Study narrows down possible pathogen(s) from imported SARI cases

The Research Institute for Tropical Medicine (RITM), through its Research and Innovation Office (RIO), conducted the 38th Anniversary Research Forum on April 22, 2019 at the RITM Auditorium. A total of six researchers presented their studies at the forum.

Science Research Specialist I Hannah Leah Morito from the Research and Development Section of the Molecular Biology Laboratory of RITM was one of the presenters of this year’s forum. The presentation entitled “Needle in a haystack” looks at determining the possible pathogens causing severe acute respiratory infections (SARI) among patients who travelled to the Philippines from the Middle East from 2014 to 2016.

On February 20, news broke out about a suspected Middle East Respiratory Syndrome Coronavirus (MERS-CoV) case from Laguna. RITM conducted the laboratory testing and later announced that the suspected case tested negative for the virus. Reports confirmed that the patient arrived from Saudi Arabia, which had an ongoing MERS-CoV outbreak at that time.

The Philippines has so far reported three cases of MERS-CoV. A MERS-CoV suspect case (or a patient-under-investigation (PUI)) is defined as a patient or a patient’s contact with SARI and a history of travel to a country with active MERS-CoV transmission, such as the Middle East.  These cases are tested for MERS-CoV using real-time PCR.  Even when samples from these cases test negative for MERS-CoV, the risk of importing pathogens causing severe respiratory disease remains.

The study aimed to perform differential diagnosis of archived upper and lower respiratory MERS-CoV-negative samples from SARI patients. Archived respiratory samples collected in 2014-2016 were tested using a multiplex PCR panel that detects bacterial, viral, and fungal human respiratory pathogens, and metagenomics analysis using next generation sequencing (NGS).

Klebsiella pneumoniae, Staphylococcus aureus, and Haemophilus influenzae bacteria associated with nosocomial and community-acquired pneumonia, were identified as the most common bacteria in the samples.  Rhinovirus, Adenovirus, and Influenza A and B were detected as the most common viruses.  Pneumocystis jiroveciii, a fungal pathogen commonly found in immunocompromised patients, was also found in a few samples.  Several co-infections were also detected in the samples.

The NGS results identified non-pathogenic viruses and species in the Pseudomonas stutzeri subgroup, which was not detected in the multiplex PCR panel.  The P. stutzeri subgroup includes opportunistic pathogens associated with nosocomial pneumonia.  Confirmation of possible disease causality may be possible with association with clinical data.

The Molecular Biology Laboratory continuously adapts and optimizes its laboratory protocols to be able to respond during outbreaks of or outbreak investigations for emerging and re-emerging infectious diseases.

by Ma. Patricia Lansang, Communication and Engagement Office

Technical Editors: E. Mercado, L. Dancel., I. Medado, & H. Morito