Phage predation, disease severity and pathogen genetic diversity in cholera patients

Abstract

Nearly a century has passed since d'Herelle and colleagues discovered phages that infectVibrio choleraeand mitigate cholera epidemics. Despite an increasingly detailed picture of the molecular mechanisms of resistance and counter-resistance that shape phage and bacterial interactions, we lack an understanding of how these interactions play out during natural infection, how they are affected by antibiotic exposure, and how they relate to clinical outcomes. To fill these gaps, we conducted a year-long, nation-wide study of diarrheal patients in the cholera-endemic setting of Bangladesh. A total of 2574 stool samples were collected from enrolled patients at hospital admission and screened forV. choleraeand virulent phages (ICP1, 2, or 3). All 282 culture positive samples, and an additional 107 culture negative but PCR positive samples, were analyzed by shotgun metagenomic sequencing. From these metagenomes, we estimated the relative abundances ofV. cholerae, phages, and members of the gut microbiome, while accounting for antibiotic exposure determined by quantitative mass spectrometry. Consistent with d'Herelle's thesis, we observed higher phage toV. choleraeratios in patients with mild dehydration, demonstrating in the modern era that phages are indicative of disease severity. Antibiotics were associated with lessV. choleraeand with mild disease; ciprofloxacin in particular was associated with several known antibiotic resistance genes. Phage resistance genes in theV. choleraeintegrative conjugative element (ICE) were associated with lower phage toV. choleraeratios. In the absence of detectable ICEs, phages shaped genetic diversity, selecting for nonsynonymous point mutations in theV. choleraegenome. Together, our results point to both antibiotics and phages as inverse correlates of disease severity, while also selecting for resistance genes or mutations within cholera patients.

Diversity ofVibrio choleraeO1 through the human gastrointestinal tract during cholera

“…Based on sequencing of V. cholerae O1 isolate genomes 8 and metagenomes 9,10 from stool, we have previously found that co-infections by distinct strains of V. cholerae O1 in humans appear to be rare in the excreted population, but these could be more common in the inoculum, especially in hyperendemic areas. Similarly, the V. cholerae O1 population in stool from single individuals contains only minor point mutations and dozens of gene content variants.…”