Paleomicrobiology Flashcards
Y. pestis
- disease
- 3 major human pandemics
- acquired via
- most common form
plague
Justinian
Black death
Modern
flea bites
- host = rodents
Bubonic plague
Y. pestis biovars
- define
- differentiated how?
= variant prokaryotic strain that differs physiologically or biochemically from other strains
sub lineage attributed as the cause of major pandemics
metabolic traits
Where did Y.pestis originate from?
Where did it spread to?
Justinian
- from E/C Africa
via Egypt to Med
Black death
- central Asia
via Caspian se to Europe
via silk routes
Modern
- China
via Hong King through shipping globally
Pneumonic plague
- process
- enters via eyes, nose, mouth
- pneumonia in lungs
(usually 100% mortality) - exit via eyes, nose, mouth
(v contagious)
Bubonic plague
- process
- enters via rat flea bite
- spreads via lymphatic system
- buboes
pneumonia
internal organ haemorrhage - exit via eyes, nose, mouth
(v contagious)
how does plague spread?
where do bacteria multiply?
overwhelming infection can lead to?
via lymphatics within macrophages
extracellularly
- cell lysis in lymph nodes, liver + spleen
multi-organ failure
pseudogene
where sequence suggests a gene in non-functional
e.g. STOP codon in middle of sequence
Who sequenced the Y. pestis genome?
Parkhill et al
What were the findings of the Y. pestis sequence?
- in terms of ancestry?
loss of many genes associated w/ ancestral enteropathogenic niche
- enterotoxins + adhesins
- many present as pseudogenes
(150 found in total)
What were the findings of the Y. pestis sequence?
- IS elements
- acquisition
- plasmids
large no.s of IS elements
- contribute to gene loss/activation
acquisition of insect toxin homologues
- adaptation to insect vector host?
several plasmids
- some common to genus
- some specific to pestis carrying virulence determinants
Y. pestis evolution
acquires series of plasmids
-> improve efficiency and virulence
e.g. virulence plasmid + phospholipase D plasmid for flea survival
+
chromosomal genes for biofilm formation + insect toxins from bacteria in soil or gut
Y. pestis paper by?
Prentice et al (2007)
black death
- killed..?
- entered country via?
- caused by?
killed ~50% of population in 1948-1949
port in Weymouth
Y. pestis
Controversy surrounding Y.pestis, Justinian + black death plagues
high mortality rates + clinical manifestation differ from modern Y. pestis
- if same pathogen, why don’t we see modern pandemics?
inconsistent PCR-based detections in ancient samples
Y. pestis
- genomic make up
chromosome + pCD1
- shared with non-pestis ancestors
pMT + PCP1 plasmids
- Y. pestis-specific plasmids
PCP1 plasmid
- features (ideal for things to look for in an ancient sample)
Y. pestis specific
high copy number (100x more than chromosome)
paleomicrobiology
- what is it
studying the genomes of ancient samples
paleomicrobiology
- major technical issues
DNA degraded into short fragments
pathogen DNA = tiny proportion of total
direct sequencing of pathogen DNA not possible
DNA extraction from ancient samples
extract pulp from molar
-> extract DNA
why are molars favoured samples?
large
often intact
enamel used for radiodating
preventing contamination
- contamination sources
- preventative measures
- microbial flora from burial site
- from lab
- cross-contamination
> gloves
UV irradiation
run 1 -ve control for 3 samples
techniques for detecting ancient pathogens
electron or optical microscope
imumunodetection
isolation + culture
PCR-based detection + sequencing
extracting out pathogen DNA (Y. pestis) from sample
- cut PCP1 plasmid sequence up into fragments
- PCP1 backbone synthesised ‘bait’ DNA
(sequences stuck to beads) - hybridise bait w/ extracted DNA
- samples eluted + sequenced using net gene sequencing
black death sequence
- techniques used
- findings
used array-based capture
- sequence using next gen
almost identical to Y.pestis strains that cause bubonic strains today
- no unique traits obvious
- perceived increased virulence of disease may not have been du to bacterial phenotype
black death
- phylogenetics
Black death strain sits at root of evolutionary tree (17 contemporary strains of Y. pestis)
-> black death strain = progenitor of present Y. pests is strains
what caused the high mortality of black death?
> malnutrition + host susceptibility
- poor weather + subsequent crop failures in years before
> pneumonic vs bubonic plague
- pneumonic ~95% fatality rate transmitted via sneezing (human-human transmission)
- bubonic ~ 45% fatality
transmitted via flea bites
> no treatments available
Justinian plague
- when?
- where?
- deaths?
AD 541-542
Eastern Roman Empire affected
no reliable no. of fatalities
Justinian plague
- sequence
tooth pulp from 2 skeletons
generated Y. pestis genome
compared to 131 sequenced Y. pestis strains from later pandemics
- construct phylogenetic tree
lineages that cause Justinian plague + black death were independent emergences from rodents into humans
Tuberculosis (TB) in a mummy
extracted lung tissue
sequenced in a single Illumia MiSeq run
<1% of reads aligned to human genome
8% aligned to M. tuberculosis reference strain
comparative genomics
identify SNPs that describe genetic variation among population
use only common DNA
use SNPS to infer phylogenetic tree
-> depicts evolutionary relationships among samples
molecular clock
DNA + protein sequences evolve at rate relatively constant over time + among different orgs
can be calibrated using temporal info from aDNA (as samples can be dated)
