Using Machine Learning Techniques and National Tuberculosis Surveillance Data to Predict Excess Growth in Genotyped Tuberculosis Clusters.

The early identification of clusters of persons with tuberculosis (TB) that will grow to become outbreaks creates an opportunity for intervention in preventing future TB cases. We used surveillance data (2009-2018) from the United States, statistically derived definitions of unexpected growth, and machine-learning techniques to predict which clusters of genotype-matched TB cases are most likely to continue accumulating cases above expected growth within a 1-year follow-up period. We developed a model to predict which clusters are likely to grow on a training and testing data set that was generalizable to a validation data set. Our model showed that characteristics of clusters were more important than the social, demographic, and clinical characteristics of the patients in those clusters. For instance, the time between cases before unexpected growth was identified as the most important of our predictors. A faster accumulation of cases increased the probability of excess growth being predicted during the follow-up period. We have demonstrated that combining the characteristics of clusters and cases with machine learning can add to existing tools to help prioritize which clusters may benefit most from public health interventions. For example, consideration of an entire cluster, not only an individual patient, may assist in interrupting ongoing transmission.

US Tuberculosis Rates among Persons Born Outside the United States Compared with Rates in Their Countries of Birth, 2012-20161.

The US Centers for Disease Control and Prevention recommends screening populations at increased risk for tuberculosis (TB), including persons born in countries with high TB rates. This approach assumes that TB risk for expatriates living in the United States is representative of TB risk in their countries of birth. We compared US TB rates by country of birth with corresponding country rates by calculating incidence rate ratios (IRRs) (World Health Organization rate/US rate). The median IRR was 5.4. The median IRR was 0.5 for persons who received a TB diagnosis <1 year after US entry, 4.9 at 1 to <10 years, and 10.0 at >10 years. Our analysis suggests that World Health Organization TB rates are not representative of TB risk among expatriates in the United States and that TB testing prioritization in the United States might better be based on US rates by country of birth and years in the United States.

Tuberculosis Infection Among People With Diabetes: United States Population Differences by Race/Ethnicity.

INTRODUCTION: Diabetes might confer a modestly increased risk of latent tuberculosis infection, which without treatment can progress to active tuberculosis disease. Three recent analyses of the National Health and Nutrition Examination Survey found a positive association between diabetes and a positive test for Mycobacterium tuberculosis infection. This study examines whether prevalence of a positive test still varies by diabetes status after stratifying by race/ethnicity. METHODS: This cross-sectional analysis used the public-use National Health and Nutrition Examination Survey 2011-2012 data sets and was conducted in 2018-2019. Interview and examination results for 5,560 adult participants yielded estimates for 219 million U.S. adults in the 4 largest race/ethnicity groups. The weighted prevalence of positive tuberculin skin test or interferon-gamma release assay by diabetes status was ascertained in each group. RESULTS: Among white and black adults, diabetes was associated with no difference in positive skin test prevalence and little difference in positive interferon-gamma release assay prevalence. The positive assay prevalence difference was +14.5% (95% CI=2.3%, 26.7%) among Hispanic and +9.9% (95% CI=1.2%, 18.6%) among Asian adults, when comparing those with diabetes with those with neither diabetes nor prediabetes. Based on assay results, 23.6% (95% CI=14.0%, 36.9%) of Hispanic and 27.2% (95% CI=19.6%, 36.5%) of Asian adults with diabetes also had latent tuberculosis infection. CONCLUSIONS: Hispanic and Asian subpopulation results drove much of the previously reported positive association between diabetes and a positive test for M. tuberculosis infection. Hispanic and Asian adults with diabetes might particularly benefit from screening and treatment for latent tuberculosis infection.

Robustness of NHANES Estimates of the US Prevalence of a Positive Tuberculin Skin Test.

