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Path 2022 > Microbio > Flashcards

Microbio Flashcards

1
Q

Causative agents of HAP

A 
More gram -ve organisms (vs CAP)
•	Enterobacteriales 31%
•	Staph aureus 19%
•	Pseudomonas spp. 17%
•	Acinetobacter baumannii 6%
•	Fungi e.g. Candida sp. 7%
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2
Q

Atypical CAP organisms

A 
Atypical = organisms without cell wall
o	Mycoplasma – epidemics every 4-6 years
o	Legionella - water coolers, AC
o	Chlamydia psittaci - birds
o	Coxiella (Q fever) – farm/domestic animals
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3
Q

CURB-65 Score

A 
Confusion
Urea >7
RR >30
BP - systolic <90 or diastolic <60
>65 years old

2 points = consider admitting
2-5 = admit + treat as severe

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4
Q

Abx guidelines for atypical CAP

A

NOT cell-wall active Abx e.g. penicillins (since they don’t have a cell wall)

Sensitive to macrolides e.g. clarithromycin
OR Tetracyclines e.g. doxycycline

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5
Q

Key features of Streptococcus Pneumoniae (CAP)

A

Gram +ve
Acute onset fever, rigors, rust coloured sputum!
May follow recent viral illness?
Tx = almost always penicillin sensitive (amoxicillin, co-amoxiclav)

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6
Q

Key features of Legionella Pneumophila (CAP)

A 
Atypical CAP
Inhalation of water droplets - AC, water coolers
Extra-pulmonary Sx
- hyponatraemia
- hepatitis
- confusion
- abdominal pain
- diarrhoea
- lymphopenia

Dx = urine/serum antigen + special buffered charcoal yeast extract culture

Tx = macrolides e.g. clarithromycin

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7
Q

Key features of Haemophilus influenzae (CAP)

A

Gram -ve
Cocco-bacilli
More common if pre-existing lung disease
Dx: chocolate agar culture

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8
Q

TB Ix Results / Diagnosis

A

CXR –> upper lobe cavitation is typical (but varies)

Auramine rhodamine stain

Ziehl-Neelsen stain

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9
Q

Key features of PCP / Pneumocystis jirovecii

A

Insidious onset

  • dry cough
  • SOB + reduced exercise tolerance
  • weight loss
  • malaise

Ix:
CXR - bat wing
Immunofluorescence of BAL
Silver stain in cytology lab

Tx = septrin (co-trimoxazole)

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10
Q

Aspergillus fumigatus lung disease - key features

A

Allergic bronchopulmonary aspergillosis (ABPA)

  • chronic wheeze
  • eosinophils
  • bronchiectasis

Aspergilloma

  • fungal ball often in pre-existing cavity
  • may cause haemoptysis

Invasive aspergillosis

  • immunocompromised
  • tx = amphotericin B
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11
Q

CAP Abx Guidelines

A

Mild-moderate:

  • Amoxicillin OR
  • Erythromycin/Clarithromycin

Moderate-severe (needing hospital)

  • Co-amoxiclav AND clarithromycin
  • If penicillin allergic: Cefuroxime AND clarithromycin
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12
Q

Reservoir for Campylobacter

A

Poultry (100% Uk chickens carry in GI tract)

Cattle

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13
Q

Ix for Campylobacter

A

Stool culture - 48-72 hours

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14
Q

Reservoir for Salmonella

A

Poultry

Amphibians/reptiles

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15
Q

Forms of Bartonella henselae infection

A

Cat scratch disease

  • macule at inoculation site
  • becomes pustular
  • regional lymphadenopathy
  • systemic sx

Bacillary Angiomatosis

  • immunocompromised people
  • skin applies
  • disseminated multi organ + vascular involvement
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16
Q

Tx for Bartonella infection

A

Erythromycin, doxycycline

+ rifampicin if immunocomprised (bacillary angiomatosis)

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17
Q

Tx for Toxoplasmosis

A

Pregnant = spiramycin

Immunosuppressed = pyrimethamine, sulfadiazine

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18
Q

Presentation of Brucellosis

A

Mimics extra pulmonary TB

  • back pain
  • orchitis
  • fever
  • focal abscesses e.g. psoas, liver
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19
Q

Tx for brucellosis

A

Doxycycline + gentamicin or rifampicin

6 weeks

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20
Q

Q fever causative organism?

