I have done MLST for some isolates of Acinetobacter baumannii which are obtained from ICU scenario in a single month. In which five genes have same clonal number in all isolates while only two genes have different clonal number. I don’t know whether this is normal are some abnormal pattern. I am curious to know the logical answer behind it.
I need to know whether this clonal change in these two genes namely gpi(glucose 6 phosphate isomerase) and gyr(gyrase) are due to the hospital stress or this isolates where originally different clones when they enter the hospital scenario.
I did some mutational analysis on these two genes for all the isolates and found that the mutations are due to silent mutation.
Can anyone guide me how I could analyse the data further to get broad understanding.
please check the attachment for easy understanding
Nithin, read on the site below
http://www.mlst.net/misc/further.asp
what looks to me is you have got clones. I would be inclined to find out what the sequence types are by putting the numbers here
http://pubmlst.org/perl/bigsdb/bigsdb.pl?db=pubmlst_abaumannii_isolates&page=profiles
The site will be down today or tomorrow due to maintenance
Secondly for hospital outbreaks PFGE is a good method to assess clonality. Use Tenover's criteria or a cut off of 85% in bionumerics. You can have a look at my papers if you want more explanation.
Hope this is helpful!
Thanks,
Bruno
Thank you very much for your quick response Bruno.
I have checked the ST and it turns out i got only one new ST which i have submitted in pubmlst to get new ID.
I did phylogenetic analysis using the partial gene sequence used in MLST to find which clone came from which (rooted tree). But iam not sure whether iam doing the right thing.
I want to know how this clones are formed. Because i believe from one wild type strain avilable in the community all should have evolved. But i have no clue of figuring this out.
I don't thing so i could do PFGE. Is their any other way to find out break using MLST data. One thing i did was i did MLST of some isolate of Acinet.B in same hospital senario after 6 months and found that same clones matched with the existing clones identified. The problem is i dont know whether it stays in the ICU for 6 month or it jumps into the ICU from community within the 6 month period.
Can you sent me some links for your papers that can guide me?
Also i will needing your help with bionumerics iam totally new to it. If you could suggest some freeware that will also help me.
Thank you very much.
Regards,
Nithin.
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