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Microbiology > Respiratory Tract Infections > Flashcards

Respiratory Tract Infections Flashcards

1
Q

How do we divide RTIs?

A

Upper and lower

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2
Q

What are the URTIs?

A

o Sinusitis
o Tonsillitis

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3
Q

What are the LRTIs?

A
  • Bronchitis
  • Pneumonia
  • Empyema
  • Bronchiectasis
  • Lung abscess
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4
Q

What do we get RTIs?

A
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5
Q
  • 18yo female; fever, cough and malaise
  • Diagnosed with flu by GP (no ABx given)
  • Attended A&E with…
    • T 38C
    • 87% sats on room air
    • Chest clear, RR 24
    • Bloods (WCC 40.8, Neut 36.3, CRP 63)
A

CXR → double heart border (‘Sail’ sign)

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6
Q
A

densely consolidated and collapsed lower lobe

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7
Q
  • 18yo female; fever, cough and malaise
  • Diagnosed with flu by GP (no ABx given)
  • Attended A&E with…
    • T 38C
    • 87% sats on room air
    • Chest clear, RR 24
    • Bloods (WCC 40.8, Neut 36.3, CRP 63)

What is the most likely organism?

A

Streptococcus pneumoniae

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8
Q

What is happening?

A
  • Alpha-haemolytic and optochin-sensitive
  • Gram-positive cocci (chains and pairs)
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9
Q

What percentage of.community-acquired pneumonia is strep. pneumoniae responsible for?

A

30-50%

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10
Q

What does acute onset of strep. pneumonia cause?

A
  • Severe pneumonia
  • Fever and rigors
  • Lobar consolidation
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11
Q

What is strep pneumonia almost always sensitive to?

A
  • Almost always penicillin-sensitive
  • Penicillin-resistance strains may be imported from Southern Europe
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12
Q

Define pneumonia.

A

inflammation of the lung alveoli

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13
Q

What is the mortality of pneumonia?

A

Patients are sick with a mortality of 5-10%

20-40% admitted to hospital

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14
Q

How does pneumonia present?

A
  • Fever
  • Cough
  • Abnormal CXR
  • Pleuritic chest pain
  • SoB
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15
Q

How do we classify pneumonia?

A
  • Community-acquired
  • Hospital-acquired/nosocomial (i.e. ventilator-associated)
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16
Q

What are the underlying factors behind pneumonia that need to be considered?

A
  • Pre-existing lung disease
  • Immunocompromise
  • Geography, seasons, epidemics
  • Travel, exposure to animals
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17
Q

Why is no microbiological ID made in most cases of CAP?

A

this is often due to difficulty obtaining a good sputum sample and because of early treatment with antibiotics

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18
Q

What are the main organisms causing CAP?

A
  • Streptococcus pneumoniae
  • Haemophilus influenzae
  • Moraxella catarrhalis
  • Staphylococcus aureus
  • Klebsiella pneumoniae
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19
Q

How do pathogens causing CAP differ by age?

A
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20
Q

What are the causative organisms of CAP?

A
  • TYPICAL (85%)
    • Streptococcus pneumoniae
    • Haemophilus influenzae
  • ATYPICAL (15%)
    • Legionella
    • Mycoplasma
    • Coxiella burnetii (Q fever) from exposure to farm animals
      • Hepatitis
      • Chlamydia psittaci (Psittacosis) from exposure to birds
        • Splenomegaly, rash, haemolytic anaemia
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21
Q

What are the symptoms of CAP?

A
  • SoB
  • Cough ± sputum
  • Fever
  • Rigors
  • Pleuritic chest pain
  • Malaise, N&V
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22
Q

What are the signs of CAP?

A
  • Pyrexia
  • Tachycardia
  • Tachypnoea
  • Cyanosis
  • Bronchial breathing
  • Crackles
  • Dullness to percussion/tactile vocal fremitus
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23
Q

What investigations should be done on CAPs?

