1. Uses of Genotyping

2. Objectives Identify uses for genotyping in TB control efforts
Explore false-positive situations
Distinguish between contact investigations and cluster investigations
Define how genotyping can support identification of new vs old infection

3. Genotyping is used to.. Detect false-positive culture results
Enhance investigations
Confirm/refute links
Identify unknown contacts
Distinguish relapse from new infection
Monitor trends and evaluate TB control program
Differentiate M. bovis and M. bovis BCG

4. False-Positive (FP)

5. False-Positive Possible causes Consequences
Clerical errors: mislabeled specimens
Laboratory cross- contamination
Clinical device contamination: bronchoscope
Consequences
Incorrect TB diagnosis
Unnecessary use of resources
Delay in correct diagnosis or treatment
Overestimation of the TB case rate
- Note these are commonly called lab contaminations but these can be caused by other sources.

6. False-Positive: Scenario
Case: 52 year-old male
Sputum specimen (one collected)
M. tb culture- positive
AFB smear negative
Chest radiograph- normal
Asymptomatic and no risk factors (i.e. HIV, drug use, incarceration, homeless shelter)
Began isoniazid, rifampin, ethambutol regimen
Developed hepatitis-medications discontinued
Condition did not worsen
Hospitalized with laryngeal cancer
Positive culture is enough to make an individual a confirmed TB case.
Treating physician did not believe he was a TB case; wanted to rule out laryngeal TB

7. False-Positive: Scenario
Hint #1:
Two TB suspects admitted at the same time
Two identical genotypes from same hospital lab within two sequential days
Of 12,000 genotypes run in Texas in 10 years, only 6 resulted in same genotype
Hint #2:
Contact investigation did not reveal any suspect cases from FP case
Clearly lab contamination… Right?

8. False-Positive (FP): Scenario
Other clues:
Only 1 specimen collected for FP patient and two specimens for the other– this was a burning question!
GENType– very rare strain
Suspected FP had no other clinical sx’s
No Epi-links between the two hospitalized individuals

9. False-Positive: Scenario
Summary of findings
In total, three specimens under review, all collected on successive days
All specimens collected at one hospital, but processed at another, all on successive days
Two genotyped specimens matched
Both individuals were in hospital on same day
No epidemiological links between the individuals
Conclusion: Second specimen was that of the “true” TB case but was mislabeled with the wrong name.

10. False-Positive: Scenario
Process for Investigation
Created a working group involving
Central Office: nurses, epidemiologists, TB Program Manager, surveillance, laboratory
Regional Office: TB Program Manager, nurses, case manager
Heartland
Held regular conference calls to discuss
Updates on case progress
Evolving questions
Discussions with local hospital staff to understand process of patient care and laboratory procedures
Moving forward
Team regularly reviews suspected false-positive cases
Working to create policies to share with regional and local programs
- If a case is reported and then reversed ALL of those cases will be reviewed

11. Enhance Investigations

12. Quick Epidemiology Overview
Along with the genotype data, we need to see if the cases are epidemiologically linked as well to determine recent transmission.
Definition of Epidemiologic link (Epi-link)
A characteristic two TB patients share that explains where and when TB could have been transmitted
Location where the two persons spent time together (6 or more hours per week)
Relationship that brought them together

13. What is an Epi-Link?
Epidemiologic links are essential to determine on-going transmission:
Person – demographic information
Place – bars, jail, homeless shelter, geographic location
Time – infectious period of index
Hours of exposure
Relates to infectious period
Elaborate on infectious period
Place can also be determined by what types of activities the individual is involved in (church choir, drinking, hobbies such as playing pool, card games)

14. Types of Epi-Links Definite Probable Possible No Epi-links
TB Case named the other OR
TB case in the same place at the same time during infectious period
TB cases in same area and shared social or behavioral traits
TB cases live in same neighborhood around the same time
TB case in the same place, but timing is off
No links identified

15. Enhance investigations
Two Types of Investigations:
Contact Investigations
Cluster Investigations

16. Contact Investigations
An investigation of persons who have shared space/time with a patient having infectious TB.
Goal:
Identify additional persons with active TB
Determine if transmission occurred between the TB patient and their contacts, and
To identify persons with latent TB infection who are candidates for treatment
Involves interviewing TB cases and suspects

