09-11-21 - Making an infection Diagnosis Flashcards
Learning outcomes
- List the main modalities for making a laboratory diagnosis of infection
- Understand the nature of the diagnostic process and the role of the infection specialist
- Define the terms sensitivity and specificity and relate them to the doctor patient interaction timelines
- Describe what specimens can be taken
- Describe the methods that are used to make a microbiological diagnosis
- Describe the impact of molecular biology on diagnostics
What 3 things does microbiology do in medicine?
1) Diagnostic advice – identifying the infecting organism
2) Treatment advice – Susceptibility test (what antibiotics may be effective)
3) Infection control – Identify clustered organisms over-represented in the community
What are 5 roles of clinical microbiologists?
1) Provide high quality diagnostic tests
2) Provide a clinical consultation service for patients with suspected infection
3) Provide clinical advice on the interpretation of diagnostic tests
4) Provide advice on therapy of serious infections
5) Manage control of infection issues within the hospital environment
What are the 4 methods in making a microbiological diagnosis?
1) Direct examination
2) Culture
3) Serology (scientific study of diagnostic examination of blood serum)
4) Molecular
What are the 2 types of direct examination methods?
What are 3 advantages and disadvantages of smear diagnosis?
What are the 3 different kinds of microscopy?
What each type be used to check for?
1) Smear diagnosis • Advantages • Rapid • Simple to perform • Cheap • Disadvantages • Not very sensitive • Not very specific • Requires considerable expertise
2) Microscopy
• Light microscopy:
1) Direct stain – can check stool for parasites
2) Gram stain – can check CSF for bacteria
3) Z-N (Ziehl-Neelsen) stain – check sputum for TB (mix of saliva and mucus coughed up from respiratory tract, typically as a result of infection)
4) Giemsa stain – check blood for malaria
• Fluorescent microscopy
1) Respiratory syncytial virus (RSV) diagnosis
2) Bacterial diagnosis of TB
• Electron Microscopy (EM)
1) Virus detection and identification
What are the 2 types of culture methods?
What are 4 advantages and 1 disadvantage of culture diagnosis?
What is 1 advantage and 3 disadvantages of MALFI-TOF?
1) Culture diagnosis • Advantages • More sensitive than a smear • Allows susceptibility testing • Allows rapid presumptive diagnosis • Allows detailed identification
- Disadvantages
- Rendered negative by antibiotics e.e patient taking antibiotics may prevent bugs from growing in the sample
2) MALDI-TOF – mass spectrometer
• Advantages
• Rapid identification of bacteria
- Disadvantages
- Does not provide susceptibilities
- Delayed by slow growth
- Of no value if antibiotics render culture negative
What is serology?
What are 7 different examples of serological techniques?
What 5 factors can be detected when making a serological diagnosis?
What type of tests are these all?
How can they help us figure out what type of infection this is?
• Serology is the scientific study of diagnostic examination of blood serum
• 7 examples of serological techniques:
1) Agglutination – antibodies clumping tother
2) Precipitation – antibodies may clump together and precipitate out of the solution
3) Complement fixation – complement system is a very potent immune reaction, and complement fixation often indicates bacterial infection
4) Virus neutralization
5) Enzyme linked immunosorbent assay (ELISA) – technique for detection of antigens in blood sample
6) Radioimmunoassay (RIA)
7) Immunofluorescence
• Last 2 are labelled antibodies fixing to specific target
• What 5 things can be detected when making a serological diagnosis:
1) Detecting high IgG concentration
2) Detecting rising or falling titres
3) Detect IgM/IgA levels
4) Measure avidity (overall strength) of binding between antibodies and antigens
5) Detecting antigens
- These are all examples of immunological tests (concerning antibodies – immunoglobulins)
- The rising and falling of levels of particular antibodies can give us insight into what is causing the infection e.g bacteria, virus, infection
What are the 2 different types of molecular diagnosis techniques?
What are the 5 different subtypes of the second type?
