Using genotyping and geospatial scanning to estimate recent mycobacterium tuberculosis transmission, United States

Using genomic epidemiology and geographic activity spaces to investigate tuberculosis outbreaks in Botswana

Background

The integration of genomic and geospatial data into infectious disease transmission analyses typically includes residential locations and excludes other activity spaces where transmission may occur (e.g. work, school, or social venues). The objective of this analysis was to explore residential as well as other activity spaces of tuberculosis (TB) outbreaks to identify potential geospatial 'hotspots' of transmission.

Methods

We analyzed data that included geospatial coordinates for residence and other activity spaces collected during 2012-2016 for the Kopanyo Study, a population-based study of TB transmission in Botswana. We included participants with results from whole genome sequencing conducted on archived samples from the original study. We used a spatial log-Gaussian Cox process model to detect core areas of increased activity spaces of individuals belonging to TB outbreaks (genotypic groups with ≤5 single-nucleotide polymorphisms), which we compared to ungrouped participants (those not in a genotypic group of any size).

Findings

We analyzed data collected from 636 participants, including 70 participants belonging to six outbreak groups with a combined total of 293 locations, and 566 ungrouped participants with a combined total of 2289 locations. Core areas of activity space for each outbreak group were geographically distinct, and we found evidence of localized transmission in four of six outbreaks. For most of the outbreaks, including activity space data led to the detection of larger areas of higher spatial intensity and more focal points compared to residential location alone.

Interpretation

Geospatial analysis using activity space data (social gathering places as well as residence) may lead to improved understanding of areas of infectious disease transmission compared to using residential data alone.

Funding

This work was supported by funding from the National Institute of Allergy and Infectious Diseases R01AI097045, R01AI147336, and R01AI170204.

Prevalence of pulmonary tuberculosis in homeless individuals in the Addis Ababa City, Ethiopia

Background

Homeless individuals are at a high risk of infection with Mycobacterium tuberculosis (M. tuberculosis) as compared to the general population. The number of homeless individuals has been increasing in Addis Ababa City during the last three decades due to the migration of rural inhabitants to the City for better living conditions. The objective of this study was to estimate the prevalence of pulmonary tuberculosis (PTB) and evaluate associated risk factors in homeless individuals in Addis Ababa City.

Methods

A total of 5,600 homeless individuals were screened for PTB symptoms using WHO guideline between February 2019 and December 2020. Sputum samples were cultured from individuals with symptoms of PTB for mycobacterial isolation. Logistic regression analysis was used to identify factors associated with PTB.

Results

The prevalence of bacteriologically confirmed cases was 1.1% (59/5,600) or 10.54 per 1000 population. Multinomial logistic regression analysis showed that being homeless for more than 5 years, body mass index (BMI) < 18.5, smoking cigarette, living in a group of more than five individuals, close contact with chronic coughers, imprisonment and HIV infection were significantly associated with the prevalence of PTB in homeless individuals (P < 0.05).

Conclusion

In conclusion, the result of this study indicated that the prevalence of PTB in homeless individuals was higher than the prevalence of PTB in the general population of Addis Ababa City requiring for the inclusion of the homeless individuals in the TB control program.

Model-based Analysis of Tuberculosis Genotype Clusters in the United States Reveals High Degree of Heterogeneity in Transmission and State-level Differences Across California, Florida, New York, and Texas

BACKGROUND

Reductions in tuberculosis (TB) transmission have been instrumental in lowering TB incidence in the United States. Sustaining and augmenting these reductions are key public health priorities.

METHODS

We fit mechanistic transmission models to distributions of genotype clusters of TB cases reported to the Centers for Disease Control and Prevention during 2012-2016 in the United States and separately in California, Florida, New York, and Texas. We estimated the mean number of secondary cases generated per infectious case (R0) and individual-level heterogeneity in R0 at state and national levels and assessed how different definitions of clustering affected these estimates.

