Micro Flashcards
What is the name of the primary granulomatous lesion of TB (often subpleural)?
Ghon focus
Presentation of TB, including 3 more serious complications
- Fever
- Night sweats
- Weight loss
- Haemoptysis
Subacute meningitis - confusion, personality change, meningism
Spinal (Pott’s disease) - back pain, discitis, iliopsoas abscess
Miliary TB - disseminated haemotgenous spread
Investigations for TB
- CXR - upper lobe cavitation (post-primary)
- Sputum sample - microscopy on Ziehl-Neelson stain, culture on Lowenstein-Jensen medium for 6 weeks (gold standard) => acid fast bacilli (red rods) seen.
- Tuberculin skin test - shows exposure (including BCG)
- IGRA - shows exposure (not BCG)
What is a more affordable and sensitive stain to Ziehl-Neelson?
Auramine-rhodamine
but less specific - more false positives. Specific = healthy patients getting correct diagnosis
First line treatment for TB
RIPE
- Rifampicin - 6 months
- Isoniazid - 6 months
- Pyrazinamide - 2 months
- Ethambutol - 2 months
Side effects of first line TB treatment
- Rifampicin - orange secretions
- Isoniazid - peripheral neuropathy
- Pyrazinamide - hepatotoxic
- Ethambutol - optic neuritis
2nd line TB treatment and prophylaxis
2nd line
• Injectables (amikacin), quinolones, linezolid
(Resistance problem)
Prophylaxis
• Isoniazid monotherapy
Clinical features of Leprosy (Mycobacterium leprae)
- Skin depigmentation
- Nodules
- Trophic ulcers
- Nerve thickening (irreversible)
Slow growing, lifelong illness
Who does Mycobacterium Avium-Intracellular complex affect and what infection does it resemble?
- Disseminated infection in immunocompromised
* Resembles TB if underlying lung disease
Who does Mycobacterium Marinarum (fish tank granuloma) affect and how does it present?
Aquarium owners
Papules/plaques
Where is Mycobacterium ulcerans (Buruli ulcer) common and how does it present?
Tropics / Australia
Painless nodules => ulceration, scarring and contractures
What is inflamed in pneumonia?
Alveoli
Score system name for pneumonia
CURB-65
3 common bacterial microorganisms that cause hospital-acquired pneumonia
- S. aureus
- Klebsiella
- Pseudomonas haemophilus
What is the definition of hospital-acquried pneumonia?
Pneumonia after >48 hours of hospital admission
How is atypical pneumonia different to typical?
Atypical
• No classic signs and symptoms
• Not in-keeping with CXR
• Don’t respond to penicillin ABx (no cell wall)
3 common bacterial microorganisms that cause bronchitis
- S. pneumoniae
- H. influenzae
- Moraxella catarrhalis
What is bronchitis?
- Inflammation of medium sized airways
* Cough with sputum for most days for 3 months, for 2 or more consecutive years
Which pathogen causing penumonia typically causes rusty-coloured sputum and is usually lobar on CXR
S. pneumonia
Which pathogen causing pneumonia is associated with recent viral infection (e.g. influenza) and shows cavitation on CXR?
S. aureus
Which pathogen causing pneumonia is associated with alcoholism and haemoptysis?
Klebsiella
What is seen on microscopy of • S. pneumonia • H. influenza • M. catarrhalis • S. aureus • K. pneumonia
- S. pneumonia: +ve diplococci
- H. influenza: -ve cocco-bacilli
- M. catarrhalis: -ve coccus
- S. aureus: +ve cocci “grape-bunch clusters”
- K. pneumonia: “-ve rod, enterobacter”
How should you treat atypical pneumonia?
Macrolides (clarithromycin) + tetracyclines (doxycline)
Name 4 causes of atypical pneumonia
- Legionella pneumophilia
- Mycoplasma pneumonia
- Chlamydia pneumonia
- Chlamydia psittaci
What can Legionella be grown on?
