Theme 2: Advanced Microbiology Flashcards
A person is described as being pyrexial when __?__
their temperature is over 38 degrees.
How does procalcitonin aid diagnosis in a patient with a suspected infection?
Differentiates between bacterial and viral
What is the most important investigation to confirm a clinical diagnosis of pneumonia?
CXR
What effect might a bacterial infection have on these lab results?
a) WCC
b) Lymphocytes
c) Neutrophils
a) WCC - raised
b) Lymphocytes - normal or low
c) Neutrophils - raised
What effect might a viral infection have on these lab results?
a) WCC
b) Lymphocytes
c) Neutrophils
a) WCC - normal
b) Lymphocytes - raised
c) Neutrophils - normal
What does sensitivity testing tell you in microbiology?
Pathogen resistance to specific antimicrobials.
Concentration of antimicrobial required to kill the organism.
What is meant by ‘empiric’ antimicrobial therapy?
Initial treatment of infection with broader spectrum antimicrobials.
What are the limitations and uses of blood cultures?
Uses: Establish presence of microorganism, determine, identify targeted therapy, provides typing information.
Limitation: Slower than direct detection, can only detect cultivable organisms, can only detect organisms at specific site.
Direct detection of microorganisms can detect either the whole organism (by __1__) or components of the organism (__2__ or __3__).
1) microscopy
2) antigen
3) nucleic acid (DNA or RNA)
What method is used to detect nucleic acid of an organism?
PCR
What method of microbial identification is usually the fastest?
Direct detection
__?__ is the transition from no antibody response to an antibody response. Identifiable as a change from a negative result on one test, to a positive result on the next.
Seroconversion
If a patient’s antibody concentration rises from 1/2 to 1/32, this would be called a __?__
‘fourfold rise in titre’
Why is antibody testing not usually able to help inform antimicrobial therapy decisions?
The convalescent sample is taken 10 days to 2-weeks after the event.
This is often too late to inform antimicrobial therapy decisions.
Describe the normal variation in temperature for a patient with fever
Fevers are usually associated with diurnal variation in temperature: increases during the early day and goes down at night.
How is fever useful in diagnostic testing?
Most commonly caused by infections.
Pyrogens secreted at sites of infection are detected by hypothalamus. Hypothalamus responds by sending signals for generating and retaining more heat.
Raised neutrophil count generally indicates ____
bacterial infection
Raised lymphocytes generally indicates ____
viral infection
True or false: raised monocytes may indicate a chronic infection.
True, though it is important to note they are also raised in acute infections
Raised eosinophil count generally indicates ____
parasitic infection
Raised basophils generally indicates ____
viral infection
Raised CRP/procalcitonin means what?
Indicates potential bacterial infection (but not definitely). Negative inflammatory markers suggest infection is less likely.
High sensitivity; low specificity.
Which of the following is true of inflammatory marker in a blood test:
a) high sensitivity; high specificity
b) low sensitivity; low specificity
c) high sensitivity; low specificity
d) low sensitivity; high specificity
c) high sensitivity; low specificity
Often picks up a bacterial infection if present (few false negatives); but also raised by a range of other things (many false positives)
How can lactate be useful as an infection test?
Raised lactate may indicate severe infections such as sepsis and meningitis.
What component is usually being identified in serology tests for infection?
Levels of antibodies (IgM, IgG). Will be raised if infection present.
Acute viral infections are generally caused by viruses with which type of nucleic acid?
RNA viruses
Influenza, measles, mumps, HAV
Chronic viral infections are generally caused by viruses with which type of nucleic acid?
DNA viruses
Herpes simplex, CMV, HIV, HBV
True or false: Viruses are obligate intracellular parasites
True
This means they can only replicate inside cells.
When should you use antivirals?
High risk patients with acute infection
Chronic viral infections - prevent further damage
Immunosuppressed
Which antivirals are herpesvirus polymerase inhibitors?
Aciclovir and ganciclovir
Which antivirals are used to treat CMV?
Ganciclovir (CMV): guanosine analogue that inhibits viral DNA polymerases.
Cidofovir (CMV retinitis in patients with AIDS): targets viral DNA synthesis by inhibiting herpesvirus polymerase
What infections are commonly treated by aciclovir?