BACKGROUND: A single 2-year National Health and Nutrition Examination Survey (NHANES) cycle is designed to provide accurate and stable estimates of conditions with prevalence of at least 10%. Recent NHANES-based estimates of a tuberculin skin test (TST) ≥10 mm in the noninstitutionalized US civilian population are at most 6.3%. METHODS: NHANES included a TST in 1971-1972, 1999-2000, and 2011-2012. We examined the robustness of NHANES-based estimates of the US population prevalence of a skin test ≥10 mm with a bias analysis that considered the influence of non-US birth distributions and within-household skin test results, reclassified borderline-positive results, and adjusted for TST item nonresponse. RESULTS: The weighted non-US birth distribution among NHANES participants was similar to that in the overall US population; further adjustment was unnecessary. We found no evidence of bias due to sampling multiple participants per household. Prevalence estimates changed 0.3% with reclassification of borderline-positive TST results and 0.2%-0.3% with adjustment for item nonresponse. CONCLUSIONS: For estimating the national prevalence of a TST ≥10 mm during these three survey cycles, a conventional NHANES analysis using the standard participant weights and masked design parameters that are provided in the public-use datasets appears robust. See video abstract at, http://links.lww.com/EDE/B636.

Epidemiology of Tuberculosis in the United States.

Although considerable progress has been made in reducing US tuberculosis incidence, the goal of eliminating the disease from the United States remains elusive. A continued focus on preventing new tuberculosis infections while also identifying and treating persons with existing tuberculosis infection is needed. Continued vigilance to ensure ongoing control of tuberculosis transmission remains key.

Factoring Prior Treatment into Tuberculosis Infection Prevalence Estimates, United States, 2011-2012.

To refine estimates of how many persons in the United States are candidates for treatment of latent tuberculosis, we removed from analysis persons who self-reported prior treatment on the National Health and Nutrition Examination Survey 2011-2012. We estimate that 12.6 million persons could benefit from treatment to prevent active tuberculosis.

Age-Period-Cohort Analyses of Tuberculosis Incidence Rates by Nativity, United States, 1996-2016.

OBJECTIVES: To assess changes in US tuberculosis (TB) incidence rates by age, period, and cohort effects, stratified according to race/ethnicity and nativity. METHODS: We used US National Tuberculosis Surveillance System data for 1996 to 2016 to estimate trends through age-period-cohort models. RESULTS: Controlling for cohort and period effects indicated that the highest rates of TB incidence occurred among those 0 to 5 and 20 to 30 years of age. The incidence decreased by age for successive birth cohorts. There were greater estimated annual percentage decreases among US-born individuals (-7.3%; 95% confidence interval [CI] = -7.5, -7.1) than among non-US-born individuals (-4.3%; 95% CI = -4.5, -4.1). US-born individuals older than 25 years exhibited the largest decreases, a pattern that was not reflected among non-US-born adults. In the case of race/ethnicity, the greatest decreases by nativity were among US-born Blacks (-9.3%; 95% CI = -9.6, -9.1) and non-US-born Hispanics (-5.7%; 95% CI = -6.0, -5.5). CONCLUSIONS: TB has been decreasing among all ages, races and ethnicities, and consecutive cohorts, although these decreases are less pronounced among non-US-born individuals.

Simple Estimates for Local Prevalence of Latent Tuberculosis Infection, United States, 2011-2015.

We used tuberculosis genotyping results to derive estimates of prevalence of latent tuberculosis infection in the United States. We estimated <1% prevalence in 1,981 US counties, 1%-<3% in 785 counties, and >3% in 377 counties. This method for estimating prevalence could be applied in any jurisdiction with an established tuberculosis surveillance system.

Statistical Method to Detect Tuberculosis Outbreaks among Endemic Clusters in a Low-Incidence Setting.

We previously reported use of genotype surveillance data to predict outbreaks among incident tuberculosis clusters. We propose a method to detect possible outbreaks among endemic tuberculosis clusters. We detected 15 possible outbreaks, of which 10 had epidemiologic data or whole-genome sequencing results. Eight outbreaks were corroborated.

Tuberculosis Among Foreign-Born Persons Diagnosed ≥10 Years After Arrival in the United States, 2010-2015.

