Module 1: Glossary

Glossary of Key Terms for Module 1

  • 7PET: the name of the current pandemic lineage of Vibrio cholerae. 7PET is the lineage of V. cholerae that has been responsible for all major outbreaks and epidemics of cholera since the 1960s. ‘7PET’ is short for ‘Seventh Pandemic El Tor’ because 7PET has caused the 7th historically recorded cholera pandemic, and isolates of the 7PET lineage have the El Tor biotype (a laboratory phenotype).

  • Biotype: a subgroup of V. cholerae bacteria that display a particular phenotype upon a certain set of biochemical laboratory tests. The biotype phenotype has been used historically to predict whether isolates of the V. cholerae causing a particular outbreak belong to the epidemic-causing 7PET lineage.

  • Biotype variants: biotypes which differ in a small number of the laboratory test results that are used to identify the El Tor biotype.

  • Cholera: a disease characterised by acute watery diarrhoea, which is caused by ingestion of Vibrio cholerae.

  • Cholera case: a patient diagnosed with cholera using standard criteria; see the WHO 2023 guidance and definitions for what they consider ‘a suspected cholera case’ and ‘a confirmed cholera case’.

  • Cholera-endemic area: see ‘endemic’.

  • Cholera toxin (Ctx, CTX, or CT): the most important virulence factor of Vibrio cholerae; cholera toxin triggers acute watery diarrhoea.

  • Clone: a group of cells produced asexually from one ancestor, to which they are genetically identical (or nearly identical).

  • DNA (Deoxyribonucleic acid): the molecule that carries genetic information of an organism.

  • Endemic: according to the CDC website, an ‘endemic’ refers to the constant presence and/or usual prevalence of a disease or infectious agent in a population within a geographic area. The WHO defines a ‘cholera-endemic area’ as “an area where confirmed cholera cases were detected during the last 3 years with evidence of local transmission (meaning the cases are not imported from elsewhere)” (WHO 2024, accessed 18th July 2024).

  • Epidemic: an unexpected increase in the number of disease cases in a specific geographical area (definition from the CDC website). An epidemic is considered to occur of a larger geographic area than an outbreak. See the WHO’s detailed technical guidance (WHO 2023) for precise definitions of what they consider to be ‘a suspected cholera case’, ‘a confirmed cholera case’, ‘a suspected cholera outbreak’, ‘a probable cholera outbreak’, or ‘a confirmed cholera outbreak’.

  • Epidemic-causing lineage of V. cholerae: a V. cholerae lineage that can cause a very large increase in the number of cases of diarrhoeal illness caused by V. cholerae in a particular town/city/region over a relatively short period of time. The 7PET lineage is the only epidemic-causing lineage of V. cholerae at present.

  • Gene: a segment of the DNA of an organism, typically hundreds or thousands of base-pairs in length. A very common type of gene is a protein-coding gene, which is a stretch of DNA which encodes (specifies the production of) a particular protein.

  • Genome: all the genetic material present in a cell or organism.

  • Isolate: an organism collected from a specific sample material e.g. from a stool sample or from river water.

  • Lineage: a group of organisms belonging to the same bacterial species, and that are genetically more closely related to each other than other members of the same species. There can be many lineages within a particular bacterial species. Different lineages of a bacterial species may have different biological characteristics, such as the ability to cause more severe disease. (Adapted from a definition by the National Cancer Institute.)

  • Metadata: non-genetic data that has been collected for bacterial isolates, such as the exact location or date of collection of the isolates.

  • Mutation: a change in the genetic material of an organism, caused by a change its DNA (e.g. the change of single base-pair in its DNA).

  • Non-epidemic lineage of V. cholerae: a V. cholerae lineage that is not an epidemic-causing lineage (see ‘epidemic-causing lineage of V. cholerae’). There are many non-epidemic lineages of V. cholerae.

  • O-antigen: a component of the surface lipopolysaccharide (LPS) of Gram-negative bacteria such as V. cholerae.

  • Outbreak: an unexpected increase in the number of disease cases in a specific geographical area (definition from the CDC website). An outbreak is considered to occur of a smaller geographic area than an epidemic. See the WHO’s detailed technical guidance (WHO 2023) for precise definitions of what they consider to be ‘a suspected cholera case’, ‘a confirmed cholera case’, ‘a suspected cholera outbreak’, ‘a probable cholera outbreak’, or ‘a confirmed cholera outbreak’.

  • Pandemic: an epidemic that has spread over several countries and usually affects many people (definition from the CDC website).

  • Pandemic lineage: a lineage of a bacterial species that is causing or caused a pandemic of a disease.

  • Phylogenetic tree: a diagram that depicts the evolutionary relationships between particular organisms, and how they descended from a common ancestor.

  • Serogroup: a subgroup of V. cholerae bacteria that share the same distinctive surface structure in their O-antigen, and so have the same laboratory phenotype when exposed to host antibodies specific for that particular type of O-antigen.

  • Strain: see ‘lineage’. Also used to refer to a single bacterial isolate that has been cultured over time in a laboratory.

  • Toxigenic V. cholerae: V. cholerae that produces the cholera toxin. Isolates of the 7PET lineage are toxigenic, but a small fraction of isolates of some other lineages of V. cholerae are also toxigenic.

  • Variant biotype: See ‘biotype variants’.

  • Viable but Non-Culturable (VBNC): a dormant state that many bacterial species enter under unfavourable conditions such as low temperature and low nutrient conditions.

  • Vibrio cholerae (V. cholerae): a curved Gram-negative rod-shaped bacterium that causes the disease cholera.

  • Virulence factor: a protein (or protein complex) that helps a bacterium to colonise a host at the cellular level.

  • WASH: ‘water, sanitation and hygiene’. These are barriers to the transmission of cholera.

  • Whole genome sequencing (WGS): the process of determining the DNA sequence of an organism’s whole genome.

Vibriowatch

In later modules of this course, you will learn how to carry out bioinformatics analyses using Vibriowatch, as well as other bioinformatics tools. If you already have cholera genomic data to analyse, and want to get going quickly, you may also be interested in our Vibriowatch tutorial.

Contact

I will be grateful if you will send me (Avril Coghlan) corrections or suggestions for improvements to my email address alc@sanger.ac.uk

Acknowledgements

Contributors to this course: Avril Coghlan, Matt Dorman, Ismail Bashir, Anne Bishop, Amber Barton, Stephanie McGimpsey, Jolynne Mokaya, Nisha Singh, Nick Thomson.