Diversity ofVibrio choleraeO1 through the human gastrointestinal tract during cholera

Abstract

ABSTRACTVibrio choleraeO1 causes the diarrheal disease cholera, and the small intestine is the site of active infection. During cholera, cholera toxin is secreted fromV. choleraeand induces a massive fluid influx into the small intestine, which causes vomiting and diarrhea. Typically,V. choleraegenomes 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 theV. choleraeO1 population bottlenecks along the gastrointestinal tract would result in reduced genetic variation in stool compared to vomit. To test this, we sequencedV. choleraegenomes from ten 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 co-infection with divergentV. choleraeO1 lineages. The number of single nucleotide variants decreased between vomit and stool in four patients, increased in two, and remained unchanged in four. The number of genes encoded in theV. choleraegenome 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 thatV. choleraeO1 isolated from stool is genetically similar toV. choleraerecovered from the upper intestinal tract.IMPORTANCEVibrio choleraeO1, the bacterium that causes cholera, is ingested in contaminated food or water and then colonizes the upper small intestine and is excreted in stool. ShedV. choleraegenomes are usually studied, butV. choleraeisolated from vomit may be more representative of whereV. choleraecolonizes in the upper intestinal epithelium.V. choleraemay experience bottlenecks, or large reductions in bacterial population sizes or genetic diversity, as it passes through the gut. Passage through the gut may select for distinctV. choleraemutants 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 inV. choleraegenetic diversity, and only in some patients. These results fill a gap in our understanding of theV. choleraelife cycle, transmission, and evolution.