The impact of phage predation on bacterial pathogens in the context of human disease is not currently appreciated. Here, we show that predatory interactions of a phage with an important environmentally transmitted pathogen, Vibrio cholerae, can modulate the evolutionary trajectory of this pathogen during the natural course of infection within individual patients. We analyzed geographically and temporally disparate cholera patient stool samples from Haiti and Bangladesh and found that phage predation can drive the genomic diversity of intra-patient V. cholerae populations. Intra-patient phage-sensitive and phage-resistant isolates were isogenic except for mutations conferring phage resistance, and moreover, phage-resistant V. cholerae populations were composed of a heterogeneous mix of many unique mutants. We also observed that phage predation can significantly alter the virulence potential of V. cholerae shed from cholera patients. We provide the first molecular evidence for predatory phage shaping microbial community structure during the natural course of infection in humans.DOI: http://dx.doi.org/10.7554/eLife.03497.001

A cholera epidemic has claimed the lives of more than 8,000 Haitians and sickened 650,000 since the outbreak began in October 2010. Early intervention in the epidemic focused on case-finding, treatment, and water and sanitation interventions for prevention of transmission. Use of oral cholera vaccine (OCV) as part of a complementary set of control activities was considered but initially rejected by policymakers. In December 2011, the Minister of Health of Haiti called for a demonstration of the acceptability and feasibility of the use of OCV in urban and rural Haiti. This paper describes the collaborative activity that offered OCV to one region of the Artibonite Department of rural Haiti in addition to other ongoing treatment and control measures. Despite logistics and cold chain challenges, 45,417 persons were successfully vaccinated with OCV in the region, and 90.8% of these persons completed their second dose.

Background Between April and June 2012, a reactive cholera vaccination campaign was conducted in Haiti using an oral inactivated bivalent whole-cell vaccine (BivWC). Methods We conducted a case-control study to estimate field effectiveness of the vaccine. Cases had acute watery diarrhea, sought treatment at one of three participating cholera treatment units from October 24, 2012 through March 9, 2014, and had a stool sample positive for cholera by culture. For each case, four controls (individuals who did not seek treatment for acute watery diarrhea) were matched by location of residence, calendar time, and age. We also conducted a bias-indicator case-control study to assess the likelihood of bias in the vaccine effectiveness (VE) study. Findings During the study period, 114 eligible individuals presented with acute watery diarrhea and were enrolled. 47 were analyzed as cases in the VE case-control study and 42 as cases in the bias-indicator study. In multivariable analyses, VE was 63% [95% confidence interval (CI): 8%–85%] by self-reported vaccination and 58% [95% CI: 13%–80%] for verified vaccination. Neither self-reported nor verified vaccination was significantly associated with non-cholera diarrhea (VE: 18% [95% CI: −208%–−78%] by self-report and −21% [95%CI: −238%–57%] for verified vaccination). Interpretation BivWC oral cholera vaccine was effective in protecting against cholera in Haiti during the study period –from 4 through 24 months after vaccination. Vaccination is an important component of epidemic cholera control efforts. Funding National Institutes of Health, Delivering Oral Vaccines Effectively project, Department of Global Health and Social Medicine at Harvard Medical School.