Buffered charcoal yeast extract
Cause of hyponatraemia in Legionella?
Diarrhoea
Risk population, presentation and test for Mycoplasma pneumonia?
Univeristy / boarding school students
• Dry cough
• Athralgia
• Erythema multiforme
(Risk SJS, AIHA)
Cold agglutinin test +ve
What can cause Chlamydia psittaci?
Birds
What are common causes of respiratory tract infections in HIV patients?
- P. jiroveci - fungus causing Pneumocystis pneumonia (desats on exercise)
- TB
- Cryptococcus neoformans
What is a common fungal cause of respiratory tract infection and its treatment in neutropenic patients?
Aspergillus spp.
Amphotericin B
What are common causes of respiratory tract infection in BM transplant patients?
Aspergillus + CMV
What type of organisms commonly cause respiratory tract infection in splenectomy patients?
Encapsulated organisms
What are common causes of respiratory tract infection in CF patients?
- Pseudomonas aeruginosa
* Burkholderia cepacia (high mortality)
How can S. pneumoniae and Legionella be diagnosed in severe CAP?
Urine antigen tests
Which diagnostic tests are useful in difficult-to-culture causes of pneumonia such as Chlamydia?
Paired serum samples
At presentation, then 10-14 days - rise in Ab level
Boat-shaped organisms seen. What is the diagnosis and the stain that was used?
PCP
Silver stain
ABx treatment for mild / moderate classical CAP
Amoxicillin
OR
Clarithromycin / doxycycline
ABx treatment for severe classical CAP
Co-amoxiclav + Clarithromycin
OR
Erythromycin
Outline CURB-65
- Confusion
- Urea > 7
- RR ≥ 30
- SBP < 90, DBP ≤ 60
- ≥ 65 yo
ABx treatment for HAP
- Ciprofloxacin +/- vancomycin
- ITU: piptazobactam + vancomycin
Aspiration pneumonia - cefuroxime + metronidazole
Legionella and Chlamydia psittaci ABx
Macrolides
S. aureus pneumonia ABx
Flucloxacillin
MRSA pneumonia treatment
Vancomycin
What is infective endocarditis and the symptoms?
Infection of innermost layer of heart - usually valves
- Fever
- Anorexia
- Weight loss
- Night sweats
Acute - SOB, chest tightness, embolic complications
Why is it important to ask about dental history if infective endocarditis is suspected?
Important route of infection
2 risk factors for infective endocarditis
- Right heart failure
* Valve replacement
What can be seen on examination in infective endocarditis?
- Changing heart murmurs
- Clubbing
- Splinter haemorrhages
- Osler’s nodes (tender)
- Janeway lesions (non-tender)
- Roth spots (fundoscopy)
- Splenomegaly
Why is tricuspid valve endocarditis more common in intravenous drug abusers?
IV reaches right heart first
2 infective agents of subacute bacterial endocarditis
- Low virulence strep (S. viridians)
* Staph. epidermis
What type of endocarditis do the following pathogens cause:
• S. aureus - IVDA
• S. pyogenes
• Coagulase negative staphylococci - prosthetics
Acute bacterial endocarditis
Empirical treatment of infective endocarditis
Native valve
• Acute: flucloxacillin
• Indolent: penicillin + gentamycin
Prosthetic valve
• Vancomycin + gentamycin + rifampicin
Which valves are most commonly involved in infective endocarditis?
Mitral + aortic valves
Outline Dukes criteria for infective endocarditis
2 major
1 major + 3 minor
5 minor
Major
• Positive blood cultures
• Echo findings - vegetations
Minor
• Predisposing heart condition or IVDA
• Fever >38 or high CRP
• Immunologic phenomena e.g. splinter haemorrages, haematuria
• Vascular phenomena
• Positive blood culture not typical of IE
Treatment for MSSA endocarditis
Flucloxacillin
What is important to note about taking blood cultures in infective endocarditis?
