According to Kerala Director of Health Services Dr K J Reena, the spike in cases is mainly due to the state's rigorous testing of all unidentified encephalitis cases.A decade after detecting its first amoebic meningoencephalitis case in 2016, Kerala is seeing an alarming surge in the fatal infection, with 133 positive cases and 33 deaths in the first five months of 2026. A major chunk of the cases, according to the health department, are granulomatous amoebic encephalitis (GAE), caused by Acanthamoeba, a free-living amoeba found mainly in contaminated water.The rise in amoebic meningoencephalitis cases is alarming, considering the state reported only eight cases between 2016 and 2023. However, the surge began in 2024, when Kerala recorded 36 positive cases and nine deaths across various districts. In 2025, the state reported 201 cases and 47 deaths. The figures have continued to rise this year, with positive cases already reaching 133 and deaths 33 till June 12.Kerala’s figures stand out in sharp contrast to the number of detected cases in other states and abroad. Since the first recorded case of PAM in 1971, India had reported only around two dozen cases till 2023. Research papers on PAM state that only 381 cases were reported globally between 1965 and 2018.According to Kerala Director of Health Services Dr K J Reena, the spike in cases is mainly due to the state’s rigorous testing of all unidentified encephalitis cases.“We are detecting more cases after all unidentified encephalitis cases are being subjected to all tests. Undetected encephalitis cases are very few in the state due to this rigorous testing and diagnosis,” Dr Reena told The Indian Express.The DHS said that earlier, most amoebic meningoencephalitis cases were Primary Amoebic Meningoencephalitis (PAM), caused by Naegleria fowleri.“Now, the PAM cases have come down in Kerala and most of the cases detected are GAE, caused by another free-living amoeba called Acanthamoeba, which is ubiquitous in water bodies, soil and even dust. Apart from the tropical climate of the state, poor quality of water is a contributing factor for the increased presence of this amoeba. Our water bodies have vegetation, which is another conducive factor for the increased presence of Acanthamoeba. Most of the affected persons are aged ones with compromised immunity. PAM has a global fatality rate of 97 per cent but GAE has a better survival rate,” she said.Story continues below this adIn 2024, the Kerala health department designed a special treatment protocol and a standard operating procedure for the management of amoebic meningoencephalitis cases — becoming the first state in India to do so. This also helped early detection and reduced the mortality rate. The first Indian to survive the fatal infection was a 14-year-old in Kerala in 2024, and he was the 11th PAM survivor in the world.Dr Anoop Kumar A S, director of Critical Care at Aster MIMS (North Kerala), also said rigorous testing is a key factor behind Kerala’s increase in cases.“Western medical literature shows that most PAM cases were detected during postmortems. Many Western countries do not have regular screening for PAM/GAE. Whereas in Kerala, we are diagnosing the cases and saving lives,” he said.Dr Anoop, who was instrumental in detecting the first Nipah case in Kerala in 2018, said water contamination can lead to an increased presence of Acanthamoeba.Story continues below this ad“Water quality is very poor in Kerala. High population density leads to contamination of water. Many households have their toilet pits close to open wells. Water bodies with high coliform bacterial counts are more likely to have a strong presence of Acanthamoeba, which feeds on various bacteria including E. coli,” he said, calling for a detailed environmental study.Several studies on the quality of well water in Kerala have reported a high presence of coliform bacteria, indicating faecal contamination. A 2018 study on the quality of well water in Thiruvananthapuram district found that 73 per cent of sampled wells were contaminated with coliform bacteria. Another study conducted in 2023 in selected blocks of Ernakulam district also showed a high prevalence of E. coli contamination in a majority of samples.A 2010 study by the Indian Institute of Science, Bengaluru, found water samples in Kerala contaminated with coliform bacteria beyond desirable limits. Shaju Philip is a Senior Assistant Editor at The Indian Express, where he leads the publication's coverage from Kerala. With over 25 years of experience in mainstream journalism, he is one of the most authoritative voices on the socio-political, religious, and developmental landscape of South India. Expertise, Experience, and Authority Decades of Regional Specialization: Shaju has spent more than two decades documenting the "Kerala Model" of development, its complex communal dynamics, and its high-stakes political environment. Key Coverage Beats: His extensive reporting portfolio includes: Political & Governance Analysis: In-depth tracking of the LDF and UDF coalitions, the growth of the BJP in the state, and the intricate workings of the Kerala administration. Crime & Investigative Journalism: Noted for his coverage of high-profile cases such as the gold smuggling probe, political killings, and the state’s counter-terrorism efforts regarding radicalization modules. Crisis Management: He has led ground-level reporting during major regional crises, including the devastating 2018 floods, the Nipah virus outbreaks, and the Covid-19 pandemic response. ... Read More Tags:KeralaThiruvananthapuram