I am currently working on my undergrad doing biofilm research for Staphylococcus aureus. Unfortunately we have lost the exact strain that we are working with. I am planning on submitting our strain for sequencing, but wanted to ask what the best primers might be. Any help would be greatly appreciated!
You can target 23s RNA or thermonuclease gene for the identification of S. aureus. These two markers are specific to S. aureus, the following paper may help you.
Article Differentiation of Staphylococcus aureus and Staphylococcus ...
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Dear Bryce, we use spa primers to check S. aureus strains. It was described by Aires-de-Sousa et al.., 2006.
spa-1113f 5-TAAAGACGATCCTTCGGTGAGC-3
spa-1514r: 5-CAGCAGTAGTGCCGTTTGCTT-3
AIRES-DE-SOUSA M., Boye K., de Lencastre H., Deplano A., Enright M.C., Etienne J., Friedrich A., Harmsen D., Holmes A., Huijsden, X.W., Kearns A.M., Mellmann A., Meugnier H., Rasheed J.K., Spalburg E., Strommenger B., Struelens M.J., Tenover F.C., Thomas J., Vogel U., Westh H., Xu J., Witte W., High interlaboratory reproducibility of DNA sequence-based typing of bacteria in a multicenter study, Journal of Clinical Microbiology (J Clin Microbiol), 44, 619-621, (2006).
Additionally, you can use multiplex PCR in attached file.
If you have a mixture of bacteria, you could firstely use selective média to isolate S aureus strains. Then, depending of the charcateristics of your strain, you could target antibiotic resistance genes, virulence genes, agr type...
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