A
  • FBC, U&E, CRP
  • BCs, Sputum MC&S
  • ABGs
  • CXR
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24
Q

What scoring system do we use to assess severity of CAP?

A
  • Confusion
  • Urea > 7 mmol/L
  • RR > 30
  • BP < 90 systolic, < 60 diastolic
  • 65+ years

2 = consider admitting

2-5 = manage as severe / consider ITU

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25
Q

Define bronchitis.

A

inflammation of medium-sized airways

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26
Q

Who is bronchitis usually seen in?

A

Smokers

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27
Q

How does bronchitis present?

A
  • Cough
  • Fever
  • Increased sputum production
  • Increased shortness of breath
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28
Q

What does a CXR usually show for bronchitis?

A

Normal

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29
Q

What organisms cause bronchitis?

A
  • Viruses
  • Streptococcus pneumoniae
  • Haemophilus influenzae
  • Moraxella catarrhalis
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30
Q

What is the tx for bronchitis?

A
  • Bronchodilation
  • Physiotherapy
  • Antibiotics
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31
Q
  • 56yo man; flu-like illness
  • Presented with cough, fever, haemoptysis, pyrexia (but not severely unwell)
  • What organism would you suspect?
    • Strep pneumonia
    • H. influenzae
    • Staph aureus
    • Klebsiella
A

Cavitation on X ray

H. influenzae

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32
Q
A
  • Gram-negative cocco-bacilli - H. influenzae
  • (stain on chocolate agar)
33
Q

What percentage of CAPs does H. influenza cause?

A

15-35%

34
Q

What resistance can H.influenzae have?

A
  • May produce beta-lactamase
35
Q

When is H.influenzae infection more common?

A

With pre-existing lung disease

36
Q
  • 62yo man; SOB
  • Confusion, smoker, 91% saturation on room air, chest exam normal, hyponatraemia
  • What is the likely organism?
    • Moraxella catarrhalis
    • Mycobacterium TB
    • Legionella
    • Staph aureus
    • CMV
A

CXR - bilateral interstitial change

Legionella pneumophilia

37
Q
A
  • It is grown on a buffered charcoal yeast extract
38
Q

How is legionella spread? What does it cause?

A
  • Spread via inhalation of infected water droplets - aerosol
  • Environmental outbreaks
  • Associated with:
    • Confusion
    • Abdominal pain
    • Diarrhoea
    • Lymphopaenia
    • Hyponatraemia
  • Can cause multi-organ failure
39
Q

What is atypical pneumonia caused by?

A
  • Pneumonia caused by organisms without a cell wall:
    • Mycoplasma
    • Legionella
    • Chlamydia
    • Coxiella
40
Q

What is atypical pneumonia caused by?

A
  • Pneumonia caused by organisms without a cell wall:
    • Mycoplasma
    • Legionella
    • Chlamydia
    • Coxiella
41
Q

What antimicrobials (don’t/do) work on atypical pneumonias?

A
  • Cell-wall active antibiotics (e.g. penicillins) do NOT work → so need agents that work on protein synthesis
    • Macrolides (clarithromycin/erythromycin)
    • Tetracyclines (doxycycline=
42
Q

What are extrapulmonary features of atypical pneumonias?

A
  • (e.g. hepatitis, hyponatraemia) – characteristic of atypical pneumonias
43
Q

What percentage of CAPs are caused by atypical pneumonias?

A
  • Account for 20% of CAP
44
Q

What characteristics are found in atypical pneumonias?

A
  • Often have a flu-like prodrome before fever and pneumonia
  • Extra pulmonary complications
45
Q

How do we diagnose legionella pneumophila and how is it treated?

A
  • Investigation: urinary antigens
  • Sensitive to macrolides
46
Q

Where do we commonly see Coxiella burnetii? How is it transmitted? How is it investigated? How is it treated?

A
  • Common in domesticated farm animals
  • Transmitted by aerosol or milk
  • Investigation: serology
  • Sensitive to macrolides
47
Q

How is chlamydia psittaci spread? How is it investigated? How is it managed?

