PH marine sediments source of antibiotics -- expert

By Ellalyn De Vera Ruiz

The abundance of actinobacteria in the Philippines' marine sediments is found to be a valuable resource of antibiotics that can treat secondary bacterial infections as a result of the coronavirus disease (COVID-19), according to an expert from the University of San Agustin (USA) in Iloilo.

Dr. Doralyn S. Dalisay (DOST / MANILA BULLETIN) Dr. Doralyn S. Dalisay

"Drugs from the vast Philippine marine sediment-derived actinobacteria offers unlimited potential to offer economic and healthcare benefits to society to fight against infectious diseases," said Dr. Doralyn Dalisay, USA's Director of Center for Chemical Biology and Biotechnology.

Citing recent reports, she said symptomatic individuals infected by COVID-19 display microbial co-infection, caused by bacteria, fungi, or virus, that may increase the risk of disease severity in humans.

"Evidence show that individuals infected with COVID-19, those that are symptomatic patients, showed secondary infections caused by bacterial infections—streptococcus pneumoniae, Klebsiella pneumoniae, and Haemophilus influenzae are on top of the list," Dalisay said.

"Surprisingly, there were opportunisitc bacterial infections observed in respiratory infection including E. coli, staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii. In this co-infection data that was published in May 11, 2020, other virus pathogens were also observed, and also some opportunistic fungal infections," she added.

She pointed out that antibiotics are important to treat the secondary bacterial infection, "not the viral infection." "It is the secondary infection that follows the initial phase of viral respiratory infection or occur during the recovery phase," the expert explained.


"What we do at University of San Agustin particularly at the Center for Chemical Biology and Biotechnology, and Center of Natural Drug Discovery and Development, we use the diverse natural resources of the Philippines to find cure against bacterial infections and cancer using marine organisms, plants, and marine invertebrates," she said.

Dalisay was a guest in a webinar titled, "The Great Web: COVID-19, Climate Change, and the Ocean, last May 26. The activity, which was part of the Philippines' celebration of the Month of the Ocean and organized by the Climate Change Commission, in partnership with Rare Philippines, highlighted the importance of oceans and the marine ecosystem as the country addresses climate change and the COVID-19 pandemic.

Dalisay specializes in marine chemical biology and microbial drug discovery. She graduated cum laude from the University of San Agustin with a degree in Pharmacy. She earned her Master of Science in Biology at the University of the Philippines-Visayas, doctorate in Microbiology at University of New South Wales in Australia and a post-doctorate fellowship to specialize on marine natural products chemistry at the University of California, San Diego.

She returned to the Philippines as a Balik Scientist of the Department of Science and Technology (DOST) in June 2015 to establish a research program on natural products drug discovery at the USA Center for Chemical Biology and Biotechnology. She holds two US patents on the use of a marine natural product for fungal infections and cancer.


The study titled "Marine Sediment-Derived Actinobacteria: New Vista for Natural Products Discovery in the Philippines" was led by Dalisay along with Dr. Jonel Saludes, Associate Vice President and Research and Global Relations Director of the Center for Natural Drug Discovery and Development of the University of San Agustin.

The project, which was supported by the National Research Council of the Philippines and the DOST, was conducted from December 2016 to November 2019.

"We went all throughout the Philippine archipelago to collect different marine sediments, bring them to the lab and get the actinobacteria to find those several number of antibiotic-producing bacteria," Dalisay said.

The team would get 1 meter sediment core from the ocean floor as sample from different sites that are "accessible by scuba or boat, and away from anthropogenic activities."

Samples were taken from Apo Island, Negros Oriental; Balicasag Island, Bohol; Batbatan Island, Antique; Crocodile Island, Aklan; Danjugan Island, Negros Occidental; Mararison Island, Antique; Nogas Island, Antique; Olotoyan Island, Capiz; Seco Island, Antique; Sumilon Island, Cebu; and Unisan Island, Guimaras.

They also took samples from Apo Reef, Occidental Mindoro; Batanes Islands, Guintinua Island, Camarines Norte; Kalanggaman, Leyte; La Januza Island, Surigao del Norte; Mantigue Island, Camiguin; Pujada Island, Davao Oriental; Quatro Islands, Leyte; White Island, Camiguin; and Tubbataha Reef, Palawan.


