Survey of Genomes - Vibrio cholerae strain El Tor N16961

In this episode from a survey of genomes, Danielle Vincent from the 2019 Hiram College Genetics course will introduce us to Vibrio cholerae El Tor N16961 and what its genome tells us about its ability to cause the dreaded disease cholera.
Welcome to Genomics Revolution. This is Danielle Vincent from the 2019 Hiram College Genetics course, and I will be your host for this episode on the genome of Vibrio cholerae El Tor N16961. Now, just to make things a bit easier, I’ll go ahead and refer to this organism as V. cholerae for the remainder of this episode. V. cholerae is a gram-negative, gamma-Proteobacterium that you may already recognize as it’s the bacterium that causes the disease Cholera (1). In 1854, during the third pandemic of Cholera, an anaethesiologist named John Snow theorized that this, at the time, unknown, disease was spreading through contaminated water. Snow mapped out 13local, public wells in London and took water samples, and he claimed to see “white, flocculent particles” in some of these samples (3). Around the same time, this organism was seen in Florence by the anatomist Filippo Pacini as he was performing autopsies on individuals that had died during this pandemic. He saw what he referred to as “vibrions”, or little elements, found in the intestinal mucosa and feces, and he believed that this was the cause of the disease (3). V. cholerae was not definitively found to be the cause of Cholera until, in 1884, German scientist, Robert Knoch, successfully isolated the bacterium in pure culture. Robert Knoch also noted that this organism was “a little bent, like a comma” (3). 
​Cholera has been known to be an epidemic in Southern Asia for over 1,000 years and has also been the cause of seven pandemics, the first starting in 1817 (1). Cholera is known to be an infection of the small intestines. People who have contracted the disease will experience severe, watery diarrhea and vomiting and can die from dehydration, even just after a few hours (3). Without treatment, this disease is very contagious and lethal. Cholera probably isn’t a disease many of us have to worry about day-to-day. However, individuals in developing countries with unsafe drinking water, poor sanitation, and limited healthcare, can easily fall victim to the disease (3). Over the years, many strains of V. cholerae with varying gene content have been found to cause Cholera in various countries, and the study of this organism is very important as it allows for advances in creating more efficient treatments.
​The originally sequenced El Toro N16961 strain of V. cholerae was found to have a genome size of  4,033,460 base pairs (1). It contains two circular chromosomes that encode for a total of 3,885 proteins, 2,770 of these proteins are found in chromosome 1 while 1,115 proteins are located in chromosome 2 (1). 
​Sequencing the genome for this bacterium has played a large role in figuring out the mechanisms in which V. cholerae functions and causes disease. Cholera toxin (CT) and the toxin-coregulated pilus (TCP) are the two main virulence factors.Cholera toxin is an ADP-ribosylating toxin that, when secreted, causes an increase in cAMP levels in the intestinal epithelial cells (2). ToxRS for example, is a transcriptional regulator that aids in the activation of the toxT promoter, and this leads to the activation of various virulence genes (2). Many studies will now use this type of knowledge to find differences between the strains of V. cholerae, as certain conditions, like temperature and pH, can cause decreases in virulence factors (2). One study looked at the expression of cholera toxin in the presence of bile acids and found that El Tor biotype strains, N16961 included, has a much lower production of cholera toxin when exposed to bile acid than say a classical strain of V. cholerae (2).
​As stated before, there are many different strains of V. cholerae, and the genome has become very crucial in differentiating the various strain types. The cholera toxin we just discussed is encoded by two genes, ctxA and ctxB, which are located on the CTXphi prophage (5). Now, epidemic or pandemic V. cholerae can broken down in to serogroups, O1 and O139 (5). The O1 serogroup contains two biotypes, classical and El Tor, like the strain we’ve been discussing. It was found that both of these biotypes have conserved the sequence for the ctxAgene while the sequence for the ctxB gene is slightly different between the two (5). There is a two base change seen at base positions 115 and 203. In the classical strains, cytosines are seen at these postitions while El Tor biotypes express thymines (5). These types of differences have been reliable markers in identifying V. cholerae biotypes and has helped convey the spread of strains in certain geographic locations. 
​Severely ill cholera patients will often be treated with antibiotics, but, unfortunately, some strains of V. cholerae have become antibiotic resistant. It seems as though strain resistance patterns evolve overtime, and, from 2007-2010, strains from Democratic Republic of the Congo were seen to be resistant to tetracyclines and ampicillin (4). Later on, from 2011-2012, many of these strains had become resistant to most antibiotics with the exception of cyclines and fluoroquinolones (4). Muchof this data has come from various genomic analyses and whole-genome sequencing. It’s quite apparent that this type of research is vital in understanding and controlling the effects of V. cholerae.
Thanks for listening. 
(1) Heidelberg, J.F. et al., 2000. Nature 406:477-84. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
(2) Hung, D.T. & Mekalanos, J.J., 2005. PNAS 102(8):3028-33. Bile acids induce cholera toxin expression in Vibrio cholerae in a ToxT-independent manner. 
(3) Lippi, D. & Gotuzzo, E., 2014. Clinical Microbiology and Infection 20:191-95. The greatest steps towards the discovery of Vibrio cholerae.
(4) Miwanda, B. et al., 2015. Emerging Infectious Diseases 21(5):847-51. Antimicrobial drug resistance of Vibrio cholerae, Democratic Republic of the Congo. 
(5) Son, M.S. et al., 2011. Journal of Clinical Microbiology 49(11):3739-3749. Characterization of Vibrio cholerae O1 EL Tor biotype variant clinical isolates from Bangladesh and Haiti, including a molecular genetic analysis of virulence genes.