17. Contact Investigations
Genotyping can help:
Identify persons involved in same chain of transmission
Confirm links
Refute Links
Identify unknown contacts

18. Challenges Missing information on TB-340’s Date of broken contact
Names of bars, restaurants, shelters, or other places of social activities
Diagnosis dates, dates of symptom onset, or other relevant dates
Unidentified contacts
Case is unwilling to reveal the name of contact
Case did not know the name of contact
Case unable to provide information (i.e. dead, dementia)
- Genotyping can assist with unidentified contacts

19. Designation of Clusters
More than one isolate has the same GENType
Unique
No matched GENType indicates it is a unique strain (i.e. not clustered)

20. Cluster Investigation
An investigation of TB patients who share epidemiologic links after genotyping results are known
Goal: To identify epidemiologic links among TB patients whose isolates have matching GENTypes to see if any contacts were missed.
Genotyping is critical to initiate cluster investigations and follows contact investigations if there is suspicion of an outbreak.
May consist of reviewing medical info or re-interviewing patient.

21. Launching a cluster investigation
Movement from PCRType to GENType, i.e. G16274
Cluster alerts from TBGIMS
Log Likelihood Ratio
Cluster investigations are not always warranted
We are here to help guide you and assist you when deciding on whether or not to launch a full investigation.
Genotyping coordinator monitors cluster alerts
Creating a workgroup to assess and determine need for further investigation
Discuss LLR
Alert levels in TB GIMS are based on geospatial concentration
Statistic: Log Likelihood Ratio (LLR)
On the county level
High (3-year LLR≥10)
Medium (3-year LLR = 5.0 to 9.99)
None (3-year LLR ≤ 4.99)

22. Possible Indicators for Ongoing Transmission/ Outbreak
Homeless clusters
Pediatric cases, drug resistant cases, other risk factors
High geographic concentration
Increasing numbers over time (Epi curve)

23. Contact Cluster Who? Contacts Cases What? New cases/suspects
Linked cases (Genotyping/Epi-links)
When?
Upon identification of case/suspect
After contact investigation and genotyping
Where?
Home/work place visit
Re-evaluation of home/work
How?
Interviewing
Record interview
Social network analysis
Re-interview cases
Record re-review
Review genotype data
Additional social network analyses
Why?
Genotyping may assist in finding missed contacts/expand contact investigations.
It can confirm Epi-links.
Identify unsuspected transmission.

24. Distinguish relapse from new infection

25. New vs Old Infection
Reactivation: when TB patient is treated & cured, but has a subsequent episode of TB disease caused by same strain of M. tuberculosis as previous episode
Reinfection: caused by 2nd infection with different strain from initial strain
Genotyping 1st & 2nd isolates from same patient: can demonstrate reactivation vs reinfection
- Reinfection: usually, though it is possible to be reinfected with the same strain if the person continues to be exposed after cure.

26. Monitor trends and evaluate TB control program

27. Monitor trends and evaluate TB control program
Monitor ongoing transmission
Identify trends- characteristics of cluster
Known high risk populations
Newly identified high risk populations
Settings
Prioritize prevention and control efforts
Monitor progress toward TB elimination goals
Quarterly Cohort Reviews
Treatment completion
Number of contacts

28. Differentiate M. bovis and M. bovis BCG

29. M. bovis and M. bovis BCG
These cases can be identified via genotyping results
M. bovis-warrants further investigation
unpasteurized dairy
contact with livestock
M. bovis BCG- no further investigation required
Verify these cases are not reported

30. Quiz Time!
TRUE OR FALSE
Genotyping is a good substitute for contact investigations.
Answer= False. Genotyping complements contact investigations but does not replace the need for good CI work!

31. Quiz Time!
Genotyping may be especially helpful in identifying places that were:
Obvious during the initial contact investigation.
Already tested during the initial contact investigation.
Overlooked (unusual settings) during the initial contact investigation.
Correct answer: C
Unusual and overlooked settings can become more clear once genotyping results have been determined.

32. Reminder Our team is here to help you:
Genotype Coordinator: TBGIMS, interpreting results
Support for cluster investigation
Guide false-positive investigations
Assist with questions for contact investigations/guidance

33. Objectives Identify uses for genotyping in TB control efforts
Explore false-positive situations
Distinguish between contact investigations and cluster investigations
Define how genotyping can support identification of new vs old infection