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Concepts Of Disease > Bacterial disease > Flashcards

Bacterial disease Flashcards

1
Q

What are the two kingdoms that make up prokaryotes

A

bacteria and archaea

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2
Q

What is the universal tree of life based on?

A

SSU rRNA

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3
Q

What does a polyphasic approach mean?

A

a combination of multiple testing methods

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4
Q

What phenotypic information can be found about mRNA in a bacterial genome?

A

proteins - cellular/cell envelope proteins or enzymes
chemotaxonomic markers - such as fatty acids, cell wall compounds and exopolysaccharides
expressed features - such as morphology, physiology, antibiotic resistance and serology

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5
Q

What is ANI?

A

compares the shared gene content between bacteria. there is a species boundary >95-6% ANI between genomes

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6
Q

What categorisation comes below species?

A

strain

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7
Q

What methods can be used to determine the genotype of a strain?

A

restriction analysis by restriction digest DNA
PCR methods to amplify
gene sequencing
MLST
rMLST
whole genome sequencing

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8
Q

What methods can be used to determine the phenotype of a strain?

A

serotyping
resistotyping
biotyping
MALDI-TOF MS to detect molecular masses of proteins

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9
Q

What does the TRAD criteria stand for?

A

typeability = how many isolates can be typed
reproduceability = will you get the same consistent results for a strain
accuracy
discriminatory power = can different strains of the same species be distinguished

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10
Q

Evaluate genetic strain typing techniques

A

more stable and discriminatory. more likely to meet the TRAD criteria

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11
Q

Evaluate phenotype strain typing techniques

A

relies on growth, there are variable phenotypes meaning that the same genetically identical strain could look phenotypically different which could make it hard to discriminate

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12
Q

Strain genotyping is a genomic method. How is this done?

A

DNA extracted and whole genome sequenced
using a global DNA database as a library of strain types

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13
Q

What is MLST and how does it work

A

multi locus sequence typing. 7 housekeeping genes which are conserved enough to amplify all strains in a species but diverse enough to distinguish strains. design facilitated by genome sequence data
all 7 MLST loci are sequenced, polymorphisms recorded (sequence differences) and alleles combined. combined alleles give the sequence type

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14
Q

What are SNP’s and why are they used

A

single nucleotide polymorphisms
look at single base changes so allow to go below the MLST level of strain typing

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15
Q

What is rMLST and why is it used

A

ribosomal MLST, compares 53 ribosomal protein subunit genes - rps genes/ they are present in all bacteria and encode proteins that stabilise selection for functional conservation, have sufficient SNP variation to diffferentiate allleles. rMLST allows rapid bacterial species identification form a genome

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16
Q

What are the pros and cons of PCR fingerprinting

A

easy resources, good typeability and strain discrimination
must be developed for each species, hard to reproduce globally, not transportable, only works at strain ;level

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17
Q

What are the pros and cons of 7 gene MLST

A

excellent typeability and strain discrimination, transportable, global databases, can extract MLST genes from genome
needs PCR and sequencing or genome sequencing, may not work in localised outbreaks involving a single MLST strain

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18
Q

What are the pros and cons of ribosomal MLST

A

works from strain to domain level, identified bacteria species and other taxonomic levels
needs genome sequencing and other genomes available for comparison

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19
Q

What are the pros and cons of SNP

A

all bacteria typeable and has greatest discriminatory resolution
but needs genome sequencing and works best within a species

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20
Q

What is dysbiosis

A

any change to the composition of resident commensal microbial communities relative to the community found in healthy individuals

21
Q

What makes up the microbiome of the body?

A

Hair
Nostril
Skin
Vagina
Oral Cavity
Oesphagus
Colon
Stomach

22
Q

How is campylobacter jejuni spread

A

zoonotic infection - spread from animals to humans

23
Q

Why is C.jejuni hard to grow in a lab

A

it is fastidious and requires certain growth conditions such as temperatures of 37-42 degrees, oxygen levels below 5%, high co2 levels of 2-10%

24
Q

Who is there in the human microbiome?

A
  • Virus
  • Fungal/ Yeast
  • Protozoa
  • bacteria
  • Archaea
25
Q

How does C.jejuni cause infection

A

c.jejuni is highly motile
produces virulence factors in host
biofilms formation allows to survive outside the host
can cross membranes and the gut lumen
immune cell detection leads to inflammation and diarrhoea

26
Q

What are the two major phyla of the gut microbiome?

A

Firmicutes
Bacteriodetes

90% in theses

27
Q

What are the symptoms of C.jejuni infection

A

gillian-barre syndrome, autoimmune diseases causing progressive weakness and paralysis due to the similarity of c.jejuni lipologosaccharides to host gangliosides so alters the nerves

28
Q

What can affects the microbiome of a baby?

