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Y2 Clinical Pathology > Advanced microbiology > Flashcards

Advanced microbiology Flashcards

1
Q

What makes up a virus

A 
Nucleic acid (DNA or RNA)
Protein (coat- structutal or enzymes - non structural)
Obligate intracellular parasites
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2
Q

What causes acute virus infections and what are some examples

A

RNA viruses

Influenza, measles, mumps, hepatitis A virus

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3
Q

What causes chronic virus infections and what are some examples

A

Generally DNA viruses
Latent (with or without recurrences): herpes simplex, cytomegalovirus
Persistent: HIV, HTLV, Hepatitis B, Hepatitis C (RNA)

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4
Q

What are examples of non-vesicular rashes

A 
Measles 
Rubella
Parovirus
Adenovirus
HHV6
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5
Q

What are examples of vesicular rashes

A

Chickenpox (HHV3)
Herpes simplex
Enterovirus

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6
Q

What are the respiratory virus syndromes

A 
Influenza A/B
Respiratory syncytial virus
Parainfluenza virus
Human metapneumovirus
Rhinovirus
Coronavirus (including SARS)
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7
Q

What are the gastroenteritis virus syndromes

A 
Rotavirus
Norovirus
Astrovirus
Sapovirus
Adenovirus (group F)
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8
Q

What are the blood borne virus syndromes

A 
Hepatitis virus:
-HBV
-HCV
Retrovirus:
-HIV 1, 2
-HTLV 1, 2
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9
Q

What are the neurological disease causing viruses

A

Cause encephalitis/meningitis

  • HSV
  • Enteroviruses
  • Rabies
  • Japanese encephalitis virus
  • Nipah virus
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10
Q

When are antivirals used

A

Acute infections in general population
Chronic infection (HIV, HBV, HCV)
Infections in immunocompromised:
-Post transplant
-Individuals receiving immunosuppressive therapies
-Patients with primary immunodeficiencies

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11
Q

How is HSV treated

A

Aciclovir

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12
Q

When should shingles and chickenpox be treated and with what

A 
Treat with aciclovir
Treat all adults with chicken pox
Treat shingles:
->60 
-involves eye
-immunocompromised
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13
Q

Who do you treat with influenza

A

High risk patients:

  • Chronic neurological, hepatic, renal, pulmonary and cardiac disease
  • Diabete mellitus
  • Severe immunosuppression
  • Age over 65
  • Pregnancy
  • Children under 6 months
  • Morbid obesity (BMI>40)
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14
Q

How are chronic virus infections treated

A

Usually lifelong:

  • antiviral toxicity can happen
  • good adherence is challenging
  • avoid emergence of resistance
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15
Q

How does a virus replicate

A 
Virus attachment to cell via receptor
Cell entry
Virus uncoating
Early proteins produced - viral enzymes
Replication
Late transcription/ translation - viral structural proteins
Virus assembly
Virus release and maturation
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16
Q

What are antimicrobial agents used for

A

Killing microorganisms while preserving the life of the patient:

  • Treatment of established infections
  • Prophylaxis (prevention) of possible infections
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17
Q

What are antibiotics

A

Chemical products of microbes that inhibit or kill other organisms

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18
Q

What are antimicrobial agents

A

Antibacterial, antifungal, antiviral
Antibiotics
Synthetic compounds with similar effect
Semi-synthetic ie modified from antibiotics

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19
Q

What is the function of bacteriostatic/fungistatic antimicrobials

A

Inhibit growth

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20
Q

What is the function of bacteriocidal/fungicidal antimicrobials

A

Kill organisms

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21
Q

What is the MIC

A

Minimum inhibitory concentration

Minimum concentration of antimicrobial agent at which visible growth is inhibited

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22
Q

What is the MBC/MFC

A

Minimum bactericidal/ fungicidal concentration

Minimum concentration of antimicrobial agent at which most organisms are killed

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23
Q

What is synergy/synergism

A

Activity of two antimicrobials given together is greater than the activity of either if given separately

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24
Q

What is antagonism

A

Activity of two antimicrobials given together is less than the activity of either if given separately

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25
Q

What are some B-lactam antibiotics

A

Penicillins:

  • Benzylpenicillin, amoxicillin, flucloxacillin
  • Relatively narrow spectrum

Cephalosporins:

