Ongoing Research Projects
Using Genomics to Trace Salmonella Transmission and Antimicrobial Resistance (AMR) in the Poultry and Swine Food Chains in Metropolitan Manila, Philippines (Salmonella GENOMICS)
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.
Direct detection of Salmonella in meat using filtration LAMP assay (Salmonella LAMP)
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.
Aptamer-based multiplex detection assay for the early detection of Leptospirosis (Lepto-Aptamer)
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.
In this study, aptamers for multiple antigens of Leptospira spp. will be selected and applied as biorecognition molecules in a paper-based LFAA. The LFAA offers a reliable and cost-efficient tool for the direct and early detection of Leptospira which in turn can aid in the surveillance and control of cases of leptospirosis in the country.
Manila Bay Monitoring Using Metagenomics for Pathogen Detection and Source-Tracking (Manila Bay Project)
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.
Source Tracking Of Microbial Contamination in Selected Lakes of Laguna, Philippines (STROLL)
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.
Combating Antibiotic Resistance in Philippine Lakes: One-Health upstream interventions to reduce the burden (ARPHILAKE-Consortium)
This study aims to implement key interventions in Greater Manila, The 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 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.
Cyst Resilience of Potentially Pathogenic Free-Living Amoebae in Urban Water Systems
This study aims to implement key interventions in Greater Manila, The 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 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.
Salmonella enterica: Characterization of virulence, antimicrobial resistance and detection in eggs, meat, and meat products (SCRAMBLE)
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.
Past Research Projects
Microbial Source Tracking (MST) in Selected Tributaries of Laguna Lake
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.
In Vitro Characterization and Molecular Detection of Antimicrobial Resistance and Identification of Virulence Genes in Salmonella enterica Isolates
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.
Analysis of Virulence-Associated Genes of Leptospira Isolated from Environmental Samples in the Philippines
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.
Molecular Detection and Identification of Leptospira spp. Isolated from Pediatric and Adult Patients in the Philippines
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.
Occurrence, Genotype Analysis and Quantitative Microbial Risk Assessment of Cryptosporidium from Bivalves in the Coastal Areas of Metro Manila
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.
Proficiency testing and validation of the developed PCR-based detection protocol of Salmonella in meat samples
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.
Development of a rapid, low-cost, semi-quantitative, LAMP-based paper strip for the identification and detection of carbapenem-resistant Acinetobacter baumannii from pure cultures
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.