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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
What are some B-lactam antibiotics
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
26
What are glycopeptides
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
27
What are some protein synthesis inhibitors
``` Aminoglycosides Macrolides Lincosamides Tetracycline, doxycycline Linezolid Mupirocin Fusidic acid ```
28
What do trimethoprim and sulphonamides do
DNA synthesis inhibitors Both agents inhibit folate synthesis Trimethoprim used to treat UTI
29
What do fluoroquinolones do and what are some examples
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
30
What is rifampicin
RNA polymerase inhibitor | Prevents synthesis of mRNA
31
What are cell membrane agents
Colistin/polymyxin E (gram negatives) | Daptomycin (gram positives)
32
What are antifungal cell wall inhibitors
Echinocandins: - Enzyme inhibitors - Inhibit B-1, 3- glucan synthase - examples: - - Anidulafungin - - Caspofungin - - Micafungin
33
What are antifungal cell membrane agents
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)
34
What agent is an antifungal protein/DNA synthesis inhibitor and how does it work
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)
35
How are antibiotic sensitivities tested
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
36
What are the steps of liquid media-microtitre plate susceptibility testing
``` Add antibiotic Add organism Incubate Read MIC Compare with breakpoint Report result ```
37
What are the steps of disk sensitivity testing
``` Add organism Add antibiotics Incubate Compare zone sizes against published breakpoint zone sizes Interpret and report results ```
38
What methods can be used to prevent antibiotic resistance
Minimise use of antibiotics | Effective infection prevention and control
39
What leads to antibiotic resistance in a patient
Exposure to antibiotics | Transmission of resistant organisms
40
What is the antibiotic era
Term used to describe the time since the widespread availability of antibiotics to treat infection
41
What is the post antibiotic era
Term used to describe the time after widespread antibiotic resistance has reduced the availability of antibiotics to treat infection
42
Why do antibiotic choices need to be individualised
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
43
What is diagnostic iteration
A procedure in which repetition of a sequence of tests yields results successively closer to a desired result (a high diagnostic probability
44
What are the two reasons to carry out a diagnostic test
Improve outcome | Provide epidemiological data
45
What are the characteristics of oral antibiotics
``` Slower absorption Diarrhoea Requires small bowel for absorption Absorption may vary No IV access required No IV access side effects Self-administration Cheaper ```
46
What are the characteristics of IV antibiotics
``` 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
When should antibiotics always be started and never be started
Always: Patients with sepsis Never: No evidence of infection Auto-immune inflammation
48
What are the benefits of early antibiotic therapy
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
What are the disadvantages of early antibiotic therapy
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
What is antibiotic stewardship
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
What are the clinical guidelines for antibiotic stewardship
``` IV to PO switch Antibiotic restriction Microbiologist support Education Use of biomarkers Audit and feedback ```
52
When should penicillin not be used
If a patient has a history of anaphylaxis or severe reaction | History of delayed type hypersensitivity, avoid where possible
53
What are some indicated side effects of antibiotic
``` Nausea/vomiting Diarrhoea/ stomach upset Headache/ dizziness Family history of allergy Thrush Metallic taste/ altered taste in mouth Lethargy ```
54
What are indication of anaphylaxis/ severe reaction when taking an antibiotic
``` Swelling (mouth/ tongue/ face etc) Problems breathing Wheals or raised rash Low blood pressure/ tachycardia Collapse/ unconsciousness Hospitalised/ needed ventilation Blistering ```
55
What are indication of possible delayed type reaction when taking an antibiotic
Itching rash Onset some days after starting antibiotic Flat rash
56
When symptoms suggest a diagnosis of infection, what other information can help identify potential pathogens
``` Travel Occupation Animal contact Hobbies Sexual history ```
57
What can blood lactate and blood gases identify
Severe sepsis | Respiratory failure
58
What are the methods of microbiological diagnosis
Culture Direct detection Immunological tests
59
What are the principles of culture
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
What is gram stain
Chemical process that distinguishes between bacterial cell walls that retain crystal violet and those that do not when stained and washed with acetone
61
What are the gram positive result meanings
Gram positive - purple | Gram negative - pink or colour of counter stain
62
What are the principles of sensitivity testing
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
What are the principles of direct detection
Detection of whole organism by microscopy Detection of component of organism: -antigen -nucleic acid (DNA or RNA)
64
What are the principles of immunological tests
``` Detection of immune response to infection: -Antibody detection -- IgM detection -- Seroconversion -- Fourfold rise in titre IFN-y release assays in tuberculosis ```
65
What are examples of passive immunity
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