Take at least 3 from different sites (new guidelines suggest 6)
(Investigations are x3 BC and echo)
Why is 6 weeks of ABx treatment needed for infective endocarditis?
Valves have poor vascular supply
What are the 3 mechanisms of GI disease
- Secretory diarrhoea with no fever or white cells in stool
- Inflammatory diarrhoea with fever and white cells in stool
- Enteric fever with little stool change
Give an example of secretory diarrhoea and its mechanism
Cholera toxin
• cAMP normally opens chloride channels in apical membrane of enterocytes
• Toxin opens chloride channels - efflux into lumen - loss of water and electrolytes
Describe the mechanism where systemic toxicity occurs in secretory diarrhoea, with reference to superantigens
- Superantigens bind to T cell receptors outside the binding site
- Cytokine release by CD4+
How can Staph aureus food poisoning spread?
Unwashed hands or skin lesions on food handlers touching food
1/3 are chronic carriers, 1/3 are transient carriers
How do you diagnose staph aureus food poisoning?
- Catalase and coagulase positive gram positive coccus - tetrads or clusters
- Gold-yellow colonies with beta haemolysis on blood agar
Mechanism and effect of staph aureus food poisoning
- Produces enterotoxin (exotoxin)
- Superantigen in GIT
- Release of IL1 and IL2
- Vomiting & watery diarrhoea
Where can Bacillus cereus come from, how does it cause food poisoning, and how does it present?
- Spores germinate in reheated fried rice
- Heat stable emetic toxin not destroyed by reheating
- Heat labile diarrhoeal toxin if not heated high enough
- Watery, non-bloody diarrhoea
- Sudden vomiting
Food cause, mechanism and effects in clostridium botulinum (Gram positive anaerobe)
Gram positive anaerobe
- Canned / vaccum packed food, honey
- Blocks ACh release from peripheral nerves
- Descending paralysis
Food cause, mechanism and effects in clostridium perfringens (Gram positive anaerobe)
Gram positive anaerobe
- Reheated meat
- Superantigen in small intestine
- Watery diarrhoea and gas-gangrene
Causes and name of disease caused by clostridium difficile (Gram positive anaerobe)
- HAI from ABx therapy (cephalosporins, cipofloxacin, clindamycin)
- Pseudomembranous colitis
Who does Listeria monocytogenes affect, what causes it, how does it present and how is it treated?
- Pregnant women
- Refridgerated food, particularly unpasteurised dairy
- Presents with watery diarrhoea, fever (little vomiting)
- Tx ampicillin
Common name for E. coli effect and where is it found?
- Traveller’s diarrhoea
* Food and water contaminated with human faeces
2 types of enterotoxins in E. coli and what do they do?
- Heat labile - stimulates adenyl cylase and cAMP
* Head stable - stimulates guanylyl cylase
Which parts of the GIT do E. coli toxins act?
Jejunum and ileum
What are the 4 types of E. coli? What do they do?
Enterotoxigenic (ETEC) - main cause of travellers diarrhoea
Enteropathogenic (EPEC) - infantile diarrhoea
Enteroinvasive (EIEC) - dysentery
Enterohaemorrhagic (EHEC) - caused by verotoxin producing 0157:H7 E. coli => HUS (anaemia, thrombocytopaenia, renal failure)
E. coli treatment
No specific treatment - self-limiting
Outline identification of Salmonella inc. antigens
TSI agar - red colonies with black centres (also produce hydrogen sulphide on XLD agar)
Non-lactose fermenting
Antigens:
• Cell wall - O
• Flagellar - H
• Capsular - Vi (virulence, anti-phagocytic)
Patient presents with slow onset fever, constipation and rose spots. What is the diagnosis, how is it transmitted, where does it multiply in the body and how is it treated?
Salmonella typhi / paratyphi
• Transmitted via water and food contaminated by human faeces
• Multiplies in Peyers patches
• Treatment with iv fluids, iv ceftriaxone, then PO azithromycin
Patient falls ill after eating undercooked poultry and eggs. What is the pathogen responsible, how do you expect them to present, which tissue is invaded and how is it treated?
