RESEARCH PROJECTS
Our projects focus on understanding and addressing key pathogenic bacterial genera, including Escherichia, Salmonella, and Leptospira. Through targeted studies, we aim to uncover insights that support public health and improve disease management.
Surveillance and Assessment of Farm Environments Using Enhanced Genetic and Genomic Detection Methods for Salmonella enterica (SAFE EGGS)
Funding Agency: Department of Agriculture Biotechnology Program Office
Project Duration: 1 year
Tools for Water Quality Management Using Emerging Sustainable Technology for Manila Bay
Funding Agency: Office of the Vice President for Academic Affairs – Emerging Interdisciplinary Research
Project Duration: 2 years
Gut Microbiome Shifts in Filipino Children Following Treatment for Soil-Transmitted Helminth Infections
Funding Agency: Office of the Vice President for Academic Affairs – Emerging Interdisciplinary Research
Project Duration: 2 years
Geospatial Artificial Intelligence-aided Antimicrobial Resistance Monitoring System for predicting antimicrobial resistance hotspots in major inland freshwater environments in Leyte, Philippines
Funding Agency: National Research Council of the Philippines
Project Duration: 2 years
Unveiling Potential Food Safety Threat (UPFOST): Use of NGS in Detection of intestinal parasitic protozoans in fresh produce from selected open-air markets and supermarkets
Funding Agency: Natural Sciences Research Institute, UP Diliman
Project Duration: 1 year
Clinical Trial I: Field Validation and Evaluation of an Aptamer-Based Lateral Flow Assay for Early Detection of Leptospirosis
Funding Agency: Department of Science and Technology – Philippine Council for Health Research and Development
Project Duration: January 2025 to January 2027
This research involves a clinical trial evaluating the performance of a developed lateral flow aptamer assay prototype for the early detection of leptospirosis. The development of this point-of-care test will enable the rapid detection of the pathogen and, consequently, facilitate proper and timely management of the disease, alleviating the burden caused by the difficulty of differentiating leptospirosis from other endemic blood-borne infections. The partner institution involved in the project will ensure the proper implementation of the clinical trial of the diagnostic test kit. Data gathered from this study will serve as a starting point for the optimization and refinement of the lateral flow prototype for its potential commercialization and public use.
Combating Antibiotic Resistance in Philippine Lakes: One-Health upstream interventions to reduce the burden (ARPHILAKE)
Funding Agency: International Development Research Centre, Canada
Project Duration: January 2023 to May 2026
This study aims to implement key interventions in Greater Manila, Philippines to reduce AMR. Interventions will focus on hospitals, small farms, and the Laguna Lake, one of the largest freshwater lakes in Asia. Better antibiotic use, point of care testing in hospitals and farms, and novel solar-powered wastewater cleaning technologies will be implemented. Their impact will be assessed by state-of-the-art molecular surveillance for antibiotic resistance genes (ARGs) and bacteria in the water before and after interventions. The study will be the most comprehensive and systematic interventions to be introduced in Asia to reduce AMR in lakes.
Effect of Serine and Cysteine Protease and Protein Kinase C Inhibitors on Encystation of Free-living Amoebae
Funding Agency: Natural Sciences Research Institute, UP Diliman
Project Duration: January 2025 to December 2025
Protease activity of free- living amoebae from environmental and urban water distribution systems
Funding Agency: Natural Sciences Research Institute, UP Diliman
Project Duration: January 2024 to December 2024
Salmonella enterica: Characterization of virulence, antimicrobial resistance and detection in eggs, meat, and meat products (SCRAMBLE)
Funding Agency: Department of Agriculture, Biotechnology Program Office
Project Duration: July 2023 to July 2025
Fecal contamination from wastewater and domestic sewage in water bodies poses great risks to human health, and determining the sources of contamination is vital for proposing measures to remediate its effects on water bodies. Currently, the presence of contamination is usually determined by monitoring levels of total and fecal coliforms, however this does not provide any information on the sources of the contamination. Hence, Microbial Source Tracking (MST) has become a new and emerging sub-discipline of microbiology–aiming to identify, and at times, quantify, the origin of fecal contaminants in bodies of water. MST can be done using either Library-Dependent or Library-Independent methods. This study aims to track the sources of fecal contamination in selected tributaries of Laguna Lake, utilizing both Library-dependent and Library-independent methods.
