Comparative Genomics to Investigate the Resistome and Bacterial Heterogeneity in the Creekside Ecosystem in Navotas City: An Exploratory Research
DOI:
https://doi.org/10.65232/rcdf2g95Keywords:
Antibiotic Resistance Gene, Antimicrobial Resistance, Creekside Bacteria, Public Health, Shotgun Metagenomic SequenceAbstract
Rapid urbanization and untreated sewage discharge have degraded aquatic ecosystems, particularly the Navotas River. This study aimed to assess antimicrobial resistance (AMR) in bacterial communities to support rehabilitation efforts. A descriptive-correlational design was employed at three creekside sites with varying levels of human activity. Triplicate water samples (600 mL/site) were collected during the first and fourth weeks of January 2025. DNA was extracted and validated using Qubit, NanoDrop, and gel electrophoresis. Shotgun metagenomic sequencing was performed via Illumina NovaSeq (15 million reads/sample). Taxonomic classification used QIIME and KRAKEN, while antimicrobial resistance genes (ARGs) were identified through Q2-RGI with the comprehensive antimicrobial resistance database (CARD). One-way ANOVA assessed differences in bacterial and ARG abundance across sites. DNA quality met sequencing requirements, and physicochemical parameters, including pH and temperature were within normal limits. A diverse microbial community with known pathogenicity was found, including Pseudomonas, Sulfitobacter, Streptomyces, and Rhodococcus. The most abundant ARG was rpoB mutant in Bifidobacterium adolescentis (35.41%), conferring rifampicin resistance, followed by rpoB2 in Nocardia (20.94%). Other notable ARGs included sul1 (8.61%) and tlrC (4.90%), which are associated with sulfonamide and macrolide-lincosamide resistance. Beta-lactamases, including VIM, NDM, OXA variants, including aminoglycoside-resistance genes were identified. No significant ARG abundance differences were found across sites (p = 0.997; p = 0.777). The presence of antibiotic-resistant bacteria and ARGs, particularly rpoB mutants and beta-lactamases, signals a silent AMR crisis in Navotas River. These findings highlight the urgent need for policy intervention and continuous AMR surveillance in aquatic environments.
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Copyright (c) 2025 Mariae Janselle Pamposa, Zamantha Bernadette Convento, Jhoanna Loraine Fabela, Khris Angelique Manalo, Duane Miguel Mariano, Eulce Jashen Regala, Hana Yesha Uthayasurian, Maria Ruth Pineda-Cortel, Sherill Tesalona (Author)
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