HSV and VZV (chicken pox and shingles)
Usually treatment only given in severe cases or for patients who are immunocompromised.
Severe cases usually involve encephalitis or disseminated HSV.
What is the mechanism of action of aciclovir?
Converted to aciclovir triphosphate, which inhibits HSV DNA polymerases, preventing viral DNA synthesis
When is aciclovir given prophylactically?
Patients with frequent reactivation of herpes virus.
Prevention of infection/reactivation following transplant (immunosuppressed).
When might it be appropriate to treat chicken pox with aciclovir?
When presenting in adults.
No need to treat children.
When might it be appropriate to treat shingles with aciclovir?
Age >60yo
Involves the eyes
Immunocompromised
What drugs are used to treat influenza in high risk patients?
Neuraminidase inhibitors:
Oseltamivir
Zanamivir
Which patients are considered high risk when deciding whether or not to treat influenza?
Chronic disease
Diabetes Mellitus
Immunosuppressed
Age >65yo
Pregnant (and two-weeks post partum)
Age <6mo
Morbid obesity (BMI >40)
What treatment is used to eradicate chronic viral infections such as HCV, HBV, and HIV?
HBV and HIV are DNA viruses that cannot be eradicated. They usually require lifelong treatment.
HCV is an exception as it is an RNA virus that causes chronic infection. Therefore, direct-acting antivirals can eradicate the virus.
HCV RNA polymerase nucleotide inhibitors (e.g. sofosbuvir) are effective at eradicating HCV.
Nucleoside reverse transcriptase inhibitors (NRTIs) are either analogues of __1__ to affect the growing chain in transcription, or the inhibit the proper functioning of __2__.
1) nucleotide bases
2) polymerase
Aciclovir and ganciclovir are ____ inhibitors
herpesvirus polymerase
Aciclovir is an analogue of ____
guanosine
What do non-nucleotide reverse transcriptase inhibitors target?
Allosteric inhibition of polymerases.
How do protease inhibitor antivirals work?
Proteases break down proteins. The viruses need protease enzymes to break down the chains they make into smaller individual enzymes necessary for the virus to function. Protease inhibitors interrupt this process.
What is Fidaxomicin used for?
Relatively new drug , solely treats C.Diff in the bowel
When is Fosfomycin likely to be used?
Effective against many resistant strains, used to treat UTIs
Beta-lactams target the ____
cell wall
Which specific types of antibiotic are classified as beta-lactams?
Any with a b-lactam ring (C-C-C-N)
- Penicillins
- Cephalosporins
- Carbapenems
- Monobactams
Benzylpenicillin and phenoxymethylpenicillin are ____ spectrum penicillins
narrow
The broader spectrum penicillins are ____ and ____
amoxicillin and pivmecillinam
Which penicillin is resistant to penicillinase?
Flucloxacillin
What class of antibiotic are these?
Cephalexin, cefuroxime, cefotaxime, ceftriaxone, ceftazidime
Cephalosporins
These are beta-lactams, therefore they target the cell wall by preventing peptidoglycan crosslinking
How do beta-lactams work?
Prevent peptidoglycan cross-linking by interfering with function of transpeptidase enzymes
What class of antibiotic are these?
Ertapenem, imipenem, meropenem
Carbapenems
These are broad spectrum beta-lactams. Therefore they target the cell wall: prevent peptidoglycan cross-linking by interfering with function of transpeptidase enzymes.
Aztreonam is a type of __1__ and is only effective __2__ bacteria.
1) monobactam (subtype of beta-lactam)
2) gram negative
Which beta-lactam is safe for use in patients with penicillin allergy?
Aztreonam
Although it is still a beta-lactam, the ring in its structure is sufficiently different.
What combinations can be used to overcome beta-lactamase?
Co-amoxiclav (augmentin): amoxicillin with clavulanic acid
Tazocin: piperacillin with tazobactam
What are some problems with using BLBLI therapy?
(BLBLIs = beta-lactam, beta-lactamase inhibitors)
- Very broad spectrum, therefore predispose to c. diff.
- Names don’t end with “-illin” or start with “cef-“. Makes it easy to forget about penicillin allergy.
