Making an Infection Diagnosis Flashcards
What does microbiology do ?
Identify the infecting organism
Susceptibility testing
Identify clustered organisms over-represented in the community.
Diagnostic advice
Identify the infecting organism
Treatment advice
Susceptibility testing
Infection control
Identify clustered organisms over-represented in the community.
What are laboratory results for ?
- Act as a doctors back up
- Alert us to patients where the clinicians suspect infection but have not bothered to contact
- Help out when antibiotics are unpredictable
- Permit collection of alert organisms and detection of outbreak samples
- Provide an intelligence system
Why don’t clinicians use microbiology results ?
The speed of progression of infection is much
faster than the time taken to generate results
(we are too slow)
They do not understand the implications of
the data.
Describe some roles of clinical microbiologist
To provide :
- high quality diagnostic tests
- a clinical consultation service for patients with suspected infection
- clinical advice on the interpretation of diagnostic tests
- advice on therapy of serious infections
Describe the process of a diagnosis
Patient doctor interaction
Differential diagnosis
Clinical specimens
Results - refinement of differential diagnosis
Diagnosis
Therapy
How to make a microbiological diagnosis ?
Direct examination
Culture
Serology
Molecular
What is serology ?
To check for the presence or level of specific antibodies in the blood.
Types of Microscopy
Light
Fluorescent
Electron microscopy
Types of light microscopy
Direct
Gram
Z-N
Giemsa
Direct light microscopy
stool - parastites
Gram light microscopy
CSF - bacteria
Z-N light microscopy
sputum - TB
Giesma light microscopy
blood - malaria
What is fluorescence microscopy used for ?
Respiratory syncytial virus
RSV diagnosis
What is electron microscopy used for ?
Virus detection and identification
Culture diagnosis features
- More sensitive than smear
- Allows susceptibility testing
- Allows rapid presumptive diagnosis
- Allows detailed identification
- Rendered negative by antibiotics
Smear diagnosis description
- Rapid
- Simple to perform
- Cheap
- Not very sensitive
*Not very specific - Requires considerable expertise
MALDI-TOF description
A positive step
- Rapid identification of bacteria
- Does not provide susceptibilities
- Delayed by slow growth
- Of no value if antibiotics render cultures negative
Serological diagnosis function
- Detect high IgG concentration
- Detect rising of falling titres
- Detect IgM/IgA
- Measure avidity of binding
- Detect antigen
Name 7 examples of serological techniques
Agglutination
Precipitation
Complement fixation
Virus neutralisation
ELISA
Radioimmunoassay
Immunofluorescence
Examples of molecular techniques
DNA hybridisation.
Nucleic acid amplification testing.
- PCR
- LCR
- Automated DNA amplification
- Real time PCR
Culture based diagnosis
- Detect high IgG concentration
- Detect rising of falling titres
- Detect IgM/IgA
- Measure avidity of binding
- Detect antigen
Examples of specimens
UTI - midstream urine
Wound - pus or swab
Meningitis - CSF and blood
Pyrexia of unknown origin - serology
Pneumonia - sputum, lavage, serology
How to test for specimens with a single pathogen ?
- Throat swab (except diphtheria suspected)
- Infection control screening
- Unusual infections e.g., pertussis
- Mtb detection
How to test for specimens where a few organisms are likely ?
CSF
STI samples
Blood
How to test for specimens with multiple pathogens ?
- Faeces
- Abscess pus
- LRTI samples
- Oral swab
- (Urine)
How to interpret clinical tests ?
- Test sensitivity and specificity
- Impact of normal flora on
- The fourth dimension- do I need a test – can I
get a test?
What is test sensitivity ?
- The ability of a test to detect all of the true positives
- Equal to the number of positives obtained divided by the total number of positives
What is test specificity ?
- Ability to identify the number of true negatives
- Equal to the number of negatives obtained divided by the number of true negatives
Normal flora
- Its everywhere
- Many of the pathogens are also colonisers
- Interpretation of all microbiology results must be made in the context of the normal flora
Normal flora in nasopharynx
Streptococci
Haemophilius
Neisseria
Mixed anaerobes
Candida
Actinomyces
Normal flora in skin
Staphylococci
Streptococci
Corynebacteria
Proprionibacteria
Yeasts
Normal flora in upper bowel
Enterobacteriaceae
Enterococci
Candida
Normal flora in lower bowel
Bactericides
Bifidobacteria
Clostridium
Peptostreptococci
Normal flora in vagina
Streptococci
Lactobacilli
Corynebacteria
Candida
Actinomyces
Mycoplasma hominid
What are the cultures like for patients with a viral infection ?
Negative cultures
Drawbacks of legionella
Grows slowly and requires specialist medium
Drawbacks of mycoplasma pneumoniae
Requires specialist medium and 14 days to grow
Drawbacks of chlamydia psittaci
chlamydophyla pneumoiae
Obligate intracellular pathogen