RESULTS

In clusters of genotypically linked TB cases that occurred within a state over a 5-year period (reference scenario), the estimated R0 was 0.29 (95% confidence interval [CI], .28-.31) in the United States. Transmission was highly heterogeneous; 0.24% of simulated cases with individual R0 >10 generated 19% of all recent secondary transmissions. R0 estimate was 0.16 (95% CI, .15-.17) when a cluster was defined as cases occurring within the same county over a 3-year period. Transmission varied across states: estimated R0s were 0.34 (95% CI, .3-.4) in California, 0.28 (95% CI, .24-.36) in Florida, 0.19 (95% CI, .15-.27) in New York, and 0.38 (95% CI, .33-.46) in Texas.

CONCLUSIONS

TB transmission in the United States is characterized by pronounced heterogeneity at the individual and state levels. Improving detection of transmission clusters through incorporation of whole-genome sequencing and identifying the drivers of this heterogeneity will be essential to reducing TB transmission.

Vitamin D and the risk of latent tuberculosis infection: a systematic review and meta-analysis

Objective

Latent tuberculosis infection (LTBI) may be a risk of developing tuberculosis (TB) and thus a health hazard. The aim of this meta-analysis is to explore the association between vitamin D and LTBI.

Methods

Databases including PubMed, Embase, Scopus, and ProQuest were electronically searched to identify observational or interventional studies that reported the association between vitamin D and LTBI. The retrieval time is limited from inception to 30 September 2021. Two reviewers independently screened literature, extracted data, and assessed risk bias of included studies. Meta-analysis was performed by using STATA 12.0 software.

Results

A total of 5 studies involving 2 case–control studies and 3 cohort studies were included. The meta-analysis result showed that the risk of LTBI among individuals was not associated with high vitamin D level (OR 0.51, 95% CI 0.05–5.65, P = 0.58). The result from cohort studies also suggested that relatively high vitamin D level was not a protective factor for LTBI (RR = 0.56, 95%CI 0.19–1.67, P = 0.300).

Conclusions

Our meta-analysis suggested that serum vitamin D levels were not associated with incidence of LTBI, and relatively high serum vitamin D level was not a protective factor for LTBI. Further RCTs are needed to verify whether sufficient vitamin D levels and vitamin D supplementation reduces the risk of LTBI.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12890-022-01830-5.

What Can Genetic Relatedness Tell Us About Risk Factors for Tuberculosis Transmission?

BACKGROUND

To stop tuberculosis (TB), the leading infectious cause of death globally, we need to better understand transmission risk factors. Although many studies have identified associations between individual-level covariates and pathogen genetic relatedness, few have identified characteristics of transmission pairs or explored how closely covariates associated with genetic relatedness mirror those associated with transmission.

METHODS

We simulated a TB-like outbreak with pathogen genetic data and estimated odds ratios (ORs) to correlate each covariate and genetic relatedness. We used a naive Bayes approach to modify the genetic links and nonlinks to resemble the true links and nonlinks more closely and estimated modified ORs with this approach. We compared these two sets of ORs with the true ORs for transmission. Finally, we applied this method to TB data in Hamburg, Germany, and Massachusetts, USA, to find pair-level covariates associated with transmission.

RESULTS

Using simulations, we found that associations between covariates and genetic relatedness had the same relative magnitudes and directions as the true associations with transmission, but biased absolute magnitudes. Modifying the genetic links and nonlinks reduced the bias and increased the confidence interval widths, more accurately capturing error. In Hamburg and Massachusetts, pairs were more likely to be probable transmission links if they lived in closer proximity, had a shorter time between observations, or had shared ethnicity, social risk factors, drug resistance, or genotypes.

CONCLUSIONS

We developed a method to improve the use of genetic relatedness as a proxy for transmission, and aid in understanding TB transmission dynamics in low-burden settings.

Population-Based Geospatial and Molecular Epidemiologic Study of Tuberculosis Transmission Dynamics, Botswana, 2012-2016

Tuberculosis (TB) elimination requires interrupting transmission of Mycobacterium tuberculosis. We used a multidisciplinary approach to describe TB transmission in 2 sociodemographically distinct districts in Botswana (Kopanyo Study). During August 2012-March 2016, all patients who had TB were enrolled, their sputum samples were cultured, and M. tuberculosis isolates were genotyped by using 24-locus mycobacterial interspersed repetitive units-variable number of tandem repeats. Of 5,515 TB patients, 4,331 (79%) were enrolled. Annualized TB incidence varied by geography (range 66-1,140 TB patients/100,000 persons). A total of 1,796 patient isolates had valid genotyping results and residential geocoordinates; 780 (41%) patients were involved in a localized TB transmission event. Residence in areas with a high burden of TB, age <24 years, being a current smoker, and unemployment were factors associated with localized transmission events. Patients with known HIV-positive status had lower odds of being involved in localized transmission.

