Unveiling bacterial community structure and antibiotic resistance genes in coastal water of Manila Bay, Philippines using metagenomic and qPCR approaches

Antibiotic resistance is no longer confined to hospitals and clinics: resistant bacteria and the genes that confer resistance persist and spread in coastal waters. Manila Bay, the main natural harbour of the Philippines and the receiving water body for Metro Manila, is exposed to domestic sewage, untreated wastewater, industrial discharges, port operations and urban runoff. Although clinical surveillance in the country has recorded high prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae, the environmental dimension of resistance has remained poorly characterised.

In a study published in the journal Emerging Contaminants, researchers from the University of the Philippines Manila reported one of the first culture-independent assessments of the bay’s bacterial communities and resistome. They sampled five locations in September and October 2021 — the South and North Harbors, the Manila International Container Terminal, the lower Pasig River and Baseco Beach — combining shotgun metagenomic sequencing (MetaPhlAn 4 and HUMAnN 3) with quantitative PCR, and characterising resistance genes against the MEGARes 3.0 database.

“Three phyla — Bacteroidota (72.5%), Firmicutes (15%) and Proteobacteria (8.5%) — accounted for more than 90% of classified reads, while the dominant genera, among them Bacteroides, Paramuribaculum, Pallieniella, Duncaniella, Phocaeicola, Helicobacter and Lactobacillus, are typically gut-associated — consistent with the high total and faecal coliform counts recorded at the sites,” shares Christian C. Ramos, corresponding author of the study. “Functional profiling showed a community geared to core metabolism and cellular maintenance, alongside efflux pumps that confer tolerance to chemical stress.”

Notably, just 0.11% of reads mapped to resistance genes, yielding 305 determinants across 34 mechanisms: tetracycline resistance dominated (71.2%), followed by macrolide–lincosamide–streptogramin (17.9%) and aminoglycoside (3.6%) resistance.

“The bacterial community we recovered reads like the signature of untreated sewage — gut-associated taxa alongside high faecal coliform counts — and it carries a resistome dominated by tetracycline and macrolide resistance,” says Ramos. “Detecting blaCTX-M, blaSHV and blaTEM at almost every site tells us that Manila Bay is not merely receiving these genes; the bay may be sustaining them.”

In particular, quantitative PCR targeting clinically relevant ESBL genes returned the most significant finding: blaCTX-M, blaSHV and blaTEM were detected at the sites — blaTEM was absent only at the container terminal — at 71 to 2,156 gene copies per millilitre, or 10⁻⁵ to 10⁻³ copies per 16S rDNA copy.

“The metagenomic survey missed them, illustrating how the two methods complement each other,” adds Ramos.

The authors noted that the study covers one season and five locations, and called for surveillance integrating clinical and environmental data to inform One Health-oriented risk assessment.

Contact author details: Christian C. Ramos, Department of Medical Microbiology, College of Public Health, University of the Philippines Manila. Email: Ccramos7@up.edu.ph

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