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%
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
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
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
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)
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
7
Q
Key features of Haemophilus influenzae (CAP)
A
Gram -ve
Cocco-bacilli
More common if pre-existing lung disease
Dx: chocolate agar culture
8
Q
TB Ix Results / Diagnosis
A
CXR –> upper lobe cavitation is typical (but varies)
Auramine rhodamine stain
Ziehl-Neelsen stain
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)
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
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
12
Q
Reservoir for Campylobacter
A
Poultry (100% Uk chickens carry in GI tract)
Cattle
13
Q
Ix for Campylobacter
A
Stool culture - 48-72 hours
14
Q
Reservoir for Salmonella
A
Poultry
Amphibians/reptiles
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
16
Q
Tx for Bartonella infection
A
Erythromycin, doxycycline
+ rifampicin if immunocomprised (bacillary angiomatosis)
17
Q
Tx for Toxoplasmosis
A
Pregnant = spiramycin
Immunosuppressed = pyrimethamine, sulfadiazine
18
Q
Presentation of Brucellosis
A
Mimics extra pulmonary TB
- back pain
- orchitis
- fever
- focal abscesses e.g. psoas, liver
19
Q
Tx for brucellosis
A
Doxycycline + gentamicin or rifampicin
6 weeks
20
Q
Q fever causative organism?
A
Coxiella burnetii
21
Q
Tx for coxiella Burnetti?
A
Doxycycline
Hydroxychloroquine
22
Q
Tx for rabies
A
Post exposure vaccine
+/- human normal immunoglobulin (no specific formation)
23
Q
Rat bite fever presentation
A
Fever
Polyarthralgia
Maculopapular rash —> purpuric
+/- Endocarditis
24
Q
Tx for rat bite fever
A
Penicillins
25
Causative organism of rat bite fever?
Streptobacillus moniliformis
| Spirillum minus
26
Viral haemorrhagic fevers
- Reservoir & disease
? Bats - Ebola
? Bats - Marburg
Rats - Lassa
Ticks - Congo Crimean haemorrhagic fever
27
HIV encephalopathy signs on imaging
Basal ganglia calcification
White matter changes
Atrophy —> enlarged ventricles
28
Methods of vertical HIV transmission
In Utero
intra partum
Breast feeding
29
Factors affecting maternal —> baby HIV transmission
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
30
Type I Antimicrobial activity pattern
Concentration dependent killing
Examples:
- aminoglycosides
- daptomycin
- fluoroquinolones
- ketolides
31
Type 2 antimicrobial activity pattern
Time dependent killing
Examples:
- carbapenems
- cephalosporins
- erythromycin
- linezolid
- penicillins
32
Type 3 antimicrobial activity pattern
Time dependent killing + moderate-prolonged persistent effects
Examples:
- azithromycin
- clindamycin
- oxazolidinones
- tetracyclines
- vancomycin
33
Beta lactam Abx MOA
Inactivate enzymes needed for terminal stages of cell wall synthesis (the penicillin binding proteins)
Induce cell lysis
34
What bacteria will beta-lactams NOT work on?
Bacteria that lack peptidoglycan cell wall
| Chlamydia, mycoplasma
35
Pattern of activity across Cephalosporin generations
Activity against gram -ve increases (and gram +ve decreases)
36
Cephalosporins
1st gen = Cephalexin
2nd gen = Cefuroxime
3rd gen = Cefotaxime, Ceftriaxone, Ceftazidime
37
Glycopeptide Abx - examples and MOA
Vancomycin, (Teicoplanin)
Binds to D-Ala, D-Ala
Prevents trans glycosidase and transpeptidase binding
Cell wall lysis as bacterium divides
38
Side effects of Glycopeptide Abx
Nephrotoxic
+/- Ototoxic
Require drug level monitoring
39
Aminoglycoside Abx - MOA and examples
Bind to 30S ribosomal subunit
Prevent elongation of polypeptide chain + cause misreading of codons along mRNA
E.g., gentamicin, amikacin, tobramycin
40
Tetracycline Abx - MOA & examples
Reversibly bind 30S ribosomal subunit
Prevent amino acyl atRNA binding to ribosomal acceptor site - inhibits protein synthesis
E.g. doxycycline
41
Side effects of doxycycline
Deposited in growing bones - do not give in children, pregnant or breastfeeding women
Teratogenic
Light sensitive rash
42
Macrolide Abx - MOA & Examples
Bind to 50S ribosomal subunit
Interfere with translocation
E.g., azithromycin, clarithromycin, erythromycin
43
Chloramphenicol MOA
Binds peptidyl transferase of 50S ribosomal subunit
| Inhibits peptide bond formation
44
Side effects/risks of chloramphenicol
Grey baby syndrome - inability to metabolise drug
| Aplastic anaemia
45
Oxazolidinone Abx - MOA & example
Binds 23S component of 50S subunit
Prevents formation of functional 70s initiation complex
E.g., linezolid
46
Most common valve affected in Infective Endocarditis in IVDU
Ticuspid
47
Acute Infective endocarditis - causative organisms
high virulence bacteria
o Strep pyogenes (Group A strep)
o Staph aureus – most common in IVDU
o CoNS – most common in prosthetic valve
48
Subacute Infective Endocarditis - causative organisms
low virulence bacteria
o Staph epidermidis
o Strep viridans
o HACEK – Haemophilus, Acinetobacter, Cardiobacterium, Eikinella, Kingella
49
How to interpret Duke's criteria in IE?