__1__ and teicoplanin are both glycopeptides that target __2__. They are only effective against gram __3__ strains.
1) Vancomycin
2) the cell wall
3) positive
Glycopeptides are unable to penetrate the outer-membrane porins of gram negative species, therefore they are ineffective against them.
How do glycopeptide antibiotics work?
The glycopeptides (vancomycin and teicoplanin) act on the cell wall.
They prevent peptidoglycan cross-linking by competitively inhibiting transpeptidases.
Vancomycin is an example of a ____ antibiotic.
Glycopeptide
Teicoplanin is an example of a ____ antibiotic.
Glycopeptide
Aminoglycosides, MLSs and tetracyclines all target ____
protein synthesis.
Aminoglycosides: gentamicin, amikacin
MLS = macrolides, lincosamides, streptogramins:
Erythromycin, clarithromycin, clindamycin
Tetracyclines:
Doxycycline, tigecycline
Which antibiotics bind to the 30s subunit of the ribosome, preventing translation of RNA into proteins?
Aminoglycosides:
Gentamicin, amikacin
Which antibiotics bind to the 50s subunit of the ribosome, preventing elongation of the protein chain?
Macrolides, Lincosamides, streptogramins (MLS):
Erythromycin, clarithromycin, clindamycin
Which antibiotics bind to the 30s subunit of the ribosome, inhibiting translation by interfering with the binding tRNA with rRNA?
Tetracyclines:
Doxycycline, tigecycline
Which antibiotics interfere with DNA by inhibiting the synthesis of folate?
Trimethoprim
Co-trimoxazole
Which antibiotics interfere with DNA synthesis by inhibiting DNA gyrase or topoisomerase IV (bacterial enzymes responsible for remodelling DNA)?
Quinolones: ciprofloxacin, levofloxacin
Why is trimethoprim not given in the the first trimester of pregnancy?
It is a folate antagonist, which could lead to spina bifida.
intended target is bacterial DNA synthesis
Which antibiotic works by binding to the cell’s DNA, leading to DNA degradation and cell death?
Metronidazole.
Only effective against anaerobic bacteria and protozoa.
Is nitrofurantoin effective against gram negative or gram positive bacteria?
Both, actually.
How do bacteria develop resistance to nitrofurantoin?
Reduced levels of nitrofuran reductase.
This enzyme is required to reduce the drug to it’s active metabolite.
What part of the cell does nitrofurantoin target?
Nitrofurantoin is an antibiotic that targets DNA to bring about cell death.
Daptomycin targets __1__ and is effective against gram __2__ bacteria.
1) plasma membrane
2) positive
Colistin targets __1__ and is effective against gram __2__ bacteria.
1) plasma membrane
2) negative
Which of the following would you choose if you wanted to target the plasma membrane of a gram negative bacteria?
a) Daptomycin
b) Nitrofurantoin
c) Colistin
d) Vancomycin
c) Colistin
Daptomycin targets the plasma membrane but is effective against G +ve species.
Nitrofurantoin targets DNA in both G -ve and G +ve species.
Vancomycin is a glycopeptide and targets the cell wall. Only effective against G +ve species.
Which antifungals target the cell wall?
Echinocandins (anidulafungin, caspofungin, micafungin)
Inhibit beta-1,3-glucan synthase, leading to construction of highly abnormal cell wall.
Why do we not use antifungals that target protein synthesis?
Fungi are eukaryotes, therefore their protein synthesis mechanisms are very similar to ours. Antifungals that targeted protein synthesis would likely kill our own cells, too.
What is the target of azoles?
Antifungals that target the plasma membrane of fungal cells. Include clotrimazole and fluconazole. They inhibit ergosterol - an essential component of the fungal cell membrane.
What is the target of Nystatin?
Antifungals that target the plasma membrane of fungal cells. They bind to ergosterol - causing physical damage to the fungal cell membrane.
What is the difference between the mechanism of action of azoles and nystatin?
Both antifungals target ergosterol in the plasma membrane.
Azoles inhibit ergosterol synthesis, whereas nystatin binds to ergosterol, causing physical damage.
Which are smaller, bacteria or fungi?
Bacterial cells are much smaller than fungal cells
Which are more complex, bacteria or fungi?
