Can a single ST belong to multiple phylogroups?

[anuradhasingh15]

Hi,

I noticed that some STs can be assigned to more than one phylogroup, although one phylogroup is usually predominant. Is this expected due to biological reasons such as recombination, or does it generally indicate a technical artefact?

Thanks.

[nickp60]

Hi @anuradhasingh15 , I haven't investigated this specifically but I wouldn't be surprised. The phylogroup is a useful label but is a pretty coarse metric; finer methods (whole genome ani, mash distances, core gene phylogeny, and sequence types) aren't always going to line up with phylogroups.

As to whether its a technical artifact, this tool is geared towards replicating the expected results from the PCR assay. Those primers can tolerate some level of variability, which we have tried to replicate with fuzzy searching, but there is the possibility that the fuzzy search misses something that the actual primers could tolerate in the pcr reaction.

If its the case where a different phylogroup is being called because one of the expected loci is absent, feel free to send it over and I can take a look. If you have the ability to run the PCR assay to validate, all the better!