Hi everyone,
I am analyzing ~1,981 Pseudomonas aeruginosa genomes and performed SNP/InDel calling using Snippy against the PAO1 reference genome. After filtering, I identified mutations in several resistance-associated genes, including oprD, ampC, pmrB, mexT, nalC, nalD, arnT, fiuA, fecA, and waaL.
Some mutations are well documented in the literature, while many appear to be unreported. Since this is a computational study using public WGS data, experimental validation is not possible.
How are such novel mutations typically handled in bacterial genomics papers? Is literature comparison and classification as putative novel variants generally acceptable, or are additional validation steps expected?
I would also appreciate recommendations for papers that use a similar Snippy-based mutation analysis approach.
Thanks!
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lavslipoprotein2204 •
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Yes, you can certainly curate the literature to identify evidence supporting the functional impact of specific mutations. If antibiogram data are also available for the corresponding samples, you can investigate potential associations. Additionally, you can prioritise variants based on their functional classification (e.g., nonsynonymous missense mutations) and assess their potential impact on protein structure and function.
Antibiogram with sequencing data example: https://www.ncbi.nlm.nih.gov/biosample/SAMN50642835