2 major OR 1 major + 3 minor OR 5 minor --> Dx of IE
50
Gonorrhoea tx?
Ceftriaxone IM 1g - uncomplicated gonorrhoea (anogenital, pharyngeal)
51
Chlamydia Tx?
Azithromycin 1g STAT or Doxycycline 100mg BD for 7 days
52
Best sample for NAAT (Chlamydia, Gonorrhoea)
```
Men = clean catch urine
Women = vaginal swab
```
53
Causative organism of Syphillis?
Treponema pallidum
• Obligate gram negative
• spirochaete
54
Tx of Syphillis?
Single dose IM Benzathine Penicillin
Doxycycline if allergic
(think this changes once latent / tertiary ? )
55
Jarisch Herxheimer reaction?
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
Ocular sign of late syphillis?
Argyll Robertson pupil = one that accommodates but does not react to light
57
Broad spectrum Abx
Co-amoxiclav
Tazocin
Meropenem
Ciprofloxacin
58
Narrow spectrum Abx
Flucloxacillin
Metronidazole
Gentamicin
59
Mechanisms of Abx resistance?
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
Examples of altered targets giving Abx resistance
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
Examples of inactivation of Abx as resistance mechanism
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
Abx most likely to cause C. diff diarrhoea?
3 Cs
clindamycin
cephalosporins
ciprofloxacin
63
Tx for C. diff diarrhoea
1st line = Oral vancomycin for ALL C. Diff
Oral metronidazole NO LONGER 1st line
+ stop offending Abx
64
HAART Regimen principles
```
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
PCP/PJP Tx?
Tx = Co-trimoxazole (septrin) + Prednisolone if hypoxia
Prophylaxis = Co-trimoxazole (septrin) OR inhaled pentamidine
66
Yeast examples?
Candida spp.
Cryptococcus (neoformans)
Histoplasma - dimorphic
Pneumocystis jiroveci
67
Mould examples?
Dermatophytes e.g. Trichophyton rubrum
(Agents of) Mucomycoses
Aspergillus
68
Ix for (deep) Candida infection?
Beta-D-glucan assay
Sabouraud-dextrose Agar culture --> raised cream coloured colonies
69
Tx for deep/invasive Candida?
Amphotericin B
+ blood cultures every 48 hrs
continue tx for at least 2 weeks from first -ve blood culture
70
Cryptococcu serotypes & pattern?
A & D - immunodeficient people, incl 'neoformans'
B & C - immunocompetent, tropical countries, incl 'gatii'
71
What medication is associated with Cryptococus infection?