Cyst resilience of potentially pathogenic free-living amoebae in urban water systems
Funding Agency: Natural Sciences Research Institute, UP Diliman
Project Duration: January 2023 to December 2023
Rapid detection of Salmonella spp. in various meat samples using shortened pre-enrichment in tandem with closed-tube loop-mediated isothermal amplification (LAMP) assay
Funding Agency: Office of the Vice Chancellor for Research and Development, University of the Philippines Diliman
Project Duration: May 2023 to April 2024
Source Tracking Of Microbial Contamination in Selected Lakes of Laguna, Philippines (STROLL)
Funding Agency: DOST – Philippine Council for Industry, Energy and Emerging Technology Research and Development
Project Duration: May 2022 to December 2024
Fecal contamination from wastewater and domestic sewage in water bodies poses great risks to human health, and determining the sources of contamination is vital for proposing measures to remediate its effects on water bodies. Currently, the presence of contamination is usually determined by monitoring levels of total and fecal coliforms, however this does not provide any information on the sources of the contamination. Hence, Microbial Source Tracking (MST) has become a new and emerging sub-discipline of microbiology–aiming to identify, and at times, quantify, the origin of fecal contaminants in bodies of water. MST can be done using either Library-Dependent or Library-Independent methods. This study aims to track the sources of fecal contamination in selected tributaries of Laguna Lake, utilizing both Library-dependent and Library-independent methods.
Manila Bay Monitoring Using Metagenomics for Pathogen Detection and Source-Tracking (Manila Bay Project)
Funding Agency: DOST – National Research Council of the Philippines
Project Duration: December 2020 to November 2023
Coastal recreational waters are continually at risk of fecal contamination, which poses a significant public health concern since fecal material often harbors pathogenic bacteria. The mission of the Manila Bay rehabilitation is to restore waters to SB level fit for swimming and contact recreation. However, recent reports still indicate high levels of fecal coliform in several areas of Manila Bay. Although quantifying fecal coliform is a standard parameter in measuring water quality and monitoring compliance, it does not account for the entire microbial pathogen community in the environment. Traditional techniques in pathogen detection such as culture-based assays, PCR, and microarrays are limited in that they are labor-intensive, unable to detect a majority of pathogens in the natural environment, and rely on the availability of prior data which make them biased toward model or well-studied organisms. With the advent of metagenomics, it is now possible to account for the total microbial diversity in a sample. This study will utilize next-generation sequencing to identify the microbial community from selected sites in Manila Bay, with a particular focus on pathogenic bacteria, as well as use the microbial community signature for microbial source tracking (MST). The results and protocols generated from this study can be used as a benchmark for the assessment of water treatment processes for the elimination of waterborne pathogens.
Direct detection of Salmonella in filtration-LAMP assay
Funding Agency: Department of Agriculture Biotechnology Program Office
Project Duration: October 2020 to December 2023
Aptamer-based multiplex detection assay for the early detection of Leptospirosis (Lepto-Aptamer)
Funding Agency: DOST – Philippine Council for Health Research and Development
Project Duration: March 2020 to December 2022
With the expected rise of cases of leptospirosis and the difficulty in its diagnosis, the development of novel diagnostic assay that is reliable, fast, and economical is essential. The use of aptamers as recognition molecule for Leptospira offers advantages over the current antibody-based assays. Aptamers have zero to low variability, are stable at room temperature, and are applicable to various assay platforms since they can be easily modified without affecting their activity. The aptamers’ nucleic acid nature and their chemical synthesis makes them less expensive than antibodies that require animals for production. Additionally, several aptamer-based assays can be developed upon the selection of aptamers against multiple factors significant for the direct and reliable detection of the pathogen. The lateral flow aptamer assay (LFAA) shows promise as a point-of-care assay, mainly overcoming instrumentation and the need for highly technical personnel in conducting the assay.
