Deciphering the ongoing evolution of Vibrio cholerae: adapting to clinically relevant evolutionary pressures

Cholera is a waterborne infectious disease affecting up to 4 million people yearly and frequently arising where sanitary infrastructure is inadequate. Cholera is caused by pathogenic strains of the aquatic bacterial species V. cholerae. While V. cholerae infections often cause no or only mild diarrhoeal symptoms, virulent infections can lead to severe dehydration and death within hours of the onset of symptoms. Acute cholera infections are commonly treated by rehydration, whereas antibiotic therapy is only administered in a subset of severely ill patients to reduce the duration of water loss. The Centre for Disease Control (CDC) recommends a single dosage of doxycycline as first-line treatment if not contradicted by the local antibiotic susceptibility patterns. If resistance to doxycycline is prevalent, azithromycin and ciprofloxacin are recommended as alternative options. Despite the scarce encounters of V. cholerae and antibiotic substances in the human gut, antimicrobial resistant V. cholerae have increased over the last decades. The mode of V. cholerae antimicrobial resistance evolution, in the human gut or in aquatic environments, remains unknown. Mobile genetic elements have played a crucial role in the evolution of pathogenic V. cholerae, as the primary virulence factor, the cholera toxin, is encoded on a lysogenic prophage CTXf. Multiple phage- and plasmid defence systems have been described within the last few months, exemplifying how V. cholerae is evolving under the pressure of these elements. Fluctuating dynamics of phages and bacteria have recently been observed during a V. cholerae infection within the human gut. However, it has not yet been established if and how these phage-pathogen dynamics impact the disease outcome of the human host. Human genetic factors have been shown to influence disease status. Cholera is an ancient disease that has affected humanity for centuries and thus impacts its evolution. Human single nucleotide polymorphisms (SNPs) in innate immune system pathways are associated with susceptibility to cholera. How these interact with well-known cholera virulence factors and whether a combined analysis of the two genome dispositions (human host and pathogen) can predict cholera susceptibility is currently unknown. In this project, I will test the following hypothesis (i) V. cholerae evolves AMR while infecting the human host (WP1); (ii) Prevalent and symptomatic V. cholerae strains are resistant to the frequent ICP1 phages; and (iii) Combining human and bacterial genomic data can explain the severity of a cholera infection (WP3). The suggested project is embedded into ongoing cholera work in the research group of Prof. B. Jesse Shapiro (Department of Microbiology and Immunology, McGill University, Montréal, Canada). It focuses on the bioinformatic analysis of clinical samples which have been isolated in collaboration with the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) (Dhaka, Bangladesh) and subjected to shotgun metagenomic sequencing. Data available for this project include (a) snapshot stool samples of 300 patients with diarrhoea, which were either culture negative (n=100) or positive (n=200) for V. cholerae, (b) longitudinally collected stool samples of 24 index patients and their household contacts, sampled at three different time points: day 0 (enrollment), day 3 and day 7 and (c) paired human/bacterial samples of 271 cholera patients and asymptomatic contacts carrying V. cholerae. I will test the above hypotheses by jointly analysing these metagenome sequences, combined with single strain bacterial genomes (sequenced for this study and from public databases), concentrations of antibiotic substances in stool samples determined by mass spectrometry, and human genome data. Overall, the knowledge gained from this study may improve strategies for antibiotic stewardship, disease prevention and pave the way for new treatment options.