Pandemic Cholera: Origins and Implications

Sahaj Shah ’21

On February 5, 2018, Jesse Shapiro presented his research findings on the origins of pandemic choleric strains from the environment, and their fate within patients to the Joint Microbiology & Immunology and Biological Sciences Seminar at the Geisel School of Medicine. Professor Shapiro is the Canada Research Chair and Assistant Professor at the Department of Biological Sciences at the Université de Montréal, interested in identifying signatures of positive natural selection in microbial genomes, particularly in Vibrio.    

Credit: Amélie Philibert, UdeM.

Credit: Amélie Philibert, UdeM.



Cholerae made an early appearance in the Soho district of London, where it was first recognized as a waterborne pathogen that caused severe diarrhea and death, if not treated in time. Cholera is easily preventable with proper oral rehydration, yet it still remains a global threat to public health, especially in the developing regions1. Within the V. Cholerae species, there are a genetically diverse collection of aquatic bacteria. One of them is the PG ‘pandemic genome’ group that, as the name suggests, has been responsible for the past seven cholera epidemics. In a regular cycle, the bacteria either perishes due to selection pressure from the environment or survives via horizontal gene transfer, where phages (viruses that infect bacteria to replicate) can integrate directly into the bacterial genome cycle. Virulence factors, molecules produced by the bacteria to enhance their ability to inhabit a niche, are also important in trying to understand the emergence and evolution of these pandemic genes.

To help us understand the origin and the rise of pandemic clones, particularly the PG group, researchers use genome-wide phylogeny, studying relationships among genes across species. John Smith and colleagues at the University of Sussex first noticed an interesting result on population structures of clonal bacteria, where he observed a uniform network to the emergence of different strains, except one pandemic offshoot, as seen in Figure 1. This offshoot, emergence of a string of different strains, is seen as the point of origin for the pandemic genes. Occasionally, one highly successful individual would arise and increase rapidly in frequency, producing a pandemic clone2. But why just one single origin? Since there are two virulence factors in play, why not different places of origin? What are the chances of emergence from multiple origins? And finally, how does the diversity of strains relate to treatment in human patients? These are the questions that Shapiro and his team seek to answer.

Figure 1: Representation of epidemic structure (Source: Smith et al)

Figure 1: Representation of epidemic structure (Source: Smith et al)

To find properties of PG that set it apart for pandemic success, Shapiro’s lab collaborated with Salvador Almagro-Moreno, a post-doctoral fellow at the Geisel School of Medicine, and aligned 22 genomes known for V. Cholerae diversity. Seven of these were from the PG group and 15 were from environmental genomes. Alignment of genomes infer phylogeny, as seen in Figure 2. The phylogeny of 22 V. Cholerae genome revealed an interesting result. The core is star like, but the PG group is only found on one of the branches, rather than being set apart. This led to two different questions: 1) What is the significance of the PG branch, just a small branch, that eventually yields pandemic success? 2) Are there virulence adaptive polymorphisms (VAPs) or other factors necessary, in addition to PG, for an epidemic? They hypothesized that the PGs had an environmental ancestor that contained alleles of the core genes, called VAPs, that essentially enhanced chances of survival for pandemic success.

In an effort to answer those questions, Shapiro and his team focused on mixed single nucleotide polymorphisms (SNPs), shaped by natural selection and found in both the environmental genome (EG) and PG. They plotted SNPs per gene versus genome position and found five candidate genes as candidate VAPs. Among the candidate VAPs, ompU gene was prevalent among the data sets that branched closer to the PG than core phylogeny, as seen in Figure 2 above, making it a compelling candidate.

Figure 2: Phylogeny of V. cholerae genomes. (Source: Shapiro et al)

Figure 2: Phylogeny of V. cholerae genomes. (Source: Shapiro et al)

This lead to the hypothesis that the PG-like alleles present in the environmental strains might confer properties conducive to virulence.

To test their hypothesis, Shapiro’s team ran biofilm assays and found that ompU and other PG genes have the same pattern of lower biofilm formation. This indicated the phenotypic similarity in the effects of PG genes and ompU. Several other tests were made to further identify candidate ompU alleles. In a recent paper, Shapiro and colleagues found several interesting results. First, they found VAPs in the environment and identified eight ompU candidate genes. Interestingly, they also developed and designed a similar approach to identifying the genetic basis of virulence that is applicable to other bacteria responsible for epidemics (e.g. E. coli, Yersinia pestis) with the correct core genomic background. In the stool samples obtained from patients, all genomes were found to be isogenic except mutations in ompU3.

Implications of this research by professor Shapiro and his team are far and wide. Some follow up leads that Shapiro and his team want to follow are: 1) Why are VAPs maintained at the environment? and 2) Is pathogen emergence limited by genetic architecture (qualitative traits) or by niche availability (the physical environment it occupies)? For example, a niche in Haiti would look different than a niche in the United States.


1) World Health Organization. (2018). Cholera. [online] Available at: [Accessed 11 Feb. 2018].

2) Smith, J., Smith, N., O’Rourke, M., & Spratt, B. (1993). How Clonal are Bacteria? Proceedings of the National Academy of Sciences of the United States of America, 90(10), 4384-4388. Retrieved from

3) B. Jesse Shapiro, Inès Levade, Gabriela Kovacikova, Ronald K. Taylor and Salvador Almagro-Moreno. Origins of pandemic vibrio cholerae from environmental gene pools. Nature microbiology Volume 2, Article Number: 16240, 19 October 2016.