Vibrio cholerae, a Gram-negative facultative anaerobe, is arguably the most well-known of the Vibrionaceae due to being the causative agent of the potentially fatal diarrheal disease cholera [Legros18]. Typically caused by the consumption of contaminated food and water sources, cholera epidemics and pandemics remain a significant threat in nations with limited healthcare and unsafe drinking water [Reidl02, Legros18]. The characteristic symptoms of cholera are caused by two main virulence factors, the toxin co-regulated pilus (TCP) and the cholera toxin (CT) [Faruque98, Vanden07]. The CT is encoded within the genome of CTXφ, a filamentous lysogenic bacteriophage which is found integrated into the genome of all toxigenic Vibrio cholerae strains [Waldor96, Reidl02, Faruque02].

There are over 200 serogroups of Vibrio cholerae, yet only two (O1 and O139) are associated with pandemics, whilst serogroup O1 is also composed of strains with two distinct biotypes, Classical, and El Tor. The first six cholera pandemics were caused by Classical biotypes of serogroup O1 whilst the El Tor biotype is responsible for the ongoing seventh pandemic, which originated in Indonesia in 1961 [Feng08, Mukhopadhyay14]. The El Tor strain was originally isolated in 1905 from the gut of pilgrims in a Sinai Peninsula quarantine camp called El Tor, from which the strain got its name [Cvjetanovic72]. By the 1970s it had reached much of Asia and parts of Africa, the Middle East, and Southern Europe; cholera outbreaks in the Americas in the 1990s, Haiti (2010-2019), and more recently Yemen (2015-present) are also part of the seventh pandemic [Cvjetanovic72, Mukhopadhyay14, Federspiel18].

The genome used for this PGDB is an updated version of the first Vibrio cholerae genome sequenced in Bangladesh in 1975 which was isolated from a 7th pandemic El Tor biotype designated Vibrio cholerae O1 biovar El Tor str. N16961 [Heidelberg00, Mutreja11]. As with other Vibrio cholerae strains, and many other members of the Vibrionaceae, the genome of Vibrio cholerae O1 biovar El Tor str. N16961 possesses two circular chromosomes; chromosome 1 encodes most essential genes and is larger (in this strain, 2.96 Mb) than chromosome 2 (in this strain, 1.07 Mb), which evidence suggests may have once been a megaplasmid [Okada05, Sozhamannan20]. In this strain, one copy of CTXφ is integrated within Chromosome 1, but variations in the target chromosome, gene arrangement and copy number are observed between biotypes [Heidelberg00, Sanchez08, Safa20].

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp11, Karp16] component of Pathway Tools software version 26.0 and MetaCyc [Caspi20] version 26.0 on 15-Dec-2021, and was improved by manual curation, bringing it to a tier 2 status. Some of the data in this PGDB were obtained from publications describing closely related strains, including Vibrio cholerae O1 C6706 [Weng21].

Development of this PGDB was supported by BioCyc subscription revenues and by grant GM080746 from the National Institute of Health.