Airborne Germs Project
Funding Agency: P&G Singapore
Project Duration: March 2020 to June 2021
Microbial source tracking of fecal indicator bacteria Escherichia
coli isolated from fresh produce in Luzon, Philippines
Funding Agency: Department of Agriculture – Bureau of Agricultural Research
Project Duration: October 2019 to October 2021
Transmission of Cryptosporidium meleagridis from bird communities to bivalves in Manila Bay, Philippines
Funding Agency: Office of the Vice Chancellor for Research And Development, University of the Philippines Diliman
Project Duration: April 2019 to February 2021
Using Genomics to Trace Salmonella Transmission and Antimicrobial Resistance (AMR) in the Poultry and Swine Food Chains in Metropolitan Manila, Philippines (Salmonella GENOMICS)
Funding Agency: Newton Fund – Department of Agriculture, Biotechnology Program Office
Project Duration: August 2018 to June 2023
Using whole genome sequencing (WGS), genomic variation between historic and new isolates of Salmonella enterica from different points along the poultry and swine food chains will be characterized. The resulting genomic variation will be used to construct phylogenies and infer transmission chains, including mathematical modeling and epidemiological analyses. Investigation of rare variants using GWAS analysis will lead to the association of genotype to drug resistant phenotypes and transmissibility. These genomic data will be validated by correlating with laboratory determined virulence and drug resistance outcomes, and other collected meta data (e.g. geographical location). This study aims to shed light on the transmissibility and drug resistance of the foodborne pathogen S. enterica using genomics.
In Vitro Characterization and Molecular Detection of Antimicrobial Resistance and Identification of Virulence Genes in Salmonella enterica Isolates
Funding Agency: Department of Agriculture, Biotechnology Implementation Unit
Project Duration: January 2018 to December 2019
Due to limited data on the prevalence of the serotype-dependent antimicrobial resistance and virulence characteristics of S. enterica in the country, management approach may be delayed or overlooked. This study focuses on, but not limited to, the multiplex assays and in vitro assays for the detection of extended spectrum beta-lactamase (ESBL) enzymes and Salmonella pathogenicity island (SPI)-mediated virulence of S. enterica. Also, it is of economic importance to report the epidemiology of multidrug resistant and/or highly virulent S. enterica in food and food producing animals. It is therefore important to identify the presence of these genes to design and implement effective measures in slaughter facilities and markets to reduce the risk of contamination and possible spread of resistance and virulence genes.
Molecular Detection and Identification of Leptospira spp. Isolated from Pediatric and Adult Patients in the Philippines
Funding Agency: Natural Sciences Research Institute, University of the Philippines Diliman
Project Duration: January 2018 to December 2018
Leptospirosis is considered a major threat to our country’s public health due to its increasing incidence particularly during rainy season. The current project aims to identify the circulating Leptospira species that can be isolated from Filipino pediatric and adult patients through DNA sequencing and to describe the disease outcome that can be observed between these age groups.
Application of loop-mediated isothermal amplification (LAMP)
assay for rapid detection of Salmonella enterica in raw meat products
Funding Agency: Office of the Vice Chancellor for Research and Development, University of the Philippines Diliman
Project Duration: August 2017 to July 2018
Development of aptadetection and aptaprecipitation assays for Trichomonas vaginalis
Funding Agency: DOST – Philippine Council for Industry, Energy and Emerging Technology Research and Development
Project Duration: July 2017 to June 2018
Proficiency testing and validation of the developed PCR-based detection protocol of Salmonella in meat samples
Funding Agency: Department of Agriculture, Biotechnology Implementation Unit
Project Duration: April 2017 to March 2018
This research involves rapid detection methods for Salmonella spp. in food, which are crucial for ensuring food safety and preventing outbreaks. Traditional methods require culture enrichment and are labor-intensive, taking 5-7 days. In contrast, molecular techniques like PCR and real-time PCR are faster and more sensitive. This project has optimized a PCR-based protocol that can detect Salmonella in swine samples and meat products within just 3 days, making it a quicker alternative to traditional culture methods. However, this protocol needs validation from an internationally accredited proficiency testing center before implementation in Department of Agriculture laboratories. It aimed to validate this protocol through proficiency testing and compare its results with those from the National Meat Inspection Service (NMIS) culture detection protocol.
Microbial Source Tracking (MST) in Selected Tributaries of Laguna Lake
Funding Agency: DOST – Philippine Council for Industry, Energy and Emerging Technology Research and Development
Project Duration: February 2017 to January 2020
Fecal contamination from wastewater and domestic sewage in water bodies poses great risks to human health, and determining the sources of contamination is vital for proposing measures to remediate its effects on water bodies. Currently, the presence of contamination is usually determined by monitoring levels of total and fecal coliforms, however this does not provide any information on the sources of the contamination. Hence, Microbial Source Tracking (MST) has become a new and emerging sub-discipline of microbiology–aiming to identify, and at times, quantify, the origin of fecal contaminants in bodies of water. MST can be done using either Library-Dependent or Library-Independent methods. This study aims to track the sources of fecal contamination in selected tributaries of Laguna Lake, utilizing both Library-dependent and Library-independent methods.