  • Cefuroxime, ceftazidime
  • broad spectrum
  • arranged into generations

Carbapenems:

  • meropenem, imipenem
  • extremely broad spectrum

Monobactams:

  • aztreonam
  • gram negative activity only
  • slightly different ring structure
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26
Q

What are glycopeptides

A

Vancomycin, teicoplanin
Large molecules, bind to terminal amino acids on NAM pentapeptides
-inhibit binding of transpeptidases and thus peptidoglycan cross linking
Gram positive activity as unable to penetrate gram negative outer membrane

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27
Q

What are some protein synthesis inhibitors

A 
Aminoglycosides 
Macrolides 
Lincosamides
Tetracycline, doxycycline
Linezolid
Mupirocin
Fusidic acid
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28
Q

What do trimethoprim and sulphonamides do

A

DNA synthesis inhibitors
Both agents inhibit folate synthesis
Trimethoprim used to treat UTI

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29
Q

What do fluoroquinolones do and what are some examples

A

Inhibit one or more of two related bacterial enzymes:
-DNA gyrase and topoisomerase IV
-Involved in remodelling of DNA during DNA replication
Examples:
-Ciprofloxacin
-Levofloxacin

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30
Q

What is rifampicin

A

RNA polymerase inhibitor

Prevents synthesis of mRNA

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31
Q

What are cell membrane agents

A

Colistin/polymyxin E (gram negatives)

Daptomycin (gram positives)

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32
Q

What are antifungal cell wall inhibitors

A

Echinocandins:

  • Enzyme inhibitors
  • Inhibit B-1, 3- glucan synthase
  • examples:
    • Anidulafungin
    • Caspofungin
    • Micafungin
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33
Q

What are antifungal cell membrane agents

A

Azoles (clotrimazole, fluconazole, voriconazol)
Terbinafine (inhibit synthesis of ergosterol (a component of fungal cell membranes))
Amphotericin B (and nystatin) (bind to ergosterol causing physical damage to the membrane)

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34
Q

What agent is an antifungal protein/DNA synthesis inhibitor and how does it work

A

5-fluorocytosine
Entry into cell requires fungal cytosine permease
Converted to 5-fluorouracil by cytosine deaminase
5-fluorouracil incorporated into fungal RNA (inhibits protein synthesis)
Metabolised to 5-fluorodeoxyuridine monophosphate (inhibits DNA synthesis)

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35
Q

How are antibiotic sensitivities tested

A

Organism is grown in presence of antibiotic
If grows in high MIC it is resistant
If killed at low MIC it is sensitive
The lower the MIC the more sensitive is the organism

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36
Q

What are the steps of liquid media-microtitre plate susceptibility testing

A 
Add antibiotic
Add organism
Incubate
Read MIC
Compare with breakpoint
Report result
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37
Q

What are the steps of disk sensitivity testing

A 
Add organism
Add antibiotics
Incubate
Compare zone sizes against published breakpoint zone sizes
Interpret and report results
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38
Q

What methods can be used to prevent antibiotic resistance

A

Minimise use of antibiotics

Effective infection prevention and control

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39
Q

What leads to antibiotic resistance in a patient

A

Exposure to antibiotics

Transmission of resistant organisms

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40
Q

What is the antibiotic era

A

Term used to describe the time since the widespread availability of antibiotics to treat infection

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41
Q

What is the post antibiotic era

A

Term used to describe the time after widespread antibiotic resistance has reduced the availability of antibiotics to treat infection

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42
Q

Why do antibiotic choices need to be individualised

A

Allergy
Elderly (need to avoid those with high risk of Cdiff infection)
Some patients can’t take oral or IV antibiotics
Renal impairment so avoid nephrotoxic drugs
Microbiology culture results may allow narrowing spectrum of antibiotics or may dictate a new antibiotic choice
Don’t exacerbate problems
Interactions

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43
Q

What is diagnostic iteration

A

A procedure in which repetition of a sequence of tests yields results successively closer to a desired result (a high diagnostic probability

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44
Q

What are the two reasons to carry out a diagnostic test

A

Improve outcome

Provide epidemiological data

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45
Q

What are the characteristics of oral antibiotics

A 
Slower absorption
Diarrhoea
Requires small bowel for absorption
Absorption may vary
No IV access required
No IV access side effects
Self-administration
Cheaper
46
Q