The majority of tuberculosis (TB) cases in the United States are attributable to reactivation of latent TB infection (LTBI) (1). LTBI refers to the condition when a person is infected with Mycobacterium tuberculosis without signs and symptoms, or radiographic or bacteriologic evidence of TB disease. CDC and the U.S. Preventive Services Task Force (USPSTF) recommend screening populations at increased risk for LTBI, including persons who have lived in congregate settings at high risk and persons who were born in, or are former residents of countries with TB incidence ≥20 cases per 100,000 population (2-4). In 2015, foreign-born persons constituted 66.2% of U.S. TB cases (5). During the past 30 years, screening of persons from countries with high TB rates has focused on overseas screening for immigrants and refugees, and domestic screening for persons who have newly arrived in the United States (6,7). However, since 2007, an increasing number and proportion of foreign-born patients receiving a diagnosis of TB first arrived in the United States ≥10 years before the development and diagnosis of TB disease. To better understand how this group of patients differs from persons who developed TB disease and received a diagnosis <10 years after U.S. arrival, CDC analyzed data for all reported TB cases in the United States since 1993 in the National TB Surveillance System (NTSS). After adjusting for age and other characteristics, foreign-born persons who arrived in the United States ≥10 years before diagnosis were more likely to be residents of a long-term care facility or to have immunocompromising conditions other than human immunodeficiency virus (HIV) infection. These findings support using the existing CDC and USPSTF recommendations for TB screening of persons born in countries with high TB rates regardless of time since arrival in the United States (2,3).

Recent Transmission of Tuberculosis - United States, 2011-2014.

Tuberculosis is an infectious disease that may result from recent transmission or from an infection acquired many years in the past; there is no diagnostic test to distinguish the two causes. Cases resulting from recent transmission are particularly concerning from a public health standpoint. To describe recent tuberculosis transmission in the United States, we used a field-validated plausible source-case method to estimate cases likely resulting from recent transmission during January 2011-September 2014. We classified cases as resulting from either limited or extensive recent transmission based on transmission cluster size. We used logistic regression to analyze patient characteristics associated with recent transmission. Of 26,586 genotyped cases, 14% were attributable to recent transmission, 39% of which were attributable to extensive recent transmission. The burden of cases attributed to recent transmission was geographically heterogeneous and poorly predicted by tuberculosis incidence. Extensive recent transmission was positively associated with American Indian/Alaska Native (adjusted prevalence ratio [aPR] = 3.6 (95% confidence interval [CI] 2.9-4.4), Native Hawaiian/Pacific Islander (aPR = 3.2, 95% CI 2.3-4.5), and black (aPR = 3.0, 95% CI 2.6-3.5) race, and homelessness (aPR = 2.3, 95% CI 2.0-2.5). Extensive recent transmission was negatively associated with foreign birth (aPR = 0.2, 95% CI 0.2-0.2). Tuberculosis control efforts should prioritize reducing transmission among higher-risk populations.

Tuberculosis Infection in the United States: Prevalence Estimates from the National Health and Nutrition Examination Survey, 2011-2012.

BACKGROUND: Reexamining the prevalence of persons infected with tuberculosis (TB) is important to determine trends over time. In 2011-2012 a TB component was included in the National Health and Nutrition Examination Survey (NHANES) to estimate the reservoir of persons infected with TB. METHODS: Civilian, noninstitutionalized U.S. population survey participants aged 6 years and older were interviewed regarding their TB history and eligibility for the tuberculin skin test (TST) and interferon gamma release assay (IGRA) blood test. Once eligibility was confirmed, both tests were conducted. Prevalence and numbers of TST positive (10 mm or greater), IGRA positive, and both TST and IGRA positive were calculated by adjusting for the complex survey design after applying corrections for item nonresponse and digit preference in TST induration measurements. To examine TST positivity over time, data from NHANES 1999-2000 were reanalyzed using the same statistical methods. The TST was performed using Tubersol, a commercially available purified protein derivative (PPD), rather than PPD-S, which was the antigen used in NHANES 1999-2000. Prior patient history of TB vaccination was not collected in this study nor were patients examined for the presence of a Bacillus of Calmette and Guerin (BCG) vaccine scar. RESULTS: For NHANES 2011-2012, TST and IGRA results were available for 6,128 (78.4%) and 7,107 (90.9%) eligible participants, respectively. There was no significant difference between the percentage of the U.S. population that was TST positive in 2011-2012 (4.7% [95% CI 3.4-6.3]; 13,276,000 persons) compared with 1999-2000 (4.3%; 3.5-5.3). In 2011-2012 the percentage that was IGRA positive was 5.0% (4.2-5.8) and double TST and IGRA positivity was 2.1% (1.5-2.8). The point estimate of IGRA positivity prevalence in foreign-born persons (15.9%; 13.5-18.7) was lower than for TST (20.5%; 16.1-25.8) in 2011-2012. The point estimate of IGRA positivity prevalence in U.S.-born persons (2.8%; 2.0-3.8) was higher than for TST (1.5%; 0.9-2.6). CONCLUSIONS: No statistically significant decline in the overall estimated prevalence of TST positivity was detected from 1999-2000 to 2011-2012. The prevalence of TB infection, whether measured by TST or IGRA, remains lower among persons born in the United States compared with foreign-born persons.

