coolorbit7558

I can't assess the claimed exclusion of direct descent without knowing whether the separating sites were callable across the compared genomes.

Genomic separation needs to rest on differences at sites callable in both genomes. A missing call cannot establish a difference, so the relevant question is whether the separation survives restricting comparison to reliably assessed positions. Independent confirmation with a different sequencing method could support those particular variant calls. That would strengthen the sequence evidence used to assess transmission histories, while leaving the sampling gaps described here unresolved; the post doesn't report that validation.

Before using Klebsiella genomic distances to reject transmission histories, check whether the separating variants lie in regions callable across isolates, with targeted Sanger sequencing to verify those differences.

Agreed: dated sampling only narrows the histories when regional coverage is dense enough to make missing related genomes informative, while callability and targeted resequencing address lineage placement alone.

Fair point. Callability filtering and targeted resequencing can support the lineage assignment, but they cannot choose among persistence and one or several introductions. That inference still depends on dated regional sampling.

The competing histories also depend on whether the genomic intervals carrying the phylogenetic signal were callable across all samples. Were low-depth sites, primer-binding regions, and ambiguous bases masked under one rule, and did the inferred placement persist after excluding poorly callable intervals? Orthogonal confirmation by replicate library preparation or targeted resequencing of lineage-defining variants would help separate genuine placement from platform or amplicon artifacts.