Analysis of Virulence-Associated Genes of Leptospira Isolated from Environmental Samples in the Philippines
Funding Agency: Natural Sciences Research Institute, University of the Philippines Diliman
Project Duration: January 2017 to December 2017
Leptospira is the causative agent of leptospirosis which is one of the prevalent infectious diseases affecting the country. Genomic analysis of Leptospira species revealed the complexity of this genera as evident in the high genetic diversity observed among isolates worldwide. The impact of this diversity accounts for the organism’s wide host range and virulence patterns, and the array of symptoms presented by infected hosts. It is therefore important to determine the association of these genetic variations with the virulence of the organism to be able to understand the mechanism for its disease pathogenesis. Establishing the molecular basis of the pathogenesis of Leptospira may reveal potential targets for leptospirosis interference. The present study aims to identify and analyze individual genes that may possibly contribute to the virulence of Leptospira isolates from the Philippines. Specifically, the study will isolate Leptospira from environmental samples obtained from geographically distinct areas in the country and identify them by DNA sequencing. Environmental isolates will be collected since human or even animal infection is usually acquired upon exposure to contaminated environment. Comparative analysis of putative virulence-associated gene sequences of Leptospira will be done subsequently to assess diversity among isolates. Results of this study are expected to provide insights on the pathogenesis of Leptospira by identifying genetic variations that may potentially cause altered transcription hence the difference in virulence patterns and in adaptive mechanisms to a variety of hosts and environment.
Occurrence, Genotype Analysis and Quantitative Microbial Risk Assessment of Cryptosporidium from Bivalves in the Coastal Areas of Metro Manila
Funding Agency: National Research Council of the Philippines
Project Duration: September 2016 to February 2019
The project focuses on carrying out hazard identification (detection of oocysts) and determining the occurrence of Cryptosporidium in bivalves from harvesting sites around Manila Bay using sucrose flotation and immunomagnetic separation (IMS) with immunofluorescence antibody assay (IFA) and PCR. The project also aims to determine the genotypes of Cryptosporidium oocysts obtained from the samples using DNA sequence and phylogenetic analyses. Furthermore, another goal of the project will be on assessing the risk of cryptosporidiosis on the healthy population of Metro Manila that regularly consumes these bivalves using Quantitative Microbial Risk Analysis.
Loop-mediated isothermal amplification (LAMP) for rapid
detection of Salmonella enterica in raw and processed meat products
Funding Agency: Natural Sciences Research Institute, University of the Philippines Diliman
Project Duration: January 2016 to December 2016
Molecular characterization of Salmonella enterica isolates from
raw and processed meat sold in selected wet markets in Metro Manila
Funding Agency: Office of the Vice Chancellor for Research And Development, University of the Philippines Diliman
Project Duration: July 2015 to June 2016
Survey of pathogens in vegetables of significance to food safety in Luzon Philippines
Funding Agency: Department of Agriculture – Bureau of Agricultural Research
Project Duration: December 2014 to September 2016
Recombinant protein expression, immunological characterization and production of de-antigenized human influenza H3 hemagglutinin
Funding Agency: Office of the Vice President for Academic Affairs, University of the Philippines System
Project Duration: November 2014 to December 2020
Development of multiplex PCR for detection of Ehrlichia canis,
Babesia canis and Hepatozoon canis in canine blood
Funding Agency: Natural Sciences Research Institute, University of the Philippines Diliman
Project Duration: January 2014 to December 2015
Diagnosis and molecular characterization of Salmonella species from slaughtered swine and other raw meat and meat products
Funding Agency: Department of Agriculture – Biotechnology Implementation Unit
Project Duration: June 2013 to June 2015
Identification and characterization of Trichomonas vaginalis
viruses (TVV) in the Philippines
Funding Agency: Office of the Vice Chancellor for Research And Development, University of the Philippines Diliman
Project Duration: February 2013 to January 2014
Microbial risk assessment of agricultural waters and produce in
