MolEpi Applications Flashcards
Case study: Germany E.coli
APPLICATION: outbreak investigation.
Cases of enterohaemorraghic E.coli in Germany associated with raw vegetable consumption.
Patients interviewed, many had been to same a hamburg market and had these cucumbers of Spanish origin from which E.coli was isolated. Spain blamed, batch sold no longer.
Further genetic analysis, found the patient e.coli isolates actually differed from that of the cucumbers and they had unique sensitivity profile, also different to that of cucumbers.
Would not have been possible without MOL epi.
Case study: SARS
APPLICATION: Identify new pathogen, outbreak investigation
Mystery pneumonia (inflamed air sacs, fluid): April 2003, 4300 cases, 250 deaths, 25 countries.
Virus? chlamydia? animal or human origin?
Took patient cells, coronavirus found.
Patients with SARS consistently tested positive for coronavirus RNA (tested by qPCR of a conserved coronavirus region).
But where did it originate?
Viral genes sequenced, no differences found (no branch length) comparing human and civet isolate sequences.
Civets COULD be natural hosts or reservoirs -> spillover to human or just a one-time cross over then transmission between humans?
As a result, civets were culled.
Also looked at bats. There is genetic diversity of coronavirus within bats, suggesting bats and corona have been coevolving.
Case Study: MRSA
APPLICATION: Source of pathogen. Colonisation vs infection.
MRSA predominantly a hospital-acquired (healthcare-associated) infection. many bacterial species can be hospital-acquired.
Increase in number of deaths MRSA contributed to in UK.
S.aureus part of many peoples normal flora. Up to 80% carry in their nose but can be deadly in bloodstream.
1960 - S.aureus acquired resistance cassette making it bind with low affinity to b-lactams.
Until 1990 - most MRSA infections hospital-related BUT numbers from within communities instead of healthcare setting have increased.
Do surgical patients get infected by their own
S. aureus flora, or by different strains particularly
adapted to infect and cause disease?
Comparing blood and nasal isolates of patients, a high percentage were infected with own skin S.aureus flora and some infected from other sources. Compared DNA fingerprints (PFGE).
Case study: Anthrax
APPLICATION: Forensics
Letter sent to a republican politician had anthrax. Many people exposed.
22 involved in outbreak, 5 died.
Source of anthrax?
- looked at postmark (new Jersey)
- Looked if similar letters sent to others.
- Compared letter strain to reference strains via multi-locus variable number tandem repeat analysis (MLVA) Like a barcode. Identical strain used in US army medical centre.
Anthrax = bacterial =Bacillus anthrasis
Normally animals, sporadic in humans from animal handling and spore inhalation. Zoonotic.
Case Study: AIDS origin
It was feared that the polio vaccine was the source of HIV infections in Nigeria and thwarted vaccination efforts.
Contaminated polio vaccine brought HIV to Nigeria in 50s? A book alleged vaccine was cultured with chimp cells which were SIV-contaminated. Sites of vaccination around the time do correlate to the HIV outbreak areas. Three studies have since refuted this claim.
Analysed RNA SIVcpz and HIV sequences.
4 chimp sub-species - 2 of which have SIV infections. Upon phylogenetic analysis, HIV nested within the SIV from troglotydes (central Africa), not schweinfurthii (East Africa). SIV from Kisangani (purported origin of polio theory) clustered with schweinfurthii.
Therefore, SIV from Kisangani, not progenitor of HIV.
Case Study: Covid
A surveillance system for “pneumonia of unknown etiology”, established in
2003, investigates this outbreak: lessons learned from previous epidemics
(SARS-CoV).
Only 1% of cases were linked to animal markets. Therefore, likely transmission between people?
Responded by mass sequencing, collaboration and pooling of data.
Many groups and consortiums established March-April 2020 worldwide.
Massive sequencing and genome submission to public databases. By October 2020: > 100,000 SARS-CoV-2 genomes available. If patient was positive by qPCR, whole genome sequenced.
Global outbreak, need global “level” of marker.
