Guide to the Application of Genotyping to Tuberculosis Prevention and Control

Tuberculosis Genotyping Case Studies: How TB Programs Have Used Genotyping

Genotyping Used to Improve Contact and Cluster Investigations

The Massachusetts Department of Public Health recently reported on their universal genotyping program and provided evidence that genotyping strengthened both their contact and cluster investigations (Miller 2002).

Table 2.1. Relationship or location of presumed transmission for 25 patients with suspected epidemiologic links detected during contact investigations that were not confirmed by subsequent genotyping results — Massachusetts, 1996–2000.

Suspected relationship/ location of transmission Number of misleading epidemiologic links
Homeless shelter 11
Household members 5
Workplace 4
Friends/social contacts 3
Non-household family members 2
Total 25

From 1996 through 2000, Massachusetts used routine contact investigations to identify 92 epidemiologic links between 984 persons with TB. Subsequent genotyping results with IS6110-based RFLP and spoligotyping confirmed that 67 (73%) of these had matching genotype patterns. In 25 (27%), however, the reported epidemiologic links were not supported by matching genotyping results. The reported relationships or locations of transmission that were revealed by genotyping to be misleading are shown in Table 2.1. In addition to identifying misleading epidemiologic links, the Massachusetts program used universal genotyping and subsequent cluster investigations to identify 21 patients who shared genotyping matches and epidemiologic links that were not found by routine contact investigations (Table 2.2). The settings of transmission for these unexpected epidemiologic links were often nontraditional, and at least one cluster consisting of three patients was the result of casual transmission. The routine contact investigations found nothing in common among the three, but the subsequent cluster investigation established that one patient had been the hairdresser of the second patient, who spent time in a college dormitory where the third patient was a security guard.

Table 2.2. Newly recognized transmission settings detected by cluster investigations, Massachusetts.

Newly recognized transmission setting Number of TB patients with newly discovered epidemiologic links
Hair salon, college building




Public housing




Long-term care facility


Fast food restaurant


Buddhist temple


Community barbecue


Neighborhood market






“Universal genotyping has proved to be an invaluable tool for the Massachusetts TB Division. Data provided through this mechanism has driven our strategic planning process. Not only can we better understand transmission trends in our state, we can also identify cross contamination more quickly as well as prove (or disprove) cases that appear to be related. It is also a key core element of our Outbreak/ High Profile Incident Response Plan and we have used it as a tool for recent outbreaks among the homeless, and a cluster of Somalian cases. It is hard to imagine now, a TB Program without genotyping.”

Sue Etkind, RN, MS
TB Prevention and Control
Massachusetts Department of Public Health