A

Coxiella burnetii

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21
Q

Tx for coxiella Burnetti?

A

Doxycycline

Hydroxychloroquine

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22
Q

Tx for rabies

A

Post exposure vaccine

+/- human normal immunoglobulin (no specific formation)

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23
Q

Rat bite fever presentation

A

Fever
Polyarthralgia
Maculopapular rash —> purpuric
+/- Endocarditis

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24
Q

Tx for rat bite fever

A

Penicillins

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25
Q

Causative organism of rat bite fever?

A

Streptobacillus moniliformis

Spirillum minus

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26
Q

Viral haemorrhagic fevers

  • Reservoir & disease
A

? Bats - Ebola
? Bats - Marburg
Rats - Lassa
Ticks - Congo Crimean haemorrhagic fever

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27
Q

HIV encephalopathy signs on imaging

A

Basal ganglia calcification
White matter changes
Atrophy —> enlarged ventricles

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28
Q

Methods of vertical HIV transmission

A

In Utero
intra partum
Breast feeding

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29
Q

Factors affecting maternal —> baby HIV transmission

A

Major = maternal viral load

Placenta - healthy is protective, toxoplasmosis or malaria co-infection causes unhealthy placenta
PPROM
1st born twin - approx double risk
Breast feeding - 4% transmission for every 6 months

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30
Q

Type I Antimicrobial activity pattern

A

Concentration dependent killing

Examples:

  • aminoglycosides
  • daptomycin
  • fluoroquinolones
  • ketolides
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31
Q

Type 2 antimicrobial activity pattern

A

Time dependent killing

Examples:

  • carbapenems
  • cephalosporins
  • erythromycin
  • linezolid
  • penicillins
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32
Q

Type 3 antimicrobial activity pattern

A

Time dependent killing + moderate-prolonged persistent effects

Examples:

  • azithromycin
  • clindamycin
  • oxazolidinones
  • tetracyclines
  • vancomycin
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33
Q

Beta lactam Abx MOA

A

Inactivate enzymes needed for terminal stages of cell wall synthesis (the penicillin binding proteins)

Induce cell lysis

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34
Q

What bacteria will beta-lactams NOT work on?

A

Bacteria that lack peptidoglycan cell wall

Chlamydia, mycoplasma

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35
Q

Pattern of activity across Cephalosporin generations

A

Activity against gram -ve increases (and gram +ve decreases)

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36
Q

Cephalosporins

A

1st gen = Cephalexin

2nd gen = Cefuroxime

3rd gen = Cefotaxime, Ceftriaxone, Ceftazidime

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37
Q

Glycopeptide Abx - examples and MOA

A

Vancomycin, (Teicoplanin)

Binds to D-Ala, D-Ala
Prevents trans glycosidase and transpeptidase binding
Cell wall lysis as bacterium divides

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38
Q

Side effects of Glycopeptide Abx

A

Nephrotoxic
+/- Ototoxic

Require drug level monitoring

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39
Q

Aminoglycoside Abx - MOA and examples

A

Bind to 30S ribosomal subunit
Prevent elongation of polypeptide chain + cause misreading of codons along mRNA

E.g., gentamicin, amikacin, tobramycin

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40
Q

Tetracycline Abx - MOA & examples

A

Reversibly bind 30S ribosomal subunit
Prevent amino acyl atRNA binding to ribosomal acceptor site - inhibits protein synthesis

E.g. doxycycline

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41
Q

Side effects of doxycycline

A

Deposited in growing bones - do not give in children, pregnant or breastfeeding women
Teratogenic
Light sensitive rash

