Pearson Talima, Furstenau Tara, Wood Colin, Rigas Vanessa, Sahl Jason, Maltinsky Sara, Currie Bart J, Mayo Mark, Hall Carina, Keim Paul, Fofanov Viacheslav
Pathogen &Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.
School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America.
bioRxiv. 2024 Jun 20:2024.06.18.599478. doi: 10.1101/2024.06.18.599478.
Genomic diversity in a pathogen population is the foundation for evolution and adaptations in virulence, drug resistance, pathogenesis, and immune evasion. Characterizing, analyzing, and understanding population-level diversity is also essential for epidemiological and forensic tracking of 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 particular traits or phylogenetic inheritance patterns. Here, we describe the theory and method of how population sequencing directly from a mixed sample can be used in conjunction with sequencing a very small number of 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 from the sputum of a single patient. We also analyzed population sequences of derived from different people and different body sites. Sequencing results confirm our ability to capture and characterize phylogenetic diversity in our samples. Our analyses of populations led to the surprising discovery that the pathogen population is highly structured in sputum, suggesting that for some pathogens, sputum sampling may preserve structuring in the lungs and thus present a non-invasive alternative to understanding colonization, movement, and pathogen/host interactions. Our analyses of samples show how comparing phylogenetic diversity across populations can reveal directionality of transmission between hosts and across body sites, demonstrating the power and utility for characterizing the spread of disease and identification of reservoirs at the finest levels. We anticipate that population sequencing and analysis can be broadly applied to accelerate research in a broad range of fields reliant on a foundational understanding of population diversity.
病原体群体中的基因组多样性是其在毒力、耐药性、发病机制和免疫逃逸方面进化与适应的基础。表征、分析和理解群体水平的多样性对于病原体来源的流行病学和法医追踪以及揭示详细的传播途径也至关重要。对于细菌而言，培养、分离并对大量单个菌落进行测序以充分采样多样性可能极其耗时且昂贵。虽然直接从混合群体中测序会显示读段之间的变异，但无法将它们关联起来以揭示与特定性状或系统发育遗传模式相关的等位基因组合。在此，我们描述了如何将直接从混合样本中进行群体测序的理论和方法与对极少数菌落进行测序相结合，以在不进行单倍型重建的情况下描述群体的系统发育多样性。为了证明群体测序在捕获系统发育多样性方面的效用，我们将同基因克隆与来自一名患者痰液的群体序列进行了比较。我们还分析了来自不同人群和不同身体部位的群体序列。测序结果证实了我们在样本中捕获和表征系统发育多样性的能力。我们对群体的分析得出了一个惊人的发现，即病原体群体在痰液中具有高度结构化，这表明对于某些病原体而言，痰液采样可能保留了肺部的结构，从而为理解定植、移动以及病原体/宿主相互作用提供了一种非侵入性的替代方法。我们对样本的分析展示了比较不同群体间的系统发育多样性如何能够揭示宿主之间以及不同身体部位之间传播的方向性，证明了在最精细层面表征疾病传播和识别病原体库的能力和效用。我们预计群体测序和分析可广泛应用于加速众多依赖对群体多样性有基本理解的领域的研究。
