I am on an investigation about molecular epidemiology of Clostridium difficile. I have characterise some isolates and I want to study their ribotypes. I will do a PCR ribotype with primers of O'Neill, but I have no access to a database of C. difficile ribotypes.
HI,
The problem with PCR ribotyping is that a general database is still not available because the data are not readily comparable from one lab to another. So a PCR profile obtained in one lab might not be exactly comparable to another one in another lab even if the same strain is analyzed. It will depend on the type of gel or capillary apparatus used to analyze the bands, the primer pairs, the PCR conditions, etc. Most labs that do PCR ribotyping of Cdiff use their own internal reference system, and a number of "reference" strains of known ribotype to compare. In my lab, we do like that and since the most clinically relevant strains are often the most prevalent (eg. ribotypes 027, 078, 001, etc) then it is easier to ask a collaborator or a reference lab to send you these reference strains that you will analyze with your unknown isolates, using the same experimental conditions.
Hope this will help!
Thank you very much! I thought that would be the answer!. The problem is that in my country there is no reference laboratory working in C. difficile and I couldn´t get the strains yet.
Hi,
if I could recommend, the best option for ribotyping is the capillary electrophoresis way. There is a new consensus protocol you can follow (see PMID: 25679978). I know, the sequencer machine is not the routine equipment in most microbiological labs but I am sure that some genetic department is near to your lab and they can help you. You can compare your electronic data (*fsa files) with other labs or with WEBRIBO database. If you need more help do not hesitate to contact me. Regards, Marcela
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