Bacterial disease Flashcards
What are the two kingdoms that make up prokaryotes
bacteria and archaea
What is the universal tree of life based on?
SSU rRNA
What does a polyphasic approach mean?
a combination of multiple testing methods
What phenotypic information can be found about mRNA in a bacterial genome?
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
What is ANI?
compares the shared gene content between bacteria. there is a species boundary >95-6% ANI between genomes
What categorisation comes below species?
strain
What methods can be used to determine the genotype of a strain?
restriction analysis by restriction digest DNA
PCR methods to amplify
gene sequencing
MLST
rMLST
whole genome sequencing
What methods can be used to determine the phenotype of a strain?
serotyping
resistotyping
biotyping
MALDI-TOF MS to detect molecular masses of proteins
What does the TRAD criteria stand for?
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
Evaluate genetic strain typing techniques
more stable and discriminatory. more likely to meet the TRAD criteria
Evaluate phenotype strain typing techniques
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
Strain genotyping is a genomic method. How is this done?
DNA extracted and whole genome sequenced
using a global DNA database as a library of strain types
What is MLST and how does it work
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
What are SNP’s and why are they used
single nucleotide polymorphisms
look at single base changes so allow to go below the MLST level of strain typing
What is rMLST and why is it used
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
What are the pros and cons of PCR fingerprinting
easy resources, good typeability and strain discrimination
must be developed for each species, hard to reproduce globally, not transportable, only works at strain ;level
What are the pros and cons of 7 gene MLST
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
What are the pros and cons of ribosomal MLST
works from strain to domain level, identified bacteria species and other taxonomic levels
needs genome sequencing and other genomes available for comparison
What are the pros and cons of SNP
all bacteria typeable and has greatest discriminatory resolution
but needs genome sequencing and works best within a species
What is dysbiosis
any change to the composition of resident commensal microbial communities relative to the community found in healthy individuals
What makes up the microbiome of the body?
Hair
Nostril
Skin
Vagina
Oral Cavity
Oesphagus
Colon
Stomach
How is campylobacter jejuni spread
zoonotic infection - spread from animals to humans
Why is C.jejuni hard to grow in a lab
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%
Who is there in the human microbiome?
- Virus
- Fungal/ Yeast
- Protozoa
- bacteria
- Archaea
How does C.jejuni cause infection
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
What are the two major phyla of the gut microbiome?
Firmicutes
Bacteriodetes
90% in theses
What are the symptoms of C.jejuni infection
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
What can affects the microbiome of a baby?
Breast fed, formula-fed, solid food
How is c.difficile spread
an opportunistic pathogen which is often healthcare associated infection where patients during a hospital stay get infected from cross-contamination
How does C.difficil work on a molecular level
produces toxin A, B and c,difficile transversase - causes cytoskeleton collapse, necrosis, apoptosis, immune cell recruitment, cytokine release and local inflammation
What is the difference in symptoms between mild and severe C.diff infection
mild = diarrhoea, high temperature and fever, loss of appetite, nausea, abdominal pain
severe = same but significant colon inflammation, gut barrier leakage, sepsis
What is metabolomics?
tool to assess dysbiosis
Compare healthy and kidney patient microbiomes/metabolomes and understand how these microbiomes affect mouse health
How can c.diff exist outside of its host?
by producing spores
Which groups are at risk of C.diff infection
older, immunosuppressed, previous antibiotic treatment, chronic kidney disease
What is End stage renal disease (ESRD) characterised by?
Is a progression of chronic kidney disease
Characterised by the accumulation of toxic metabolites in the blood stream
Why do patients with C.diff often have recurring infections
as soon as antibiotic treatment ends the infection rises again. is then suppressed by antibiotics again. cycle continues
How can donor microbiota be used to treat C.diff
using microbiota sample from family or anonymous donor, screened for suitability and the samples are homogenised, liquified and transplanted
How can a known mix of microbial communities be used to treat C.diff
mix of probiotics and common facilities from the gut microbiome delivered in capsules
What is culture dependent sampling?
Selective agar to grow certain types of microorganisms
Biochemical assays e.g API testing
What is culture independent sampling?
• 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
What are the advantages and Disadvantages of shotgun metagenomic sequencing?
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
What are advantages and disadvantages of 16sRNA>
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
Describe Kochs postulate
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.