A
  • Spread from birds by inhalation
  • Investigation: serology
  • Sensitive to macrolides
48
Q
  • 74yo woman
  • SOB, fever (38.5C), right-sided pleuritic chest pain, reduced percussion note & decreased air entry right base
  • PMHx IHD, CABG, AF;
  • DHx warfarin
  • Otherwise well
  • Admitted → commended on cefuroxime and doxycycline  continued to spike fevers
    • What is the possible diagnosis?
      • A) Tuberculosis
      • B) Empyema
      • C) Mesothelioma
      • D) MRSA pneumonia
      • E) Aspiration pneumonia
A
  • CXR → homogenous shadowing with meniscus level of right side (CT → empyema with collapsed lung underneath)
  • Empyema
49
Q
A
  • These are difficult to treat because they have a wall around them and the pus itself is very acidotic which inactivates the antibiotics → hence why she continued to spike fevers even on ABx
50
Q

Why do patient fail to improve on treatment for empyema?

A
  • Empyema/abscess
  • Proximal obstruction (tumour)
  • Resistant organisms (travel hx)
  • Not receiving/absorbing antibiotics
  • Immunosuppression
  • Other diagnosis (lung cancer, cryptogenic organising pneumonia
51
Q
A

Bilateral interstitial changes

SARS-CoV-2

52
Q
A

Focal changes - SARS-CoV-2

53
Q
  • 21yo male, from Ecuador
  • Cough and WL
  • U&Es normal
  • Hb 10.4
  • WCC 9.8
  • HIV -ve
  • CRP 173
  • Alb 31
  • What is the causative organism?
    • A) Staphylococcus aureus
    • B) Aspergillus fumigatus
    • C) Mycobacterium tuberculosis
    • D) Haemophilus influenzae
    • E) Pneumocystis jiroveci
A
  • CXR  right-sided apical shadowing → diagnosed TB
54
Q

What are clues for a dx of TB?

A
  • Clues: Geographical exposure/Ethnicity, Prolonged prodrome, Fevers, Weight loss, Haemoptysis
  • CXR: classically upper lobe cavitation (but can vary)
55
Q
A
  • TB
  • Staining:
    • An auramine stain and a Ziehl-Neelsen stain will be done
    • Red rods are the acid-fast bacilli
56
Q

Define HAP.

A
  • A pneumonia onset >48 hours in hospital
57
Q

What do patients with HAP usually have?

A
  • Patients have often had previous antibiotics and maybe even ventilation
  • Bronchial lavage is desirable (differentiate upper respiratory from lower respiratory flora)
58
Q

What is the aetiology of hospital acquired acquired pneumonias?

A

Enterobacteriaciae (e.g. E. coli, K. pneumoniae)

59
Q
  • 64yo retired general
  • Treated for lymph node TB
  • Increasing SOB, non-productive cough, chest exam normal
  • What organism is likely to have caused this?
  • A) Aspergillus fumigatus*
  • B) Influenza*
  • C) Mycoplasma pneumoniae*
  • D) Cytomegalovirus (CMV)*
  • E) Pneumocystis jiroveci*
A
  • CXR → bilateral ground-glass shadowing (“bat’s wing”)
  • Pneumocystitis jirovecii
60
Q

What type of organism is pneumocystitis jirovecii? Where is it found?

A

Protozoan

Ubiquitous in the environment

61
Q

What is the presentation of pneumocystis jirovecii? What sign would you see on XR?

A
  • Dry cough
  • Weight loss
  • SOB
  • Malaise

Bat’s wing

62
Q

What are the Ix and Mx of pneumocystis jieovecii?

