Iam working with clinical strains isolated from the same hospital and patients with similar background (all CF patients in a CF center).
We have the complete sequence of the strains and they are quiet similar but I could find a statistical or value that can be used to demostrate if the strain are related or are isogenic. How many SNPs had to have in their sequence to be consider a diferent strain and no an isogenic strain with some mutations?
Also if anybody know about an article or something about this specific problem (delucidate isogenic or close related) please let me know!
Thanks!!
I don't believe that number of SNPs is a way of defining new bacterial strains. Microbiologists normally do so based on morphological/biochemical features. I've attached a review of the topic for you. In general, you can have a lot of SNPs and still be looking at the same strain. Over the years many microorganisms have been sequenced and inserted into databases.
You can definitely search your sequence against a database of known sequences (BLAST). You will most definitely get a hit matching a sequence from an already sequenced organism, up to a confidence value. If all your sequences match the same strain you can be almost certain that the sequence belongs to that particular organism (this will most likely be the case).
If this is not the case i.e. your sequences match known sequences poorly and the top matches belong to different strains then you may be looking at something new.
Thank you for your answer! I understand what you say but my doubt is that Isogenic strains have to be genetically identical with the same polymorphism in all the genes. But when you have mutation in the strain due to different stress (antibiotics for example). The new resistant strain is still isogenic with some SNPs or is consider a new strain?. There is a value or something that could guve you the beakpoint or is more a theorical thing without a practical way to show that!?
Here is the article I was trying to add. I don't think there is a number specified anywhere; what I was saying is that you can have a number of SNPs and it will still be the same strain, unless you characterize it as a new one based on new properties such as the fact that it is resistant.
You can try determining what confers the resistance by looking into what is the common thing between the resistant mutants and identifying what is the molecular entity the drug normally interacts with (it probably targets a protein, but possibly the resistant strain doesn't let the drug inside, across its outer membrane).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC130684/
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