Beyond the ‘brain-eating’ amoeba: India’s silent struggle with neglected amoeba infections
Globally, Entamoeba histolytica, the parasite behind amoebiasis, causes 55,000-1,00,000 deaths annually — 9,229 deaths in India alone in 2021 — making it the third deadliest parasitic disease after malaria and schistosomiasis. Yet, neither has WHO listed it under Neglected Tropical Diseases nor has any country, including India, launched a national eradication programme against this amoeba
Amoebas are generally associated with diarrhoea, dysentery, or an occasional liver abscess. But in recent years, the so-called “brain-eating amoeba” has made its way into public headlines, while other, more silent amoeba continue to quietly burden millions across the country. Together, these parasites may be far more dangerous than most realise.
The brain-eating amoeba: Rare but deadly
The spotlight has recently fallen on Naegleria fowleri, a free-living amoeba infamously known as the “brain-eating amoeba.” It enters through the nose, usually while swimming or bathing in warm, untreated water. Once inside, it travels to the brain, causing primary amoebic meningoencephalitis (PAM) a disease that kills over 97% of patients worldwide according to the Center for Disease Control and Prevention (CDC), Atlanta, U.S.
Kerala has become the epicentre of this health scare. In 2024, the state reported 29 such cases with five deaths (a 26% case fatality rate), far lower than the global average, but still alarming. This marked a sharp rise from just eight cases recorded between 2016 and 2023. The threat continues in 2025, with Kerala reporting nine fresh cases, including a nine-year-old girl and a three-month-old infant. Five patients have already died.
Doctors stress that prevention is the only reliable defence, as no guaranteed cure exists once Naegleria reaches the brain. Experts advise avoiding warm stagnant water, using boiled or filtered water for nasal rinses or religious ablutions, and seeking immediate medical help if fever, nausea, headache, or confusion follow water exposure. To improve outcomes, Kerala has established specialised molecular labs for early detection, a move praised by health authorities.
The wider burden
While Naegleria makes headlines because of its dramatic attacks, there are other rare infections that are caused by equally deadly amoebas that are also free-living. People need to be aware about other amoeba infections, their symptoms and preventive measures.
Acanthamoeba keratitis (AK), is a rare infection but it poses a major threat to vision. Every year, it affects about 23,561 individuals worldwide. Compared with countries such as Tunisia and Belgium, which record as low as 0.2 cases per million, India has one of the highest national rates of up to 15.2 cases per million. Acanthamoeba accounts for about 1% of all cultures from suspected infectious keratitis, a condition that causes corneal ulcer and frequently results in excruciating pain, redness, vision loss, blindness, or even death if left untreated. People who wear contact lenses should be careful as this type of keratitis is prevalent in this population.
The two most prevalent pathogenic species associated with eye infections are Acanthamoeba castellanii and Acanthamoeba polyphaga, which can be present in water, soil or air. These amoebae also cause a rare and fatal disease of the central nervous system called ‘granulomatous amoebic encephalitis’ (GAE) mainly in immunocompromised patients. Out of 30 paediatric cases reported worldwide between 1960 to 2020, 14 (46%) were from India. Due to its rare occurrence, GAE is challenging to diagnose, leading to death due to delayed treatment.
While Naegleria and Acanthamoeba kill people quickly and brutally, destroying the brain or eyes in a matter of days to weeks, a more insidious amoeba that does not get the same attention is Entamoeba histolytica. E. histolytica does not cause dramatic damages to the body and so fail to make headline news. However, it is responsible for slowly damaging the gut and liver of a large number of people.
The silent menace: Entamoeba histolytica
Entamoeba histolytica, the parasite behind amoebiasis, is far more common and is generally not considered to be of concern. This amoeba spreads through contaminated food and water. Infected individuals may suffer abdominal pain, mild diarrhoea, or severe dysentery with blood and mucus. More dangerously, the parasite can eat through the intestine, enter the bloodstream, and travel to vital organs like the liver, lungs, or brain, forming abscesses that can kill if untreated.
Globally, E. histolytica infects 50 million people annually and causes between 55,000 and 1,00,000 deaths as per the global burden of disease study, making it the third deadliest parasitic disease after malaria and schistosomiasis. India bears the heaviest burden in the world: prevalence in communities ranges from 3% to 23%, depending on sanitation and diagnostic practices. In 2021, India recorded 9,229 deaths due to this disease. Despite the huge annual death toll, amoebiasis remains a neglected disease. Neither has the World Health Organization (WHO) listed it under Neglected Tropical Diseases (NTDs) nor has any country, including India, launched a national eradication programme against this amoeba.
Why amoebiasis is hard to eradicate
Amoebiasis due to E. histolytica is generally dismissed as “easily treatable.” The reality is far more complex. Most infected people never show symptoms but shed millions of infectious cysts daily in their stool. These ‘carriers’ keep disease transmission alive. The cysts survive in the environment, spreading infection in areas with poor sanitation and unsafe drinking water. Clinical symptoms of diarrhoea- abdominal pain and fever overlap with other gastrointestinal diseases. Most Indian labs still use microscopic stool examination for diagnosis, which is not a reliable test. Nearly 45% of cases are misdiagnosed.
Additionally, another amoeba, E. moshkovskii, which was not usually detected in Indian patients is being reported more frequently in India, suggesting that it may have become endemic. Microscopy also misses low parasite counts if samples are old or poorly preserved. Blood antibody tests cannot distinguish between past and current infections. Molecular tests such as PCR are recommended but costly, not widely available, and sometimes return false negatives. The most widely used drugs are metronidazole and tinidazole which kill only the active disease-causing stage (trophozoites), not the cysts that spread infection. As a result, the infection cycle continues.
Worse, reports now show increasing resistance and reduced efficacy of these drugs, with some cases of treatment failure. Long term, high-dose use has also been linked to liver damage. Importantly, no new drug has been developed in the last 60 years for this parasite.
Amoebiasis treatment is more complicated than simply administering medication. Since many parasite carriers do not exhibit any symptoms, they fail to seek help and unintentionally keep spreading the infection. At the same time, many countries find it difficult to supply everyone with clean food, safe drinking water, and adequate sanitation. Even when these things are available, many people do not always practice good hygiene. This indicates that a combination of medical care, improved hygiene, and awareness is needed to break the cycle, not just medications.
India’s health goals and the way forward
India has a track record of success with targeted national missions, with significant progress in controlling other parasitic diseases. Kala-azar elimination programme has reduced deaths significantly since the 1990s. The filariasis programme has led to zero deaths due to this disease in India, and the malaria elimination programme has also reduced deaths sigificantly. Yet amoebiasis, which killed 9,229 Indians in 2021 and costs the country 0.7 million Disability Adjusted Life Years (DALYs) has been largely ignored. Research funding for amoebiasis remains shockingly low compared to malaria and leishmaniasis.
The Sustainable Development Goals (SDG) 2030 call for “good health and well-being for all”. Achieving this will be impossible without addressing so-called “easily treatable” diseases like amoebiasis. In view of the increased frequency of rare amoebic infections like Naegleria, India should launch a National Mission for these amoebic infections, focusing on public education on hygiene and safe food practices, improved sanitation and clean drinking water, investment in accurate diagnostic technologies, along with research for new drugs to break the infection cycle.
If India commits to combating amoebiasis with the same vigour as malaria and kala-azar, it could save tens of thousands of lives, reduce recurrent infections and improve the health of millions, and raise the country’s standing in the global health index. For a nation aspiring to meet its SDG 2030 health targets, this fight is not optional, it is essential.
