Whole Genome Sequencing: Local Perspective Shameer Poonja, MPH CDC Public Health Advisor Los Angeles County TB Program

Los Angeles County TBCP TB Controller Admin. Genotype Cluster ID and Assessment Data Mgmt and IT Education and Evaluation Epidemiology and Research Medical Consultation, Patient Services and Reporting CI Monitoring and Assessment Unit – Coordinate CI referral form TB Surv, CMaP, CI Core Teams Provide CI Assurance/Support/Feedback to CHS Request isolates for expedited genotyping Coordinate any additional TBCP CI activities Coordinate TBCP Health Officer Log Genotype Cluster ID and Assessment Provide Cluster support Contact Investigation Monitoring and Assessment

TBCP Genotype Cluster ID and Assessment: Cluster investigation Begins with referral to the cluster team TBCP – surveillance, medical consultation, CI Team CA TBCB Outbreak Team CDC TBGIMS Weekly review of genotype results Establish a picture of the cluster Create a line list of all cases with the same genotype Collecting all known information about cases Document known epi links Review national distribution of genotype pattern Request expedited genotyping

Cluster investigation (2) Develop transmission hypothesis Risk factors Country of birth, ethnicity, and age Employment Geographic location (sites and settings) Assess likelihood of transmission or TB outbreak Notify CI Core Team of concerning clusters Collection of additional information Re-interview patients Maintain priority cluster list Develop transmission hypotheses Identify characteristics common to all or most cases, including infectiousness and other clinical characteristics, in hypotheses development. Utilize readily available contact rosters to identify if and how cases may be linked. Conduct a preliminary cluster review considering information from TB GIMS such as the number of cases, date range (epidemiologic curve), genotype distribution, and geographic area. In addition, consider how complete the available data is, how the cluster was identified, risk factors of known cases, and any known epidemiological or social links that are known. Rank clusters as low, medium or high likelihood of transmission Low likelihood of transmission – upon initial listing of cases and review of information the cases in the cluster are either part of common genotype with know reported association or time span between cases does not suggest recent transmission Medium likelihood of transmission – are ones clusters that suggest possible/probable recent transmission (2-3 years) and CI within these clusters require on-going monitoring. High likelihood of transmission – clusters with known/confirmed recent transmission. Assess for the likelihood of a TB outbreak or an exposure among a small limited number of close contacts. Notify CI Core team of concerning clusters Low – no followup Medium - Many times cases within these clusters will require additional information from DPHN. For open, ongoing Cis would try to provide recommendations to the CI Core Team to help focus the investigation and resources. High – CIs within these clusters require greater oversight and additional targeted activities. Provide technical assistance to CI Core Teams in on-going investigations  Prioritize and assign responsibilities for the investigation If the cluster is deemed to warrant further investigation, prioritize the cluster following CDC guidance.

Cluster investigation challenges Large national clusters (common genotypes) Determine if exposure is currently taking place Extent of transmission Cross jurisdictional exposure

Local jurisdiction example: G00020 Cluster summary National distribution show that the G00020 cluster is common genotype: XXX cases nationwide, XX different states reporting a case and 16 cases reported by California between 2010 – 3/2015 Sub – cluster 1 (2014-2015) TBCP Medical consultation with district and CI Team 4 cases Commercial site and family/social sites of exposure Determined to be an outbreak Sub-cluster 1: Index case 1a. presented with a cough in 8/2013 and attended regular meetings at VS. During his CI, 1b was identified and tested QFT positive on 5/29/14. She had a normal CXR and started INH on 7/23/14. It is unclear if she finished treatment but she presented with symptoms in 12/2014. Her daughter, 1c was discovered through a small discrepancy in what seemed to be a normal CXR. She had no signs or symptoms.

Patient 1A 1B 1C 1D Age 51 46 14 49 COB Mexico U.S. HC Pacoima Meds Started 4/4/2014 1/17/2015 2/26/2015 4/7/2015 Smear Positive (4+) Positive (1+) Negative Culture Positive Cavitary No Yes Risk factor none Employment student Epi link friend mother daughter sister

Timeline of exposures

Social network

Social network (2) 1B had 11 different sites of exposure Attended birthday party Large family network with family that was estranged Family experienced multiple testing due to continued exposure to several cases Daughter attended LAUSD school and CI was initiated at school (assigned seats in their classrooms) 4 hrc – 1 converter 26 med – 3 converted 1 teacher - negative

Local jurisdiction example: G00020 Cluster summary National distribution show that the G00020 cluster is common genotype: 125 cases nationwide, 17 different states reporting a case and 85 cases reported by California Sub – Cluster 2 (2016) CI Core Team and Cluster Unit review of genotype results 4 cases (multiple jurisdictions) Household/social setting sites of exposure Determined to be a cross-jurisdictional outbreak Progress notes from 4/13/15 Additional cases - matches G00020 JB - lives 3 miles from VS- notified nurse and inquired about any relation he may have 2B matched G00020- staff contacted nurse about any relation he may have to VS. DPHN reported that 2B has no relation to VS KG has no relation to VS per DPHN- FM has no relation to Vida Saludable per DPHN- 2D – call from DPHN at Monrovia His sister was diagnosed with TB and completed treatment Sept of 2015, her DP# is 906032, and she was followed in Pomona. My index was not evaluated at the time of his sister’s diagnosis as he had no contact with her during her infectious period. Upon interview with my index and his mother, I found that there was a cousin that visited the family often from Mexico that was diagnosed and treated for TB in the past (has prison history). Mom stated that he was treated and followed up in different jurisdiction (I figure crossing the border for treatment and follow up). His name is 1A . I was just curious to see if there was any genotype info that you have access to on him to see if there could be a match with him. The belief is that the household was all exposed to the same source and the activation is happening at different times. These two siblings were born in the US and at one point did live in the same household, could be when this cousin visited. There is a third sibling, US born, that was found to be TB II with sisters CI but he refused LTBI. Now with brother a possible TB III, he is reconsidering!

