I have sequenced various bacterial genomes, and what I need to know is whether these isolates are clonal or not. There are several percentages of similarity among these isolates, yet I do not know what is the lowest percentage to consider genomes as clonals nonetheless.
Thanks in advance for your time.
I have read a paper where they talked about TZMD ( Tetranucleotide-derived Z-value Manhattan Distance) which can differentiate between clonal and non-clonal strains.@ Jesus Rojas
I would say it depends on the species of bacteria, some may mutate a bit more frequently than others due to differences in doubling time (growth rate) and other factors. Some bacteria have better DNA damage and repair enzymes than others.
One case that was very extensively studied and published on, was the case of Bacillus anthracis following the 9/11 attacks. Hundreds of isolates and strains or lineages were studied by complete genome sequencing, which was much harder to do back in those days, than it is today. Differences in lineages or isolates were just a few single base changes over the complete genome. But there are also many other cases of a similar nature, involving the tracing of outbreaks of Sigella toxin producing E. coli or outbreaks of hospital-acquired vs community acquired drug resistant bacteria.
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As told before, this depends a lot on the species.
For enteric bacterial pathogens I often set a threshold at 5 SNPS within the core genome. Actually it should be no more than 5 SNPs over the whole genome but this is difficult to detect as current sequencing technologies often deliver false positive SNPs.
Hello
To get clonality of two strains, you should use the in silico MLST available at https://cge.cbs.dtu.dk/services/MLST/
It's impossible to have two identical genomes even with identical clones. It's linked to naturally occuring mutations. In addition, when sequencing a genome, you are not sure that you have the exact sequence of your genome (reads quality, assembly, size, ...etc.)
As far as I know there is no magic value to say X is a clone and Y is not a clone. Biology is like that: lots of grey.
There are several metrics in use. Chose on that you can live with. All should agree that clones will look like each other while non clones will look different
First you have to evaluate the level of différentiation between your bacterials, your will see the difference between them is significant or not.
If the difference is not significant, you can do the clonale test that will allow you to get if all individuals tend to be clones or not and what the level of similarity beteen. For this test you can use poppr R package (there is a function for clonale test), it shows rbarD index and its probabilty of significance.
If the percentage of similarity between your individuals is high that means the considered individuals are not significantly different, in that case we can do the clonale test. otherwise, the similarity is low so the tested individuals are different, a structuration can be found.
Depending on what you want to compare and refer as cloning I would say that there’s no percentage of compliance between bacterial strains.
Genomial cloning and comparison is all about specific match, genomics expression, virulence or other abilities/potencies and specific cohesion of specific genes or DNA sequences.
otherwise bacterial strains can be seen as clonal in their colonies;
it’s all about certain genes or even nucleotides that the similarity and mutations are marked
There is no cut off for SNP, but when you get less than 20,you can take them as clonal, you can add Ortho ANI score which must be more than 98,6%
It differs from one genera to another. But at average nucleotide identity level the similarity should be 99.5%.
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