Infectious Diseases Flashcards
What is tuberculosis
A contagious, debilitating (consuming) bacterial disease spread by airborne droplets
Coughing, speaking, sneezing
Left untreated, one person with tuberculosis will infect 10-15 people (R0)
What bacterium causes tuberculosis
Mycobacterium tuberculosis
Slow growing, difficult to kill, waxy coat
What imaging test can detect TB
X-ray showing multiple cavities, also lungs can undergo necrosis
What is a TB granuloma
Chronic granulomatous inflammatory responses
In the centre it is necrotic and liquified leading to cavities
Bacteria can grow in these cavities which may be released into the bronchus, coughed and spread
How many people with TB present with symptoms
Exposure - only 30% get infection - of this 5% progress to active disease while 90% have latent TB
How can you detect latent TB
A mantoux test (injection of TB Abs) shows reaction in latent infection
When is TB latency problematic
When the person is immunosuppressed
Why can TB become quickly resistant
High bacterial load in TB (unique) = many organisms, that can eventually gain resistance
How do you treat TB
Antibiotics - firstly streptomycin, however TB rapidly became resistant to this
4 drug combination trial - standard short course of 4 drugs for 6 months
Overcomes mutation rates, 95% effective with relapse rate 3-4%
Treatment must contain multiple drugs to which organisms are susceptible
What is the phases and drugs used in treatment of TB
Intensive phase - RHZE for 2 months
Continuous phase - RH for 4 months
Can last longer e.g. when infection of meninges
What drugs are used to treat TB
Isoniazid (INH/H) Rifampicin (RIF/R)
Pyrazinamide (PZA/Z)
Ethambutol (EMB/E)
What is the mechanism of action for isoniazid
Isoniazid (INH/H) – inhibits synthesis of mycolic acid, required for mycobacterial cell wall
What is the mechanism of action for rifampicin
It inhibits bacterial RNA polymerase
What is the mechanism of action for pyrazinamide
It binds to the ribosomal protein S1 (RpsA) and inhibits translation + other possible mechanisms
What is the mechanism of action for ethambutol
It inhibits arabinosyl transferases involved in cell wall biosynthesis of arabinogalactans
What is the molecular mode of action of isoniazid
Analogue of nicotinic acid
It’s a prodrug that is activated by catalase peroxidase inside the bacteria produced by KatG
This then adducts with Iso-NADH, binding the lipid synthetase preventing mycolic acid synthesis
These enzymes are coded by Inh A
What is the molecular mode of action of isoniazid
PZA is also a prodrug, activated inside the bacteria by pyrazinamidase , coded by PncA gene forming pyrazinoic acid
Why does it take so long to treat TB
TB therapy takes 6 months to treat as it grows rapidly forming biofilms inside granulomas
Initial rapid kill curve by sterilising effect of INH
There is a second persistent population who no longer are turning over their cell walls and their metabolic pathways are slowed down thus the prodrugs aren’t activated - thus becoming drug tolerant
What factors impact response to treatment
Due to many host factors
Disease type and extent meningeal, bone lung TB
Immuno-competence
Bacterial strain
Genotype-phenotype
Antibiotic resistance
What increases the chance of a patient having drug resistant TB
Patient has spent time with someone with active drug-resistant TB disease
Patient does not take their medicine regularly or does not take all of their medicine
Patient develops active TB disease after having taken TB medicine in the past
Patient comes from area of the world where drug-resistant TB is common
What is MDR and XDR
Moderately and extremely drug resistant
What is the difference between MDR-TB and XDR TB
MDR-TB = resistant to INH and RIF (RH)
XDR-TB is MDR-TB resistant to any fluroquinolone (levofloxacin, moxifloxacin and ofloxacin) and at least one of three injectable second-line drugs (capreomycin, kanamycin and amikacin)
What are TB drug resistance mechanisms
Barrier mechanisms - decreased permeability and efflux pump
Degrading or inactivating enzymes - e.g. β- lactamases
Modification of pathways involved in drug activation or drug metabolism
E.g. katG and isoniazid resistance
Drug target modification - e.g. rpoB and rifampicin resistance
Target amplification - e.g. inhA and isoniazid resistance
Too much enzyme that IZH cannot fully target
How can you detect drug resistance
Standard methods - culture and phenotypic drug susceptibility testing (DST) - weeks to months
Delays during which patients receive sub-optimal therapy
Additional resistance and further spread of drug resistant TB
What are the conventional phenotypic, and the genotypic methods of drug resistance
Conventional – Phenotypic
Using solid and liquid media
Absolute concentration, resistance ratio and proportion susceptibility testing
Time consuming - weeks
Genetic tests for mutations in target
Rapid, predictive only
Needs accurate databases of mutations
What is geneXpert
PCR in a cartridge which quantitates amount of TB DNA and identified rpoB gene
Identifies if it is TB and if there is rpoB mutation resistance to rifampicin
There are 5 probes - if one probe fails to bind, it shows there’s resistance to RIF within the rpoB gene
What drugs can we confidently predict resistance for
High confidence calls
INH - katG or inhA SNPs
RIF - rpoB SNPs - codons 507-533
Quinolone - gyrA SNPs
What are the difficulties when determining the impact of mutations?