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42
Q

Macrolide Abx - MOA & Examples

A

Bind to 50S ribosomal subunit
Interfere with translocation

E.g., azithromycin, clarithromycin, erythromycin

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43
Q

Chloramphenicol MOA

A

Binds peptidyl transferase of 50S ribosomal subunit

Inhibits peptide bond formation

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44
Q

Side effects/risks of chloramphenicol

A

Grey baby syndrome - inability to metabolise drug

Aplastic anaemia

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45
Q

Oxazolidinone Abx - MOA & example

A

Binds 23S component of 50S subunit
Prevents formation of functional 70s initiation complex

E.g., linezolid

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46
Q

Most common valve affected in Infective Endocarditis in IVDU

A

Ticuspid

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47
Q

Acute Infective endocarditis - causative organisms

A

high virulence bacteria
o Strep pyogenes (Group A strep)
o Staph aureus – most common in IVDU
o CoNS – most common in prosthetic valve

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48
Q

Subacute Infective Endocarditis - causative organisms

A

low virulence bacteria
o Staph epidermidis
o Strep viridans
o HACEK – Haemophilus, Acinetobacter, Cardiobacterium, Eikinella, Kingella

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49
Q

How to interpret Duke’s criteria in IE?

A

2 major OR 1 major + 3 minor OR 5 minor –> Dx of IE

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50
Q

Gonorrhoea tx?

A

Ceftriaxone IM 1g - uncomplicated gonorrhoea (anogenital, pharyngeal)

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51
Q

Chlamydia Tx?

A

Azithromycin 1g STAT or Doxycycline 100mg BD for 7 days

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52
Q

Best sample for NAAT (Chlamydia, Gonorrhoea)

A 
Men = clean catch urine
Women = vaginal swab
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53
Q

Causative organism of Syphillis?

A

Treponema pallidum
• Obligate gram negative
• spirochaete

54
Q

Tx of Syphillis?

A

Single dose IM Benzathine Penicillin
Doxycycline if allergic

(think this changes once latent / tertiary ? )

55
Q

Jarisch Herxheimer reaction?

A

Seen few hours after Abx Tx in syphillis

Presentaion: 
Flu like Sx - Headache, myalgia
tachycardia, mild hypotension
hyperventilation
can induce early labour or foetal distress

Tx

  • aspirin every 4 hours fo 24-48 hrs
  • steroids in CVS or neuro syphillis - can be fatal

Resolves within 24h

56
Q

Ocular sign of late syphillis?

A

Argyll Robertson pupil = one that accommodates but does not react to light

57
Q

Broad spectrum Abx

A

Co-amoxiclav

Tazocin

Meropenem

Ciprofloxacin

58
Q

Narrow spectrum Abx

A

Flucloxacillin

Metronidazole

Gentamicin

59
Q

Mechanisms of Abx resistance?

A
  1. Chemical modification or inactivation of antibiotic
  2. Alteration or replacement of target
  3. Reduced accumulation of Abx - increased efflux or reduced uptake
  4. Bypass Abx sensitive step
60
Q

Examples of altered targets giving Abx resistance

A

MRSA
- mecA gene encodes novel penicillin-binding protein (2a) with low affinity for beta-lactams

Streptococcus pneumoniae
- stepwise mutations in penicillin-binding protein genes

61
Q

Examples of inactivation of Abx as resistance mechanism

A

Beta lactamases

  • Staph aureus & gram -ve bacilli
  • NOT the mechanism in MRSA & pneumococci

Extended spectrum beta lactamases

  • can also break down cephalosporins
  • more common in E. coli, Klebsiella
62
Q

Abx most likely to cause C. diff diarrhoea?

A

3 Cs

clindamycin
cephalosporins
ciprofloxacin

63
Q

Tx for C. diff diarrhoea

A

1st line = Oral vancomycin for ALL C. Diff
Oral metronidazole NO LONGER 1st line

+ stop offending Abx

64
Q

HAART Regimen principles

A 
3 different ARV from 2 or more classes:
NNRTI
NRTI
Integrase inhibitors
Protease inhibitors

E.g. Bictegravir (II) + tenofovir alafenamide (NRTI) plus emtricitabine (NNRTI)

65
Q

PCP/PJP Tx?

