AcrB mutation in S. Typhi

marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

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AcrB mutation in S. Typhi #93

Closed fahadkhokhar closed 3 years ago

fahadkhokhar commented 3 years ago

Hello! Uploading genomes to PathogenWatch - it seems that the azithromycin resistance mutation acrB R717L in S. Typhi is not being picked up. The R717Q mutation is correctly identified.

bkille commented 3 years ago

Hi @fahadkhokhar, sorry for the delay. Can you elaborate on this error a bit more? Are you using Parsnp to align a group of genomes and noticing that the alignment doesn't report the R717L variant?

fahadkhokhar commented 3 years ago

Hi, this seems to have been resolved in the latest update from Pathogenwatch.