Salmonella enteritidis
- No fever
- Diarrhoea
- Invasion of epithelial and subepithelial tissue of bowels
- Self-limiting, no tx
Is shigella lactose fermenting and does it produce hydrogen sulphide? Furthermore, what are the cell wall and polysaccharide antigens?
- Non-lactose fermenting
- Doesn’t produce hydrogen sulphide
Antigens:
• Cell wall- O
• Polysaccharide - A-D, indentifies species
Which part of the GIT does shigella invade, how does it present, what treatment should be avoided, and which group of people are at higher risk of contracting the infection?
Invasion of mucosa of distal ileum and colon
Fever and severe bloody diarrhoea
Avoid abx
Increased MSM risk
Patient has rice water stool with no inflammatory cells. What is the pathogen responsible, how it transmitted, what leads to the watery stool, how it treated, and what is the epidemic subset?
Vibrio cholerae
• Food and water contaminated with human faeces e.g. shellfish
• A + B subunits - increased cAMP opens Cl- channel at apical membrane, efflux of Cl- to lumen
• Supportive tx
O1 group - epidemic subset
Patient in Japan presents with diarrhoea. He has been eating raw seafood (oysters) recently. Treated successfully with doxycycline. What is the pathogen responsible?
Vibrio parahaemolyticus
A HIV-positive shellfish handler was eating shellfish for dinner. He cut himself by accident at dinner, cleaned it up and went for a swim in the sea. He presented with cellulitis, diarrhoea, and vomiting, and has become septic. What is the responsible pathogen and what abx could be considered?
Vibrio vulnificus
• Treatment with doxycline
Which genus of gram-negative bacteria are comma shaped and late lactose fermenters? Are they oxidase positive?
Vibriosis
• Oxidase positive
Which genus of gram-negative bacteria are comma or S shaped? Are they oxidase positive?
Campylobacter
• Oxidase positive
Patient presents with a headache and fever, followed by abdominal cramps and bloody, foul-smelling diarrhoea. He admits to drinking unpasteurised milk and having a BBQ with chicken the other day. The BBQ from the garden may not have been cleaned either. What is the responsible pathogen and how should this be treated?
Campylobacter jejuni
• If immunocompromised or >5 days: macrolides e.g. erythromycin
How is Yersinia enterolitica transmitted, what temperature does it prefer, how does it present, and what other manifestations is it associated with?
- Food contaminated with domestic animals faeces
- Prefers 4 degrees (cold enrichment)
- Enterocolitis, mesenteric adenitis with necrotising granulomas
- Associated with reactive arthritis and erythema nodosum
Patient (MSM) has returned from camping where he cooked food over a fire and drank water from the stream. He has no fever, but foul-smelling non-bloody diarrhoea. He also has RUQ pain. What is the pathogen responsible, what is the cause of the RUQ pain, and how would this be treated? How could aquiring this infection through the contaminated water be prevented?
Entamoeba histolytica • Foul-smelling non-bloody diarrhoea (motile trophozoite in diarrhoeal, non-motile cyst in non-diarrhoeal) • RUQ pain - liver abscess • Treat with metronidazole • Boiling water and water filters
Flask-shaped ulcer seen on histology. Pathogen also detected in ELISA string test, stool microbiology and serology (invasive disease).
What is the pathogen responsible?
Entamoeba histolytica
Which part of GIT does Cryptosporidium parvum infect, how does it present, and how is it treated in aduts/kids?
- Infects jejunum
- Severe diarrhoea in immunocompromised
- Treat with paromomycin, or nitazoxanide in kids
Oocysts seen in stool by modified Kinyoun acid fast stain. Pathogen responsible?
Cryptosporidium parvum
Pear shaped trophozoite seen in traveller/hiker/mental hospital. Pathogen responsible and infection it is similar to.