Multidrug-resistant tuberculosis in the United States, 2011-2016: patient characteristics and risk factors

OBJECTIVE: To determine risk factors for multidrug-resistant tuberculosis (MDR-TB) and describe MDR-TB according to three characteristics: previous TB disease, recent transmission of MDR-TB, and reactivation of latent MDR-TB infection.SETTING and DESIGN: We used 2011-2016 surveillance data from the US National Tuberculosis Surveillance System and National Tuberculosis Genotyping Service and used logistic regression models to estimate risk factors associated with MDR-TB.RESULTS: A total of 615/45 209 (1.4%) cases were confirmed as MDR-TB; 111/615 (18%) reported previous TB disease; 41/615 (6.7%) were attributed to recent MDR-TB transmission; and 449/615 (73%) to reactivation. Only 12/41 (29%) patients with TB attributed to recent transmission were known to be contacts of someone with MDR-TB. For non-US-born patients, the adjusted odds ratios of having MDR-TB were 32.6 (95%CI 14.6-72.6) among those who were known to be contacts of someone with MDR-TB and 6.5 (95%CI 5.1-8.3) among those who had had previous TB disease.CONCLUSION: The majority of MDR-TB cases in the United States were associated with previous TB disease or reactivation of latent MDR-TB infection; only a small proportion of MDR-TB cases were associated with recent transmission.

Geographic analysis of latent tuberculosis screening: A health system approach

Background

Novel approaches are required to better focus latent tuberculosis infection (LTBI) efforts in low-prevalence regions. Geographic information systems, used within large health systems, may provide one such approach.

Methods

A retrospective, cross-sectional design was used to integrate US Census and Duke Health System data between January 1, 2010 and October 31, 2017 and examine the relationships between LTBI screening and population tuberculosis risk (assessed using the surrogate measure of proportion of persons born in tuberculosis-endemic regions) by census tract.

Results

The median proportion of Duke patients screened per census tract was 0.01 (range 0–0.1, interquartile range 0.01–0.03). The proportion of Duke patients screened within a census tract significantly but weakly correlated with the population risk. Furthermore, patients residing in census tracts with higher population tuberculosis risk were more likely to be screened with TST than with an IGRA (p<0.001).

Conclusion

The weak correlation between patient proportion screened for LTBI and our surrogate marker of population tuberculosis risk suggests that LTBI screening efforts should be better targeted. This type of geography-based analysis may serve as an easily obtainable benchmark for LTBI screening in health systems with low tuberculosis prevalence.

Contextualizing tuberculosis risk in time and space: comparing time-restricted genotypic case clusters and geospatial clusters to evaluate the relative contribution of recent transmission to incidence of TB using nine years of case data from Michigan, USA

PURPOSE

Novel approaches must address the underlying factors sustaining the tuberculosis (TB) epidemic in the United States, specifically what maintains new Mycobacterium tuberculosis (Mtb) transmission.

METHODS

Culture-confirmed TB cases reported to the Michigan Department of Health and Human Services (2004-2012) were analyzed for time-restricted genotypic and/or geospatial clustering. Cases with both types of clustering were used as a proxy for recent, local transmission. Modified, multivariate Poisson regression models were fit to estimate this prevalence in relation to various individual- and neighborhood-level demographic and socio-economic variables.

RESULTS

Those individuals that were spatially clustered were 1.7 times as likely to also be time-restricted genotypically clustered. The prevalence of recent, local transmission was higher among U.S.-born cases, males, and non-Hispanic blacks. Moreover, people living in neighborhoods in the highest poverty quartile had 13.8 times the prevalence of recent, local transmission compared with those in the lowest poverty neighborhoods.