Cross resistance
No DST (drug susceptibility) data for new SNP’s
DST and MICs (minimum inhibitory concentration) for drugs unknown
Compensatory and secondary mutations
How is WGS used for TB
Genome wide mutation screening
Public health monitoring - tracking strains
Why is WGS beneficial for TB treatment and monitoring
Quick, unbiased, cost effective and can help improve databases
However requires bioinformatics, good databases and many studies - not sure if accurate
Gives evidence based advice, allowing faster and more effective treatment for better patient outcomes
Reduces onwards transmission and chance of further resistance
What other factors influence TB treatment
Other risk factors/comorbidities e.g. HIV, genetic susceptibility to poor response to TB, latent TB etc.
Why might you use a drug for a patient with TB resistant to that drug
It may be a weak resistance, with a low MIC falling within the therapeutic index
Thus you only need to increase the concentration
Pyrazinamide is a drug used for most if not all cases of TB - when might it not be used
When the evidence shows the strain is 100% resistant, there is no point wasting resources if you are 100% sure it wont work
How may drug dosage be influence by drug susceptibility tests
By finding out the MIC and prescribing drugs at higher concentrations than the MIC, if safe to do so
What are some of the clinical considerations when choosing a treatment
Drug side effects
Injectables need long central line – risk of infection and venous thrombosis
HEPA filtered negative pressure isolation room until culture negative for 6 weeks
Unpleasant for patients, expensive and difficult to manage for hospital
Poor compliance
Longer you wait for testing = drug resistance thus use empirical treatment first
False +ve/negative
-ve = ineffective treatment
+ve = unnecessary side effect
What is an example of a viral STI and its effects
Viral - trichomoniasis
This targets mainly women, causing vaginal discharge, preterm birth, increased incidence of HIV, miscarriage and other complication including bacterial vaginosis
What is an example of bacterial STI’s and its effects
Bacterial - syphilis, gonorrhoea, chlamydia, mycoplasma genitalium
Syphilis behaviours like a virus which causes a systemic long term illness
Gonorrhoea and chlamydia infect primarily the lower tracts
They can infect mucosal surfaces e.g. in pharynx, rectum and cause inflammation
Can cause blocking of the fallopian tubes, infertility, preterm birth miscarriage
Mycoplasma genitalium- recently recognised STD
Gonorrhoea and mycoplasma genitalium have developed antimicrobial resistance
What is the public health impact of gonorrhoea
It does not tend to cause mortality now
Caused severe pelvic inflammatory disease, ectopic pregnancies, infertility
Gonorrhoea in eyes of foetus after birth can cause blindness
Can cause endocarditis (affecting heart lining) via disseminated gonococcal infection
It can increase risk of HIV transmission and acquisition though taking ART can make it safer
Antimicrobial resistance needs to be monitored
What is gonorrhoea
Samples taken from discharge, gram stained
Gram negative intracellular diplococcus - inside neutrophils
A lipid membrane inside and outside of the cell wall
Where is gonorrhea found within a patient
Gonorrhoea can be in back of throat, cervix or rectum which cannot be detected easily
Thus a antimicrobial culture result needs to come back before a molecular test
Treatment given to prevent spread, but it cannot be personalised thus resistance may develop
What is GRASP
A UK system to collect samples from STI clinics and microbiology labs
These are then tested to see prevalence of resistance and the region form which it came
Finds the rates of resistance in England/wales to which drug - determining which drug to avoid
What common drug resistances are seen in the UK
Ciprofloxacin resistance has increased rapidly
Ceftriaxone and spectinomycin resistance has so far remained low
However in other countries there are so
