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使用核心基因组多位点序列分型（cgMLST）和生命识别号（LIN）编码分类系统来了解……的种群结构。 注：原文中“Understanding the population structure of ”后面缺少具体内容。

Understanding the population structure of using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system.

作者信息

Yassine Iman, Jolley Keith A, Bray James E, Jansen van Rensburg Melissa J, Patel Fadheela, Sheppard Anna E, Zar Heather J, Allen Veronica, Tow Lemese Ah, Maiden Martin Cj, Nicol Mark P, Brueggemann Angela B

机构信息

Nuffield Department of Population Health, University of Oxford.

Department of Biology, University of Oxford.

出版信息

bioRxiv. 2025 May 4:2025.04.30.651387. doi: 10.1101/2025.04.30.651387.

DOI:10.1101/2025.04.30.651387
PMID:40654840
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12247924/
Abstract

is an important cause of infectious exacerbations of chronic obstructive pulmonary disease and otitis media. Previously, seroresistant (SR) and serosensitive (SS) lineages that differed in virulence potential were described, which raised questions about their evolutionary relationship and species classification. To investigate the population structure of , we developed a core-genome multilocus sequence typing (cgMLST) scheme using 1,319 core genes, and a life identification number (LIN) barcode classification system. Whole-genome analyses of nearly 2,000 genomes confirmed two divergent SR and SS lineages with distinct evolutionary trajectories. SR genomes were more conserved, while SS genomes exhibited greater genetic variability. Virulence gene analyses revealed lineage-specific variations in ubiquitous surface proteins (UspA1 and UspA2) and lipooligosaccharide (LOS) types, and SR genomes had more diverse LOS variants. The β-lactamase gene, and the bacteriocin cluster, were more common in SR, which suggested different selective pressures and ecological adaptation. This cgMLST scheme and LIN code system provides a robust method for characterising , distinguishes between SR and SS lineages, and offers a unified framework for population structure analyses. Implemented within PubMLST, this open-access resource facilitates high-resolution genomic studies and supports the scientific community in understanding the evolutionary complexity of .

摘要

是慢性阻塞性肺疾病和中耳炎感染性加重的重要原因。此前，已描述了毒力潜力不同的血清抗性（SR）和血清敏感（SS）谱系，这引发了关于它们的进化关系和物种分类的问题。为了研究的种群结构，我们使用1319个核心基因开发了一种核心基因组多位点序列分型（cgMLST）方案和一个生命识别号（LIN）条形码分类系统。对近2000个基因组的全基因组分析证实了两个具有不同进化轨迹的不同SR和SS谱系。SR基因组更保守，而SS基因组表现出更大的遗传变异性。毒力基因分析揭示了普遍存在的表面蛋白（UspA1和UspA2）和脂寡糖（LOS）类型的谱系特异性变异，并且SR基因组具有更多样化的LOS变体。β-内酰胺酶基因和细菌素簇在SR中更常见，这表明存在不同的选择压力和生态适应性。这种cgMLST方案和LIN编码系统为表征提供了一种强大的方法，区分了SR和SS谱系，并为种群结构分析提供了一个统一的框架。在PubMLST中实施后，这个开放获取资源促进了高分辨率基因组研究，并支持科学界理解的进化复杂性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/88afdf1c1a24/nihpp-2025.04.30.651387v1-f0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/cc93436f6459/nihpp-2025.04.30.651387v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/36a865babc5a/nihpp-2025.04.30.651387v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/b5b0fd5e4ea3/nihpp-2025.04.30.651387v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/a5592d91770b/nihpp-2025.04.30.651387v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/6af185f91412/nihpp-2025.04.30.651387v1-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/5b64bbbb23da/nihpp-2025.04.30.651387v1-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/2855fb492397/nihpp-2025.04.30.651387v1-f0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/88afdf1c1a24/nihpp-2025.04.30.651387v1-f0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/cc93436f6459/nihpp-2025.04.30.651387v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/36a865babc5a/nihpp-2025.04.30.651387v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/b5b0fd5e4ea3/nihpp-2025.04.30.651387v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/a5592d91770b/nihpp-2025.04.30.651387v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/6af185f91412/nihpp-2025.04.30.651387v1-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/5b64bbbb23da/nihpp-2025.04.30.651387v1-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/2855fb492397/nihpp-2025.04.30.651387v1-f0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e6f/12247924/88afdf1c1a24/nihpp-2025.04.30.651387v1-f0008.jpg

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