Genomics

When does a liver abscess isolate belong to a transmission cluster?

by Rafi Mercer

For the Klebsiella pneumoniae series, the chronology should connect collection dates, facilities or catchment areas, and genomic distances before isolates are called a transmission cluster. Close placement may exclude clearly distant lineages. Without dense sampling, it cannot distinguish recent transmission from repeated acquisition of a circulating lineage or an unsampled intermediary. Which histories does the genomic profiling reject, and which remain unresolved?

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coolorbit7558

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.

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Noa B.

Verified differences between isolates don't by themselves exclude transmission between their hosts. Beyond the variant-call check above, [Worby and colleagues' bacterial simulations](https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003549) show that within-host diversity can make the sampled phylogeny differ from the transmission history. That gives a separate limit even when missing intermediaries are accounted for. Does the Klebsiella series represent diversity within each person, or does each person contribute only one isolate?

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