MIC cut off varies between drugs - 1.25 for ceftriaxone
And you don’t want more than 5% of population with that resistant strain
What is the physical properties of mycoplasma genitalium
Atypical class of bacteria - a mollicute, related to gram positives
No cell wall, not susceptible to penicillin
Lost ability to synthesise essential amines for survival and become parasitic and dependant on hosts
What are the genomic properties of mycoplasma genitalium
The genome size is small - 580kb, coding for <500 genes
Does not have the genes to synthesise various essential amines
What conditions can mycoplasma genitalium cause
Cervicitis, pelvic inflammatory disease, preterm birth, spontaneous abortion and may cause infertility
What three drug classes may be used to treat mycoplasma genitalium
Macrolides - bind 50S subunit targeting 23S rRNA
Quinolones - bind DNA gyrase and topoisomerase IV
Tetracyclines - bind 30S ribosomal subunit
What bacterium can cause genital discharge and pus
Pus could indicate chlamydia or gonorrhoea, trichomonas, and mycoplasma genitalium
How is genital discharge investigated
Microscopy - however this cannot inform resistance
How can point of care testing be used in STI clinics
PoC testing can help discriminate between the different causes of genital discharge
Rapid tests can test within hours
Done at microfluidic level which makes it faster
What is the rapid test paradox
Molecular testing in labs tend to be accurate
Sensitivity (true positives, ruling out false results) and specificity
Important in STI’s as it can cause emotional distress for false results
BUT certain populations may not return e.g. live far, not mobile
Then you may prioritise speed over sensitivity
You may also pretreat them before they come back
What is GeneXpert in TB and STI usage
Random access platforms
They have individuals modules/shelves which runs samples independently within 90mins
Realtime PCR
Expensive
Can test for chlamydia, gonorrhoea, trichomonas and HPV
Sample first - samples taken first, then put into geneXpert, wait, consultation and hopefully by the end the result is available
What is the Binx health IO system
Microfluidic cartridge test - chambers where the sample in inserted and flows through
Describe the process within the binx health io system
The DNA is extracted and goes into two different PCR chambers which amplify the targeted genes, there’s are them split into two more chambers for detection
Can look for multiple different diagnoses - up to 24!
Looks for molecular resistance markers
What factors need to be considered to reduce transmission of resistant pathogens/what factors determine the R0 value
Biology of pathogen
Sexual behaviour of patients e.g. partner change
Duration of infectiousness
What are the
mechanisms of resistance in gonorrhoea
Cell wall alteration - penicillin and cephalosporins
Change in porin protein channels preventing antibiotics entering cells
Changes in gene control of transporters e.g. efflux pumps which normally pump toxins
actively pump out antibiotics
Penicillin resistance due to mobile genetic elements - plasmids which can produce beta-lactamase
Ribosomal disruptors - macrolides
Fluroquinolones can be passed by mutations in topoisomerases
Topoisomerases are needed for unwinding of DNA for replication
Describe fluoroquinolone action
Fluroquinolones targets topoisomerases II/DNA gyrase A which prevents unwound DNA from twisting
Topoisomerase do this by cutting the DNA and reattaching it - thus inhibition = DNA twist = no replication
It also targets topoisomerase IV or ParC/E e.g. moxifloxacin
This is involved in the circular chromosome
What codon change in topoisomerases in gonorrhoea can confer resistance
Codon 91 Ser to Phe and codon 95 Asp to = resistance
How can you test for codon 91 and 95 changes in gonorrhoea topoisomerase
PCR
This can be used to identify those who are susceptible to fluoroquinolones
Why might WGS be used
It can help predict strains accurately
It has fast turn around - but it does depend on the platform e.g. NGS Vs long-read
