Joseph Sandeep J, Bommana Sankhya, Ziklo Noa, Kama Mike, Dean Deborah, Read Timothy D
Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Department of Pediatrics, University of California San Francisco, Oakland, California, USA.
bioRxiv. 2023 Jan 26:2023.01.25.525576. doi: 10.1101/2023.01.25.525576.
, a gram-negative obligate intracellular bacterium, commonly causes sexually transmitted infections (STIs). Little is known about transmission within the host, which is important for understanding disease epidemiology and progression. We used RNA-bait enrichment and whole-genome sequencing to compare rectal, vaginal and endocervical samples collected at the same time from 26 study participants who attended Fijian Ministry of Health and Medical Services clinics and tested positive for at each anatomic site. The 78 genomes from participants were from two major clades of the phylogeny (the "prevalent urogenital and anorecta"l clade and "non-prevalent urogenital and anorectal" clade). For 21 participants, genome sequences were almost identical in each anatomic site. For the other five participants, two distinct strains were present in different sites; in two cases, the vaginal sample was a mixture of strains. The absence of large numbers of fixed SNPs between strains within many of the participants could indicate recent acquisition of infection prior to the clinic visit without sufficient time to accumulate significant variation in the different body sites. This model suggests that many infections may be resolved relatively quickly in the Fijian population, possibly reflecting common prescription or over-the-counter antibiotics usage.
is a bacterial pathogen that causes millions of sexually transmitted infections (STIs) annually across the globe. Because lives inside human cells, it has historically been hard to study. We know little about how the bacterium spreads between body sites. Here, samples from 26 study participants who had simultaneous infections in their vagina, rectum and endocervix were genetically analyzed using an improved method to extract DNA directly from clinical samples for genome sequencing. By analyzing patterns of mutations in the genomes, we found that 21 participants shared very similar strains in all three anatomic sites, suggesting recent infection and spread. For five participants two strains were evident, indicating multiple infections. This study is significant in that improved enrichment methods for genome sequencing provides robust data to genetically trace patterns of infection and transmission within an individual for epidemiologic and pathogenesis interrogations.
沙眼衣原体是一种革兰氏阴性专性细胞内细菌，通常引起性传播感染（STIs）。关于其在宿主体内的传播情况知之甚少，而这对于理解疾病流行病学和进展至关重要。我们使用RNA诱饵富集和全基因组测序来比较从26名研究参与者同时采集的直肠、阴道和宫颈样本，这些参与者前往斐济卫生和医疗服务部诊所就诊，且在每个解剖部位检测出沙眼衣原体呈阳性。参与者的78个沙眼衣原体基因组来自沙眼衣原体系统发育的两个主要分支（“常见泌尿生殖道和肛门直肠”分支以及“非常见泌尿生殖道和肛门直肠”分支）。对于21名参与者，每个解剖部位的基因组序列几乎相同。对于其他五名参与者，不同部位存在两种不同的沙眼衣原体菌株；在两个案例中，阴道样本是菌株的混合物。许多参与者体内不同沙眼衣原体菌株之间缺乏大量固定单核苷酸多态性（SNPs），这可能表明在就诊前近期感染了沙眼衣原体，且没有足够时间在不同身体部位积累显著变异。该模型表明，斐济人群中的许多沙眼衣原体感染可能相对较快得到解决，这可能反映了常见的处方或非处方抗生素使用情况。
沙眼衣原体是一种细菌病原体，全球每年导致数百万例性传播感染（STIs）。由于沙眼衣原体生活在人体细胞内，一直以来很难进行研究。我们对该细菌在身体部位之间的传播方式了解甚少。在此，我们使用一种改进方法对26名在阴道、直肠和宫颈同时感染的研究参与者的样本进行基因分析，该方法可直接从临床样本中提取沙眼衣原体DNA用于基因组测序。通过分析基因组中的突变模式，我们发现21名参与者在所有三个解剖部位共享非常相似的沙眼衣原体菌株，表明近期感染并传播。对于五名参与者，有两种明显的沙眼衣原体菌株，表明存在多重感染。这项研究的重要意义在于，改进的基因组测序富集方法为从基因上追踪个体内沙眼衣原体感染和传播模式以进行流行病学和发病机制研究提供了可靠数据。