A

NOTE: the walk test (attaching an oxygen saturation probe and asking the patient to walk) will show desaturation on exertion

  • Investigations: bronchoalveolar lavage
  • Treatment: co-trimoxazole (septrin)
  • Prophylaxis: co-trimoxazole
63
Q
A

Pneumocystis jirovecii

64
Q
  • 22yo man, chemotherapy for leukaemia
  • Prolonged neutropenia (<1.0), fevers, raised inflammatory markers
  • ABx so far : meropenem, ciprofloxacin, vancomycin, tazocin, ganciclovir

A)MRSA

B)Aspergillus sp.

C)Mycobacterium tuberculosis

D)CMV

E)Pseudomonas aeruginosa

A
  • CT thorax : non-specific (interstitial) changes on the CT scan → Aspergillus fumigatus
65
Q

What are the different presentations of aspergillum fumigatus?

A

Allergic bronchopulmonary aspergillosis

  • Chronic wheeze
  • Eosinophilia
  • Bronchiectasis

Aspergilloma

  • Fungal ball, often in pre-existing cavity
  • May cause haemoptysis

Invasive aspergillosis

  • Immunocompromised
  • Treatment: amphotericin B
66
Q
A

Aspergillus fumigatus

67
Q

What infections are you likely to get with

  • HIV
  • Neutropenia
  • BM transplant
  • Splenectomy
A
  • HIV → PCP, TB, Atypical mycobacteria
  • Neutropoenia → Fungi (e.g. Aspergillus spp)
  • Bone Marrow Transplant → CMV
  • Splenectomy → Encapsulated organisms (S. pneumoniae, H. influenzae, malaria)
  • Anything can do anything
68
Q

What different samples can be sent in LRTIs

A
  • Sputum/induced sputum
  • Blood cultures
  • BAL
  • Pleural fluid
  • Antigen tests
  • Antibody tests
  • Immunofluorescence
  • PCR
69
Q

For what should antigen tests be sent?

A
  • Limited urine antigen tests available for:
    • Legionella pneumophila
    • Streptococcus pneumoniae
  • Send in severe CAP
70
Q

When should antibody tests be collected? What are we looking for? What are the most useful organisms to test for?

A
  • Only useful on paired serum samples (one acutely unwell and another when getting better)
  • Usually collected on presentation and 10-14 days later
  • Looks for a rise in antibody level over time
  • Most useful organisms to send antibody tests for because they are difficult to culture:
    • Chlamydia
    • Legionella
71
Q

What does immunofluorence do? What is it used for? What is the most common one used?

A
  • Antibody is labelled with fluorescent dye
  • Often used in virology
  • PCP immunofluorescence is the most commonly used one in microbiology labs
  • PCP may also be detected by Silver stain in cytology labs
72
Q

How would you choose abx tx for RTI?

A
73
Q

Describe the abx framework

A
74
Q

What is the empirical therapy of CAP?

A
  • Each hospital has its own guidelines
    • Mild-Moderate: Amoxicillin [OR erythromycin/clarithromycin]
    • Moderate-Severe
      • Needing hospital admission: Co-amoxiclav (augmentin) AND clarithromycin
      • Allergic: Cefuroxime AND clarithromycin
75
Q

What is the empirical therapy of HAP?

A
75
Q

What is the empirical therapy of HAP?

A
76
Q
  • 21yo man, no PMHx, smoker, drinker
  • Presented cough, SOB, sats 89% room air, hypotensive
  • How would you treat this pt?
    • A)Amoxicillin
    • B)Piperacillin/tazobactam and vancomycin
    • C)Co-amoxiclav
    • D)Co-amoxiclav and clarithromycin
    • E)Rifater, isoniazid, pyrazinamide and ethambutol
  • What other mx should be given?
A
  • CXR : RUZ pneumonia
  • Co-amoxiclav and clarithromycin
  • Fluid resuscitation
  • Supplemental O2
  • Senior support requested
77
Q

How do we prevent pneumonia?

A
  • Smoking cessation
  • Vaccination:
    • Childhood immunisation schedule
    • Adults → influenza annually, pnemovax every 5 years

Microbiology (19 decks)

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