Advanced microbiology Flashcards
What makes up a virus
Nucleic acid (DNA or RNA) Protein (coat- structutal or enzymes - non structural) Obligate intracellular parasites
What causes acute virus infections and what are some examples
RNA viruses
Influenza, measles, mumps, hepatitis A virus
What causes chronic virus infections and what are some examples
Generally DNA viruses
Latent (with or without recurrences): herpes simplex, cytomegalovirus
Persistent: HIV, HTLV, Hepatitis B, Hepatitis C (RNA)
What are examples of non-vesicular rashes
Measles Rubella Parovirus Adenovirus HHV6
What are examples of vesicular rashes
Chickenpox (HHV3)
Herpes simplex
Enterovirus
What are the respiratory virus syndromes
Influenza A/B Respiratory syncytial virus Parainfluenza virus Human metapneumovirus Rhinovirus Coronavirus (including SARS)
What are the gastroenteritis virus syndromes
Rotavirus Norovirus Astrovirus Sapovirus Adenovirus (group F)
What are the blood borne virus syndromes
Hepatitis virus: -HBV -HCV Retrovirus: -HIV 1, 2 -HTLV 1, 2
What are the neurological disease causing viruses
Cause encephalitis/meningitis
- HSV
- Enteroviruses
- Rabies
- Japanese encephalitis virus
- Nipah virus
When are antivirals used
Acute infections in general population
Chronic infection (HIV, HBV, HCV)
Infections in immunocompromised:
-Post transplant
-Individuals receiving immunosuppressive therapies
-Patients with primary immunodeficiencies
How is HSV treated
Aciclovir
When should shingles and chickenpox be treated and with what
Treat with aciclovir Treat all adults with chicken pox Treat shingles: ->60 -involves eye -immunocompromised
Who do you treat with influenza
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)
How are chronic virus infections treated
Usually lifelong:
- antiviral toxicity can happen
- good adherence is challenging
- avoid emergence of resistance
How does a virus replicate
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
What are antimicrobial agents used for
Killing microorganisms while preserving the life of the patient:
- Treatment of established infections
- Prophylaxis (prevention) of possible infections
What are antibiotics
Chemical products of microbes that inhibit or kill other organisms
What are antimicrobial agents
Antibacterial, antifungal, antiviral
Antibiotics
Synthetic compounds with similar effect
Semi-synthetic ie modified from antibiotics
What is the function of bacteriostatic/fungistatic antimicrobials
Inhibit growth
What is the function of bacteriocidal/fungicidal antimicrobials
Kill organisms
What is the MIC
Minimum inhibitory concentration
Minimum concentration of antimicrobial agent at which visible growth is inhibited
What is the MBC/MFC
Minimum bactericidal/ fungicidal concentration
Minimum concentration of antimicrobial agent at which most organisms are killed
What is synergy/synergism
Activity of two antimicrobials given together is greater than the activity of either if given separately
What is antagonism
Activity of two antimicrobials given together is less than the activity of either if given separately
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
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
What are some protein synthesis inhibitors
Aminoglycosides Macrolides Lincosamides Tetracycline, doxycycline Linezolid Mupirocin Fusidic acid
What do trimethoprim and sulphonamides do
DNA synthesis inhibitors
Both agents inhibit folate synthesis
Trimethoprim used to treat UTI
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
What is rifampicin
RNA polymerase inhibitor
Prevents synthesis of mRNA
What are cell membrane agents
Colistin/polymyxin E (gram negatives)
Daptomycin (gram positives)
What are antifungal cell wall inhibitors
Echinocandins:
- Enzyme inhibitors
- Inhibit B-1, 3- glucan synthase
- examples:
- Anidulafungin
- Caspofungin
- Micafungin
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)
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)
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
What are the steps of liquid media-microtitre plate susceptibility testing
Add antibiotic Add organism Incubate Read MIC Compare with breakpoint Report result
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
What methods can be used to prevent antibiotic resistance
Minimise use of antibiotics
Effective infection prevention and control
What leads to antibiotic resistance in a patient
Exposure to antibiotics
Transmission of resistant organisms
What is the antibiotic era
Term used to describe the time since the widespread availability of antibiotics to treat infection
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
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
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
What are the two reasons to carry out a diagnostic test
Improve outcome
Provide epidemiological data
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
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
When should antibiotics always be started and never be started
Always:
Patients with sepsis
Never:
No evidence of infection
Auto-immune inflammation
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
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
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
What are the clinical guidelines for antibiotic stewardship
IV to PO switch Antibiotic restriction Microbiologist support Education Use of biomarkers Audit and feedback
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