A

Breast fed, formula-fed, solid food

29
Q

How is c.difficile spread

A

an opportunistic pathogen which is often healthcare associated infection where patients during a hospital stay get infected from cross-contamination

30
Q

How does C.difficil work on a molecular level

A

produces toxin A, B and c,difficile transversase - causes cytoskeleton collapse, necrosis, apoptosis, immune cell recruitment, cytokine release and local inflammation

31
Q

What is the difference in symptoms between mild and severe C.diff infection

A

mild = diarrhoea, high temperature and fever, loss of appetite, nausea, abdominal pain
severe = same but significant colon inflammation, gut barrier leakage, sepsis

32
Q

What is metabolomics?

A

tool to assess dysbiosis
Compare healthy and kidney patient microbiomes/metabolomes and understand how these microbiomes affect mouse health

33
Q

How can c.diff exist outside of its host?

A

by producing spores

34
Q

Which groups are at risk of C.diff infection

A

older, immunosuppressed, previous antibiotic treatment, chronic kidney disease

35
Q

What is End stage renal disease (ESRD) characterised by?

A

Is a progression of chronic kidney disease
Characterised by the accumulation of toxic metabolites in the blood stream

36
Q

Why do patients with C.diff often have recurring infections

A

as soon as antibiotic treatment ends the infection rises again. is then suppressed by antibiotics again. cycle continues

37
Q

How can donor microbiota be used to treat C.diff

A

using microbiota sample from family or anonymous donor, screened for suitability and the samples are homogenised, liquified and transplanted

38
Q

How can a known mix of microbial communities be used to treat C.diff

A

mix of probiotics and common facilities from the gut microbiome delivered in capsules

39
Q

What is culture dependent sampling?

A

Selective agar to grow certain types of microorganisms
Biochemical assays e.g API testing

40
Q

What is culture independent sampling?

A

• 16s rRNA gene- a component of the 30S (small) subunit o the bacterial ribosome
• Due to slow rates of evolution in this gene it is used to measure the evolutionary distance between organisms
• Provide up to species-level resolution but typically genus level is expected
• Whole genome (shotgun) sequencing
• Metagenomics- the collection of genomes and genes rod the members of a micro iota
• Enhanced species detection
• Increased detection of diversity
• Increased insight of function derived from identified gene

41
Q

What are the advantages and Disadvantages of shotgun metagenomic sequencing?

A

ADVATNAGES
* Provides more information on the community than species identification i.e AMR gene
* Greater discrimination of species
* Provides information on non-bacterial/archaeal community members
* Can be used to determine community-community and community-host relationships
Disadvatanges
* most costly and requires higher computing power
* Higher DNA concentrations required within samples
* Sampling strategy influences the bias of the data generated
* Results generated are only as good as the databases available

42
Q

What are advantages and disadvantages of 16sRNA>

A

Advantages
* Cheap and easy
* Carried out on low conc samples
* There are several large, open access, curated databases for use during analysis

Disadvantages
* The number of rRNA copies in each species is variables- this can skew abundance estimates
* Multiple steps introduce sample bias- and contamination - need to analyse carefully
* Data outputs are relatively limited- genus indetificatio only data
* Abundance data generated is relative (not absolute

43
Q

Describe Kochs postulate

A

The microorganisms must be found in abundance in all organisms suffering from the diseases but should not be found in healthy organisms.
The microorganism must be isolated from a diseased organism and grown in pure culture.

The cultured microorganisms should cause disease when introduced into a healthy organism.

The microorganisms must be reisolated Ron the inoculated disease experimental host and identified as being identical to the original specific causative agent.

44
Q

What is the one health concept?

A

there are complex connections between human, wild and domesticated animals and environmental health

45
Q

What are vector borne diseases and how are they transmitted

A

infections transmitted via bites from parasites - such as malaria, lyme disease, dengue fever, plague, typhus, sleeping sickness

46
Q

What are zoonotic infections and examples

A

infections transmitted by close contact with animals
such as rabies, salmonella, cobid, ebola, taxoplasmosis,

47
Q

What is DALY and QALY

A

disability adjusted life years and quality adjusted life years (with intervention)

48
Q

Why may underestimation of GI infections occur

A

symptoms clearing within 2-3 days
symptoms only being mild
difficulty getting GP appointments

49
Q

What factors may impact the future burden of GI tract infections

A

warm weather and moisture optimising bacteria growth
deforestation
AMR
illegal and poorly regulated livestock production
AMR
climate change

Concepts Of Disease (8 decks)

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