Abstract：
Vibrio cholerae O1 causes the diarrheal disease cholera, and the small intestine is the site of active infection. During cholera, cholera toxin is secreted from V. cholerae and induces a massive fluid influx into the small intestine, which causes vomiting and diarrhea. Typically, V. cholerae genomes are sequenced from bacteria passed in stool, but rarely from vomit, a fluid that may more closely represents the site of active infection. We hypothesized that V. cholerae O1 population bottlenecks along the gastrointestinal tract would result in reduced genetic variation in stool compared to vomit. To test this, we sequenced V. cholerae genomes from 10 cholera patients with paired vomit and stool samples. Genetic diversity was low in both vomit and stool, consistent with a single infecting population rather than coinfection with divergent V. cholerae O1 lineages. The amount of single-nucleotide variation decreased from vomit to stool in four patients, increased in two, and remained unchanged in four. The variation in gene presence/absence decreased between vomit and stool in eight patients and increased in two. Pangenome analysis of assembled short-read sequencing demonstrated that the toxin-coregulated pilus operon more frequently contained deletions in genomes from vomit compared to stool. However, these deletions were not detected by PCR or long-read sequencing, indicating that interpreting gene presence or absence patterns from short-read data alone may be incomplete. Overall, we found that V. cholerae O1 isolated from stool is genetically similar to V. cholerae recovered from the upper intestinal tract.
OBJECTIVE: Vibrio cholerae O1, the bacterium that causes cholera, is ingested in contaminated food or water and then colonizes the upper small intestine and is excreted in stool. Shed V. cholerae genomes from stool are usually studied, but V. cholerae isolated from vomit may be more representative of where V. cholerae colonizes in the upper intestinal epithelium. V. cholerae may experience bottlenecks, or large reductions in bacterial population sizes and genetic diversity, as it passes through the gut. Passage through the gut may select for distinct V. cholerae mutants that are adapted for survival and gut colonization. We did not find strong evidence for such adaptive mutations, and instead observed that passage through the gut results in modest reductions in V. cholerae genetic diversity, and only in some patients. These results fill a gap in our understanding of the V. cholerae life cycle, transmission, and evolution.
OBJECTIVE: Vibrio cholerae O1, the bacterium that causes cholera, is ingested in contaminated food or water and then colonizes the upper small intestine and is excreted in stool. Shed V. cholerae genomes from stool are usually studied, but V. cholerae isolated from vomit may be more representative of where V. cholerae colonizes in the upper intestinal epithelium. V. cholerae may experience bottlenecks, or large reductions in bacterial population sizes and genetic diversity, as it passes through the gut. Passage through the gut may select for distinct V. cholerae mutants that are adapted for survival and gut colonization. We did not find strong evidence for such adaptive mutations, and instead observed that passage through the gut results in modest reductions in V. cholerae genetic diversity, and only in some patients. These results fill a gap in our understanding of the V. cholerae life cycle, transmission, and evolution.
摘要：
霍乱弧菌O1引起腹泻病霍乱,小肠是活跃感染的部位。霍乱期间,霍乱毒素由霍乱弧菌分泌，并诱导大量液体流入小肠，导致呕吐和腹泻。通常,霍乱弧菌基因组从粪便中通过的细菌测序，但很少因为呕吐物,一种可能更接近地代表活动性感染部位的液体。我们假设与呕吐物相比，沿着胃肠道的霍乱弧菌O1种群瓶颈会导致粪便遗传变异减少。为了测试这个，我们对10例霍乱患者的霍乱弧菌基因组进行了测序，这些患者有配对的呕吐物和粪便样本。呕吐物和粪便的遗传多样性都很低，与单一感染人群一致，而不是与不同的霍乱弧菌O1谱系合并感染。4名患者从呕吐物到粪便的单核苷酸变异量减少,增加了两个，四个保持不变。8例患者的呕吐物和粪便之间的基因存在/缺失变异减少，2例增加。组装的短阅读测序的Pangenome分析表明，与粪便相比，毒素共同调节的菌毛操纵子更频繁地包含来自呕吐物的基因组缺失。然而,这些缺失没有通过PCR或长读测序检测到，这表明仅从短读数据解释基因存在或缺失模式可能是不完整的。总的来说,我们发现从粪便中分离的霍乱弧菌O1与从上肠道回收的霍乱弧菌在遗传上相似。
目的：霍乱弧菌O1，引起霍乱的细菌，摄入受污染的食物或水中，然后在小肠上部定植，并在粪便中排泄。通常研究粪便中的霍乱弧菌基因组，但从呕吐物中分离出的霍乱弧菌可能更能代表霍乱弧菌在上肠上皮定植的地方。五、霍乱可能会遇到瓶颈，或者细菌种群规模和遗传多样性的大幅减少，当它穿过肠道时。通过肠道的传代可以选择适应于存活和肠道定植的不同霍乱弧菌突变体。我们没有找到这种适应性突变的有力证据，相反，观察到通过肠道导致霍乱弧菌遗传多样性的适度减少，只有一些病人。这些结果填补了我们对霍乱弧菌生命周期理解的空白，传输,和进化。
目的：霍乱弧菌O1，引起霍乱的细菌，摄入受污染的食物或水中，然后在小肠上部定植，并在粪便中排泄。通常研究粪便中的霍乱弧菌基因组，但从呕吐物中分离出的霍乱弧菌可能更能代表霍乱弧菌在上肠上皮定植的地方。五、霍乱可能会遇到瓶颈，或者细菌种群规模和遗传多样性的大幅减少，当它穿过肠道时。通过肠道的传代可以选择适应于存活和肠道定植的不同霍乱弧菌突变体。我们没有找到这种适应性突变的有力证据，相反，观察到通过肠道导致霍乱弧菌遗传多样性的适度减少，只有一些病人。这些结果填补了我们对霍乱弧菌生命周期理解的空白，传输,和进化。
