search

klebgenomics / Kaptive

GNU General Public License v3.0
44 stars 21 forks source link

Klebsiella oxytoca and Klebsiella aerogenes #38

Open abrozzi opened 2 months ago

abrozzi commented 2 months ago

Dear all, do you know if these two species share the same gene cluster for O-antigen and can be typed using Kaptive, similar to K. pneumoniae?

Bests, -A

kelwyres commented 1 month ago

Hi, Great question. I suspect there is at least some degree of sharing of these loci with the other Klebs species but I would expect the K. pneumo database is missing much of the diversity in these other species. Similar to the situation for the capsule db- if you find a really good match (high identity, high coverage no missing and no extra genes with no big length discrepancy) it is likely correct but there will be lots of genomes that don't have good matches. We have a capsule db for K oxytoca that we hope to release soon and plans for an O locus db but I don't have timeframe on the latter. Please do let us know if this is something you might be looking into so we don't duplicate efforts later.

Thanks, Kelly

fengyuchengdu commented 1 month ago

for Klebsiella aerogenes complex, try this as described in https://doi.org/10.1016/j.celrep.2024.114602