ArticleProceedings of the National Academy of Sciences of the United States of America2025
Population sequencing for phylogenetic diversity and transmission analyses.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistantMicrobial genomics · 2026Article
- A Bayesian Framework for the Network Analysis of Transmission Dynamics in Infectious Disease.Journal of molecular evolution · 2026Article
- Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistantmedRxiv : the preprint server for health sciences · 2026Article
- High-throughput targeted amplicon screening tool for characterizing intrahost diversity inMicrobial genomics · 2025Article
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12 authors.
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Abstract
Genomic diversity in pathogen populations is foundational for evolution and adaptation. Understanding population-level diversity is also essential for tracking sources and revealing detailed pathways of transmission and spread. For bacteria, culturing, isolating, and sequencing the large number of individual colonies required to adequately sample diversity can be prohibitively time-consuming and expensive. While sequencing directly from a mixed population will show variants among reads, they cannot be linked to reveal allele combinations associated with phylogenetic inheritance patterns. Here, we describe the theory and method for using population sequencing directly from a mixed sample, along with a minimal number of individually sequenced colonies, to describe the phylogenetic diversity of a population without haplotype reconstruction. To demonstrate the utility of population sequencing in capturing phylogenetic diversity, we compared isogenic clones to population sequences of
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