Bacterial cells are uniform simple structures
Fungal cells may have a complex structure and the same organism may have many different forms (hyphae, spores etc)
Define bacteriostatic
An agent with the capacity to inhibit the growth of bacteria.
E.g. protein synthesis inhibitors to stop organism growing and dividing.
Define bacteriocidal
An agent with the capacity to kill bacteria.
E.g. cell wall agents, such a penicillin.
Define minimum inhibitory concentration (MIC)
Minimum concentration of antimicrobial agent at which visible growth is inhibited
Define minimum bactericidal concentration (MBC)
• Minimum concentration of antimicrobial agent at which most organisms are killed
True or false: An organism with a low MIC (e.g. 0.1 mg/L) is likely to be a resistant strain.
False.
A low MIC indicates a sensitive organism. It means only a small amount of antimicrobial is required to inhibit that organism.
What terms describes this relationship:
“Activity of two antimicrobials given together is greater than the sum of their activity if given separately”
Synergism
What terms describes this relationship:
“One antimicrobial agent diminishes the activity of another”
Antagonism
What terms describes this relationship:
“Activity of one antimicrobial is unaffected by the addition of another agent”
Indifference
What is meant by ‘selective toxicity’, when referring to antimicrobial agents?
The agent must be able to kill the target organism without damaging the host.
Either:
- target isn’t present in human cells; or,
- target is inaccessible in human cells
Why are cell-wall agents ideal when treating infections?
Bacteria and fungi both have cell wall, but animals do not. Therefore these agents have great potential for selective toxicity.
What are bacterial cell walls made of?
Peptidoglycan
What are fungal cell walls made of?
beta-1,3-glucan
A large polymer of UDP glucose
Which antimicrobials target cell walls?
Beta-lactams (antibacterial)
Glycopeptides (antibacterial)
Echinocandins (antifungal)
Which beta lactams are extremely broad spectrum and generally used only as a last resort?
Carbapenems
Which enzyme confers resistance to penicillins and cephalosporins?
Extended spectrum b-lactamase (ESBL)
Which enzyme confers resistance to just some penicillins?
Staphylococcal b-lactamase.
Narrow spectrum of resistance.
What is tazocin used for?
Tazocin (pieracillin-tazobactam) is a b-lactam/b-lactamase inhibitor (BLBLI) combination used to treat bacterial infections that would be resistant to piperacillin on its own.
True or false: MRSA is resistant to glycopeptides
False
Glycopeptides (vancomycin, teicoplanin) are mainly used to treat staphylococcus aureus infections caused by MRSA, which is resistant to b-lactams.
Which antibiotics target protein synthesis?
Aminoglycosides (gentamicin, amikacin)
Macrolides, lincosamides, streptogramins (MLS Abx: erythromycin, clarithromycin, clindamycin)
Tetracyclines
(tetracycline, doxycycline, tigecycline)
Oxazolidinones
(Linezolid)
Mupirocin (anti-MRSA nasal ointment)
Which agents target the cell membrane?
Antibacterial: colistin (G-), daptomycin (G+)
Antifungal: Azoles, terbinafine (athletes foot), amphotericin B
What does rifampicin target?
Antibiotic targets RNA synthesis
Streptococci are resistant to aminoglycosides (e.g. gentamicin). What type of resistance is this?
Innate.
Their resistance is facilitated by a fundamental property of the species - impermeable cell wall - and therefore this is innate, rather than acquired.
What makes anaerobes innately resistant to aminoglycosides?
Aminoglycosides take advantage of O2-dependent active transport, something anaerobes don’t have.
Define MIC
Minimum Inhibitory Concentration
The minimum concentration of antimicrobial which inhibits microbial growth.
Match these interactions to the drugs below. Each can be used once, more than once, or not at all:
a) Enhance anticoagulant effect
b) Serotonin syndrome
c) Ototoxicity with furosemide
d) Reduces excretion of methotrexate
e) Hyperkalaemia with ACE inhibitors
f) Alters phenytoin concentrations
g) Increased nephrotoxicity with aminoglycosides
h) Nephrotoxicity with cyclosporin
i) Hyperkalaemia with ACE inhibitors
j) Increased plasma digoxin concentrations
1) Penicillins/beta-lactams
2) Quinolones (ciprofloxacin)
3) Macrolides (clarithromycin)
4) Trimethoprim
5) Glycopeptides
6) Linezolid
7) Aminoglycosides
1) Penicillins/beta-lactams: d
2) Quinolones (ciprofloxacin): f
3) Macrolides (clarithromycin): a, f, j
4) Trimethoprim: e, h
5) Glycopeptides: g
6) Linezolid: b
7) Aminoglycosides: c
Which adverse effect is most commonly associated with penicillins?
