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Selective pressures
factors in the environment that influence which organisms survive and reproduce as a result of gene gain, loss, rearrangement, mutation etc
Selective pressure with a net positive effect
will be maintained
Selective pressure with a net negative effect
will be removed from the population
Microbial genomes can change rapidly via
SNPs (Single Nucleotide Polymorphisms)
Genomic epidemiology can be used for __ _
trace the zoonotic or geographic origins of an outbreak, investigate transmission chains, or estimate when an epidemic started
Vertically and horizontally inherited DNAs have
different evolutionary histories
For the most part, DNA in core chromosomes in inherited
Vertical gene transfer
Evolutionary history should be determined from what type of gene transfer
Vertically inherited DNA
The Haitian V. cholerae isolates were essentially identical, consistent with them being clonally-related. What does this mean and what is the implication of this regarding transmission?
It indicates that the isolates share a common ancestor, suggesting that the outbreak is due to a single source of infection
Cholera climatic hypothesis
non-pathogenic V. cholerae, indigenous in Haiti, was given the right
environment and evolved into a pathogenic strain
Cholera human transmission hypothesis
pathogenic V. cholerae was introduced to Haiti by individuals (e.g., UN aid workers) who had been infected in their home countries
Are mobile genetic elements taken into account when discussing common ancestry
No. They primarily involve horizontally inherited genes.
Regarding the 2010 cholera outbreak in Haiti, what
genomic data supported the conclusion that the
outbreak occurred following the transmission of
pathogenic V. cholerae from Nepalese aid workers?
Haitian and Nepalese V. cholerae isolates had
essentially identical core genomes
mobile genetic elements
are genetic materials that can move between different locations within a genome or between different organisms
Mobile genetic elements normally encode
Clusters of genes that encode virulence
Virulence factor-encoding mobile genetic elements are often
Highly variable in both their presence and gene content between isolates.
Symbionts and avirulent relatives of pathogens often contain a few of the same virulence- associated genes because ____
They have different advantages that can help them survive in the environment (not just in a host) like escaping amoebas
Legionella virulence factor IcmT facilitates escape of the bacterium from human macrophages, so why would a nonvirulent strain have this mobile genetic element?
Although they don’t escape macrophages, the gene can help them escape from amoebas
If a strain of S. aureus doesn’t have the exfoliating toxin mobile gene element then ___
It cannot cause staphylococcal scalded skin syndrome
Gut symbionts can serve as reservoirs for ___
antibiotic resistance genes
Why do livestock and human gut symbionts harbor so much resistance
As the host is exposed to antibiotics, we are selecting for resistant bacteria in the body
Why have specific regions of fungal genomes have been identified that show evidence of accelerated rates of evolution?
a consequence of repeat-driven genome expansion
and recombination (microbes with high amounts of repeat DNA)
Are virulence genes usually conserved?
No, variation within virulence genes in common
Any thoughts on why genes
encoding cell surface proteins
often show this variability within these virulence genes?
Immune evasion
Genome reduction and pseudogenes are common in ___
pathogens
generalists
Can infect multiple host types
Host adapted
infect specific host species
If one isolate has a lot of pseudogenes compared to another, what does this mean for host specificity?
More pseudogenes means more likely to be host adapted and very limited to that niche. Other isolate may be generalist
The greater number of pseudogenes present in host-adapted strains indicates that, compared to generalist strains
host-adapted strains are under less-stringent selection for a variety of genetic functions
Why do host adapted strains undergo gene reduction?
Loss of unnecessary genes that would just be a metabolic burden, also mutations are more likely to be deletions since they weren’t needed anyway.
Many antibiotic-resistance traits are encoded by
A single gene that can be easily identified
Any potential issues in using the
presence / absence of resistance
genes to determine resistance?
may not always correlate with phenotypic resistance due to factors such as gene regulation, mutations, or the presence of other compensatory mechanisms.
“one health” initiative
global approach to enhance human health via the
understanding that human and animal health are interdependent and bound to the health
of the ecosystems in which they exist
Genomic surveillance
is the systematic monitoring of genetic data from pathogens to track changes in their genomes, helping to identify outbreaks and resistance patterns.
capsular switching
a serotype targeted by the vaccine escapes vaccine coverage by switching out the capsule genes to that of a non-targeted serotype
Why does capsular switching occur
strong selective pressure to avoid binding/killing by the
antibodies induced by the vaccine towards the capsule
Capsular switching has serious implication with
vaccine efficacy
the presence of pathogen DNA does not automatically mean that the pathogen is causing disease. Any thoughts on why this is?
Person could be a carrier or have in in their natural microbiome
