LEPTOSPIROSIS risk is not just a post-typhoon hazard hiding in floodwaters-it is a year-round reality embedded right in Metro Manila’s waterways.
Researchers from the University of the Philippines Diliman College of Science (UPD-CS) and the Philippine Genome Center (PGC) have discovered that Leptospira-the bacteria responsible for leptospirosis-is continuously present in the entire length of Estero de Paco, that passes through a a heavily populated urban community in Manila.
Unlike popular belief that the deadly bacteria only spike in floodwaters after torrential rains, the new findings reveal that the pathogen lives persistently in both the soil and water, spread evenly across the estero regardless of season.
Screening 448 bacterial isolates taken from five different sites along Estero de Paco, the team confirmed Leptospira at every single location. Statistically, there was no difference in bacterial concentration whether tested upstream or downstream, in water or in soil.
‘Most people picture leptospirosis risk as something you catch from an obvious flood puddle after a typhoon,’ said Ram Julius L. Marababol, lead researcher on the studies. ‘What our data show is that the bacteria aren’t waiting for a flood to arrive-they are already living in the soil and water of an ordinary city waterway all year round.’
Senior author Windell L. Rivera emphasized that the absence of isolated ‘hotspots’ fundamentally changes how public health officials must tackle the issue.
‘The old model of pointing to one contaminated spot and cleaning it up isn’t going to be enough,’ Rivera explained. ‘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.’
In addition to proving the bacteria’s pervasive presence, the team isolated two strains carrying the lipL32 gene-the definitive genetic marker for disease-causing lineages.
Through advanced genetic sequencing, the researchers identified the species as Leptospira yasudae, a pathogenic strain capable of infecting both humans and animals. This marks the first time L. yasudae has ever been sequenced in the Philippines.
Fewer than ten complete genomes of L. yasudae exist globally. Analysis showed that the Philippine strains are genetically distinct from the only two other recorded genomes worldwide (found in Mayotte and Brazil), suggesting Metro Manila’s waterways may harbor a unique, locally evolved lineage.
The complete draft genome-a 4.5-million-base-pair blueprint-was deposited in Microbiology Resource Announcements.
While leptospirosis has long been classified as a neglected tropical disease, experts warn that cases are steadily shifting toward rapidly urbanizing, densely populated cities. In Metro Manila, inadequate drainage, informal settlements, and frequent flooding create prime conditions for the bacteria to spill over into human populations.
The researchers clarified that their current data does not yet measure human infection rates from these specific strains or link them directly to recent case spikes. However, proving that a dangerous pathogen is genetically embedded throughout a key urban waterway proves that public health strategies, flood-season monitoring, and civic warning systems need an immediate overhaul.
The studies were supported by the Department of Science and Technology (DOST) and conducted by the Pathogen-Host-Environment Interactions Research Laboratory at UP Diliman in partnership with the PGC.