TB Genotyping and Whole Genome Sequencing in California CTCA Educational Conference March 7, 2017 Martin Cilnis, MPH, MS Tuberculosis Control Branch California Department of Public Health

Potential Uses of Genotyping Confirm or refute outbreaks Identify lab cross-contamination Identifying possible sources of TB in children Distinguish TB relapse from reinfection Uncover linkages and settings not found by traditional contact investigations (CI) Measure success of TB control Define accuracy of contact and source case investigations Many uses of genotyping

TB Genotyping Coverage in California, 2011-2016 2015 National Objective 94% High genotyping coverage in CA, exceeds national objective, high confidence that genotyping clusters are capturing culture-positive CA cases, 90% in 2016 is because 2016 isolates are still being submitted by local health departments

How Do We Learn About Outbreaks? CDC Outbreak Detection Using TB Genotyping TB genotype cluster alerts: Generated when a genotype has a higher than expected concentration within a county compared to other counties in the US in a 3-year window Large outbreak surveillance: ≥10 TB cases in a 3-year period related by recent transmission Notifications from local health departments Several ways CA TBCB learns about possible outbreaks

CDC TB Genotype Cluster Alerts in CA, 2011-2016 The number of genotype alerts have increased since 2011. Some of these alerts were indeed incident or prevalent outbreaks, however, some also are not outbreaks or other recent transmission events. We take each genotype alert seriously and, depending on our outbreak team’s assessment, minimal to extensive resources could be expended to investigate a cluster. WGS can help prioritize which genotype clusters to investigate. Potential question: Why has there an increase in cluster alerts? We don’t have a definitive answer: some genotype clusters alert more than once, some of the clusters are recent transmission or incident outbreaks, some are prevalent outbreaks occurring over multiple years, some are common genotypes that are not recent transmission. Improved genotyping coverage in CA might explain a small percent of the increase. We also learn about clusters or outbreaks through communication with local health departments and monitoring of genotypes via our watch lists. Note: a genotype can have more than one alert. The graph includes the multiple alerts because the outbreak response team examines each alert.

Steps of a TB Genotype Cluster Investigation TB genotype cluster alert received by TB outbreak team Prioritize genotype clusters Higher priority Lower/no priority Notify local health departments Monitor genotype Investigation can be a variety of things, e.g., review patient charts, discuss cluster with case managers, re-interview cases, expand contact investigations. In a time of diminishing public health resources, it is important to prioritize the clusters that are important to investigate and not spend time on false positive alerts. Whole genome sequencing could help with the cluster prioritization. WGS could help with cluster prioritization and investigation. Investigation Implement interventions

Cluster investigation ≠ “Just another TB contact investigation” Cluster investigations more challenging Aim: Interrupt transmission by identifying contacts AND where, when and from whom patient was infected Scope: Multiple patients; often multiple LHDs Timeframe of interest: 2-3 years Methods: Not yet well-established; tools not widely available Training: Not yet readily available; few SMEs; not yet seen as core competency for staff Differences between genotype cluster investigation and a contact investigation

Outcomes for Alerted TB Genotype Clusters, 2016 47 alerts for 40 county-clusters 26 (55%) higher priority clusters 27 outcomes Prior outbreaks with new cases: 13 (48%) New outbreaks: 9 (33%) Confirmed/probable outbreaks: 3 (33%) Suspected outbreaks: 6 (67%) No evidence of an outbreak: 3 (11%) Limited transmission: 5 (100%) Cross-contamination: 2 (7%) Outcomes of genotype clusters that were alerted in 2016: (outcomes based on cluster investigation findings before WGS was available) Prior outbreaks with new cases (i.e., growth of genotype clusters associated with prior outbreaks; new cases assessed by CA TBCB and cluster re-prioritized) New outbreaks (i.e., genotype clusters alerted in 2016 that were determined to be suspected, probable, or confirmed outbreaks) No evidence of an outbreak (i.e., cluster investigation found some epi links among cases but not enough to reach the defined threshold of a suspected, probable, or confirmed outbreak) Cross-contamination (i.e., the alerted genotype cluster was due to lab cross-contamination not previously known by the LHD or local PHL) For reference only: WGS was requested for 17 of the higher priority county-clusters; WGS results were reported for 12, outcomes were reaffirmed by WGS except for 4 clusters where WGS refined possible transmission links (i.e., excluded clustered cases, included cluster cases, identified sub-clusters)

Genotyping Report No epi/clinical data Key data fields: Case name and DOB Specimen collection date Genotype Accession Number Genotyping Lineage Comments Genotype report is sent by encrypted email from CA TBCB to local health departments, Excel spreasheet contains data for your jurisdiction since the beginning of the genotyping service in 2004, has many data fields, however, there are some key data fields, contain no epi or clinical data, however, the report itself can be useful (examples on next slides).

Example: Refute suspected transmission Suspected 5-person outbreak among foreign-born adults living in same city 3 with culture-confirmed TB 2 with suspected TB and pending cultures All diagnosed within 2-month period 4 attend the same school, 2 are friends, and 2 lived at same apartment complex Genotypes for 3 culture-pos patients did not match!! Can stand down from outbreak investigation unless new genotype matches found The report can be used to look-up case names genotypes to determine if whether transmission has occurred

Example: Evaluate outbreak containment 3 6 4 2 3 4 Outbreak Contained? New Transmission? The report can be used to monitor for new cases in a genotype associated with an outbreak

Methods Used in TB Molecular Analysis Whole Genome Sequencing Various molecular analysis methods have been used for TB, MIRU-VNTR analyze a small portion of the Mtb genome (~1%) while WGS analyzes over 90% of the genome (more discriminatory) Current genotyping methods Source: A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Guthrie JL, Gardy JL. Ann N Y Acad Sci. 2016 Dec 23. doi: 10.1111/nyas.13273

TB WGS in California, 2013-2016 41 clusters 32 (78%) clusters with complete WGS results (35 outcomes) 9 (22%) clusters with pending WGS results 14 (40%) refuted as an outbreak 21 (60%) outbreak not refuted WGS outcomes for 41 clusters. 40% of clusters were refuted as an outbreak but in most of these clusters, sub-clusters of cases were identified which suggest transmission (the focus of investigation can be on the sub-cluster of cases rather than the entire cluster) 60% of clusters were not refuted as outbreaks, most were confirmed and probable outbreaks indicating that WGS and the cluster investigation findings aligned 11 (79%) limited transmission 14 (67%) confirmed and probable outbreak

Summary State TB Control Branch prioritizes alerted genotype clusters for investigation Genotype cluster investigation are different from contact investigations Most of the prioritized county-clusters were known new outbreaks or prior outbreaks with new cases WGS can help elucidate chains of transmission and help focus on cases with closely-related WGS

Thank you! Martin Cilnis, MPH, MS Epidemiologist, Outbreak Prevention and Control Section, Tuberculosis Control Branch, California Department of Public Health 510-620-3015 martin.cilnis@cdph.ca.gov