Hi Rory,

This question intrigued me, so here is just an idea of how I might go about it.

I am fairly sure It's possible to detect the SCC type straight from illumina short reads using SRST2 (https://github.com/katholt/srst2). You would need to compile a custom database of known SCC types such as those listed on http://www.staphylococcus.net/. Simply put, the algorithm uses a very sensitive and fast read aligner to map the WGS data to a set of reference sequences (i.e. the SCC sequence database) and provides a robust and accurate match to the best allele/sequence. I have done something similar for conjugative transposons in C. difficile. The SRST2 website does offer a guide for custom database set up.

Cheers

Dan

Thanks for the advise. I have downloading SRST2 but I am having problems running it due to the fact the latest version of bowtie2 I downloaded on homebrew is not compatible. I download an old version and put it to PATH but it still saying that it not compatible when I run SRST2 and I cannot seem to remove bowtie2 from homebrew.

I agree with Daniel - www.staphylococcus.net provides a nice search tool if you can identify a contig spanning the SCCmec region. You can just paste the contig in and hit "submit". Alternatively, I find the primers from Zheng et al (2005) (also found referenced on the staphylococcus.net website) useful to use as probes for relatively short read data. With luck, one of your "short" reads spans the 250-800 bp regions used to identify different SCCmec types. Good luck!