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Purpose: To investigate the actinomycetes from an extreme environment for their inhibitory potential against methicillin-resistant Staphylococcus aureus (MRSA), and the metabolic fingerprinting of the active strains.

Methods: A total of 80 actinomycetes strains were recovered from Cholistan desert, Pakistan. The isolated strains were identified by morphological, biochemical and physiological characterization and by 16S rRNA gene sequencing. The antimicrobial activity of the selected actinomycetes strains against MRSA was determined by agar well and disc diffusion assays. All the strains were screened against MRSA for the identification of potent antimicrobial producers. Further, validation of MRSA, strains was carried out using a portion of mec-A gene (533bp) of five strains including A1, A6, A7, A8 and A9, amplified and sequenced.

Results: The desert actinomycetes strains exhibited promising antimicrobial activity against MRSA with zone of inhibition of up to 25 mm recorded in agar diffusion and disc diffusion assays. The MRSA strains also showed maximum genetic similarity with methicillin-resistant Staphylococcus aureus in GenBank. Most of the actinobacterial strains exhibited 99 % genetic similarity with the genus Streptomyces, including strains AFD6, AFD12, AFD23, AFD25, and AFD26 while isolate AFD18 has 100 % similarity with a Pseudonocardia, named Saccharothrix xinjiangensis.

Conclusion: The results reveal that actinomycetes from the desert ecosystem studied are significant producers of useful antimicrobial agents, and should be explored further for novel drug candidates against MRSA.