. Cyanobacteria and other microbes form dense microbial mats and biofilms in stagnant freshwater or marine habitats. Free-living amoebae feed on cyanobacteria, other bacteria and organic debris and colonize biofilms as secondary inhabitants. Such biofilms are resistant to environmental stressors, disinfectants and biocides providing a protective refuge and supporting the persistence of free-living amoebae even in adverse conditions²¹.