Understand the basic concepts of epidemiology and what is meant by target population, sample size and what biases are important to consider
no. of occurancies of diseases in different groups of people
prevention of illness and managment of diseases patients via planning and evaluation of strategies
measurement of disease outcomes in relation to population risk
target population
group of individuals that the intervention intends to conduct research in and draw conclusions from
sample size & sample selection
-> too small: unrepresentative
-> systematic sampling errors due to placebo effect => random sorting
aetiology
comparing disease rates in groups w. different levels of exposure -> heterogenity
Provide details on why time trends are important for surveillance/monitoring and standardisation and quality control in epidemiological studies
monitoring/surveillance
increased/decreased incidence & changes in distribution
identification of emerging problems & assessment of effektiveness of interventions
changing standards of diagnosis and data recording -> successful integration and conversion
standardisation & quality control
long term
over decades
Describe briefly what is meant by infectious disease terms: endemic, epidemic, outbreak, pandemic and zoonosis
infectious disease
illness caused by microorganism w. spread potential btw. people or from animal to a person
endemic
baseline level of disease usually present in a community
epidemic/outbreak
sudden increase in no. of cases of a disease above normal levels in a region
-> outbreak: increase in a smaller geographical area
pandemic
epidemic spread across several countries/continents
zoonosis
transmission from vertebrate animal to people by direct contact or carried from animal to human by a vector
Know that John Snow is considered the ‘father’ of the epidemiology field and his work on the Soho Cholera outbreak
cholera epdemic in Soho in 1845
through asking district about symptoms accurance, duration, etc.
outbreak source public water pump found
oral-faecal transmission
Describe what is meant by burden of disease and how it is measured, and differences between high income and low to middle income countries (communicable/infectious vs. non communicable diseases)
health status of a population w. mortality + suffering focus
-> mortality + morbidity = burden of disease in DALY (Disability Adjusted Life Years)
=> loss of 1 year in good health
LMICs: higher communicable/infectious disease rates due to poverty, poor hygiene, no medication, no clear water & food, etc. (> 60 % diarrhoeal & other infections)
List some of the top bacterial infectious diseases globally and bacterial pathogens associated with historical pandemics
globally
tuberculosis
malaria
influenza
diarrhoeal disease
measles
historically
Y. pestis/plagues
HIV
SARS
Ebola
cholera
Provide details on what notifiable bacterial pathogens cause the biggest burden of disease in Germany (and understand how this differs from what might be seen globally and/or in LMICs)
SarsCoV-19
campylobacter ententis
norovirus gastroenteritis
-> due to better health care system not so much due to hygiene but more like lifestyle choices (undercooking BBQ) or seasonal common bacterial infections or hospital gained
Describe the chain of infection and provide examples of transmission routes for infectious diseases (e.g. faecal-oral route, air-born/water-droplets)
showing spread of infections and possible points to break chain of transmission
infectious agent
reservoir
portal of entry/portal of exit
model of transmission
direct contact
indirect contact (e. g. zoonosis, Rickettsia)
droplets (Mycobacterium tuberculosis)
airborne (Mycobacterium tuberculosis)
fecal-oral (Salmonella, E. coli)
susceptible host
List approaches that can be used to break the chain, and thus reduce spread and/or infection rates
good food preparation
good hygiene
treating drinking water
quarantine
testing
protected sex
clean surgical equipments & needles
education on infection prevention
Provide an basic overview of serotyping and phage typing methods using Salmonella as an example
Serotyping
testing for 3 major antigens to gain more insight and compare to Kaufman-White reference catalouge for identification
-> Vi, O (somatic), H (flagellar)
Phage typing
specific targeting of virus by phages -> using lyse ability for particular strains
usual issues w. phenotypic methods, reproducibility, etc.
