Topic 6: Evolution and You: Bacteria and Viruses Flashcards
Parascitism
One organism benefits
One suffers
Commensalism
One organism benefits, the other is not affected
Mutualism
Both organisms benifit
Microbiome
The totality of microbes in an environment (can be a human)
3 enterotypes in human microbiome
What do bacteria do for us? (6 things)
How many kcals do mice need if they are in a sterile environment?
help
metabolism physiology maturation of immune system energy balance susceptibility to disease behavior
Mice living in a sterile environment need 30% more kcals
Where do bacteria come from (in microbiome)
Babies get some in utero and continue to get some over the first few years
The appendix - function
and when did we evolve it/why?
Darwin thought this had been evolved and was a left over, no longer useful
Actually, likely evolved to repopulate the gut with good bacteria.
In primate evolution
Individuals lived in low density populations
Occasionally alone
Useful to have a reserve of bacteria in case of illness
The appendix evolution
Evolved in two independent times
for marsupials and for ancestors of mammals and rodents (lost in the lineages of tree shrews and lemurs)
Urbanization
Big increase in urbanization globally
Increased pop density and sanitation issues
Possible that appendixes are less useful today
Cholera
Drink infected water
Moves into small intestine
Grow flagella and go into intestinal walls
Reproduce
Illness - watery diarrhea
Lots of spread into place there has historically not been any. Due to human movement.
Haiti - free since the 1800s Earthquake Aid workers from Nepal Not much infrastructure cos of hurricane Sandy Big outbreaks
Problems with urbanization
Unfamiliar bacteria
Bacteria in the wrong place
Strep pneumoniae
Usually colonises human skin
In other places, skin abcesses, and other serious health conditions
Staph
Skin
MRSA exists
What has helped cut down infections (2 things)
Sanitation development
Antibiotics
Penicillin
Alexander Fleming observed agar plate around blue-green mold was clear of bacteria
Found that the mold produced a substance that killed bacteria and called it penicillin
Florey and Chain researched how to make larger quantities. A woman in Peoria, Illinois brought in a moldy cantaloupe.
Very fast to produce. By 1942 was enough to use on ww2. By 1943 was an antibiotic resistant strain
Natural selection and antibiotic resistence
Population mutates as normal
Introduce antibiotics
Some have resistant characteristics
The antibiotics create a selection pressure in favor of these genes
The frequency of these alleles will be greater in the next generation
3 ways antibiotics can work
Attack cell wall synthesis
Attack nucleic acid synthesis
Attack protein synthesis
Ways bacteria target antibiotics (3)
Drug modification - change the drug so it does not work
Drug degradation - break down the drug
Reduce accumulation -0 prevents bacteria getting inside or the build up of it
Bacterial plamids
Contain DNA, often of stuff that is important for survival
Can replicate independently of the bacterial chromatid
Horizontal gene transfer - bacteria
Donor makes a Philus and connects to recipient
Plasmid duplicates
Basses between the two cells
Both not have plasmid
5 ways bacteria gain antibiotic resistence
From other bacteria (horizontal transmission)
From viruses - gets infected but gains DNA
From dead bacteria
From the environment
From reproduction (fission)
Bacterial fission
Very fast (hours)
Asexual, all offspring would have resistant alleles
The generation time is also really fast so there is plenty of opportunity for mutation
Microbiome and antibiotics
Take antibiotics for an infection
Selection pressure, only bacteria with genes for resistance survive
In the process, good bacteria can also be depleted
These dead bacteria can be replaced by another species, altering the local ecology in your environment
There is lots of resistence
Bacteria find new methods of resistance quicker than we develop antibiotics.
Factors impeding antibiotic development
Not profitable - only used for a little bit and we are discouraging their use.
Lifestyle drugs offer better returns
only 5/25 big drug companies still have programs
MRSA and Agriculture
What has the EU done about this?
Higher levels of MRSA are observed in ppl near agricultural livestock operations. Because fresh air is pumped in for the animals and old air out with loads of stuff including bacteria
EU and Scandinavia have all addressed this and forbidden the use in livestock of antibiotics to increase growth
Aim for overall improvement of animal health and hygiene
Selectively about what infections warrant treatment with antibiotics
Guidelines for abx use in humans
Take the full course
Only prescribe when you KNOW its bacterial ie not viral
Hard cos diagnosis is via symptoms so easy to confuse bacterial and viral
Avoid treating the wrong disease
When prescribed antibiotics have no effect on viruses, they do affect all other bacteria. Might cause issues. Provides a selection pressure for the bacteria.