A field-validated approach using surveillance and genotyping data to estimate tuberculosis attributable to recent transmission in the United States.

Tuberculosis genotyping data are frequently used to estimate the proportion of tuberculosis cases in a population that are attributable to recent transmission (RT). Multiple factors influence genotype-based estimates of RT and limit the comparison of estimates over time and across geographic units. Additionally, methods used for these estimates have not been validated against field-based epidemiologic assessments of RT. Here we describe a novel genotype-based approach to estimation of RT based on the identification of plausible-source cases, which facilitates systematic comparisons over time and across geographic areas. We compared this and other genotype-based RT estimation approaches with the gold standard of field-based assessment of RT based on epidemiologic investigation in Arkansas, Maryland, and Massachusetts during 1996-2000. We calculated the sensitivity and specificity of each approach for epidemiologic evidence of RT and calculated the accuracy of each approach across a range of hypothetical RT prevalence rates plausible for the United States. The sensitivity, specificity, and accuracy of genotype-based RT estimates varied by approach. At an RT prevalence of 10%, accuracy ranged from 88.5% for state-based clustering to 94.4% with our novel approach. Our novel, field-validated approach allows for systematic assessments over time and across public health jurisdictions of varying geographic size, with an established level of accuracy.

Controlling the last known cluster of Ebola virus disease - Liberia, January-February 2015.

As one of the three West African countries highly affected by the 2014-2015 Ebola virus disease (Ebola) epidemic, Liberia reported approximately 10,000 cases. The Ebola epidemic in Liberia was marked by intense urban transmission, multiple community outbreaks with source cases occurring in patients coming from the urban areas, and outbreaks in health care facilities (HCFs). This report, based on data from routine case investigations and contact tracing, describes efforts to stop the last known chain of Ebola transmission in Liberia. The index patient became ill on December 29, 2014, and the last of 21 associated cases was in a patient admitted into an Ebola treatment unit (ETU) on February 18, 2015. The chain of transmission was stopped because of early detection of new cases; identification, monitoring, and support of contacts in acceptable settings; effective triage within the health care system; and rapid isolation of symptomatic contacts. In addition, a "sector" approach, which divided Montserrado County into geographic units, facilitated the ability of response teams to rapidly respond to community needs. In the final stages of the outbreak, intensive coordination among partners and engagement of community leaders were needed to stop transmission in densely populated Montserrado County. A companion report describes the efforts to enhance infection prevention and control efforts in HCFs. After February 19, no additional clusters of Ebola cases have been detected in Liberia. On May 9, the World Health Organization declared the end of the Ebola outbreak in Liberia.

Characteristics of tuberculosis cases that started outbreaks in the United States, 2002-2011.

A review of 26 tuberculosis outbreaks in the United States (2002-2011) showed that initial source case-patients had long infectious periods (median 10 months) and were characterized by substance abuse, incarceration, and homelessness. Improved timeliness of diagnosis and thorough contact investigations for such cases may reduce the risk for outbreaks.

Trends in tuberculosis - United States, 2013.

In 2013, a total of 9,588 new tuberculosis (TB) cases were reported in the United States, with an incidence rate of 3.0 cases per 100,000 population, a decrease of 4.2% from 2012. This report summarizes provisional TB surveillance data reported to CDC in 2013. Although case counts and incidence rates continue to decline, certain populations are disproportionately affected. The TB incidence rate among foreign-born persons in 2013 was approximately 13 times greater than the incidence rate among U.S.-born persons, and the proportion of TB cases occurring in foreign-born persons continues to increase, reaching 64.6% in 2013. Racial/ethnic disparities in TB incidence persist, with TB rates among non-Hispanic Asians almost 26 times greater than among non-Hispanic whites. Four states (California, Texas, New York, and Florida), home to approximately one third of the U.S. population, accounted for approximately half the TB cases reported in 2013. The proportion of TB cases occurring in these four states increased from 49.9% in 2012 to 51.3% in 2013. Continued progress toward TB elimination in the United States will require focused TB control efforts among populations and in geographic areas with disproportionate burdens of TB.