Understand how molecular tools are replacing phenotypic methods in epidemiology and their general advantages
simplify, accelerate, precise detection & identification
-> first step in data stratification via taxonomic classification
subtyping for knowledge gain of old & emerging infectious diseases
combination of genetic, phenotypic, spatial & temporal data
-> evolution of virulence & phenotypic traits over time
genomic differences among different lineages/clones of same species
List some of the older and newer methods used in molecular epidemiology (also see previous lectures for details)
older
newer
PFGE
WGS
Gram-staining methods
MALDI-TOF-MS
Briefly explain how molecular approaches allow insights into infectious agents, pathogenesis and transmission
specific genome sequence for specific virulence factor, phenotype etc.
identification of sources/reservoirs
circulation of microbial strains -> problematic/not problematic (spread, virulency, drug resistance, regional)
identification of transmission probability (basic reproductive no. - R0)
identifcation of between-community transmission patterns
-> phylogenetic, sociodemographic, behavioral
Describe what is meant by genomic epidemiology and describe the terms pan-, core- and accessory-genomes
discipline of mapping, sequencing, analysing and comparing genomes
-> antibiotic-resistance genes + virulence traits relation, monitoring
pan-genome: entire gene set of all strains of a species
core-genome: genes present in all strains like housekeeping genes, regulatory functions
variable/accessory genome: genes not present in all strains, present in a handfull or unique, including mobilomes
Briefly describe a typical bioinformatics work flow for processing WGS data
Understand how SNP/SNV data is used in genomic epidemiology
detection of small and frequent changes in genome
mapping & identification of differences from reference genome w. high resolution via SNP
-> phylogenetic reconstruction
species or subspecies specific differences via SNVs
true point mutations (not from sequencing errors etc)
Briefly describe the principles behind core- and whole-genome MLST for typing bacterial pathogens
standardised and user-friendly bioinformatics approaches for typing bacterial pathogens
-> definition of a scheme
=> large data collections of genomes of a species required
core-genome MLST (cgMLST)
allele-profile generation via gene-by-gene method and genome assembly to a scheme of core genes
-> pre-defined threshold
—> dep. on population structure + diversity of species in question
whole-genome MLST (wgMLST)
extension of cgMLST via set of accesory loci
Enterococcus faecalis
Listeria monocytogenes
Chlamydia trachomatis
Vibrio cholerae
Klebsiella pneumoniae
Shiga toxin-producing E. coli
Describe how and why genomes are annotated and some of the bioinformatic tools that are used to determine erotypes/serovars of pathogens and/or understand AMR determinants
prediction of gene functions
organism’s functional capability
annotation based on gene ontology, reconstruction of metabolic pathways, assigning gene functions based on functional reconstruction
querying against specialised databases
CARD (virulence factors + AMR)
Kaptive/Enterobase (serotyping information fro mWGS data)
List two public health platforms currently used in tracking/tracing bacterial pathogens
PulseNet (US, detection of foodborne infections causing outbreaks)
IRIDA project (Canada-wide, freely available, genomic epidemiology analysis platform)
Understand how different genomic approaches have been used in public health situations with a focus on the presented case studie of Salmonella
Salmonella
identification and characterising via qPCR, biochem. properties, serology, phage-typing
identification of (sub-) species via PHE KmerID + Enterobase
comparing of eBG/ST w. PHE database -> discovering relatedness
determination of AMR via reference mapping
Understand how different genomic approaches have been used in public health situations with a focus on the presented case studie of Clostridium perfringens
Clostridium perfringens
typing of toxins
distinguishing btw sstrains within a single species
reconstruction of transmission routes/outbreaks -> narrow down search area => identification of source (foodborne, so food provider)
detection of emerging lineages
recognising epidemic clones w. specific pathogenicity
Understand how different genomic approaches have been used in public health situations with a focus on the presented case studie of Yersinia pestis
Y. pestis
ancient DNA analysis
predominantly environmental + opportunistic gastroenteric pathogen => aquisation of few virulence factors enough
interference w. spread through diversity/regional analysis
Understand how different genomic approaches have been used in public health situations with a focus on the presented case studie of Staphylococcus aureus
Staphylococcus aureus
daily surveillance of nosocomial, hospital-aquired infection -> overlaps in time, place and other factors linked together
assessment of probability of outbreak & need for further investigation
family clustering to identify patient zero
Understand how different genomic approaches have been used in public health situations with a focus on the presented case studie of AMR
AMR
rapid spatiotemproal evolution of AMR w. repeating patterns in emergence and spread od amr
-> expansion, geographical dissemination -> aquisation of specific AMR determinant
=> evolutionary process prediction, minimisation of spread via strategies
mobile AMR genes as cause identified
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