Evaluating Estimates of Recent Tuberculosis Transmission Using Epidemiologic and Whole-Genome Sequencing Data, Los Angeles County, California, 2014-2018

OBJECTIVES: Estimating the percentage of tuberculosis cases in a population attributable to recent transmission, compared with reactivation of past infections, is crucial for public health decision-making. This study evaluated a previously published plausible-source case (PSC) method for estimating recent transmission in Los Angeles County (LA County) against a reference standard based on epidemiologic and whole-genome sequencing data. METHODS: We analyzed tuberculosis cases diagnosed in LA County from 2014 through 2018 using surveillance data. Cases were classified as consistent or inconsistent with recent transmission using the PSC method and a stepwise review of epidemiologic links and single nucleotide polymorphisms (Epi/SNP). We compared classifications from both methods and assessed discrepancies. RESULTS: Of 2949 tuberculosis cases in LA County, 650 had epidemiologic and whole-genome sequencing data for evaluating recent transmission; 44 were excluded due to missing genotyping data, including 7 pediatric patients aged <15 years. The Epi/SNP review classified 195 (30%) cases as consistent with recent transmission, while the PSC method attributed 301 (46%) cases to recent transmission. The 2 methods agreed on 454 (70%) cases. Discrepancies arose from genetic diversity, geographic distance, nonmatching genotypes, and diagnosis timing. Performance varied by race and ethnicity, nativity, lineage, history of homelessness, and substance use. CONCLUSIONS: The PSC method accurately classified more than two-thirds of tuberculosis cases included in a cluster investigation in LA County. However, findings underscore the need to refine the PSC method by integrating whole-genome sequencing data, including nongenotyped cases in pediatric patients, and reevaluating the geographic and timing criteria to enhance completeness and inform public health interventions aimed at interrupting tuberculosis transmission.