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GENOMIC EPIDEMIOLOGY - Coggle Diagram

- - - - online data archives
      - centralised resources
      - global collaboration
  - - - outbreak investigations
      - transmission between cases
      - source of infection (food item, water source, etc.)
    - - surveillance (space-time clusters)
      - chains of transmission
      - distinguish relapse and reinfection
      - mixed infections
    - - population structure and prevalent strains
      - phylogeography
      - identify determinants of distribution
        
        virulence factors
        
        antibiotic resistance
      - evolution of infecting strain
      - emergence of new pathogens or virulent clones
      - epidemic growth rate
    - - strain variation
      - genome variations
      - time-scale emergence and frequency
- - - - 3 simultaneous carriage isolates had v similar antiobiograms (P11/12 & P13)
      - infection control reviewed MRSA data for prior 6 months
        
        13 more infants with MRSA positive screens (P1-10), 3 not shown
        
        8 (P2, P4-10) had same antibiograms as P11/12
        
        P1,3 and 3 others had dissimilar antibiograms, were discounted
        
        11 cases linked (P2, P4-13)
      - isolates from 3 discrete periods
    - - a further patient, P14, screened MRSA
      - positive, with same antibiogram after this
    - - v closely related to major lineage ST22
      - 3 others were ST1, ST8 and ST22
      - P1 and P3 not considered linked due to differing antbiograms, but WGS shows them to be ST2371
    - - All MRSA isolates since the start of the outbreak traced
        
        15 had similar antibiograms to ST2371
        
        further isolates after P14 also analysed, 4 more potential ST2371 detected
        
        10/19 were ST2371, WGS showed closely related to SCBU patient isolates
      - What was the transmission network for this?
        
        records gave clear link between 9 of the isolates and the SCBU outbreak
        
        infant to mother trasmission
        
        mother to mother in post natal ward
        
        P16/17 had been SCBU patients during the outbreak by screened as MRSA-negatice at the time
        
        2 mothers contact with mothers of MRSA+ve infants from SCBU
        
        P24 mother of an infant, P18, who was on SCBU for 5 days but thought to be MRSA negative
      - further case isolated 4 days post deep clean
        
        how?
        
        154 staff members screened
        
        1 positive for ST2371
        
        relieved of clinical duties and decolonised
        
        multiple colonies from this person analysed by WGS
        
        clear link to SCBU outbreak
        
        demonstrates use of WGS in true outbreak investigation
        
        confirmation of links
        
        ability to trace clone evolution during outbreak
        
        study is mainly retrospective
        
        next step is for routine WGS of all isolates
- - - - serotyping
      - phage typing
      - PFGE
        
        still very widely used even though old
      - VNTR
      - MLST
        
        multilocus sequence typing for strain differentiation
        
        genes are picked that we know are in all strains and not connected through Linkage disequilibrium
        
        same numbers = same SNPs
        
        salmonella typhi phylogeny - MLST
        
        almost no variation among strains
        
        seven genes picked don't have significant discriminatory power within the organism
        
        have to use whole genome - whole genome sequencing
    - - identification of epidemiologically linked isolates
      - related cases share the same strain
      - unrelated cases have a different strain
      - unrelated isolates may appear the same depending on ability of typing method to discriminate and relatedness of isolates
    - - as sequencing costs fall
        
        whole genome sequencing has replaced other typing approaches
        
        genomic epidemiology replaces molecular epidemiology
        
        Improving understanding in various ways
- - - - common commensal organism in animals and birds
      - contaminated food, untreated water, unpasteurised milk
      - contact with infected animals
      - can be spread from person to person by the faecal-oral route
    - - diarrhoea (may contain blood or mucus)
      - fever
      - nausea, vomiting
      - abdominal pain
    - - meningitis
      - urinary tract infections
      - septicemia
      - reactive arthritis (rare, often short term)
      - Guillain-barre syndrome (rare type if paralysis)
    - - several potential sources
    - - risk assessment
      - case control studies
      - outbreak investigation
      - natural experiments
        
        unique opportunity to assess the contribution of chicken quantitatively was presented by the "dioxin crisis" in Belgium in 1999 which led the authorities to remove all domestically produced poultry products
        
        comprised approximately 1/2 poultry available at retail, with imported meat remaining available
        
        40% reduction in the incidence of human campylobacteriosis after this withdrawal