Abstract
The Vibrio cholerae biotype “El Tor” is responsible for all of the current epidemic and endemic cholera outbreaks worldwide. These outbreaks are clonal, and it is hypothesized that they originate from the coastal areas near the Bay of Bengal, where the lytic bacteriophage ICP1 (International Centre for Diarrhoeal Disease Research, Bangladesh cholera phage 1) specifically preys upon these pathogenic outbreak strains. ICP1 has also been the dominant bacteriophage found in cholera patient stools since 2001. However, little is known about the genomic differences between the ICP1 strains that have been collected over time. Here, we elucidate the pan-genome and the phylogeny of the ICP1 strains by aligning, annotating, and analyzing the genomes of 19 distinct isolates that were collected between 2001 and 2012. Our results reveal that the 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 these V. cholerae-associated bacteriophages.
Highlights
Vibrio cholerae is a globally-distributed bacterium and is the causal agent of the disease cholera, which is a potentially severe intestinal illness that affects ~1–5 million people and is responsible for up to ~140,000 deaths annually [1]
It is becoming increasingly theorized that this region is the source of most, if not all, global cholera outbreaks [3,4,27], and gaining a better understanding of this co-evolving predator is an important area of ongoing cholera research
We have performed a comprehensive phylogenetic analysis on all available, well-sequenced ICP1 isolates to elucidate their genetic divergence over time, and to provide a platform on which to develop future
Summary
Vibrio cholerae is a globally-distributed bacterium and is the causal agent of the disease cholera, which is a potentially severe intestinal illness that affects ~1–5 million people and is responsible for up to ~140,000 deaths annually [1]. Epidemic disease outbreaks sweep across the globe periodically This has been traced back to a single lineage that has emerged from the Bay of Bengal region in multiple waves over the last half-century [3]. It is hypothesized that the Bay of Bengal serves as a reservoir where the El Tor strains circulate throughout the year, and exchange genetic material and undergo ecological selection before infiltrating coastal communities. They are subsequently transported by infected individuals to larger cities where they can be transmitted globally [5,7]. This mechanism is thought to create a bottleneck for strains, and results in the clonality of outbreaks
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