A

Tx = Co-trimoxazole (septrin) + Prednisolone if hypoxia

Prophylaxis = Co-trimoxazole (septrin) OR inhaled pentamidine

66
Q

Yeast examples?

A

Candida spp.
Cryptococcus (neoformans)
Histoplasma - dimorphic
Pneumocystis jiroveci

67
Q

Mould examples?

A

Dermatophytes e.g. Trichophyton rubrum
(Agents of) Mucomycoses
Aspergillus

68
Q

Ix for (deep) Candida infection?

A

Beta-D-glucan assay

Sabouraud-dextrose Agar culture –> raised cream coloured colonies

69
Q

Tx for deep/invasive Candida?

A

Amphotericin B

+ blood cultures every 48 hrs

continue tx for at least 2 weeks from first -ve blood culture

70
Q

Cryptococcu serotypes & pattern?

A

A & D - immunodeficient people, incl ‘neoformans’

B & C - immunocompetent, tropical countries, incl ‘gatii’

71
Q

What medication is associated with Cryptococus infection?

A

T cell immunosuppressants e.g. Tacrolimus (CN inhibitor)

72
Q

Gold standard IX for Cryptococcus infection

A

Microscopy –> halo on India ink staining

73
Q

Agents used for Cryptococcus Tx

A

Induction: Amphotericin B + flucytosine

Consolidation & Maintenance (or mild pulmonary disease only): Fluconazole

74
Q

Key Ix findings in Aspergillosis infection

A

CT –> halo sign
Galactomannan antigen detection
cultured on Czapek dox agar

75
Q

Risk factors for Mucormycoses

A

Diabetic

Immunosuppresed

76
Q

Manifestations of Mucormycoses

A

Rhinocerebral

  • orbital & facial cellulitis = black eschars (pus)
  • retro orbital extension = proptosis, chemosis, blindness
  • brain involvement = reduced GCS

Pulmonary

Cutaneous

77
Q

Causative organism for fungal infection causing Black Eschar (pus)

A

Rhinocerebral mucormycosis

Rhizopus
Rhizomucor
Mucor

78
Q

Mangement of Mucormycoses

A

Ambisome / Posaconazole

Surgical debridement

79
Q

Dermatophyte infections - common names

A

Tinea pedis = Asthlete’s foot, Trichophyton rubrum usually

Tinea corporis = body/abdomen
Tinea captitis = scalp
Tinea cruris = groin

80
Q

Causative organism for Seborrheic dermatitis

A

Malassezia globosa/furfur

81
Q

Tinea versicolor - key features?

A

Aka pityriasis versicolor

Skin depigmentation in individuals with dark skin

Tx = ketoconazole shampoo or antifungal cream

82
Q

How does onychomycosis Tx differ from Athlete’s foot?

A

Topical rarely effective

1st line = terbinafine

BUT usually wait to confirm Dx as serious side effects e.g., pancytopenia, agranulocytosis, hepatic derangement

83
Q 
HIV drugs MOA:
Tenofovir
Raltegravir
Nevirapine
Saquinavir
Maraviroc
A 
Tenofovir = NRTI
Raltegravir = integrase inhibitor
Nevirapine = NNRTI
Saquinavir = protease inhibitor
Maraviroc = CCR5 antagonist
84
Q

Beta haemolytic Streptococcus

A

Group A - strep pyogenes

Group B - strep agalactiae

85
Q

y haemolytic Streptococcus

A

Enterococci e.g. E. faecalis

86
Q

alpha haemolytic streptococcus

A

Strep pneumoniae.

Strep viridans.

87
Q

CSF analysis results in Bacterial meningitis

A

Turbid
High WCC - polymorphs
Low glucose
High protein?

