Antimicrobial resistance and bioactive metabolites of Serratia marcescens CAB03 from a Palk Bay coral reef

Abstract

Antimicrobial-resistant pathogens are poorly understood and pose emerging threats to coral reef ecosystems. Coral-associated microbial diversity is crucial for reef resilience; however, there is a limited understanding of opportunistic pathogens from Indian reefs. Here, we report the identification of Serratia marcescens CAB03, which may be associated with coral disease, isolated from Acropora cythera of Palk Bay coral reef, India. Whole genome sequencing of S. marcescens CAB03 produced 24 contigs (total G + C 59.7 %) and 4713 predicted genes. Identification of functional annotation revealed 17 antimicrobial resistance (AMR) genes, including three copies of the adeF gene, which encapsulates a resistance-nodulation-division (RND) efflux system that provides resistance to tetracyclines and fluoroquinolones. At the same time, related genes were also associated with resistance to β-lactams, aminoglycosides, macrolides, glycopeptides, and disinfectants, suggesting that this strain may have multidrug resistance potential. Further secondary metabolite prediction revealed biosynthetic gene clusters for ririwpeptide, a cyclic lipopetide with membrane-disrupting antibacterial and anticancer activity, and prodigiosin, which has gained notoriety for its antimicrobial, anticancer, and immunosuppressant activities as a red-colored pigment. Genome-based evidence clearly indicates that S. marcescens CAB03 is a contributor to coral health degradation through the proliferation of AMR bacteria and also a potential repository of bioactive compounds for pharmaceutical purposes. We used whole-genome sequencing here to address a long-standing knowledge gap regarding AMR bacteria associated with coral from Indian reefs. This study illustrates the need for genomic surveillance and conservation for AMR bacteria, ideally and more generally advances the study of microbial metabolites for drug discovery. Linking pathogen genomic profiles to reef health and advances in applied biotechnology reveal new reasons for coral reef conservation and provide new sources of data for potential drug development.