Giardia lamblia, similar to Entamoeba histolytica
How does rotavirus present and how much exposure is needed for lifelong immunity
- Watery diarrhoea
* 2x exposure - immunity
How are UTI symptoms in children <2 years different to >2 years?
Non-specific i.e. failure to thrive, vomiting, fever
rather than frequency, dysuria, flank pain
Diagnosis of UTI
Differentiate between coliforms / non-coliform UTI
• Urine dipstick - positive nitrites = coliform, -ve nitrites +ve leucotyes = non-coliform
Why are urine samples often contaminated?
Urethral areas aren’t sterile, even though bladder urine is sterile
Which cells seen on microscopy are indicative of contamination of urine sample? And which are indicative of infection?
Contamination - squamous epithelial cells
Infection - white cells (sterile pyuria) - consider STI, TB, bladder neoplasm, prior abx treatment
Treatment for UTI in women andn men
Women
Nitrfurantoin
or Trimethoprim if low risk of resistance and EGFR >45
Men
Levofloxacin or ciprofloxacin
Treatment for pyelonephritis
Co-amoxiclav +/- gentamicin
Treatment for candida UTI (caused by indwelling catheter)
No benefit of treating asymptomatic infection
3 pathogens causing surgical site infections and presentation
- S. aureus
- E. coli
- P. aeruginosa
• Failure to heal
Which layers does a deep incisional surgical site infection reach?
Fascial and muscle layers
What number of microorganisms increases risk of surgical site infection?
> 10^5
Most common microorganism in osteomyelitis
S. aureus
General treatment for osteomyelitis
- IV ABx for at least 6 weeks
2. Debridement
Pathophysiology of septic arthritis
- Bacterial proliferation in synovial fluid
- Inflammatory response
- Joint damage - exposure of fibronectin
- Bacteria (most common S. aureus) adhere to fibronectin
Diagnosis and treatment for septic arthritis
- Synovial fluid aspiration (WBC >50,000)
- Blood culture
- ESR and CRP
- ABx: 2 weeks IV, 4 weeks oral
- Joint drainage
3 features of prosthetic joint infection
- Joint never right after operation
- Early failure
- Sinus tract
Common microorganism in prosthetic join infection
Coagulase negative staphylococci (more common than S. aureus)
Diagnosis and treatment for prosthetic joint infection
- X-ray - loosening (bone loss)
- Joint aspiration - higher WCC in hip vs knee
- Intraoperative 5x tissue specimens - >3 identical organisms = PJI
- Remove prosthesis and dead bone
- Re-implant with antibiotic impregnated cement
Treatment for MRSA surgical site infection
IV linezolid
Cause of C. diff
Gut flora disturbed by Abx, particularly
• Clindamycin
• Cephalosporins
• Ciprofloxacin
Spore ingestion
-> pseudomembranous colitis etc.
Treatment for C. diff
ORAL metronidazole
3 main causative organisms of acute meningitis (hours-days)
- N. meningitis
- Strep pneumoniae
- H. influenzae B
3 causative organisms of meningitis in neonates
- Group B Strep
- Listeria
- E. coli
2 causes of chronic meningitis. What does CT show?
TB or Cryptococcus
Leptomeningeal enhancement on CT
2 risk factors of meningitis (N. men and S. pneu)
- Complement deficiency
* Hyposplenism
Treatment for bacterial meningitis. What would you consider if consciousness was reduced?
Resus
Ceftriaxone and corticosteroids
Cover listeria with ampicillin
Don’t use corticosteroids under 3 months
Consider IV acyclovir if consciousness affected to cover encephalitis
Cause of bacterial and amoebic encephalitis
Bacterial - Listeria
Amoebic - Naegleria fowleri (lives in warm water)
Imaginging of spinal infections
MRI > CT
What’s the most common infection of the CNS, organisms implicated and age group affected?
Aseptic meningitis
Cocksackie group B and echovirus
< 1 year