+ve Gram stain/microscopy

88
Q

CSF analysis results in viral (aseptic) meningitis

A

Clear
High WCC - mononuclear (lymphocytes)
Normal glucose
High protein?

Negative gram stain/microscopy

89
Q

CSF analysis results in TB meningitis

A

Clear or slightly turbid
High WCC - mononuclear or polymorphs
Low glucose
High protein

Negative gram stain/microscopy OR scanty acid fast bacilli

90
Q

Purulent meningitis management

A

A-E assessment + resusitate

Abx:
Ceftriaxone (cefotaxime in neonates instead)
+ amoxicillin/ampicillin if neonate, elderly or immunosuppressed

+ steroids in adults

91
Q

When would a CT head be done before LP?

A

(In meningitis/encephalitis where):

  • Raised ICP
  • Focal neuro deficit
  • GCS 12 or below
  • Seizures
92
Q

Empirical Tx for encephalitis

A

IV aciclovir 10mg/kg TDS

likely will give meningitis Abx as difficult to distinguish - IV ceftriaxone +/- amoxicillin/ampicillin

93
Q

Definition of R0

A

Number of people that 1 sick person will infect, on average

If <1, transmission is halted

94
Q

Indications to defer a live attenuated vaccine

A

Receiving high dose oral steroids (incl asthma exacerbation)

Received Ig in last 3 months

95
Q

Pattern of Hep B clearance by age?

A

90% clearance if >5 years old

10% in neonates

96
Q

Serology of Hep B ACUTE infection

A

HBeAg - marker of infectivity

HBsAg
HBcAb (acute IgM)

97
Q

Serology of Hep B CHRONIC infection

A

HBSAg

HBcAb (IgG)

98
Q

Serology of Hep B PAST infection

A

HBsAb

HBcAb

99
Q

Serology of Hep B Vaccination

A

HBsAb

100
Q

Hep C ‘curative’ Tx

A

-previrs e.g. telaprevir
NS3/4 protease inhibitors

-asvirs e.g. ledipasvir
NS5A inhibitors

-buvirs e.g. sofosbuvir
Direct polymerase inhibitors

101
Q

Mycobacterium avium complex (MAC) Tx regimen

A

Clarithromycin/azithromycin
Rifampicin
Ethambutol
+/- Amikacin/Streptomycin

102
Q

Pattern of protection of BCG vaccine

A 
will not protect against pulmonary TB
70-80% effective against severe childhood TB
Some protection against CNS infection
Protection wanes
Little evidence in adults
103
Q

TB Treatment regimen

A

Rifampicin
Isoniazid
Pyrazinamide
Ethambutol

ALL for 2 months then R + I for 4 more

104
Q

Main TB drug side effects

A

Rifampicin - orange secretions
Isoniazid - peripheral neuropathy
Pyrazinamide - hepatotoxicity
Ethambutol - optic neuritis

105
Q

Most powerful RF for SSI after cardiothoracic surgery?

A

Staph aureus carriage

106
Q

Exceptions to giving no Tx (except catheter removal) in Candiduria?

A

Renal transplant pt

Patients undergoing elective UT surgery

107
Q

Pyelonephritis Tx regimen

A

Admit

IV co-amoxiclav + gentamicin

108
Q

Types of viral detection

A

Indirect - identifies immune response to virus e.g. serology

Direct - identifies fragments of virus e.g. PCR for viral genetic material

109
Q

Serological screening BEFORE immunosuppression

A 
HIV
Hep B, C
EBV
CMV
HSV
Varicella zoster
HTLV
110
Q

Monitoring during immunosuppression (Via PCR)

A

CMV
EBV
BK (renal & BM transplant)
Adenovirus (paediatric BM transplant)

111
Q

Prophylaxis for HSV in immunosuppression?

A

Bone marrow transplant - for 1 month (until engraftment)

Solid organ transplant - 3-6 months + if undergoing Tx for rejection

112
Q

Tx of Shingles in the immunocompromised?

