A paper published this week in the scientific journal Biocontaminant and highlighted by ScienceDaily on June 6, 2026, has triggered a new round of expert warnings about an emerging and largely invisible public health threat lurking in the water systems of American cities.

Free-living amoebae (FLA) are tiny single-celled organisms found in soil, lakes, rivers, and man-made water systems. Scientists say they are becoming a bigger public health concern as rising temperatures and aging water systems create better conditions for them to grow. Researchers describe them as an "overlooked risk" that needs more attention, especially in cities with old water infrastructure and hot summers, such as Chicago and Houston.

The best-known type, Naegleria fowleri, or the "brain-eating amoeba," causes a rare but almost always deadly brain infection called primary amoebic meningoencephalitis (PAM). It happens when warm contaminated water enters the nose, usually during swimming in warm freshwater lakes or rivers. Symptoms start with headache, fever, and nausea, then quickly progress to confusion, seizures, and coma. The death rate is over 97%, and only a few people in the U.S. have survived since 1962. Cases have been reported in 15 states, with Texas having the most infections due to its warm freshwater conditions and long swim season.

The Trojan Horse Problem: Why Amoebae Are More Dangerous Than They Appear

Naegleria fowleri is the best-known type in a larger group of free-living amoebae that also includes Acanthamoeba, which can cause eye infections from contact lenses and deadly brain infections in people with weak immune systems; Balamuthia mandrillaris, which causes a rare and often fatal brain disease; and Vermamoeba vermiformis, which may cause respiratory illness.

The Biocontaminant paper warns that the main risk is not just direct infection, but a "Trojan Horse" effect where free-living amoebae act as host cells for dangerous bacteria and viruses, protecting them from disinfectants like chlorine and UV light. One key example is Legionella pneumophila, which causes Legionnaires' disease. It can survive inside Acanthamoeba in pipes, cooling towers, and water systems, then spread and trigger pneumonia outbreaks when released.

Why Chicago and Houston Are at Elevated Risk

Chicago and Houston share two main risk factors that make free-living amoebae more concerning. First, both cities have old water systems, with some pipes and infrastructure dating back to the early and mid-1900s. Aging pipes, low-flow areas, and sediment buildup can create warm, still water where microbes can grow. Naegleria fowleri and Acanthamoeba both thrive in these conditions, especially during hot summers when water systems are under more heat stress.

Second, both cities are seeing rising water temperatures due to the urban heat island effect. This same effect has contributed to extreme heat deaths in places like Maricopa County and has raised concerns for events like the World Cup at NRG Stadium. In Chicago and Houston, it also warms water in distribution systems, making conditions more suitable for Naegleria fowleri to survive and multiply.

The researchers note that climate change increases water temperature globally, with regions that never faced the problem before now seeing new infections. Houston's documented Naegleria fowleri cases from recreational water exposure in recent years, and Chicago's aging water main system — where the Metropolitan Water Reclamation District and Chicago Department of Water Management continue to address lead service line replacements — represent the two dimensions of the FLA risk: direct infection from warm recreational water, and infrastructure-facilitated Legionella amplification through the Trojan Horse mechanism.

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What Residents in Chicago and Houston Should Know

For people in both cities, the risk of getting Naegleria fowleri from tap water is extremely low. It only causes infection when warm contaminated water goes up the nose, and city tap water is not a common source. Most cases come from swimming in warm freshwater like lakes, reservoirs, or slow rivers in summer, using untreated well water for nasal rinsing, or diving in warm freshwater. It is very rare in the U.S., with about three cases a year, but it is almost always deadly.

A more realistic concern in cities is Legionella, a bacteria that causes Legionnaires' disease. It has been linked to cooling towers, fountains, hotel hot water systems, and hospital plumbing in cities like Chicago and Houston. It causes severe pneumonia with fever, cough, and shortness of breath, and mainly affects older adults, smokers, and people with weak immune systems or lung disease. Outbreaks have happened in cities including New York, Chicago, Atlanta, and Houston, often traced to building water systems.

The CDC's Legionella prevention resources provide guidance for building managers on water management plans that reduce Legionella risk — guidance that many building owners in both cities' older commercial and residential stock have not yet implemented.