Amoebic meningoencephalitis emerges a major health concern in Kerala

Anaya, a Class IV student at Government Lower Primary School, Korangad, near Thamarassery in Kozhikode district looked exhausted as she returned home on August 13 evening. Her father K.V. Sunoop and mother N.P. Rambeesa thought the child must have been feeling tired as she had attended dance rehearsal sessions for an Independence Day event.

As night progressed, Anaya felt feverish and started vomiting. “My brother initially suspected she had leptospirosis, gave Anaya a tablet, and asked Rambeesa to take her to the Thamarassery Taluk Hospital the next day,” Sunoop’s sister, K.V. Soumya, says. Though she was admitted to the hospital on August 14, Anaya’s condition worsened by afternoon. She passed away while being rushed to the Government Medical College Hospital (MCH), Kozhikode, in the evening.

Subsequent lab results showed that she was infected with amoebic meningoencephalitis, a rare but fatal brain infection caused by free-living amoebae found in freshwater, lakes and rivers. In the next two weeks, at least nine people undergoing treatment for fever at the MCH tested positive for the infection. Four of them, including Anaya’s seven-year-old brother and a three-month-old child, are from Kozhikode, three others are from Malappuram, while two are from Wayanad.

Doctors say that two types of fatal amoebic encephalitis infections are commonly found: primary amoebic meningoencephalitis (PAM) and granulomatous amoebic encephalitis (GAE).

PAM is caused by the Naegleria fowleri species, commonly termed as “brain-eating amoeba” as it destroys the brain tissue leading to the death of the patient. Children, teenagers, and young adults are vulnerable to it. The infection has a high fatality rate due to delayed diagnosis and a rapid onset. Some of the early symptoms of PAM are similar to that of bacterial meningitis, while those of the GAE can be akin to encephalitis, meningitis or brain abscess.

From Anaya’s partly-completed house at Anapparapoyil, a narrow, undulating, grass-covered rocky path on a steep slope leads to a tiny pond on their neighbour’s premises. “She used to take bath in the knee-deep waters there along with her two brothers,” says Soumya though the source of the infection is yet to be identified. Officials at the taluk hospital have tied a band around the pond with a notice declaring a ban on venturing into the waters.

Around 12 km from Anaya’s house, Abdussamad of Kolathakkara, near Omassery, is perplexed that his neighbour’s three-month-old child has been diagnosed with amoebic encephalitis and a lab test showed the presence of the free-living amoeba in his well. “They used to pump water for their domestic use from here. Health officials are now chlorinating it every three days,” he says.

T.S. Anish, Professor of Community Medicine, and nodal officer of the Kozhikode-based Kerala One Health Centre for Nipah Research and Resilience, says climate change is one of the main reasons for the spurt in amoebic encephalitis cases in Kerala in recent years. “Because of the rise in atmospheric temperature, microorganisms such as amoeba Naegleria fowleri that thrive in high-temperature environments have got a prominence in the environment in the past decade or so,” he says.

“Species such as Naegleria fowleri mainly feed on bacteria and algae. The contamination caused by coliform bacteria, commonly found in faecal matter, is high in our water sources such as wells, ponds, and rivers,” he says.

C. Shubin, Malappuram District Surveillance Officer, notes that a combination of specific factors comes together to cause the disease. “These include significant amoebic growth in stagnant water with optimal temperature and biomass, followed by water entering the nasal cavity, often through a pre-existing deformity or opening,” he says.

According to R. Aravind, Head of the Department of Infectious Diseases, Government Medical College, Thiruvananthapuram, there are over 400 species of free-living amoebae in the environment. “However, only Naegleria fowleri, Acanthamoeba spp., Vermamoeba vermiformis, Balamuthia mandrillaris, Paravahlkampfia francinae, and Sappinia are considered to be highly harmful to humans. Kerala has reported amoebic infections caused by Naegleria fowleri, Vermamoeba vermiforis as well as Acanthamoeba. A majority of the recent infections are due to Naegleria fowleri and Acanthamoeba spp. While Naegleria fowleri is considered to be the most dangerous of these pathogens, Acanthamoeba spp. is the most pervasive one recovered even from soil,” he says.

The local community is on alert with 14 cases and four deaths reported from Malappuram district so far this year.

