1. Using Whole Genome Sequencing Analysis in Genotype Cluster Investigation
Perspectives from Los Angeles County Tuberculosis Control Program
Wendy Noboa, MS
Shameer Poonja, MPH
Public Health Advisor
The Centers for Disease Control and Prevention

2. Conflict of Interest Statement
I have no conflicts of interest to declare.

3. Objectives
Los Angeles County’s (LAC) process of integrating Whole Genome Sequencing (WGS) data into genotype cluster investigation practices
Case studies using WGS analysis
Identify outbreaks and outbreak cases with greater precision
Refute outbreaks
Intervene to interrupt recent TB transmission
Explore added value, advantages, and challenges of using WGS analysis

4. Integrating WGS into Genotype Cluster Investigations

5. LAC’s Genotype Investigation Process
When a genotype cluster is identified as a priority it is assigned to a LAC staff member for investigation 1
Genotype cluster investigation process begins by gathering data on all cluster cases 2
Assess the likelihood of recent transmission or the potential for a TB outbreak 3
Review epidemiological data alongside WGS data 4
Based on results of investigation, public health intervention is discussed or resources are reallocated 5

6. Requesting WGS Analysis
Criteria for requesting WGS phylogenetic analysis:
Cluster is of high suspicion for ongoing recent transmission
Cluster is a potential TB outbreak
(Outbreak = 4 cases with definite epi-links within 3 year period)
Cluster is rare or unique to LAC
What can WGS analysis help answer:
Confirm or refute the presence of a TB outbreak
Exclude cases that are genetically distant and not associated with recent transmission
Identify and focus interventions

7. Real-world Case Studies

8. Genotype Cluster A Cluster of 12 cases
9 cases were born outside of the US in Central America
10 cases live within the same neighborhood
7 cases had definite epi-links
Family members
2 children <5 years
Co-workers in the construction industry
Social media
Cluster hypothesis:
Index case transmitted TB to his sister and a co- worker.
Index’s sister then gave it to two social contacts and their children.
Two cases work in construction industry and suspected to be in the same chain of transmission as the Index case.

9. Genotype Cluster A
Cases with this shared genotype were originally assumed to be in the same chain of recent transmission 9 18 8
MRCA 7 2 7 2 3 6 6 2
Case with definite epi-link 1 11 10
Case with no known epi-link 10
Non LA County 7 12

10. Identify how this case might be linked to the outbreak
Genotype Cluster A
Lessons Learned:
Identify how this case might be linked to the outbreak 9 18
Epi-linked cases are within 0-3 SNPS suggesting recent transmission and helping confirm outbreak 8
MRCA
Outlier cases with no epi-links are excluded (not recent transmission) 7 2
Non-LAC cases have TB genetically distant from outbreak strain = multijurisdictional outbreak unlikely 7 2 3 6 6 2 1 11 10 10
One case with no known epi-links but genetically similar to other outbreak cases. Warrants intensified investigation
Case with definite epi-link
Non LA County
Case with no known epi-link 12
Additional public health intervention can be supported for all outbreak cases

11. Genotype Cluster B Homeless US born Homeless Drug use Incarceration
HIV +
Homeless
Drug use
US born
Incarceration
US born
2009
2009
2009
2010
2010
2012
2014
2016
2016
HIV +
Homeless
Drug use
Incarceration
Alcohol use
US born
Alcohol use
Homeless
US born
Homeless
Drug use
Incarceration
Alcohol use
US born
No known risk factors

12. Genotype Cluster B
2016
2010 2 3
2010 1
2009 1 9 5
2016
2009 1 1
2014 2 2
2009
2012

13. Genotype Cluster B HIV + Homeless Homeless Drug use Drug use
US born
Genotype Cluster B
Homeless
Drug use
Incarceration
US born
2016
2010 2 3
No known risk factors
2010 1
2009
Alcohol use 1
HIV +
Homeless
Drug use
Incarceration
Alcohol use
US born
Homeless
US born 5
2016
Homeless
US born
Homeless
Drug use
Incarceration
Alcohol use
US born
2009 1
2014 2 2
Incarceration
US born
2009
2012

14. Genotype Cluster B Sub-cluster A Sub-cluster B 2016 2010 2010 2009
2014
2009
2012

15. Advantages and challenges of using WGS data

16. Advantages of Using WGS Data
Helps confirm or refute TB outbreaks
Identify cases in the same chain of recent transmission
Exclude cases not in the same chain of recent transmission
Helps to focus genotype cluster investigations
Phylogenetic trees are a visual tool to share evidence of recent transmission and influence the use of public health resources

17. Challenges of Using WGS Data
WGS data can be intimidating
Technical terms and concepts
WGS data alone cannot be used to determine directionality of transmission
Detailed and complete epidemiologic and clinical data is needed
If WGS does not support hypothesis
Back to the drawing board to reassess transmission event
To get the full picture, WGS analysis may require special requests
Retrospective WGS
Requests for isolates outside the local jurisdiction
Requests for isolates from closely related genotypes

18. Conclusions
WGS is a tool that can be used in conjunction with traditional epidemiologic investigation methods
Documentation of clinical and epidemiological data is necessary for WGS analysis
Request WGS analysis
Work closely with the State TB Control Branch to determine which isolates are most appropriate to request for WGS analysis
Do not be intimidated
Incorporating WGS analysis does not require a team of investigators
The State TB Control Branch can help with interpreting results and training and the Centers for Disease Control and Prevention has a number of scientific resources
We are all learning together

19. Acknowledgements Los Angeles County Tuberculosis Control Program
California State TB Control Branch
CDC Division of TB Elimination
CDC Division of TB Elimination - Surveillance, Epidemiology and Outbreak Investigations Branch
CDC Center for State, Tribal, Local, and Territorial Support – Public Health Associate Program
Contact Information:
Wendy Noboa, PHA, (213) ,
Shameer Poonja, PHA, (213) ,

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