Allergic reactions
Co-amoxiclav is commonly associated with:
a) Prolonged QT interval
b) Disulfiram reaction with alcohol
c) Optic neuropathy
d) Cholestatic jaundice
d) Cholestatic jaundice
Which of these is most likely to cause tendonitis:
a) Ciprofloxacin
b) Amoxicillin
c) Metronidazole
d) Linezolid
a) Ciprofloxacin
Quinolones are linked with tendonitis and prolonged QT interval.
What are the main adverse effects associated with macrolides (e.g. clarithromycin)?
Diarrhoea
Which antibiotic is associated with erythema multiforme?
Trimethoprim
Which antibiotics can have ototoxic and nephrotoxic side effects?
Glycopeptides and aminoglycosides
What adverse effects are associated with linezolid?
Optic neuropathy and blood disorders
Which antibiotics are to be avoided in pregnancy?
Quinolones (ciprofloxacin): Arthropathy
Trimethoprim (folate antagonist): teratogenic in 1st trimester
Aminoglycosides: Ototoxicity
Nitrofurantoin: Neonatal haemolysis
What is passive immunity?
Transfer of antibodies from one source to a person. Usually short-term.
Examples include:
- transfer from mother to baby
- Ig injection
- blood transfusion
What is active immunity?
Long-lasting immunity produced by the immune system in response to antigens.
Examples include:
- Exposure to pathogen (live, attenuated, components)
- Vaccination
What pathogens cause meningitis?
Viruses, bacteria, mycobacteria, fungi, parasites
What is the main investigation for meningitis?
Lumbar puncture
What are normal CSF results?
Opening pressure: 5-20 cm H2O
Appearance: Clear
WBC count: less than 3
Cell differentiation: N/A
Protein: 0.2-0.5
Glucose: 0.6
What CSF results are characteristic of bacterial meningitis?
Raised pressure
Turbid appearance
WBC >500
Mainly polymorphs (essentially neutrophils)
Raised protein (>1, bacteria are proteins)
Low glucose (the bacteria are using it)
What CSF results are indicative of viral meningitis?
Normal pressure
Clear appearance
Raised WBC <1000
Mainly lymphocytes
Protein <1
Glucose normal or raised
What specific tests are indicated when investigating ?meningitis?
Lumbar puncture
Blood cultures
PCR
FBC, U and Es, LFTs clotting, glucose, CRP
What specific test is used for investigation of encephalitis?
CSF PCR (viral specifically)
Is lumbar puncture a suitable investigation for suspected brain abscess?
No - lumbar puncture should be discouraged as it is not very sensitive and the risk outweighs the benefit in this instance.
What investigations are indicated when you suspect a brain abscess?
Pus sampling from drain/biopsy
Blood cultures
What investigations aid diagnosis of rhinosinusitis?
No investigations helpful unless severe case.
If severe:
- pus sample from operative sinus lavage
- Blood investigations
What investigations may aid diagnosis of pharyngitis?
Majority do not require sampling.
If evidence of bacterial infection, send swabs.
Consider:
- EBV virology
- Diphtheria swab
- Pus sample if Quinsy abscess
What is the best investigation for confirming influenza?
PCR
Very high sensitivity and specificity
How is severity of community acquired pneumonia assessed?
CURB65 score
Confusion Urea Respiratory rate BP Age over 65
(low = 0-1, mod-severe = 2-5)
According to NICE, which patients require investigations for pneumonia?
Those with a CURB65 score 2 or above.
Sputum, blood cultures, atypical screen
What does an atypical screen look for in pneumonia patients?
Urine for legionella antigen
Nose/throat for mycoplasma PCR
Serum for any other atypical causes of pneumonia
How is TB exposure tested?
