Lecture 10: Practice of diagnosis in the clinical setting Flashcards
Why is pathogen identification important?
Aids in the diagnosis/ confirmation of infection at a given site
Knowledge of how that organism can cause infection n
Inform antimicrobial susceptibility testing
Enhance antimicrobial stewardship
Help determine periods of increased incidence
Help to curtail outbreaks
Aids in pathogen surveillance and predicting trends
What are the main methods of pathogen identification?
Microscopy
Culture and sensitivity
Serology
Molecular methods
What are the molecular methods for detecting pathogens?
NAATs
PCR
WSG
What are the advantages of molecular tests?
Rapid
Often easy to use
Can detect very small amounts of material
Can be highly sensitive and specific
Can detect infectious agents during incubation period
What does detection of mutations allow for?
Help clinician optimise medical therapy
Consider isolation and barrier nursing to prevent ongoing transmission of infection to others
Why is rapid identification of the presence of organisms useful?
In outbreak situations where rapid results are required
Where isolation facilities are limited
What microorganisms do not grow on traditional media?
Viruses
Chlamydia
Mycoplasma
What are the limitations of the identification of bacteria through molecular methods?
Detects presence of gene/ DNA (not if it is expressed)
Does not differentiate between live and dead microorganisms
Genotypic not phenotypic antimicrobial susceptibility profile
What is the definition of an outbreak?
2 or more linked cases of an illness in space and time
Greater than expected rate of infection compared with usual background rate
Suspected, anticipated or actual event involving microbial contamination of food
Why are management of outbreaks important?
Surveillance of organisms can lead to early detection
Early detection can help contain outbreaks and prevent transmission
Can curtail outbreaks
Reduction in illness
What is the outbreak management framework?
Case definition
Confirm diagnosis in known cases
Determine background incidence of disease
Case-finding
Data collection
Descriptive epidemiology
Microbial investigation
How does microbiology/ virology testing help?
Surveillance: organisms identified are routinely submitted to PHE
Confirms diagnosis and if outbreak has occurred
Informs the epidemiology
Identifies which patients meet the case definition
Why is a microbiologist liaised with after investigation?
Implications of lab results
Further human and environmental samples
What types of typing are useful?
PFGE
MLST
MLVA
Whole genome sequencing
What is the reason for typing results?
To assess the relationship between microbial isolates
What are VNTR used for?
Identifying community strains and clusters
Used in hospitals for periods of increased incidence of communicable pathogens
What is multiple-locus variable-number tandem repeat analysis (MLVA)?
Phylogenetic clusters of related MLVA types classified into MLVA complexes
MVLA can detect genetic differences between strains of highly homogenous species
What is multi-locus sequence typing (MLST)?
Can characterise isolates that cannot be cultured from clinical material
What is pulse-field gel electrophoresis typing (PFGE)?
Generates distinctive pattern of fragment sizes for each bacterial strain
Useful for relatedness
Commonly used in reference laboratories
What questions should be asked upon someone becoming ill on a general medical ward?
Time of admittance? Symptoms starting?
Ward layout? Patients in relation to each other?
Any other patients, staff, visitors in last 48 hours?
What has been eaten?
Patient contacts?
When testing is occurring, what can happen on the ward in the meantime?
Infection prevention and control liaise with clinical microbiologist
Consider more likely diagnosis based on clinical findings
Consider options to isolate symptomatic patients
Depends on - ward layout, number of patients affected
Who should be present at an outbreak meeting?
Infection prevention and control
Microbiologist or infectious disease physician
Director of infection prevention and control
Chief nurse or medical director
Trust executive
What factors affect whether a bay or ward is shut?
Type of organism
Route of transmission
Number of patients and staff affected
Acuity of ward
Bed situation of hospital
What is the effect of ward closures?
Affect patient healing
Visitors cannot come
Treatments affected (e.g. physio)
Contacts have to be isolated
What is the advantage of ward closures??
Can curtail outbreaks
Prevent ongoing transmission
Facilitate discharged
What is a period of increased incidence?
2 or more patients with the same organism over a 28 day period connected in time and space
