Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
mSphere. 2021 Mar 3;6(2):e01302-20. doi: 10.1128/mSphere.01302-20.
, an obligately intracellular bacterium, is the most prevalent cause of bacterial sexually transmitted infections (STIs) worldwide. Numbers of U.S. infections of the urogenital tract and rectum have increased annually. Because is not easily cultured, comparative genomic studies are limited, restricting our understanding of strain diversity and emergence among populations globally. While Agilent SureSelect target enrichment RNA bait libraries have been developed for whole-genome enrichment and sequencing of directly from clinical urine, vaginal, conjunctival, and rectal samples, public access to these libraries is not available. We therefore designed an RNA bait library (34,795 120-mer probes based on 85 genomes, versus 33,619 probes using 74 genomes in a previous one) to augment organism sequencing from clinical samples that can be shared with the scientific community, enabling comparison studies. We describe the library and limit of detection for genome copy input, and we present results of 100% efficiency and high-resolution determination of recombination and identical genomes within vaginal-rectal specimen pairs in women. This workflow provides a robust approach for discerning genomic diversity and advancing our understanding of the molecular epidemiology of contemporary STIs across sample types, geographic populations, sexual networks, and outbreaks associated with proctitis/proctocolitis among women and men who have sex with men. is an obligate intracellular bacterium that is not easily cultured, which limits our understanding of urogenital and rectal transmission and impact on morbidity. To provide a publicly available workflow for whole-genome target enrichment and sequencing of directly from clinical urine, vaginal, conjunctival, and rectal specimens, we developed and report on an RNA bait library to enrich the organism from clinical samples for sequencing. We demonstrate an increased efficiency in the percentage of reads mapping to and identified recombinant and identical genomes in paired vaginal-rectal samples from women. Our workflow provides a robust genomic epidemiologic approach to advance our understanding of strains causing ocular, urogenital, and rectal infections and to explore geo-sexual networks, outbreaks of colorectal infections among women and men who have sex with men, and the role of these strains in morbidity.
淋病奈瑟菌是一种专性细胞内细菌，是全球最常见的细菌性性传播感染（STI）病原体。美国泌尿生殖道和直肠感染的数量逐年增加。由于淋病奈瑟菌不易培养，比较基因组研究受到限制，限制了我们对全球人群中菌株多样性和出现的理解。虽然安捷伦公司已经开发了用于从临床尿液、阴道、结膜和直肠样本中直接进行全基因组富集和测序的 SureSelect 靶向富集 RNA 诱饵文库，但这些文库无法公开获取。因此，我们设计了一种 RNA 诱饵文库（基于 85 个基因组的 34795 个 120 -mer 探针，而前一个文库使用 74 个基因组有 33619 个探针），以增加从临床样本中测序的生物体数量，并可以与科学界共享，从而能够进行比较研究。我们描述了该文库和基因组拷贝输入的检测限，并展示了在女性阴道-直肠标本对中 100%的效率和高分辨率确定重组和相同基因组的结果。该工作流程提供了一种稳健的方法，可以辨别基因组多样性，并推进我们对不同样本类型、地理人群、性网络以及与男性和男男性行为者的直肠结肠炎相关的流行性病原体的分子流行病学的理解。淋病奈瑟菌是一种专性细胞内细菌，不易培养，这限制了我们对泌尿生殖道和直肠淋病奈瑟菌传播和发病的理解。为了提供一种从临床尿液、阴道、结膜和直肠标本中直接进行全基因组目标富集和测序的公共可用工作流程，我们开发并报告了一种 RNA 诱饵文库，用于从临床样本中富集用于测序的生物体。我们证明了将读取映射到 的百分比增加，并且在女性的阴道-直肠样本对中鉴定了重组和相同的 基因组。我们的工作流程提供了一种稳健的基因组流行病学方法，可以推进我们对引起眼部、泌尿生殖道和直肠感染的 菌株的理解，并探索地理性网络、女性和男男性行为者中的结直肠感染爆发以及这些菌株在发病中的作用。