The group of Dalisay was able to isolate 3,371 marine sediment-derived actinobacteria, which they consider as the "drug discovery biobank in the Philippines."

"The Philippines is so rich when it comes to these natural resources, this is a drug discovery for antibiotics, anti-viral compounds or anti-cancer that we can use during pandemic or we can use during those instances that we need drugs to treat diseases," she said.

The researchers found that actinobacteria were most prevalent in Negros Occidental sediment samples, which yielded the highest total percentage of culturable actinobacteria (20 percent, 580 isolates), followed by southern Antique (12 percent, 348 isolates), and Sulu Sea (8 percent, 247 isolates).

"Our target are the ESKAPE pathogens, namely Enterococcus faecium, Staphyloccocus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter spp. These are the types of bacteria that co-infect COVID-19 patients. They are multidrug resistant, virulent, and can cause respiratory diseases and opportunistic bacterial infections," Dalisay pointed out.

Out of the 3,371 isolates, she further explained that the initial screening showed 771 isolates exhibited bioactivities against multidrug resistant pathogens.

"Isolates from all the collection sites exhibited bioactivities against one of the test pathogens, with Negros Oriental having the highest hit rate (85, 77 percent) followed by Davao Oriental with 77 percent (33 out of 45 isolates), and Eastern Camiguin with 64 percent (85 out of 133 isolates), and Western Leyte having the lowest hit rate with only 1 percent," she explained.

A secondary screening was done to make sure the 771 isolates will be further filtered out for false positive results, Dalisay noted. Out of the 771, there were 169 isolates, with most of the bioactive antibiotic producing isolates coming from southern Antique, followed by Sulu Sea, Tubbataha Reefs, and Negros Occidental.

In the confirmatory screening of the 169 isolates, the team of scientists were able to find 38 lead isolates.

"These 38 lead isolates targeted seven types of pathogen from MDRSA, MRSA, E. coli and P. aeruginosa, 17 from multidrug-resistant staphylococcus aureus (MDRSA), seven from methicillin resistant staphylococcus aureus (MRSA), five from Acinetobacter baumannii, and two from Escherichia coli," Dalisay said.

Out of the 38, eight were found to be very potent against multidrug resistant staphylococcus aureus when compared to the Tetracycline antibiotic, she cited. This was identified in actinobacteria from sediments derived from Romblon.


Dalisay proudly announced that the study has been peer-reviewed and published in a Switzerland scientific journal called Frontiers in Microbiology on April 24, 2020.

"The findings in this study provide evidence on the potential of marine sediment-derived Streptomyces strains from Romblon, Philippines as a source of antibiotics against S. aureus ATCC BAA-44," the journal stated. It has proven that "streptomyces thriving in underexplored niches, such as marine sediments are resource for potential antibacterial compounds that are of diverse chemical characteristics."

"Moreover, we have demonstrated that Philippine marine sediment-derived S. griseorubens strain DSD069 is a natural bacterial strain that can produce anthracycline shunt metabolites 1 and 2, with potential as antibiotic leads to combat ABR (antibiotic resistance)," it said.

Dalisay said the antibiotic "has not been reported by anyone in the world." "This is the first time this was isolated and this happened to be in the Philippines. It has a very strong MIC (minimum inhibitory concentration) against multidrug-resistant staphylococcus aureus."


In another study, Dalisay said: "We were specifically looking at the richness of sediments for antibiotic-producing actinobacteria particularly collected in Gigantes Islands in Iloilo."

The study is being supported by the Tuklas Lunas Center Program of the Philippine Council for Health Research and Development and DOST.

Dalisay said her team is currently working on three different types of antibiotic-producing actinobacteria from Iloilo marine sediments active against ESKAPE pathogens.

"Harnessing the antibiotics from Iloilo marine sediment-derived actinobacteria is not a one-night progress, it is a long process. It is important to invest in research so that when it comes there will be a pandemic of new bacterial infection or new viral infection our country is ready to fight these kinds of diseases," she said.