T cell immunosuppressants e.g. Tacrolimus (CN inhibitor)
72
Gold standard IX for Cryptococcus infection
Microscopy --> halo on India ink staining
73
Agents used for Cryptococcus Tx
Induction: Amphotericin B + flucytosine
Consolidation & Maintenance (or mild pulmonary disease only): Fluconazole
74
Key Ix findings in Aspergillosis infection
CT --> halo sign
Galactomannan antigen detection
cultured on Czapek dox agar
75
Risk factors for Mucormycoses
Diabetic
| Immunosuppresed
76
Manifestations of Mucormycoses
Rhinocerebral
- orbital & facial cellulitis = black eschars (pus)
- retro orbital extension = proptosis, chemosis, blindness
- brain involvement = reduced GCS
Pulmonary
Cutaneous
77
Causative organism for fungal infection causing Black Eschar (pus)
Rhinocerebral mucormycosis
Rhizopus
Rhizomucor
Mucor
78
Mangement of Mucormycoses
Ambisome / Posaconazole
| Surgical debridement
79
Dermatophyte infections - common names
Tinea pedis = Asthlete's foot, Trichophyton rubrum usually
Tinea corporis = body/abdomen
Tinea captitis = scalp
Tinea cruris = groin
80
Causative organism for Seborrheic dermatitis
Malassezia globosa/furfur
81
Tinea versicolor - key features?
Aka pityriasis versicolor
Skin depigmentation in individuals with dark skin
Tx = ketoconazole shampoo or antifungal cream
82
How does onychomycosis Tx differ from Athlete's foot?
Topical rarely effective
1st line = terbinafine
BUT usually wait to confirm Dx as serious side effects e.g., pancytopenia, agranulocytosis, hepatic derangement
83
```
HIV drugs MOA:
Tenofovir
Raltegravir
Nevirapine
Saquinavir
Maraviroc
```
```
Tenofovir = NRTI
Raltegravir = integrase inhibitor
Nevirapine = NNRTI
Saquinavir = protease inhibitor
Maraviroc = CCR5 antagonist
```
84
Beta haemolytic Streptococcus
Group A - strep pyogenes
| Group B - strep agalactiae
85
y haemolytic Streptococcus
Enterococci e.g. E. faecalis
86
alpha haemolytic streptococcus
Strep pneumoniae.
Strep viridans.
87
CSF analysis results in Bacterial meningitis
Turbid
High WCC - polymorphs
Low glucose
High protein?
+ve Gram stain/microscopy
88
CSF analysis results in viral (aseptic) meningitis
Clear
High WCC - mononuclear (lymphocytes)
Normal glucose
High protein?
Negative gram stain/microscopy
89
CSF analysis results in TB meningitis
Clear or slightly turbid
High WCC - mononuclear or polymorphs
Low glucose
High protein
Negative gram stain/microscopy OR scanty acid fast bacilli
90
Purulent meningitis management
A-E assessment + resusitate
Abx:
Ceftriaxone (cefotaxime in neonates instead)
+ amoxicillin/ampicillin if neonate, elderly or immunosuppressed
+ steroids in adults
91
When would a CT head be done before LP?
(In meningitis/encephalitis where):
- Raised ICP
- Focal neuro deficit
- GCS 12 or below
- Seizures
92
Empirical Tx for encephalitis
IV aciclovir 10mg/kg TDS
likely will give meningitis Abx as difficult to distinguish - IV ceftriaxone +/- amoxicillin/ampicillin
93
Definition of R0
Number of people that 1 sick person will infect, on average
If <1, transmission is halted
94
Indications to defer a live attenuated vaccine
Receiving high dose oral steroids (incl asthma exacerbation)
| Received Ig in last 3 months
95
Pattern of Hep B clearance by age?
90% clearance if >5 years old
| 10% in neonates
96
Serology of Hep B ACUTE infection
HBeAg - marker of infectivity
HBsAg
HBcAb (acute IgM)
97
Serology of Hep B CHRONIC infection
HBSAg
| HBcAb (IgG)
98
Serology of Hep B PAST infection
HBsAb
| HBcAb
99
Serology of Hep B Vaccination
HBsAb
100
Hep C 'curative' Tx
-previrs e.g. telaprevir
NS3/4 protease inhibitors
-asvirs e.g. ledipasvir
NS5A inhibitors
-buvirs e.g. sofosbuvir
Direct polymerase inhibitors
101
Mycobacterium avium complex (MAC) Tx regimen
Clarithromycin/azithromycin
Rifampicin
Ethambutol
+/- Amikacin/Streptomycin
102
Pattern of protection of BCG vaccine
```
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
TB Treatment regimen
Rifampicin
Isoniazid
Pyrazinamide
Ethambutol
ALL for 2 months then R + I for 4 more
104
Main TB drug side effects
Rifampicin - orange secretions
Isoniazid - peripheral neuropathy
Pyrazinamide - hepatotoxicity
Ethambutol - optic neuritis
105
Most powerful RF for SSI after cardiothoracic surgery?