Direct transmission
Person to person contact
Eg Ebola/HIV
Droplet transmission - sneezing
Influenza and COVID-19
Large/small droplets
Large 5-10um are respiratory droplets
Small under 5nm are respiratory nuclei
Indirect, Airborne transmission
Droplet nuclei from evaporated droplets or dust particles. Suspends virus or bacteria in the air and then it enters a new host after the last host has long left
Eg TB, chicken pox, smallpox. measles
Vector
Indirect
like mosquitoes
Malaria
Waterborne
Indirect
Cholera
The balancing act for viral infection
Natural selection should favor a balance between virulence and transmissibility
Fitness of virus depends on how virulent and transmissible it is
Scale
Outbreak is a sudden increase in the are above that expected based on recent xp
Epidemic is when the term outbreak goes beyond a small or restricted area
Pandemic is an epidemic that spread through a large region eg continents or worldwide
Outbreak - your town
Epidemic - your province
Pandemic - countries across the world
Viruses have influenced human dna
Cos we have had them for so long
many translocations
Why are viruses adaptable?: Simple construction
Viral genome can be DNA or RNA
Protein coat or capsid
Some have a lipid membrane or envelope
They don’t replicate themselves so need less DNA or equipment
Fewer genes and equipment
Why are viruses adaptable?: Short generation time
DNA/RNA comes in small packets
Easily picked up and quickly transcribed or incorporated into the host genome (so reproduce fast)
Why are viruses adaptable?: High mutation rates
Especially in RNA viruses
RNA polymerase has no proof reading ability
So more frequent errors during copying
Can make it hard to generate vaccines as the genetic sequence is always changing
Influenza viruses are divided into types based on
Their H and N proteins
H let them into cells
N let them out
Antigenic drift
In host species, viruses can undergo slow or limited evolution
Over time, antibodies might not recognize their new forms. The antigens change
Seasonal flue and drift
As it moves from the south to the north, it mutates via drift, which is why the flu vaccine is updated 2x a year
Antigenic shift
Large changes occur because a cell is infected by multiple species of virus for example multiple species
When this happens, people have no immunity to the new hybrid form
H1N1 2009 - swine flu
Bird virus and human virus combined in a pig cell with swine virus.
Transmitted to human then human to human
Was highly transmissible but not highly virulent
1918 Spanish Flu
Killed 2.5% of global population
3 waves in a year. 2nd was the worst which is odd because you would expect greater immune response
Healthy young adults died
Really fast. Infected people were asymptomatic and carrying out daily life then got sick and died
Huge immune response which destroyed the hosts own cells
Ebola
Natural host is the fruit bat
Got into humans either directly from a bat or via other mammals
Early symptoms were not bad, late included GI bleeding and death.
How does ebola kill
Infects macrophages
Release cytokines
These recruit more macrophages
and signal to increase the permeability of blood vessels
Blood clots and leaks form in vessels
Uses up all the coagulation proteins
Abnormal bleeding in skin and elsewhere = fatal
Why was Spanish flu worse than Ebola
Ebola transmission requires close contact with person or body fluids
If Ebola is hard to transmit, why did it hit so bad?
Rapid urbanization of African countries
but without:
durable housing
Clean water
Sufficient living space
Healthcare
How was Nigeria spared in Ebola?
Legendary doctor caught it and quarantined their only case
She dide from it
Challenges with a pandemic like Ebola
To control it
1 - recognize the illness
2 - prevent contact by quarantine/ppe/disposal of waste/proper burial
Covid
Bats are a reservoir
Have passed to humans via many intermediary animals
Has genetic similarity to bat coronavirus, the first sars-cov and mers-cov
Covid transmission in three studies
Using case studies to work transmission out
1) restaurant did a schematic of the place and worked out where the infected person had sat and where people got sick.
Waiters who handled their plate did not get sick
Showed contact was less of an issue and that it was unlikely to be airborne as many did not get sick. Most likely droplet.
2)Call center in south Korea
First case on 10th floor, second on 11th. Dense areas around the 2nd case got hit hard
3) train analysis
2300 index pts
73000 contacts
Made a map of where they sat and how long they were there for
Found that proximity and time spent there were the two big things
COVID effects
Normally mild to moderate pneumonia
In rare cases cytokine storm
Brakes of immune system stop working
massive effects on multiple systems
Things that influence covid transmission (4 things)
Environment - indoor/outdoor, ventilation, long term care facilities
Contact pattern - Prox to index case, time of contact, duration of contact, activity
Socioeconomic factors - poverty, job insecurity, long working hours, household crowding
Host factors - Age, infectiousness, severity, host defense factors
Positivity rates
A high positivity rate indicates there are likely more cases than we know about
This depends on the numbers of cases and tests done
Can also be measure by the number of tests you need before a positive
Patterns of responses
Those who responded early did well but often increased later. Once there is a lot of cases, it is hard to do anything to stop it. Cannot be controlled without a vaccine.
Appx death rate
3%
Vaccines
Hard to make first of all
Then hard to distribute: environment, infrastructure etc makes vaccinating enough people a challenge
Ideally you get herd immunity when there is not enough hosts left for the virus and it burns out
Without vaccine getting to here requires too many deaths
Until a vaccine
Limit contact, wear masks
Limit travel
Bottom up methods to prevent viruses
Monitor across globe where people eat bushmeat
Try to get them to not take already dead animals (as they might have disease)
Get them to sample blood of each kill
Can be analyzed
