How to retrieve the latest SCCmec types in the output

[pany-vet]

Hi,

I noticed that the software outputs only contain the hits from SCCmec type I ~ type IVh. The same is shown in both the example test data and our genome sequences. I have checked the directory of the SCCmec reference data. The database also includes the SCCmec type VII, VIII, X, and XI. However, I can't find relevant results of the latest SCCmec types in the outputs. I tried to use a genome carrying SCCmec-XI as an input file, but couldn't get the hit of XI in the result.

I would like to know, how to make the software output the latest types? And, how to update the SCCmec typing database (type XII or later)?

Thank you guys. @rpetit3

[rpetit3]

Hi @pany-vet

I've started this issue https://github.com/staphopia/staphopia-sccmec/issues/4 where I plan on adding the newer SCCmec types.

I unfortunately do not have a time line on this though, since it would have to be completed in my free time. I will try to revisit this soon to see if I'll be able to complete this sooner than later.

Thank you! Robert

[REMOUS-MAX]

Hi @rpetit3

How are you doing, thanks for your usual effort to better this useful tool. Please did you manage to add the newer sccmec types?

[rpetit3]

@pany-vet and @REMOUS-MAX - Quite the coincidence! I have actually been thinking about this over the last week.

One question I have is, do either of you have a list of S. aureus samples that have a lab validated SCCmec Type and raw genomic sequencing? I'm hoping to put together a test set to validate new changes

[REMOUS-MAX]

I have S. Aureus raw reads but the Sccmec have not been validated. @rpetit3 do you need those with newer Sccmec types?

[rpetit3]

I think it would be useful to have a set of public samples with a known SCCmec type (e.g. pcr tested). Just to have a set to test against.

[REMOUS-MAX]

@rpetit3 I will ask around in my department to see if I can get some to share with you

[rpetit3]

Thank you so much!