Staph aureus carriage
106
Exceptions to giving no Tx (except catheter removal) in Candiduria?
Renal transplant pt
| Patients undergoing elective UT surgery
107
Pyelonephritis Tx regimen
Admit
| IV co-amoxiclav + gentamicin
108
Types of viral detection
Indirect - identifies immune response to virus e.g. serology
Direct - identifies fragments of virus e.g. PCR for viral genetic material
109
Serological screening BEFORE immunosuppression
```
HIV
Hep B, C
EBV
CMV
HSV
Varicella zoster
HTLV
```
110
Monitoring during immunosuppression (Via PCR)
CMV
EBV
BK (renal & BM transplant)
Adenovirus (paediatric BM transplant)
111
Prophylaxis for HSV in immunosuppression?
Bone marrow transplant - for 1 month (until engraftment)
| Solid organ transplant - 3-6 months + if undergoing Tx for rejection
112
Tx of Shingles in the immunocompromised?
Antiviral + analgesia
IV if disseminated
+ steroids if Ramsay Hunt (facial nerve involvement --> palsy, hearing)
+ topical steroids if Herpes Zoster Ophthalmicus
113
Tx of Chickenpox in immunocompromised?
Antiviral 7-10 days
| Given IV until no new lesions then PO until all lesions crusted over
114
Tx of post-transplant lymphoproliferative disease
Rituximab
Reduce immunosuppression
+ Monitor EBV levels
115
CMV prophylaxis/monitoring strategy in immunosuppression
HSCT: viral load 2x/week + Tx if reactivation (until suppressed)
Solid organ: 100 days prophylaxis - Valganciclovir
116
Diagnosis of JC virus/progressive multifocal leukoencephalopathy
MRI
| CSF - PCR
117
What groups get Progressive multifocal leukoencephalopathy?
HIV+ve - was reducing with ART
Other immunosuppression esp Natalizumab (anti T cell) in MS
118
Influenza Tx in immunosuppressed
Resistance / severe (ICU) / immunosuppressed= Zanamivir inhaled or IV
Otherwise = Oseltamivir oral for 5 days
119
Main immunosuppressive medications that can cause HepB reactivation?
B cell agents e.g. Rituximab
IL-6 inhibitors (COVID Tx)
120
Malaria Diagnosis
Thick blood film = identify parasites
Thin blood film = identify species
121
Features of severe Falciparum malaria
```
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
Tx for severe Falciparum malaria
IV artesunate
123
Tx for mild Falciparum malaria
Artemisin combo Tx
- E.g. Riamet
- Artemether + Lumefantrine
124
Tx of Neurocysticercosis
Anti-convulsants
Anti-parasitics / Cestocidal
- Praziquantel
- Albendazole
Steroids
- esp if heavy infection - cesticidals alone may be fatal!
+/- surgery e.g. shunt if hydrocephalus
125
Indications for treating VZV?
Chickenpox in adult
Zoster in adults >50
Primary infection or re-activation in immunocompromised person
Neonatal chickenpox
HSV Encephalitis - IV Tx
126
Treatment regimen for HSV Encephalitis
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
CMV Tx options
Ganciclovir/Valganciclovir
- CMV disease in immunocompromised
- neonatal congenital CMV
- + IV Ig if pneumonitis
Foscarnet
- Ganciclovir contraindicated or resistance
- CMV retinitis
Cidofovir = 3rd line
128
EXCEPTION to Foscarnet being 2nd line for CMV?
Foscarnet 1st line for pre-engraftment period of BM transplant
(Val)ganciclovir causes BM toxicity
Also used for CMV retinitis - intravitreal formulation
129
Indications to consider Palivizumab Tx in bronchiolitis
Pre-term
Severe underlying heart or lung disease
SCID
Long term ventilation
130
Mechanisms of drug resistance in HSV
Mutations in viral thymidine kinase (95%) or viral DNA polymerase (5%)
Cross resistance to (val)ganciclovir as well as (val)aciclovir
131
Mechanisms of drug resistance in CMV
Protein kinase UL97 mutation most common
Others:
- DNA polymerase UL54
- UL56 terminase
132
Types of antiviral drug resistance assays
Genotypic
- used for HIV, Hep B & C, CMV
Phenotypic
- used for HSV