What is the one health concept?
there are complex connections between human, wild and domesticated animals and environmental health
What are vector borne diseases and how are they transmitted
infections transmitted via bites from parasites - such as malaria, lyme disease, dengue fever, plague, typhus, sleeping sickness
What are zoonotic infections and examples
infections transmitted by close contact with animals
such as rabies, salmonella, cobid, ebola, taxoplasmosis,
What is DALY and QALY
disability adjusted life years and quality adjusted life years (with intervention)
Why may underestimation of GI infections occur
symptoms clearing within 2-3 days
symptoms only being mild
difficulty getting GP appointments
What factors may impact the future burden of GI tract infections
warm weather and moisture optimising bacteria growth
deforestation
AMR
illegal and poorly regulated livestock production
AMR
climate change
Describe Helicobacter Pylori
Gram negative, spiral shaped with polar flagella
A common gastric infection in 50% of the worlds population
Usually acquired during childhood
Transmission: Fecal-oral or oral-oral route
Infections are usually asymptomatic
Clinical complications range from gastric/Duodenal ulcers, gastric atrophy and ultimately gastric cance
What are the symptoms of peptic ulcer disease?
Dull, gnawing ache, occurs 2-3
hours after a meal
• Relieved by antacid medications
• Accepted cause pre 1982 was
stress and dietary factors
• Treatment: antacids,
antidepressants, surgery (relapse
in 25% of cases), gastrectomy
WHAT IS A gastric ulcer? What can it lead To?
- An open sore which doesnt heal
In stomach or duodenum
Can lead to internal bleeding, perforation, obstruction of food, cancer
What is the role of the flagella?
Bacterial mobility and Chemotaxis to colonise under mucosa
What is the role of urease?
Neutralised gastric acid
What is the role of urease?
Neutralised gastric acid
What is the role of Lipopolysaccharides?
Adhere to host cells- during inflammation
How H.pylori colonisation of the stomach occur?
STEP 1: H. pylori flagella propel the organism
towards the mucosa
STEP 2: Extracellular urease is produced by H.
pylori, which locally raises the pH of the
stomach. Urease protects the bacterium from
the stomach’s acid defence barrier.
STEP 3: Collagenase and mucinase assist the
bacteria in reaching the stomach’s epithelial
lining.
STEP 4: Adhesins such as BapA or HpaA allow
H. pylori to bind to host cells.
STEP 5: Tissue damage follows the release of
vacuolating cytotoxin (VacA) and neutrophil-
activating protein (NAP).
STEP 6: CagA injected into host epithelial cells
activates host signal transduction pathways
that can stimulate growth, possibly leading to
cancer.
STEP 7: Type I H. pylori strains may then
invade gastric phagocytic and epithelial cells.
What are the diagnostic tools of peptic ulcer disease?
- Upper GI endoscopy- biopsy taken for histology or urease teat
- Urea breath test
- Stool antigen test
Serology- Antibody test
What is the mechanism of the urea breath test
UREA +water +urease > ammonia and co2
What is the treatment of peptic ulcer disease?
- Was antacids and anti-depressants
- Focus now is on antibiotic therapy
OFFER a twice daily course of treatment with :
• Triple or quadruple therapy:
➢ a proton pump inhibitor (PPI) & gastric mucosal protective agent
and
➢ amoxicillin and
➢ either clarithromycin or metronidazole.
• Complicated 14 day treatment protocol, expensive,
increases chance of AMR development
What is the antibiotic mechanisms of action against H.pylori?
Inhibitors of nucleic
acid synthesis:
➢Quinolones (e.g.
levofloxacin) - BS
➢Rifampicin - BS
➢Nitroimidazoles (e.g.
metronidazole) - NS
Inhibitors of ribosome
synthesis:
➢ Macrocyclic lactone
(clarithromycin) - BS
➢Tetracyclines - BS
Inhibitors of cell wall
synthesis:
➢ β-lactams
(amoxicillin) – BS
What are the H.pylori resistance strategies
- Mutation of gene encoding
antimicrobial target: nucleic acid
synthesis - Mutation of gene encoding
antimicrobial target: protein & cell
wall synthesis - Changes in bacterial barrier function
Secretion of enzyme & virulence
factors
- Changes in bacterial barrier function
- Escape mechanisms: Coccoid
formation & Induced autophag
What is the future treatment options for H.pylori?
• Dual target precise therapy (specific to
pathogen)
e.g. Targeting H. pylori urease/ mucolytic activity
(but many side-effects)
• Medicinal plant extracts
e.g. turmeric and Bryophyllum pinnatum
• Drug re-purposing
e.g. intervolin (anti-tumour), nitazoxanide (anti-
protozoal)
• New generation PPI (acid suppression)
plus amoxicillin dual therapy
• Ongoing research into vaccine
What are the features of an ideal antibiotic?
Narrow spectrum, selective/targeted towards pathogen(s), low resistance, non toxic, cheap
