Characterization and antibacterial efficacy of Streptomyces sp. NELs-40 against Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) presents a critical therapeutic challenge, and Streptomyces species are promising sources of novel antimicrobials.

This study aimed to characterize Streptomyces sp. strain NELs-40 genomically, optimize its antimicrobial production, evaluate its efficacy against MRSA ATCC 43300, and identify its bioactive metabolites.

Genomic DNA was sequenced (Illumina HiSeq X10) and assembled (SOAPdenovo2). Taxonomic classification was determined through 16S rRNA, ANI, AAI (CompareM), and dDDH (TYGS). Synteny analysis was performed using Clinker. Biosynthetic gene clusters (BGCs) were predicted with antiSMASH v4.2.0. Antimicrobial production was optimized via Plackett-Burman design. Antibacterial activity was assessed through well diffusion, MIC determination, and anti-biofilm assays. Bioactive metabolites were analyzed by GC-MS and tested for thermal, pH, and enzymatic stability.

Genomic analysis revealed a complete genome of 7,973,786 bp with 71.76% GC content, harboring 6,872 protein-coding genes and 49 biosynthetic gene clusters (BGCs). Of these, 30 clusters were associated with antimicrobial compound biosynthesis, representing diverse classes including polyketides and nonribosomal peptides. Taxonomic classification was confirmed by comparison with two reference genomes. Against the S. parvus reference genome, NELs-40 exhibited ANI of 99.6%, AAI of 98.31%, and dDDH of 88.70%. Against S. parvus A612, the values were ANI of 98.50%, AAI of 98.77%, and dDDH of 90.70%. Statistical optimization identified pH as the primary factor affecting antimicrobial production (p < 0.05). The ethyl acetate extract demonstrated potent activity against MRSA ATCC 43300, producing inhibition zones of 37 mm, an MIC of 125 μg/mL, and 32.25% biofilm inhibition. GC-MS analysis identified 23 compounds, predominantly 9-octadecenoic acid methyl ester, pyrrolo[1,2-a]pyrazine-1,4-dione derivatives, caryophyllenyl alcohol, and sesquiterpenes. The extract maintained optimal activity at pH 6.0-7.0 and temperatures up to 40 °C, with significant activity loss above 60 °C. The extract also demonstrated resistance to proteolytic enzymes, indicating non-proteinaceous characteristics.

Streptomyces sp. strain NELs-40 is a promising source of novel antimicrobial agents against drug-resistant pathogens, with extensive biosynthetic capacity, diverse chemistry, and potent activity against MRSA.