Kerala is grappling with a surge in amoebic fever cases, also known as Primary Amoebic Meningoencephalitis (PAM), caused by the brain-eating amoeba Naegleria fowleri. The state has reported 69 confirmed cases and 19 deaths so far in 2025, nearly double last year’s tally of 36 cases and nine fatalities.
Health officials say infections are now being detected across multiple districts, unlike in earlier years when cases were linked to specific water sources. Recently, a 17-year-old student in Thiruvananthapuram contracted the disease after swimming in a public pool, prompting authorities to shut the facility and test its water quality. Several other patients remain in critical condition at hospitals.
Experts say the sharp rise in cases reflects multiple factors.
"Warmer temperatures have made freshwater bodies more hospitable to the amoeba, while poor sanitation in some wells and tanks has increased risks. Improved diagnostic capacity has also led to more cases being identified than in the past," says Dr K K Vijyan, leading internist in Kerala.
A major global study published in The Lancet Infectious Diseases confirms that PAM is deadly in about 98 percent of cases. According to this report, Karachi, a major coastal city in Pakistan, is emerging as a hotspot for this infection. The first case of PAM in Karachi was reported in 2008, and by October 2019, there had been 146 cases. In just a decade, Pakistan recorded more cases than the US did in half a century, where 142 cases were reported between 1968 and 2019.
While most PAM cases in the US occur in children under 14, in Pakistan the majority are adults aged 26–45. This difference suggests that the strain in Pakistan may be genetically unique. Most infections in Pakistan happen during summer and before the monsoon season, and scientists are examining how climate change—longer, hotter summers and higher humidity—may be helping amoebas thrive in water, the study found.
There are 20 known species of Naegleria, but only N. fowleri infects humans. Its disease-causing mechanisms are not fully understood, which makes the infection so severe and rapidly fatal. Studying the amoeba’s genetic makeup could reveal why it is so deadly. Scientists are particularly interested in identifying unique genetic markers, new genes, and genes obtained from horizontal gene transfer. Whole-genome studies of the Pakistani strain could uncover these differences and help improve diagnosis and prevention.
Finally, there is an urgent need to educate the public on using boiled or properly treated water for nose rinsing to reduce the risk of infection, suggests the Lancet study.
The infection, though rare, is highly lethal. While global survival rates are extremely low, Kerala has recorded a few recoveries thanks to faster diagnosis and improved intensive care.
The state government has intensified surveillance and prevention efforts. Laboratories in Thiruvananthapuram have been equipped for advanced PCR and genomic testing, while water bodies, wells, and swimming pools are being chlorinated. Public awareness drives are underway to warn against swimming in untreated water and to promote precautionary steps such as using nose clips.
However, the scattered spread of infections poses challenges for health authorities, as no single source can be isolated and treated. Treatment remains difficult because the disease progresses rapidly, leaving doctors with little time to intervene once symptoms appear.
"The key challenge in treating PAM is its rapid spread to brain cells. The amoeba enters through the olfactory nerve in the nose when a person swims in stagnant or contaminated ponds and lakes, making the disease highly fatal,” explains Dr. Vijayan.
Despite these challenges, Kerala’s quicker detection, ICU preparedness, and research collaborations have helped improve survival compared to global trends. Still, the rise in cases is a reminder of the urgent need for stronger water safety measures and sustained public cooperation.
What next
The state government’s immediate focus is on preventing fresh infections through chlorination, water testing, and awareness campaigns.
"However, long-term control will depend on better sanitation practices, climate-linked monitoring of water sources, and continued investment in diagnostics and scientifically designed research," says Prof. Dr Sai Gopinath, a leading physician and medical researcher.
While the outbreak is limited in scale compared to other epidemics, its high fatality rate makes it a pressing public health concern. Vigilance, early detection, and preventive action will be crucial in containing further spread.