Heaf test
Mantoux test
IGRA (interferon G-releasing assay)
If a patient presents with pulmonary symptoms of TB, what investigations should be carried out?
CXR
3 sputum samples
Microscopy and culture for 8 weeks
PCR
What does M, C and S stand for?
Microscopy, culture, and sensitivity (M, C and S)
When should you investigate diabetic foot ulcers?
If non-infected, no investigation necessary
Mild infection: wound swab
Mod-severe infection: debride wound then collect living tissue sample
True or false: Bacteriuria is an indication for antibiotic prescription
False.
Only prescribe Abx when bacteriuria is accompanied by symptoms of UTI (increased frequency, dysuria)
Which generally requires the longer treatment: UTI or prostatitis?
Prostatitis
Majority of febrile UTIs will have prostatitis. Half of recurrent UTIs will have prostatitis
If you suspect a patient has epididymo-orchitis, what do you need to investigate?
Urine to test for UTI
Urine to test for chlamydia and gonorrhoea (rule out STI)
If severe: bloods/cultures, USS +/- drainage (if abscess)
How many stool samples would you normally send off when investigating infectious diarrhoea?
3
Multiple tests improves likelihood of picking up parasite
What non-invasive tests can be used to investigate H Pylori?
Urea breath test
Stool sample
Serum antibody test
**UBT and stool sample indicate active infection; serum test may be positive from previous or active infection.
When would you order a biopsy urease test?
Investigating H Pylori
Which pathogens are most likely to cause liver abscesses?
Pyogenic (bacteria)
Hydatid
Amoebic
How might you investigate a suspected liver abscess?
Pus sample (if safe to drain)
Stool for OCP (ova, cysts, parasite)
Bloods and cultures
Hydatid serology
Imaging
What investigations are important if you suspect endocarditis?
Blood cultures
- 3 sets of cultures should be taken at different times within first 24 hours
Echo
- Transthoracic echo (TTE)
- Transoesophageal echo (TOE)
TOE always indicated in suspected prosthetic valve endocarditis (PVE)
Other tests:
- FBC, CRP, U and Es, LFTs
- Serology for Bartonella, Chlamydia, Coxiella, Brucella
- Valve tissue: M,C and S and PCR
What tests should be used to investigate vascular graft infections?
3 blood cultures over 24 hours
Imaging
Tissue/fluid sample
How should you investigate viral hepatitis?
For Hep A, B, C:
- Serology antibody and antigen detection
- PCR
How do the serum antibody levels change over time in Hep A infection?
Acute phase: high IgM
Chronic phase: high IgG
IgM increases initially and then decreases, eventually disappearing.
IgG increases later and slower, but last longer.
True or false: Chronic-phase Hep-A can be detected by PCR of stool.
False, stool sample PCR can detect early stages of Hep A.
What serum antibody is observed when investigating Hep C?
IgG
After Hep C infection, the antibody persists for the rest of the person’s life, regardless of whether or not the infection is cleared.
What pathogen causes syphilis?
Treponema pallidum
How does primary-phase syphilis present?
Ulcers on and around genitals
How does secondary-phase syphilis present?
Widespread rash over palmar and plantar surfaces
Systemic illness
How does tertiary-phase syphilis present?
Following a long latent period, patients develop gummatous infection: fleshy growths/swellings over the skin.
Associated neurological and cardiovascular problems.
Clavulanic acid inhits the activity of which enzyme?
Beta-lactamase
What term means the activity of two antimicrobials given together is greater than the sum of their activity if given separately?
Synergism
Vertical transmission of auto-antibodies from mother to foetus and breastfeeding are examples of __?__ immunity
Passive
__?__ testing helps inform decisions on which antimicrobial agents to use in an infection
Sensitivity
Which drug used to treat tuberculosis targets RNA synthesis?
Rifamycin
Azidothymidine is an example of a ____ ____ ____ inhibitor
nucleoside reverse transcriptase
The C in CURB65 stands for?
Confusion
Terbinafine is commonly used to treat which types of infection?
Fungal infections, e.g.:
- Pityriasis versicolor
- Athletes foot
- Jock itch
Lamivudine is a __1__ analogue used in the treatment of __2__
1) cytosine
2) HIV