A

Antiviral + analgesia
IV if disseminated

+ steroids if Ramsay Hunt (facial nerve involvement –> palsy, hearing)

+ topical steroids if Herpes Zoster Ophthalmicus

113
Q

Tx of Chickenpox in immunocompromised?

A

Antiviral 7-10 days

Given IV until no new lesions then PO until all lesions crusted over

114
Q

Tx of post-transplant lymphoproliferative disease

A

Rituximab
Reduce immunosuppression

+ Monitor EBV levels

115
Q

CMV prophylaxis/monitoring strategy in immunosuppression

A

HSCT: viral load 2x/week + Tx if reactivation (until suppressed)

Solid organ: 100 days prophylaxis - Valganciclovir

116
Q

Diagnosis of JC virus/progressive multifocal leukoencephalopathy

A

MRI

CSF - PCR

117
Q

What groups get Progressive multifocal leukoencephalopathy?

A

HIV+ve - was reducing with ART

Other immunosuppression esp Natalizumab (anti T cell) in MS

118
Q

Influenza Tx in immunosuppressed

A

Resistance / severe (ICU) / immunosuppressed= Zanamivir inhaled or IV

Otherwise = Oseltamivir oral for 5 days

119
Q

Main immunosuppressive medications that can cause HepB reactivation?

A

B cell agents e.g. Rituximab

IL-6 inhibitors (COVID Tx)

120
Q

Malaria Diagnosis

A

Thick blood film = identify parasites

Thin blood film = identify species

121
Q

Features of severe Falciparum malaria

A 
Hypoglycaemia <2.2
Seizures / impaired consciousness
Renal & hepatic impairment
Acidosis <7.3
Pulmonary oedema / ARDS
Bleeding / DIC
Shock - <90/60
Haemoglobinuria
Anaemia <80
Parasitaemia >2%
122
Q

Tx for severe Falciparum malaria

A

IV artesunate

123
Q

Tx for mild Falciparum malaria

A

Artemisin combo Tx

  • E.g. Riamet
  • Artemether + Lumefantrine
124
Q

Tx of Neurocysticercosis

A

Anti-convulsants

Anti-parasitics / Cestocidal

  • Praziquantel
  • Albendazole

Steroids
- esp if heavy infection - cesticidals alone may be fatal!

+/- surgery e.g. shunt if hydrocephalus

125
Q

Indications for treating VZV?

A

Chickenpox in adult

Zoster in adults >50

Primary infection or re-activation in immunocompromised person

Neonatal chickenpox

HSV Encephalitis - IV Tx

126
Q

Treatment regimen for HSV Encephalitis

A

IV Acyclovir 10mg/kg IMMEDIATELY - do not delay for Ix results

Continue for 14-21 days if confirmed
Repeat LP towards end of course, before stopping Tx

127
Q

CMV Tx options

A

Ganciclovir/Valganciclovir

  • CMV disease in immunocompromised
  • neonatal congenital CMV
    • IV Ig if pneumonitis

Foscarnet

  • Ganciclovir contraindicated or resistance
  • CMV retinitis

Cidofovir = 3rd line

128
Q

EXCEPTION to Foscarnet being 2nd line for CMV?

A

Foscarnet 1st line for pre-engraftment period of BM transplant

(Val)ganciclovir causes BM toxicity

Also used for CMV retinitis - intravitreal formulation

129
Q

Indications to consider Palivizumab Tx in bronchiolitis

A

Pre-term
Severe underlying heart or lung disease
SCID
Long term ventilation

130
Q

Mechanisms of drug resistance in HSV

A

Mutations in viral thymidine kinase (95%) or viral DNA polymerase (5%)

Cross resistance to (val)ganciclovir as well as (val)aciclovir

131
Q

Mechanisms of drug resistance in CMV

A

Protein kinase UL97 mutation most common

Others:

  • DNA polymerase UL54
  • UL56 terminase
132
Q

Types of antiviral drug resistance assays

A

Genotypic
- used for HIV, Hep B & C, CMV

Phenotypic
- used for HSV

Path 2022 (12 decks)

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