What are the characteristics of IV antibiotics

A 
Faster/instantaneous absorption
Diarrhoea
No bowel required for absorption
Absorption rate can be varied
IV access required
IV access side effects (thrombophlebitis, thrombosis and infection)
Medical staff required for administration
More expensive
47
Q

When should antibiotics always be started and never be started

A

Always:
Patients with sepsis

Never:
No evidence of infection
Auto-immune inflammation

48
Q

What are the benefits of early antibiotic therapy

A

Mortality and morbidity benefit
If clinically stable:
-narrow spectrum antibiotics may be administered and the response assessed
- Oral antibiotic may be administered and the response assessed
Prevent infection metastases

49
Q

What are the disadvantages of early antibiotic therapy

A

May reduce the time available to do cultures:
- reduced chance of giving targeted therapy
- reduced chance of getting a diagnosis (the pathogen may give diagnosis)
May reduce time to do investigation so over treatment is possible
May increase chance of giving wrong antibiotic or not enough
Insufficient time to check allergies

50
Q

What is antibiotic stewardship

A

A coherent set of actions which promote using antimicrobials responsibly
Inter-professional effort across the continuum of care
Involves timely and optimal selection, dose and duration of antimicrobial
For the best clinical outcome for the treatment or prevention of infection
Minimal toxicity to the patient
Minimal impact on resistance and adverse events eg C. diff

51
Q

What are the clinical guidelines for antibiotic stewardship

A 
IV to PO switch
Antibiotic restriction
Microbiologist support
Education
Use of biomarkers
Audit and feedback
52
Q

When should penicillin not be used

A

If a patient has a history of anaphylaxis or severe reaction

History of delayed type hypersensitivity, avoid where possible

53
Q

What are some indicated side effects of antibiotic

A 
Nausea/vomiting
Diarrhoea/ stomach upset
Headache/ dizziness
Family history of allergy
Thrush
Metallic taste/ altered taste in mouth
Lethargy
54
Q

What are indication of anaphylaxis/ severe reaction when taking an antibiotic

A 
Swelling (mouth/ tongue/ face etc)
Problems breathing
Wheals or raised rash
Low blood pressure/ tachycardia
Collapse/ unconsciousness
Hospitalised/ needed ventilation
Blistering
55
Q

What are indication of possible delayed type reaction when taking an antibiotic

A

Itching rash
Onset some days after starting antibiotic
Flat rash

56
Q

When symptoms suggest a diagnosis of infection, what other information can help identify potential pathogens

A 
Travel
Occupation
Animal contact
Hobbies
Sexual history
57
Q

What can blood lactate and blood gases identify

A

Severe sepsis

Respiratory failure

58
Q

What are the methods of microbiological diagnosis

A

Culture
Direct detection
Immunological tests

59
Q

What are the principles of culture

A

Isolation of viable pathogen enables:
Identification- immediate or by further testing
Typing - To establish organism relatedness
Sensitivity testing - to direct antimicrobial therapy
Not applicable to non-cultivable micro-organisms
Needs to be done before antibiotics are started

60
Q

What is gram stain

A

Chemical process that distinguishes between bacterial cell walls that retain crystal violet and those that do not when stained and washed with acetone

61
Q

What are the gram positive result meanings

A

Gram positive - purple

Gram negative - pink or colour of counter stain

62
Q

What are the principles of sensitivity testing

A

Requires viable micro-organisms - usually bacteria or fungi
Culture of micro-organism in the presence of antimicrobial agent
Work out if the concentration of antimicrobial that will be available in the body is high enough to kill the micro-organism
Solid or liquid media

63
Q

What are the principles of direct detection

A

Detection of whole organism by microscopy
Detection of component of organism:
-antigen
-nucleic acid (DNA or RNA)

64
Q

What are the principles of immunological tests

A 
Detection of immune response to infection:
-Antibody detection
-- IgM detection
-- Seroconversion
-- Fourfold rise in titre
IFN-y release assays in tuberculosis
65
Q

What are examples of passive immunity

A

Transfer from mother to unborn baby
Maternal antibodies can protect the baby for up to a year against illnesses to which the mother is immune

