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

1. 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

2. 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

3. 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.

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

5. 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 ( )
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.

6. 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

7. Timeline of exposures

8. Social network

9. 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

10. 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 G 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 , 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!

11. 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

12. 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/ /17/2016
129 days
2B IP
10/19/ /24/2015

13. G00020 WGS results of Los Angeles isolates, June 2016
Total G 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

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

15. WGS Minus four outliers
1D, Los Angeles, 4/ B, 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

16. 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

17. Local jurisdiction example: G15969

18. 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)

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

20. 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

21. 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

22. 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

23. 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

24. 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