Uses of Genotyping

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

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

False-Positive (FP)

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.

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

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?

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

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.

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

Enhance Investigations

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

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)

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

Enhance investigations Two Types of Investigations: Contact Investigations Cluster Investigations

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

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

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

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)

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.

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)

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)

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.

Distinguish relapse from new infection

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.

Monitor trends and evaluate TB control program

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

Differentiate M. bovis and M. bovis BCG

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

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!

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.

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

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