Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period

Abstract

The Vibrio cholerae biotype El Tor is responsible for all current epidemic and endemic cholera outbreaks worldwide. These outbreaks are clonal and are hypothesized to originate from the coastal areas near the Bay of Bengal where the lytic bacteriophage ICP1 specifically preys upon these pathogenic outbreak strains. ICP1 has also been the dominant bacteriophage found in cholera patient stool since 2001. However, little is known about its genomic differences between ICP1 strains collected over time. Here we elucidate the pan-genome and phylogeny of ICP1 strains by aligning, annotating and analyzing the genomes of 19 distinct isolates collected between 2001 and 2012. Our results reveal that ICP1 isolates are highly conserved and possess a large core-genome as well as a smaller, somewhat flexible accessory-genome. Despite its overall conservation, ICP1 strains have managed to acquire a number of unknown genes as well as a CRISPR-Cas system, which is known to be critical for its ongoing struggle for co-evolutionary dominance over its host. This study describes a foundation on which to construct future molecular and bioinformatic studies of this V. cholerae-associated bacteriophages.