Profiling of Pharmaceutical Sludge Microbiome, Resistome and Secondary Metabolites Using Metagenomics

Antibiotic manufacturing sites act as the hotspot for the dissemination of antibiotic resistance. The present study explores the resistome and secondary metabolites profile associated with the sludge of two pharmaceutical industries located in Delhi and Mysore, India. It confirmed that the pharma sludge contains complex microbiome and resistome. The presence of antibiotic-resistant genes (ARGs), class I integrons, and secondary metabolite genes (NRPs and PKs) was confirmed using PCR. Metagenomic tools like ResFinder 3.2, DeepARG, BusyBee, MG-RAST, and CoMET universe were used to analyze pharmaceutical sludge metagenome. Proteobacteria was found abundant in both metagenomes, followed by firmicutes & bacteriodetes. KEGG analysis predicted the expression of vancomycin, Pandrug, antifolate resistance pathway in both metagenomes. Resfinder predicted the presence of aminoglycoside, macrolide, and sulphonamide resistance genes in both metagenomes. DeepARG analysis classified ARGs in 28 (Arbro) & 27 (Mysore) ARG category and 431 & 368 ARG class. Further, CoMET universe indicated the presence of biosynthetic gene clusters like type II polyketide biosynthesis, Nonribosomal polypeptide biosynthesis, vancomycin & tetracycline, and macrolide biosynthesis. The present study provides primary insight about the diversity of secondary metabolites clusters present in pharmaceutical sludge. Microbes residing in such environment grows under higher selection pressure and produce various secondary metabolites. These metabolites could be exploited for the discovery of novel metabolites with antimicrobial potential and combating AMR. In future, the author aims to clone metagenome in expression vector (BAC/YAC vectors) for the discovery of novel secondary metabolites.

The online version contains supplementary material available at 10.1007/s12088-024-01349-9.