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
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
What are indication of possible delayed type reaction when taking an antibiotic
Itching rash
Onset some days after starting antibiotic
Flat rash
When symptoms suggest a diagnosis of infection, what other information can help identify potential pathogens
Travel Occupation Animal contact Hobbies Sexual history
What can blood lactate and blood gases identify
Severe sepsis
Respiratory failure
What are the methods of microbiological diagnosis
Culture
Direct detection
Immunological tests
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
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
What are the gram positive result meanings
Gram positive - purple
Gram negative - pink or colour of counter stain
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
What are the principles of direct detection
Detection of whole organism by microscopy
Detection of component of organism:
-antigen
-nucleic acid (DNA or RNA)
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
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
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
What is the benefit of vaccination
Active immunity occurs without disease or disease complications
What is immunologic memory
The persistence of protection for many years after natural infection or vaccination
What is an antigen
Anything that can be bound by an antibody
What are antigenic determinants or epitopes
Small parts of molecules that antibodies specifically interact with
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
What is secondary immune response and which antibody is related to this response
Faster and more powerful
Mainly IgG antibody
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
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
What are some passive immunisations
Tetanus Botulism Hep B Rabies Varicella
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
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
What is the purpose of Adjuvant
Needed in inactivated/killed vaccines
Keeps vaccine at injection site
Activates antigen presenting cells
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
How can the pathogenic organism be eliminated
Environmental cleaning and decontamination
Equipment decontamination
Antisepsis
Antibiotic prophylaxis
What is antisepsis
Disinfection applied to damaged skin or living tissues
Examples:
Surgical skin prep
MRSA decolonisation
When is antibiotic prophylaxis done
Perioperative
Post-exposure
What can be done to remove source/reservoir
Hand hygiene
Environmental cleaning and decontamination
What can be done to minimise transmission
Hand hygiene Personal protective equipment Equipment decontamination Source and protective isolation Use of disposable equipment
What are the issues with transient bacteria
Easily picked up and transferred
Easily removed
Important cause of HCAI
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
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
When to use soap and water
Visibly soiled hands
Contact with particular infection eg C diff, viral gastro-enteritis
When to use alcohol gel
Suitable for most activities when visiting clinical area
Upon entry and exit
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
What is sterilisation
Complete killing or removal of all types of micro-organisms
What are the sterilisation methods
Heat (moist, dry)
Chemical (gas, liquid)
Filtration
Ionising radiation (used for single use disposable equipment)
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
Why are local samples taken
From source of infection
Assist with diagnosis
What bug causing infection, what drug to treat patient with
Why are general samples taken
As part of investigation of sepsis
Blood cultures
FBC, U and Es, LFTs, clotting, CRP
What are CNS infections
Meningitis
Encephalitis
Brain abscess
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
What is the CNS infection, encephalitis and how is it investigated
Inflammation of brain
Usually viral (Herpes viruses)
CSF requesting viral PCR specifically
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
What are ear nose ant throat infections
Ear: Acute otitis media, otitis externa
Nose: sinusitis
Throat: pharyngitis (viral/bacterial), diphtheria
What are respiratory infection
Influenza
Pneumonia
Pulmonary TB
Atypical infection (immunocompromised)
What is pulmonary TB
Disease which requires an exposure and then reactivation at a later stage in life to produce the pulmonary symptoms
What are skin and skin structure infections
Localised:
- Impetigo
- Erysipelas
- Cellulitis
Sever/extensive:
-necrotising fasciitis
Diabetic foot infection
What are the urinary tract infections
Lower UTI and Upper UTI
Prostatitis
Epididymo-orchitis
What are the GI tract infections
Infectious diarrhoea:
- Viral gastroenteritis
- Bacterial
- Parasitic infection
- Clostridium difficile infection
H-pylori infection
Liver abscess
Cholangitis/ cholecystitis
Diverticulitis
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
What is complicated diverticulitis
Abscess
Fistula
Perforation
Obstruction
What are vascular infections
Heart valves (endocarditis)- Native, prosthetic Vessels- Mycotic aneurysms, prosthetic vascular graft infections (PVGI)
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
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
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