Non-injection drug use, Smoker Employment Shipping and Receiving Patient 2A 2B 2C 2D Age 24 20 2 22 COB   USA HC Pomona Monrovia Meds Started 2013?  2/3/2015 2/26/2015 12/2/2015 Smear PO (2+) N/A PO(3+) Culture PO Cavitary No Yes (on CT scan) Risk Factor(s) TB contact, <5 years Non-injection drug use, Smoker Employment Shipping and Receiving Mechanist Epi link cousin Contact to SR and sister to KJ Son FJ Contact to SR and brother to FJ

Family 2 Outbreak Infectious Timeline Exposure to 2A 1/1/2013 2013 Jan May Sep 2014 May Sep 2015 May Sep 2016 2016 177 days 2D IP Today 8/25/2015 - 2/17/2016 129 days 2B IP 10/19/2014 - 2/24/2015

G00020 WGS results of Los Angeles isolates, June 2016 Total G00020 isolates Isolates WGS Requested* done pending n % Los Angeles 21 16 76% 10 63% 6 37% * WGS was requested for isolates from cases diagnosed 2013-present

G00020 WGS results for selected TB cases in Los Angeles Counties, Jan 2016

WGS Minus four outliers 1D, Los Angeles, 4/2015 1B, Los Angeles, 1/2015 1A, Los Angeles, 5/2014 , non LAC case 8/2012* WGS Minus four outliers Pending WGS for LAC cases: 1C 2C 2D 2A, 2/2012** 2B , 2/2015

Summary WGS results Two clusters were determined to be unique No additional investigation activities were pursued to connect these two sub-clusters Future actions – document questions for future G00020 cases in both geographic areas Program activities Make requests for WGS monthly WGS supported the results of basic case investigation and interviews and genotyping

Local jurisdiction example: G15969

Background Genotype has been in Los Angeles County (LAC) for at least 14 years GENType G15969 since 2007 G15969 is not unique to LAC As of April 1, 2015 there are 23 G15969 cases reported in CA in this genotype cluster* 19 (83%) of these are reported by LAC** * Three additional 1-off clusters reported in CA (G15973, G17331 and G15968) ** One additional clinical cases (2011)

G15969 in CA, 2007-2014 Los Angeles County All G15969 cases are in Southern CA. Majority are in LAC. Los Angeles County

Prior Investigation PCR00765 was initially brought to our attention by State TBCB Outbreak Team in 2008 None of these cases had MIRU2 typing Review of LAC TB Control Program charts identified 7 cases had epi links to other cases and formed 3 separate epi-linked clusters No known links between the epi-linked clusters In 2008, PCR00765 had 16 cases in California, of which 9 3 cases linked to family/social setting 2 cases linked to family/social setting were in LAC. Many of the clustered cases were Mexican-born but the most recent cases were among U.S.-born blacks

G15969 Investigation Review of 15 patient charts reported between 2010 – 2013 Possible contamination of one case 2011 3 cases reported drug and ETOH 4 HIV positive cases (4- live in close proximity) 3 cases worked construction -Home Depot (Western/Sunset) 4 cases reported incarceration 2 cases had 3.3 hour overlap at MCJ in November 2008 but neither case was infectious at that time Summary of chart review done 12/12/13- ten charts reviewed (of these 10): 1 investigate possible contamination between 2 cases. Both patients were at a local hospital and had sputum collected 6/16/11. Request was sent to see if an lab investigation took place in 2011. 2 drug and ETOH was reported among three cases 3. three HIV positive cases (plus one pending case). All three newly diagnosed. 2 cases lived in close proximity. Chart was not fully reviewed but her contacts all had different names (could this be a rehab center/housing program-need chart to answer this question). TB staff spoke with one of these cases and she states that the address on file is her mother’s house (case lived outside the house in a trailer). Mother is very social and often takes in people that need housing. 4. three cases worked construction. One of these was a painter and another did dry wall. They both picked up work at Home Depot. A third case –retired construction worker. 5. two cases reported history of homelessness . Possible overlap??? 6. One case had verified homeless history in HMIS 7. four patients reported history of incarceration

WGS Results And Epi Links 16 isolates with WGS results, of which 13 are from LAC Possible epi links: three cases live in close proximity, HIV+ Red square: 2 cases with possible epi-links among cases who live in the same neighborhood; have the same WGS profile which suggests that they are in the same chain of transmission but need more data to determine transmission links Red line: possible epi-link – the case lives in the same neighborhood; however, WGS refutes transmission among these cases Possible epi links: Construction worker/Day Laborers at Home Depot (illustrated in green) Green square: possible epi-link among day laborers; however, WGS refutes transmission among these cases Green line: possible epi-link between construction workers; however, WGS refutes transmission among these cases Overall, results indicate that this cluster is not an outbreak (more than 1-2 SNPs differences between most of the cases) Light Circles: Less infectious cases (sputum smear negative and non-cavitary CXR) Dark Circles: More infectious cases (sputum smear positive and/or non-cavitary CXR) Dark Square: More infectious case with a 1-off MIRU2

Summary WGS and epidemiologic link data show that G15969 is unlikely to be a large outbreak A pair of cases shared the same WGS profile: 2010 cases with HIV who lived close to each other (possible epi link) Limitations: not all of the cases in the cluster had WGS done

Suggested Next Steps for Discussion When new LAC G15969 cases appear: Ensure a complete contact investigation around each case Do not, as a matter of routine, perform a cluster investigation around newly identified G15969 cases However, if a epi link to another G15969 case, determine when and where transmission occurred