None has taken a dip in the placid pond at Cholakkal, near Malappuram, since the death of a 16-year-old boy in June third week. It is presumed that he developed meningoencephalitis after he took a bath in the pond with crystal clear water. “Many others who bathed in the pond along with him got fever out of fear,” says Faseela Kolakkattil, a resident of Chemmankadavu, near Cholakkal.

In September 2024, Navaikulam panchayat, about 37 km north of Thiruvananthapuram city in Varkala taluk , was in the grip of fear . Three Plus Two students had taken bath in the Maadankavu pond in Maruthikkunnu ward, out of whom one was diagnosed with the infection. The Navaikulam panchayat authorities acted swiftly, putting up flex boards on the banks of almost all the 40 ponds and a few canals warning people against venturing into them.

The messaging was done carefully to avoid creating a scare while ensuring that the people take sufficient care. A year after, the scare seems to have passed as the warning boards have been removed after the cleaning of the ponds. “No cases have been reported from the area after the cleaning and people now use some of these ponds,” says H. Savad, panchayat member of Maruthikunnu ward.

“My son spent 45 days in the hospital. Since we rushed him to the Government Medical College Hospital, Thiruvananthapuram, right when we noticed some symptoms, his situation did not get worse. He got really good care there and recovered well,” says the father of the boy from Navaikulam who was diagnosed with the disease. The doctor checks on him once in a while. “Now, he is fine and will be joining a professional course soon,” he says.

However, another 23-year old who developed symptoms around the same time last year after venturing into the waters near Sambranikodi in Kollam still faces difficulties occasionally. .

In addition to Navaikulam, the rural suburb of Athiyannoor, near Thiruvananthapuram, also witnessed a cluster of cases in seven youths, who all tested positive for the disease and later recovered. This was a rare case of a cluster, while the rest have all been sporadic cases. 

Health officials say the State started reporting sporadic amoebic encephalitis cases from 2016 and almost all the patients succumbed to the infection till 2023. It was a challenge to identify the causative organism as the samples had to be sent to the Post Graduate Institute of Medical Education and Research, Chandigarh, for confirmatory diagnosis.

In 2024, the State government came out with a set of guidelines for the diagnosis and management of the infection in the wake of recurring cases and deaths. Patients with acute meningitis symptoms such as fever, stiff neck, and confusion are now asked if they have a history of nasal exposure to freshwater 14 days before the symptom onset.  Children could be more vulnerable as their cribriform plate that separates the nasal cavity and the skull has more porous openings compared with adults.  The cerebro-spinal fluid (CSF) of such patients are then sent for lab tests for free-living amoebae, including Naegleria fowleri. The recommended multi-drug regimen and supportive therapy should start on patients diagnosed with PAM through CSF microscopy.

Dr. Aravind says the introduction of miltefosin, an anti-parasitic drug whose supply was limited earlier, in the antibiotic cocktail, was a major turning point. Till then, only 11 surviving cases of Naegleria fowleri PAM were reported globally. But, by October 2024, a total of 14 of the 19 infected persons in Kerala in the previous five months survived.

Doctors say testing is more aggressive now, especially in north Kerala districts such as Kozhikode in the context of the recurring Nipah outbreak in the region, to find out the exact cause of any case of acute encephalitis syndrome (AES), an inflammation of the brain. “Even more than one rare case is considered an outbreak. Whenever AES cases are noticed, clinicians check the presence of the amoeba in the CSF. So, more cases are being reported now. However, source detection could be difficult in the case of those affected by Acanthamoeba spp. as it is ubiquitous,” Dr. Aravind says. 

He also highlights the need for early diagnosis of the pathogen and timely treatment for saving lives. The State Public Health Lab in Thiruvananthapuram is capable of detecting five harmful species of free-living amoebae, Dr. Aravind adds.

Keeping the waterbodies clean is one of the ways to reduce the cases of the infection, says Dr. Anish. Well water should be chlorinated at regular intervals and overhead water tanks should be cleaned. “Any chance of contaminated water entering the nose should be avoided. Care must be taken that hygienic water is used for religious rituals in which water is dripped into the nose of children,” he cautions.

The State government is planning an intensive cleanliness drive on August 30 and 31 by involving local bodies, Haritha Kerala Mission, and the Water Resources department. Health Minister Veena George has asked for chlorinating all waterbodies and cleaning all water tanks.

The still waters of ponds and other waterbodies may appear inviting. But beneath the placid water sheaths, there could be a lurking pathogen.

(With inputs from Abdul Latheef Naha in Malappuram)