Injection of human immunoglobulin

66
Q

What is active immunity

A

Usually long lasting immunity produced by the immune system in response to antigens
Antigen can be from natural infection or from vaccination
Immune system makes antibodies to help destroy antigens

67
Q

What is the benefit of vaccination

A

Active immunity occurs without disease or disease complications

68
Q

What is immunologic memory

A

The persistence of protection for many years after natural infection or vaccination

69
Q

What is an antigen

A

Anything that can be bound by an antibody

70
Q

What are antigenic determinants or epitopes

A

Small parts of molecules that antibodies specifically interact with

71
Q

What is primary immune response and which antibody is related to this response

A

Develops in the weeks following first exposure to an antigen

Mainly IgM antibody

72
Q

What is secondary immune response and which antibody is related to this response

A

Faster and more powerful

Mainly IgG antibody

73
Q

How do antibodies produce immunity

A

Antibodies produced from B lymphocytes
Antigen binds to antibody which triggers clonal expansion
1st wave of IgM production followed by IgG production
IgG binds tightly to antigen and through simultaneous complement binding facilitates the destruction of the antigen-bearing microorganism
When infection resolved levels of IgG decline
One set of the IgG producing B lymphocytes persist with the ability to recognise that specific antigen crating immunological memory

74
Q

What are some active immunisations

A

Live: MMR, BCG, yellow fever, varicella

Inactivated organisms: pertussis, typhoid, IPV

Components of organisms: influenza, pneumococcal

Inactivated toxins: diptheria, tetanus

75
Q

What are some passive immunisations

A 
Tetanus 
Botulism
Hep B
Rabies
Varicella
76
Q

What are the advantages and disadvantages of live vaccines

A

Advantages:

  • Single dose sufficient for long lasting immunity
  • Strong immune response
  • Local and systemic immunity produced

Disadvantages:

  • Potential to revert to virulence
  • Contraindicated in immunosuppressed patients
  • Interference by viruses or vaccines and passive antibody
  • poor stability
  • potential for contamination
77
Q

What are the advantages and disadvantages of inactivated/killed vaccines

A

Advantages:

  • Stable
  • Constituents clearly defined
  • Unable to cause the infection

Disadvantages:

  • Need several doses
  • Local reactions common
  • Adjuvant needed
    • Keeps vaccine at injection site
  • -activates antigen presenting cells
  • Shorter lasting immunity
78
Q

What is the purpose of Adjuvant

A

Needed in inactivated/killed vaccines
Keeps vaccine at injection site
Activates antigen presenting cells

79
Q

What is the purpose of infection prevention and control

A

Activities undertaken with the aim of breaking the chain of infection:

  • eliminate pathogenic organism
  • remove source/ reservoir
  • minimise transmission
  • eliminate exit and entry
  • reduced susceptibility to infection
80
Q

How can the pathogenic organism be eliminated

A

Environmental cleaning and decontamination
Equipment decontamination
Antisepsis
Antibiotic prophylaxis

81
Q

What is antisepsis

A

Disinfection applied to damaged skin or living tissues
Examples:
Surgical skin prep
MRSA decolonisation

82
Q

When is antibiotic prophylaxis done

A

Perioperative

Post-exposure

83
Q

What can be done to remove source/reservoir

A

Hand hygiene

Environmental cleaning and decontamination

84
Q

What can be done to minimise transmission

A 
Hand hygiene
Personal protective equipment
Equipment decontamination
Source and protective isolation
Use of disposable equipment
85
Q

What are the issues with transient bacteria

A

Easily picked up and transferred
Easily removed
Important cause of HCAI

86
Q

What is resident bacteria

A

Aid in protecting us from colonisation with other harmful species
Only removed when undertaking a surgical/aseptic procedure to reduce the risk of contamination when inserting invasive devices or performing surgery

87
Q

What are the 5 moments for hand hygiene at the point of care

A 
Before patient contact
Before aseptic task
After body fluid exposure risk
After patient contact
After contact with patient surroundings
88
Q

When to use soap and water

A

Visibly soiled hands

Contact with particular infection eg C diff, viral gastro-enteritis

89
Q

When to use alcohol gel

A

Suitable for most activities when visiting clinical area

Upon entry and exit

90
Q

What is decontamination

A

A combination of processes that removes or destroys contamination so that infectious agents or other contaminants cannot reach a susceptible site in sufficient quantities to initiate infection or other harmful response

