What is epidemiology?
The study of the distribution and determinants of health-related states or events in specified population and the application of the study to control of health problems (J.M. Last 1988)
What do you call the study where you compare disease rates in groups with differing levels of exposure?
etiology
What is
Illness caused by microorganisms, such as bacteria, viruses, parasites or fungi, that can spread from one person to another or from an animal to a person?
Describes the baseline level of a disease usually present in a community?
An increase, often sudden, in the number of cases of a disease above normal levels in a region. An outbreak sometimes refers to an increase in a smaller geographical area?
An epidemic that has spread across several countries or continents and usually affects a large number of people?
A type of infectious disease that originates in vertebrate animals and moves to people. It can be spread by direct contact or carried from animals to humans by a vector such as a biting insect?
Name examples for World’s deadliest infectious diseases (2018).
Tuberculosis
Malaria
Influenza
Diarrhoeal disease
HIV/AIDS
Measles
What is Gastroenteritis - Campylobacter?
What are the links in the chain of infection?
• infectious agent
• reservoir
• portal of exit
• model of transmission
• portal of entry
• susceptible host
What are ways of transmission?
What is Bacteriophage susceptibility?
ability of a given phage to lyse a particular strain
What is the first step in data stratification of bacteria isolated during epidemiology investigation
Taxonomic classification (species level)
• 16S rRNA vs. WGS
Multiple techniques have been employed to assay genomic differences among different lineages or clones of the same species • e.g.
Pulsed Field Gel Electrophoresis (PFGE) and Multi-locus sequence typing (MLST)
Identification of infectious diseases’ sources/reservoirs
is a
Circulation of microbial strains
Identification of infectious diseases’ transmission probability
Identification of between-community transmission patterns
Genomics
Genomic elements that shape the bacterial community and are used to ‘define’ species
entire gene set of all strains of a species
includes core genome and variable/accessory genome
genes present in all strains
typically includes housekeeping genes for cell envelope or regulatory functions
genes not present in all strains of a species
includes genes present in two or more strains or even genes unique to a single strain only
e.g. genes for strain specific adaptation such as antibiotic resistance • the mobilome e.g. plasmids may be included in this genome
What is whole-genome MLST?
MLST: multilocus sequence typing
core-genome MLST (cgMLST) or whole- genome MLST (wgMLST)
core-genome MLST …
whole-genome MLST …
E#Give examples where for several bacteria, serotype and capsule type information can be derived from WGS data
e.g. Kaptive and Enterobase
Whatis the integrated Rapid Infectious Disease Analysis (IRIDA) project
Canada-wide public sector consortium to develop a freely available, genomic epidemiology analysis platform
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