the Philippines
Funding Agency: Office of the Vice-President for Academic Affairs, University of the Philippines System
Project Duration: November 2012 to October 2013
Development of a loop-mediated isothermal amplification
(LAMP) assay for rapid detection of Trichomonas vaginalis in clinical specimens
Funding Agency: Natural Sciences Research Institute, University of the Philippines Diliman
Project Duration: January 2012 to December 2013
Development of a loop-mediated isothermal amplification
(LAMP) assay for the rapid detection of Entamoeba histolytica in stool samples
Funding Agency: Natural Sciences Research Institute, University of the Philippines Diliman
Project Duration: January 2011 to December 2011
Comparison of microscopy, culture, PCR and antibody-based
assay for the detection of Blastocystis hominis in human stool
Funding Agency: Office of the Vice-Chancellor for Research and Development, UP Diliman
Project Duration: November 2010 to April 2011
Molecular and phylogenetic analysis of Philippine Trichomonas
spp. isolates from human and animal hosts
Funding Agency: Commission on Higher Education
Project Duration: January 2010 to December 2010
Immunodetection of Entamoeba histolytica antigen in feces using a sensitive diffraction biosensor
Funding: Emerging S&T Grant, University of the Philippines
Project Duration: September 2009 to August 2010
Profiles of Entamoeba histolytica-specific immunoglobulin A, G,
M in human sera
Funding Agency: Natural Sciences Research Institute, UP Diliman
Project Duration: January 2009 to December 2010
Isolation and structure elucidation of the anti-quorum sensing compounds from Terminalia catappa leaves
Funding Agency: Natural Sciences Research Institute, UP Diliman
Project Duration: January 2009 to December 2009
Molecular identification of human Trichomonas spp. isolated in
the Philippines
Funding Agency: Office of the Vice-Chancellor for Research and Development, UP Diliman
Project Duration: June 2008 to May 2009
The biology of a trichomonad isolated from pig fecal samples
Funding Agency: Natural Sciences Research Institute, UP Diliman
Project Duration: January 2008 to December 2008
Development of naturally derived bioactive products from endemic plant species in Kanawan, Morong, Bataan Forest Area
Funding: Emerging S&T Grant, University of the Philippines
Project Duration: March 2007 to February 2009
Development of salivary IgA antibody detection kit for accurate
diagnosis of amebiasis
Funding: Emerging S&T Grant, University of the Philippines
Project Duration: March 2007 to February 2009
Molecular characterization of Acanthamoeba spp. isolated from contact lens storage cases, soil and water
Funding: Office of the Vice-Chancellor for Research and Development, UP Diliman
Project Duration: October 2006 to September 2007
Molecular and phylogenetic analysis of Blastocystis isolates in the Philippines from human and animal hosts
Funding Agency: Department of Agriculture – Bureau of Agricultural Research
Project Duration: November 2005 to November 2006
Development of immunoassay for detection of anti-Blastocystis hominis-specific IgG in serum samples
Funding Agency: Natural Sciences Research Institute, UP Diliman
Project Duration: January 2005 to December 2005, and January 2007 to December 2007
Genetic diversity of Cryptosporidium spp. in the Philippines
Funding: Office of the Vice-Chancellor for Research and Development, UP Diliman
Project Duration: July 2003 to January 2005
Genetic diversity of Philippine Blastocystis hominis isolates by riboprinting
Funding Agency: Natural Sciences Research Institute, UP Diliman
Project Duration: January 2003 to December 2004
Multilocus genotypic analysis of Cryptosporidium isolates from
farm animals in the Philippines
Funding Agency: International Foundation for Science
Project Duration: November 2002 to October 2003
Development of antibody and PCR-based detection assays for
accurate diagnosis and epidemiology of human Cryptosporidium parvum infections in the Philippines
Funding Agency: Natural Sciences Research Institute, UP Diliman
Project Duration: January 2001 to December 2002
Molecular epidemiology of Entamoeba histolytica and
Entamoeba dispar in the Philippines
Funding: Japanese Government Ministry of Education, Science, Sports and Culture (Monbusho) Research Grant
Project Duration: January 2001 to March 2003
Modes of transmission of Entamoeba histolytica and Cryptosporidium parvum infections in the Philippines
Funding: Japanese Government Ministry of Education, Science, Sports and Culture (Monbusho) Research Grant
Project Duration: April 2000 to March 2003