Lecture 10: Practice of diagnosis in the clinical setting

Question 1

Why is pathogen identification important?

Answer 1

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

Question 2

What are the main methods of pathogen identification?

Answer 2

Microscopy
Culture and sensitivity
Serology
Molecular methods

Question 3

What are the molecular methods for detecting pathogens?

Answer 3

NAATs
PCR
WSG

Question 4

What are the advantages of molecular tests?

Answer 4

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

Question 5

What does detection of mutations allow for?

Answer 5

Help clinician optimise medical therapy

Consider isolation and barrier nursing to prevent ongoing transmission of infection to others

Question 6

Why is rapid identification of the presence of organisms useful?

Answer 6

In outbreak situations where rapid results are required

Where isolation facilities are limited

Question 7

What microorganisms do not grow on traditional media?

Answer 7

Viruses
Chlamydia
Mycoplasma

Question 8

What are the limitations of the identification of bacteria through molecular methods?

Answer 8

Detects presence of gene/ DNA (not if it is expressed)

Does not differentiate between live and dead microorganisms

Genotypic not phenotypic antimicrobial susceptibility profile

Question 9

What is the definition of an outbreak?

Answer 9

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

Question 10

Why are management of outbreaks important?

Answer 10

Surveillance of organisms can lead to early detection

Early detection can help contain outbreaks and prevent transmission

Can curtail outbreaks

Reduction in illness

Question 11

What is the outbreak management framework?

Answer 11

Case definition

Confirm diagnosis in known cases

Determine background incidence of disease

Case-finding

Data collection

Descriptive epidemiology

Microbial investigation

Question 12

How does microbiology/ virology testing help?

Answer 12

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

Question 13

Why is a microbiologist liaised with after investigation?

Answer 13

Implications of lab results

Further human and environmental samples

Question 14

What types of typing are useful?

Answer 14

PFGE

MLST

MLVA

Whole genome sequencing

Question 15

What is the reason for typing results?

Answer 15

To assess the relationship between microbial isolates

Question 16

What are VNTR used for?

Answer 16

Identifying community strains and clusters

Used in hospitals for periods of increased incidence of communicable pathogens

Question 17

What is multiple-locus variable-number tandem repeat analysis (MLVA)?

Answer 17

Phylogenetic clusters of related MLVA types classified into MLVA complexes

MVLA can detect genetic differences between strains of highly homogenous species

Question 18

What is multi-locus sequence typing (MLST)?

Answer 18

Can characterise isolates that cannot be cultured from clinical material

Question 19

What is pulse-field gel electrophoresis typing (PFGE)?

Answer 19

Generates distinctive pattern of fragment sizes for each bacterial strain

Useful for relatedness

Commonly used in reference laboratories

Question 20

What questions should be asked upon someone becoming ill on a general medical ward?

Answer 20

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?

Question 21

When testing is occurring, what can happen on the ward in the meantime?

Answer 21

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

Question 22

Who should be present at an outbreak meeting?

Answer 22

Infection prevention and control

Microbiologist or infectious disease physician

Director of infection prevention and control

Chief nurse or medical director

Trust executive

Question 23

What factors affect whether a bay or ward is shut?

Answer 23

Type of organism

Route of transmission

Number of patients and staff affected

Acuity of ward

Bed situation of hospital

Question 24

What is the effect of ward closures?

Answer 24

Affect patient healing

Visitors cannot come

Treatments affected (e.g. physio)

Contacts have to be isolated

Question 25

What is the advantage of ward closures??

Answer 25

Can curtail outbreaks

Prevent ongoing transmission

Facilitate discharged

Question 26

What is a period of increased incidence?

Answer 26

2 or more patients with the same organism over a 28 day period connected in time and space