Using genomics to track the dissemination of Yersinia pestis strains

1
Using genomics to track the dissemination of
Yersinia pestis strains
2
Transmission cycle of plague
A useful diagram illustrating the transmission
cycle of the plague by Neil Chamberlain
Transmission Cycles of Plague is available for
educational use from microbelibrary.org
3
Y. pestis and plague

• Nearly all plague infections are zoonotic with
  humans being accidental hosts
• Two different transmission cycles of Y. pestis
  infection
• zoonotic
• human to human
• Zoonotic (pertaining to animals) plague
  transmission due to the bite of infected fleas or
  contact with infected animals
• Zoonotic plague is further divided into
• urban
• sylvatic (rural) plague
• The second type involves the pneumonic
  transmission of infection between humans.

Information from Neil Chamberlain Transmission
Cycles of Plague www.microbelibrary.org
4
Sylvatic plague cycle

• Infection of wild mammals, (usually rodents),
  involves the passing of plague from mammal to
  mammal by fleas (Xenopsylla cheopis) infected
  with Y. pestis.
• Mammal to mammal passage of Y. pestis can occur
  by direct contact but is less common.
• Many of these mammals are relatively resistant to
  the lethal effects of Y. pestis infection.
• Squirrels, rabbits, and field rats can all serve
  as long-term reservoirs for the plague bacterium
  (enzoonotic plague).
• Other mammals are highly susceptible to the
  lethal effects of Y. pestis, resulting in rapid
  spread of plague among the animals with large
  numbers dying in the community (epizoonotic
  plague e.g., prairie dogs).
• If humans enter these areas they acquire the
  infection via flea bites or direct contact with
  infected animals.

5
Urban plague cycle

• Involves the passing of plague from mammal to
  flea to mammal.
• Mammal to mammal passage of Y. pestis can occur
  by direct contact but is less common.
• These mammals, frequently rats, are usually
  highly susceptible to the lethal effects of Y.
  pestis.
• As a result, large numbers of these animals die
  (epizoonotic plague).
• The infected fleas, lacking their more common
  rodent hosts, then bite and infect humans.
• Direct contact with infected animals can also
  result in human infection.

6
Vehicle of transmission Fleas

• The flea draws viable Y. pestis organisms into
  its intestinal tract. These organisms multiply in
  the flea and block the flea's proventriculus.
• Some Y. pestis in the flea are then regurgitated
  when the flea gets its next blood meal, thus
  transferring the infection to a new host.
• While growing in the flea, Y. pestis loses its
  antiphagocytic capsular layer.
• The male oriental rat flea, Xenopsylla cheopis,
  is the primary vector of plague in most large
  plague epidemics in Asia, Africa, and South
  America. Both male and female fleas can transmit
  the infection.

7
Human infections

• Following flea bites or by direct contact with
  infected animals usually result in bubonic
  plague.
• Most of the unencapsulated organisms are
  phagocytosed (ingested) and killed by
  polymorphonuclear leukocytes (PMNs or
  neutrophils) in the human host.
• A few bacilli are taken up by tissue macrophages.
  
• The macrophages are unable to kill Y. pestis and
  provide a protected environment for the organisms
  to synthesize their capsular and other virulence
  factors.
• The Y. pestis are taken to the draining lymph
  nodes by the macrophages.

8
Human infection cont.

• The encapsulated intracellular organisms then
  kill the macrophage and are released into the
  extracellular environment, where they resist
  phagocytosis by the PMNs.
• The Y. pestis multiply rapidly and cause a
  hemorrhagic inflammatory response making the
  lymph nodes hot, swollen, tender, and
  hemorrhagic.
• This gives rise to the characteristic black
  buboes responsible for the name of this disease
  bubonic plague.

9
Human infection cont.

• In a relatively short period of time the bacteria
  get out of the swollen lymph nodes and into the
  bloodstream.
• Then they infect the liver, spleen, and lungs.
  Bacteremia (bloodstream infection septicemic
  plague) occurs rapidly if not treated and
  mortality rates can be as high as 75.
• A severe bacterial pneumonia can develop
  pneumonic plague. Patients expel large numbers of
  viable organisms during coughing fits.
• Other humans inhale these viable organisms and
  develop pneumonia.
• The spread of Y. pestis via droplets from human
  to human is also known as the demic plague cycle.
  
• Spread from person to person can be very rapid
  and has in the past caused epidemics with
  mortality rates over 90, if untreated.

10
Historic 3 pandemics of plague
-Pandemic is defined as an epidemic that spreads
throughout the human population across a large
region such as a continent or worldwide -1st
pandemic 550 A.D. Confined mainly to Africa and
some parts of the Middle east -2nd pandemic
originated in Central Asia and spread via trading
routes into Europe (Killed 30-60 of European
population) -3rd pandemic started in 1850s in
Chinas Yunnan province and was confined mainly
to Asia
11
Identifying the causative agent of the plague
-French researcher Paul-Louis Simond postulated a
connection between human and rodent plague and
identified the flea as a possible vector -In
1894, in Hong Kong, bacteriologist Alexandre
Yersin isolated the responsible bacterium
(Yersinia pestis) and determined the common mode
of transmission -A short time later, Japanese
physician and researcher Shibasaburo Kitasato
independently identified the plague bacillus
(after mis-identifying the bacterium at an
earlier point).
12
As of 2010 there are 7 complete and 14 draft Y.
pestis genomes
Traditionally the strains are classified as
biovars (Antiqua, Mediaevalis, Orientalis, and
other) based on the following phenotypic
characteristics -Antiqua East Africa
(glycerol positive, arabinose positive, and
nitrate positive) -Mediaevalis Central Asia
(glycerol positive, arabinose positive, and
nitrate negative) -Orientalis Central Asia
(glycerol negative, arabinose positive, and
nitrate positive)  -other (ie Microtus,
Pestoides) not consistent for above phenotypes
13
Paleomicrobiology
-The prefix paleo comes from the Greek work
palaios, meaning ancient -Bacterial
colonization of dental pulp can occur during
bacteremia -Bacteremia (also known as plague
septicaemia with Y. pestis) is the presence of
bacteria in the blood
14
Extraction of bacterial DNA from dental pulp
-Some historians believed that a flu-like virus
and not Y. pestis was responsible for the 1st and
2nd pandemics -DNA detected in dental pulp
confirm that Y. pestis was the cause -Which
biovar(s) are most similar to the Y. pestis
strain(s) from the dental pulp from the corpses?
15
11 categories of virulence factors for Y. pestis
-Adhesion -Antigen -Effectors -Insect
effectors -Host barriers -Up regulated in human
plasma
-Iron acquisition -Phage component -Regulator -Sec
retion -Invasion
16
Known or putative virulence factors for Y. pestis
separated into categories (n148 genes)
17
Use of genomic tools to study Y. pestis
Concepts in this module that you will
address 1) Mutations that affect the production
of a fully functional gene product that has
phenotypic consequences (insertions, deletions,
single nucleotide polymorphisms SNPs) to study
the genes glpD, napA, and araC 2)
Paleomicrobiology investigation Determine which
biovar(s) have the most similar genes to the
amplified sequences from the dental pulp of 3
corpses. 3) Use of genome alignments Determine
an island that is unique to the four genomes for
strains that infect humans and is absent in Y.
pestis strain 91001. 4) Determine the
conservation of a virulence factor in the five
strains in the genome alignment. Determine if it
is a fully functional product in strain 91001.