First-ever Philippine genome of a globally rare Leptospira species, pulled straight from the soil of an ordinary Manila estero, forces a rethink of where flood-season infection risk actually lives
MANILA, PHILIPPINES — 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 and the Philippine Genome Center now show that the picture may be worse than health workers assumed, 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 Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, UP Diliman, investigated the presence of Leptospira in Estero de Paco, one of Metro Manila’s many narrow, engineered urban waterways that run through densely populated, flood-prone communities. What they found: the bacteria were not confined to a single dirty puddle or a known contamination point. Screening 448 isolates recovered from soil and water at five sites along the estero, the team confirmed Leptospira at every site they tested, with statistically no significant difference in how much was found upstream, downstream, in soil, or in water. In plain terms, there was no “safe” stretch of estero and no “hotspot” to avoid. The entire waterway behaved as one continuous, evenly loaded reservoir for the bacteria.
Buried inside that reservoir, the researchers isolated and confirmed two strains carrying the lipL32 gene, the molecular signature restricted to the genus’s dangerous, disease-causing lineages. Genetic sequencing identified them as Leptospira yasudae, a pathogenic species capable of infecting humans and animals, that had never before been sequenced from anywhere in the Philippines. The team’s phylogenetic analysis also found the local strains were measurably diverged from the only two other L. yasudae genomes on record worldwide, isolated a hemisphere away in Mayotte and Brazil, raising the possibility that Manila’s waterways are harboring their own locally evolved lineage of the pathogen.
That discovery is now permanently on the scientific record: in a companion paper published in Microbiology Resource Announcements, the same team deposited the first complete draft genome of L. yasudae recovered from Philippine soil, a 4.5-million-base-pair blueprint of a pathogen that, until now, genomic science had barely looked at in this part of the world. It is only the 10th such genome ever sequenced globally.
“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 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. Windell L. Rivera, senior author and Marababol’s supervisor at the Philippine Genome Center. “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,” with incidence 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 research team is careful to note what their data do not yet show: this study did not measure how many people have been infected by these specific strains, and it does not establish that this bacterium is the cause of any recent rise in reported cases. What it does establish, using rigorous culture-based isolation, molecular screening, and Bayesian phylogenetics, is that a confirmed pathogenic lineage of Leptospira is genetically embedded across an entire Manila waterway rather than confined to isolated pockets, a finding the authors say should directly inform how the country designs its flood-season surveillance and its public health messaging.
Both studies were supported by the Department of Science and Technology, Philippines (Project No. 9258), and were conducted at the Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, in partnership with the Philippine Genome Center.
About the research
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.
Media contact
Ram Julius L. Marababol, Philippine Genome Center, University of the Philippines System, Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman | Email: [email protected]
PGC Research / Ram Julius L. Marababol