Estimated rate of reactivation of latent tuberculosis infection in the United States, overall and by population subgroup.

We estimated the rate of reactivation tuberculosis (TB) in the United States, overall and by population subgroup, using data on TB cases and Mycobacterium tuberculosis isolate genotyping reported to the Centers for Disease Control and Prevention during 2006-2008. The rate of reactivation TB was defined as the number of non-genotypically clustered TB cases divided by the number of person-years at risk for reactivation due to prevalent latent TB infection (LTBI). LTBI was ascertained from tuberculin skin tests given during the 1999-2000 National Health and Nutrition Examination Survey. Clustering of TB cases was determined using TB genotyping data collected by the Centers for Disease Control and Prevention and analyzed via spatial scan statistic. Of the 39,920 TB cases reported during 2006-2008, 79.7% were attributed to reactivation. The overall rate of reactivation TB among persons with LTBI was estimated as 0.084 (95% confidence interval (CI): 0.083, 0.085) cases per 100 person-years. Rates among persons with and without human immunodeficiency virus coinfection were 1.82 (95% CI: 1.74, 1.89) and 0.073 (95% CI: 0.070, 0.075) cases per 100 person-years, respectively. The rate of reactivation TB among persons with LTBI was higher among foreign-born persons (0.098 cases/100 person-years; 95% CI: 0.096, 0.10) than among persons born in the United States (0.082 cases/100 person-years; 95% CI: 0.080, 0.083). Differences in rates of TB reactivation across subgroups support current recommendations for targeted testing and treatment of LTBI.

Using statistical methods and genotyping to detect tuberculosis outbreaks.

BACKGROUND: Early identification of outbreaks remains a key component in continuing to reduce the burden of infectious disease in the United States. Previous studies have applied statistical methods to detect unexpected cases of disease in space or time. The objectives of our study were to assess the ability and timeliness of three spatio-temporal methods to detect known outbreaks of tuberculosis. METHODS: We used routinely available molecular and surveillance data to retrospectively assess the effectiveness of three statistical methods in detecting tuberculosis outbreaks: county-based log-likelihood ratio, cumulative sums, and a spatial scan statistic. RESULTS: Our methods identified 8 of the 9 outbreaks, and 6 outbreaks would have been identified 1-52 months (median=10 months) before local public health authorities identified them. Assuming no delays in data availability, 46 (59.7%) of the 77 patients in the 9 outbreaks were identified after our statistical methods would have detected the outbreak but before local public health authorities became aware of the problem. CONCLUSIONS: Statistical methods, when applied retrospectively to routinely collected tuberculosis data, can successfully detect known outbreaks, potentially months before local public health authorities become aware of the problem. The three methods showed similar results; no single method was clearly superior to the other two. Further study to elucidate the performance of these methods in detecting tuberculosis outbreaks will be done in a prospective analysis.

Using routinely reported tuberculosis genotyping and surveillance data to predict tuberculosis outbreaks.

We combined routinely reported tuberculosis (TB) patient characteristics with genotyping data and measures of geospatial concentration to predict which small clusters (i.e., consisting of only 3 TB patients) in the United States were most likely to become outbreaks of at least 6 TB cases. Of 146 clusters analyzed, 16 (11.0%) grew into outbreaks. Clusters most likely to become outbreaks were those in which at least 1 of the first 3 patients reported homelessness or excess alcohol or illicit drug use or was incarcerated at the time of TB diagnosis and in which the cluster grew rapidly (i.e., the third case was diagnosed within 5.3 months of the first case). Of 17 clusters with these characteristics and therefore considered high risk, 9 (53%) became outbreaks. This retrospective cohort analysis of clusters in the United States suggests that routinely reported data may identify small clusters that are likely to become outbreaks and which are therefore candidates for intensified contact investigations.