91
Q

What is sterilisation

A

Complete killing or removal of all types of micro-organisms

92
Q

What are the sterilisation methods

A

Heat (moist, dry)
Chemical (gas, liquid)
Filtration
Ionising radiation (used for single use disposable equipment)

93
Q

What is disinfection

A

Removal or destruction of sufficient numbers of potentially harmful micro-organisms to make an item safe to use
Achieved by use of chemical disinfectants

94
Q

Why are local samples taken

A

From source of infection
Assist with diagnosis
What bug causing infection, what drug to treat patient with

95
Q

Why are general samples taken

A

As part of investigation of sepsis
Blood cultures
FBC, U and Es, LFTs, clotting, CRP

96
Q

What are CNS infections

A

Meningitis
Encephalitis
Brain abscess

97
Q

What is the CNS infection, meningitis and how is it investigated

A

Inflammation of the meninges
Caused by viruses, bacteria, mycobacteria, fungi, parasites
Lumbar puncture to collect cerebrospinal fluid
Blood cultures
Blood for bacterial PCR
FBC, clotting, U and Es, LFT, Glucose, CRP

98
Q

What is the CNS infection, encephalitis and how is it investigated

A

Inflammation of brain
Usually viral (Herpes viruses)
CSF requesting viral PCR specifically

99
Q

What is the CNS infection, brain abscess and how is it investigated

A

Wide aetiology:
bacterial, mycobacterial, fungal, parasitic
Patient history can narrow down diagnosis
LP should be discouraged as rarely positive and high risk
Local sampling:
-Pus (surgical biopsy/ drainage -> gram, culture, sensitivity (PCR))
-Blood cultures

100
Q

What are ear nose ant throat infections

A

Ear: Acute otitis media, otitis externa
Nose: sinusitis
Throat: pharyngitis (viral/bacterial), diphtheria

101
Q

What are respiratory infection

A

Influenza
Pneumonia
Pulmonary TB
Atypical infection (immunocompromised)

102
Q

What is pulmonary TB

A

Disease which requires an exposure and then reactivation at a later stage in life to produce the pulmonary symptoms

103
Q

What are skin and skin structure infections

A

Localised:

  • Impetigo
  • Erysipelas
  • Cellulitis

Sever/extensive:
-necrotising fasciitis

Diabetic foot infection

104
Q

What are the urinary tract infections

A

Lower UTI and Upper UTI
Prostatitis
Epididymo-orchitis

105
Q

What are the GI tract infections

A

Infectious diarrhoea:

  • Viral gastroenteritis
  • Bacterial
  • Parasitic infection
  • Clostridium difficile infection

H-pylori infection
Liver abscess
Cholangitis/ cholecystitis
Diverticulitis

106
Q

What investigation should be done for infectious diarrhoea

A 
Stool sample
For parasitic infection, 3 stool samples needed
Bloods: FBC, clotting, UandEs, LFT, CRP
Blood cultures
Abdominal imaging: plane film or CT
107
Q

What is complicated diverticulitis

A

Abscess
Fistula
Perforation
Obstruction

108
Q

What are vascular infections

A 
Heart valves (endocarditis)- Native, prosthetic
Vessels- Mycotic aneurysms, prosthetic vascular graft infections (PVGI)
109
Q

How should endocarditis be investigated

A

Three sets of blood cultures taken at different times during first 24 hours
Echocardiography
FBC, CRP, U and Es, LFTs
Serology for bartonella, chlamydia, coxiella, brucella
Valve tissue is valve replaced: M, C and S and PCR

110
Q

How should vascular graft infections be investigated

A

Three sets of blood cultures taken at different times during first 24 hours
Imaging: CT, PET, WBC scan fluid around graft, fistulae
Tissue/fluid from around graft for culture or PCR

111
Q

What are the viral hepatitis (A,B,C) investigations

A

Based on serology +/- PCR
Serology comprises antigen and antibody detection
PCR detects DNA or RNA from living or dead organisms
Usually presence of DNA/ RNA suggests active infection

Y2 Clinical Pathology (11 decks)

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