What is active immunity
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
What is the benefit of vaccination
Active immunity occurs without disease or disease complications
68
What is immunologic memory
The persistence of protection for many years after natural infection or vaccination
69
What is an antigen
Anything that can be bound by an antibody
70
What are antigenic determinants or epitopes
Small parts of molecules that antibodies specifically interact with
71
What is primary immune response and which antibody is related to this response
Develops in the weeks following first exposure to an antigen | Mainly IgM antibody
72
What is secondary immune response and which antibody is related to this response
Faster and more powerful | Mainly IgG antibody
73
How do antibodies produce immunity
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
What are some active immunisations
Live: MMR, BCG, yellow fever, varicella Inactivated organisms: pertussis, typhoid, IPV Components of organisms: influenza, pneumococcal Inactivated toxins: diptheria, tetanus
75
What are some passive immunisations
``` Tetanus Botulism Hep B Rabies Varicella ```
76
What are the advantages and disadvantages of live vaccines
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
What are the advantages and disadvantages of inactivated/killed vaccines
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
What is the purpose of Adjuvant
Needed in inactivated/killed vaccines Keeps vaccine at injection site Activates antigen presenting cells
79
What is the purpose of infection prevention and control
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
How can the pathogenic organism be eliminated
Environmental cleaning and decontamination Equipment decontamination Antisepsis Antibiotic prophylaxis
81
What is antisepsis
Disinfection applied to damaged skin or living tissues Examples: Surgical skin prep MRSA decolonisation
82
When is antibiotic prophylaxis done
Perioperative | Post-exposure
83
What can be done to remove source/reservoir
Hand hygiene | Environmental cleaning and decontamination
84
What can be done to minimise transmission
``` Hand hygiene Personal protective equipment Equipment decontamination Source and protective isolation Use of disposable equipment ```
85
What are the issues with transient bacteria
Easily picked up and transferred Easily removed Important cause of HCAI
86
What is resident bacteria
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
What are the 5 moments for hand hygiene at the point of care
``` Before patient contact Before aseptic task After body fluid exposure risk After patient contact After contact with patient surroundings ```
88
When to use soap and water
Visibly soiled hands | Contact with particular infection eg C diff, viral gastro-enteritis
89
When to use alcohol gel
Suitable for most activities when visiting clinical area | Upon entry and exit
90
What is decontamination
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
What is sterilisation
Complete killing or removal of all types of micro-organisms
92
What are the sterilisation methods
Heat (moist, dry) Chemical (gas, liquid) Filtration Ionising radiation (used for single use disposable equipment)
93
What is disinfection
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
Why are local samples taken
From source of infection Assist with diagnosis What bug causing infection, what drug to treat patient with
95
Why are general samples taken
As part of investigation of sepsis Blood cultures FBC, U and Es, LFTs, clotting, CRP
96
What are CNS infections
Meningitis Encephalitis Brain abscess
97
What is the CNS infection, meningitis and how is it investigated
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
What is the CNS infection, encephalitis and how is it investigated
Inflammation of brain Usually viral (Herpes viruses) CSF requesting viral PCR specifically
99
What is the CNS infection, brain abscess and how is it investigated
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
What are ear nose ant throat infections
Ear: Acute otitis media, otitis externa Nose: sinusitis Throat: pharyngitis (viral/bacterial), diphtheria
101
What are respiratory infection
Influenza Pneumonia Pulmonary TB Atypical infection (immunocompromised)
102
What is pulmonary TB
Disease which requires an exposure and then reactivation at a later stage in life to produce the pulmonary symptoms
103
What are skin and skin structure infections
Localised: - Impetigo - Erysipelas - Cellulitis Sever/extensive: -necrotising fasciitis Diabetic foot infection
104
What are the urinary tract infections
Lower UTI and Upper UTI Prostatitis Epididymo-orchitis
105
What are the GI tract infections
Infectious diarrhoea: - Viral gastroenteritis - Bacterial - Parasitic infection - Clostridium difficile infection H-pylori infection Liver abscess Cholangitis/ cholecystitis Diverticulitis
106
What investigation should be done for infectious diarrhoea
``` Stool sample For parasitic infection, 3 stool samples needed Bloods: FBC, clotting, UandEs, LFT, CRP Blood cultures Abdominal imaging: plane film or CT ```
107
What is complicated diverticulitis
Abscess Fistula Perforation Obstruction
108
What are vascular infections
``` Heart valves (endocarditis)- Native, prosthetic Vessels- Mycotic aneurysms, prosthetic vascular graft infections (PVGI) ```
109
How should endocarditis be investigated
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
How should vascular graft infections be investigated
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
What are the viral hepatitis (A,B,C) investigations
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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