1) DNA hybridization
2) Nucleic acid amplification testing
• Polymerase Chain Reaction (PCR)
• Ligase chain reaction (LCR)
• Automated DNA amplification
• Real time PCR – subset of PCR that is a bit more rapid and sensitive
• QPCR – tells us how many organisms are present as well
What are 5 examples of specimens taken in response to different conditions?
1) Urinary tract infection (UTI) - Midstream urine (MSU) –
2) Wound - Pus or swab
3) Meningitis - CSF and blood
4) Pyrexia (elevation of body temperature above normal variation) of unknown origin (PUO) - Blood for culture + serology
5) Pneumonia - Sputum, lavage (washing out of body cavity with water or medicated solution), serology
What are 3 ways specimens can be classified?
1) Single pathogen sought
2) Limited multiple pathogens sought
3) Many pathogens sought
How can specimens with a single pathogen be obtained?
What then occurs?
What infections may be found in the specimen?
What will be found in this specimen?
- Specimens with a single pathogen can be obtained through a throat swab (except if diphtheria is suspected – serious infection)
- Infection control screening tests can then occur
- Unusual infections may be found in the sample, such as pertussis
- This method is also useful for MTB (Mycobacterium tuberculosis) detection
- We will find a variety of organisms within this sample, but only one infection-causing pathogen e.g we will only find MTB in a TB specimen, because it is a TB infection
What are 3 examples of specimens where a few pathogens are likely?
1) CSF – cerebrospinal fluid
2) STI sample - variety of possible STIs
3) Blood – septicaemia (when bacteria enter the blood stream, and trigger blood poisoning, which causes sepsis) and bacteraemia (bacteria in the blood) can be caused by a range of organisms/pathogens
What are 5 examples of specimens with many pathogens?
1) Faeces
2) Abscess pus
3) LRTI samples (Lower respiratory tract infection)
4) Oral swab
5) Urine? – may be in single pathogen category, but passes through urinary tract and picks up many organisms, which can be difficult to differentiate between pathogens and non-pathogens
What are 3 pieces of evidence of a positive diagnosis?
How are true positives/negatives obtained?
1) Sensitivity
• The capacity to detect a small number of organisms
• The ability of a test to detect all of the true positives
• Important if very few organisms are taken from a sample
• Equal to the number of positives obtained divided by the total number of positives
2) Specificity
• Getting it right without getting false negatives/positive’s
• Ability to identify the number of true negatives
• Equal to the number of negatives obtained divided by the number of true negatives
3) Predictive value of a positive/negative test (PVP/PVN)
• Predictive value for a particular test to get it right or wrong
• Based on Sensitivity/specificity
• True positives/negatives are obtained through very in-depth testing
What are the 3 things that are needed to interpret clinical tests?
1) Test sensitivity and specificity
2) Impact of normal flora on tests
• How likely is it that normal flora from various parts of the body is picked up as part of the testing protocol? E.g skin, gut
• Why we ask for midstream urine
3) The fourth dimension
• Do I need a test? – Different doctors may come to different decisions as to whether a test for infection is needed based on the patients’ symptoms – may present with signs of infection, or maybe it could be other things and a test is not required right now
• Can I get a test? – based on resources or may not be required or sensible (ill patient that doesn’t have time for a test, as they can be slow)
What must interpretation of microbiology results be made in the context of?
What does a person’s normal flora affect?
Where is normal flora found?
What does the normal flora consist of?
When can normal flora cause health issues?
- The interpretation of all microbiological results must be made in the context of normal flora
- A person’s normal flora will affect how well they are on a day-to-day basic i.e everyone has different flora and will respond differently to the same illness/infection
- Normal flora is found everywhere, except areas such as blood, bladder and CSF, where it is unusual for bacteria to be present
- Many pathogens are also colonisers in the normal flora of the body, and will only cause illness in immunocompromised individuals
When may infections (such as UTIs) not need laboratory diagnosis?
