Leptospirosis is one of the Philippines’ most persistent and least talked-about health threats: a bacterial disease carried in contaminated water and soil, spiking every year the moment the rains and the floodwaters come. Two new peer-reviewed studies out of the University of the Philippines – Diliman College of Science (UPD-CS) and the Philippine Genome Center (PGC) now show that the picture may be worse than health workers assumed. This is not because the bacterium is new, but because of where scientists just found it living, and how completely it has settled in.

Researchers Ram Julius L. Marababol and Dr. Windell L. Rivera of the UPD-CS Institute of Biology’s (IB) Pathogen-Host-Environment Interactions Research Laboratory investigated the presence of Leptospira in Estero de Paco, an urban waterway that passes through densely populated and flood-prone communities in Metro Manila. They collected soil and water samples from five sites along the estero and tested 448 bacterial isolates. 

The team detected Leptospira at all five sites, with no statistically significant difference in its presence between upstream and downstream areas or between soil and water samples. This suggests that Leptospira was not concentrated in just one part of the estero. Instead, the bacteria were detected throughout the waterway, showing that contamination can extend across different parts of an urban waterway rather than being limited to a single visible source.

Within the bacteria they collected from Estero de Paco, the researchers identified two strains of Leptospira carrying the lipL32 gene, a genetic marker commonly associated with pathogenic Leptospira. Genetic sequencing identified the strains as Leptospira yasudae, a species known to infect humans and animals. This is the first time L. yasudae has been genetically sequenced from a sample collected in the Philippines. The researchers also compared the Philippine strains with the only two other L. yasudae genomes currently available, which came from Mayotte and Brazil. Their analysis showed that the Philippine strains were genetically distinct from these previously sequenced strains, suggesting that L. yasudae in the Philippines may represent a previously undocumented local lineage.

The discovery also led to another first for Philippine science. In a companion paper published in “Microbiology Resource Announcements,” the researchers reported the first complete draft genome of L. yasudae recovered from Philippine soil. The genome contains about 4.5 million base pairs of genetic information and is only the 10th L. yasudae genome sequenced worldwide, adding a rare Philippine reference to the growing genetic record of the species.

“Most people picture leptospirosis risk as something you catch from an obvious flood puddle after a typhoon,” said Marababol, lead researcher on both studies. “What our data show is that the bacteria carrying the potential to make people sick aren’t waiting for a flood to arrive; they are already living in the soil and water of an ordinary city waterway, spread evenly across it, all year round.”

“The absence of isolated hotspots is itself the alarming part,” added Dr. Rivera, senior author and Marababol’s supervisor at the PGC. “It means the old model of pointing to one contaminated spot and cleaning it up isn’t going to be enough. If an entire waterway is functioning as a single, connected reservoir, then surveillance and intervention have to be rethought at the scale of the whole system, not a handful of sampling points.” 

The findings land at a pointed moment. Leptospirosis is formally classified as a neglected tropical disease, but public health literature cited in the researchers’ own papers describes an epidemiology that has been “undergoing a marked shift.” The incidence is now climbing specifically in dense, rapidly urbanizing, and inadequately drained cities like Metro Manila, where informal settlements, weak waste management, and recurring flooding create ideal conditions for the bacteria to move from animal reservoirs into human contact. The disease is also widely recognized as underdiagnosed, meaning official case counts are likely to understate how often Filipinos are actually exposed.

The researchers are careful to point out what their findings do not show. The study did not determine how many people have been infected by these specific strains, nor does it establish that the bacteria are responsible for any recent increase in reported leptospirosis cases. What the study does show is that pathogenic Leptospira was detected across multiple sites along Estero de Paco, rather than being concentrated in a single area. Using bacterial culture, molecular testing, and genetic analysis, the researchers confirmed the presence of these strains and examined their relationship to other Leptospira strains. The findings highlight the need to consider the widespread presence of Leptospira in urban waterways when planning flood-season disease surveillance and communicating leptospirosis risks to the public.

Both studies were supported by the Department of Science and Technology (Project No. 9258), and were conducted at the Pathogen-Host-Environment Interactions Research Laboratory of the UPD-CS IB in partnership with the PGC.

References:

Culturable Leptospira spp. Exhibit No Detectable Spatial or Matrix-Associated Structuring in Estero de Paco, Manila, Philippines. Marababol, R.J.L. & Rivera, W.L. BMC Microbiology (2026), Article in Press. DOI: 10.1186/s12866-026-05480-z

Draft Genome Sequence of Leptospira yasudae Strain Ss3a1f from Estero De Paco, Manila, Philippines. Marababol, R.J.L. & Rivera, W.L. Microbiology Resource Announcements, Vol. 15, Issue 7 (2026). DOI: 10.1128/mra.00547-26. Genome data deposited in NCBI GenBank under BioProject PRJNA1459639.