CONCLUSIONS

Our results suggest geographic areas with high concentration of TB cases are likely driven by ongoing transmission, rather than enclaves of individuals who have reactivated a case of latent TB. Furthermore, efforts to continue reducing Mtb transmission in the United States, and other low-incidence settings, must better identify community-level sources of risk, manifested through the complex social interactions among people and their environments.

Association between vitamin D and latent tuberculosis infection in the United States: NHANES, 2011-2012

Background

Latent tuberculosis infection (LTBI) is a precursor of active tuberculosis diseases and an important issue in the United States and worldwide. The association between vitamin D deficiency and LTBI is poorly understood.

Methods

From 2011 to 2012, the National Health and Nutrition Examination Survey (NHANES) assessed LTBI (according to tuberculin skin testing and QuantiFERON^®-TB Gold In-Tube) and measured serum levels of vitamin D. We evaluated the association between LTBI and vitamin D using multivariate logistic regression models adjusted for known confounders.

Results

The LTBI group had a lower 25-hydroxyvitamin D [25(OH)D] level than the non-LTBI group (p=0.0012). The adjusted risk of LTBI was significantly higher among participants with serum 25(OH)D levels <12 ng/ml (adjusted OR [aOR], 2.27; 95% CI, 1.40-3.66) and 12-19 ng/ml (aOR, 1.75; 95% CI, 1.25-2.46) compared to those with a level ≥30 ng/ml. The higher risk of LTBI among the participants with serum 25(OH)D levels <12 ng/ml and 12-19 ng/ml remained unchanged in both male and summer season subgroups.

Conclusions

A low serum 25(OH)D level was significantly associated with the risk of LTBI in this US cohort.

Genomic Investigation of a Mycobacterium tuberculosis Outbreak Involving Prison and Community Cases in Florida, United States

We used whole-genome sequencing to investigate a tuberculosis outbreak involving U.S.-born persons in the prison system and both U.S.- and foreign-born persons in the community in Florida over a 7-year period (2009-2015). Genotyping by spacer oligonucleotide typing and 24-locus mycobacterial interspersed repetitive unit-variable number tandem repeat suggested that the outbreak might be clonal in origin. However, contact tracing could not link the two populations. Through a multidisciplinary approach, we showed that the cluster involved distinct bacterial transmission networks segregated by country of birth. The source strain is of foreign origin and circulated in the local Florida community for more than 20 years before introduction into the prison system. We also identified novel transmission links involving foreign and U.S.-born cases not discovered during contact investigation. Our data highlight the potential for spread of strains originating from outside the United States into U.S. "high-risk" populations, such as prisoners, with subsequent movement back to the general community.

Understanding Tuberculosis Transmission in the United Kingdom: Findings From 6 Years of Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeats Strain Typing, 2010-2015

Genotyping provides the opportunity to better understand tuberculosis (TB) transmission. We utilized strain typing data to assess trends in the proportion of clustering and identify the characteristics of individuals and clusters associated with recent United Kingdom (UK) transmission. In this retrospective cohort analysis, we included all culture-confirmed strain-typed TB notifications from the UK between 2010 and 2015 to estimate the proportion of patients that clustered over time. We explored the characteristics of patients in a cluster using multivariable logistic regression. Overall, 58.5% of TB patients were concentrated in 2,701 clusters. The proportion of patients in a cluster decreased between 2010 (58.7%) and 2015 (55.3%) (P = 0.001). Being a clustered patient was associated with being male and UK-born, having pulmonary disease, having a previous TB diagnosis, and having a history of drug misuse or imprisonment. Our results suggest that TB transmission in the UK decreased between 2010 and 2015, during which time TB incidence also decreased. Targeted cluster investigation and extended contact tracing should be aimed at persons at risk of being in a transmission chain, including UK-born individuals with social risk factors in clusters with a high proportion of patients having pulmonary disease.

Prospects for Tuberculosis Elimination in the United States: Results of a Transmission Dynamic Model

We estimated long-term tuberculosis (TB) trends in the US population and assessed prospects for TB elimination. We used a detailed simulation model allowing for changes in TB transmission, immigration, and other TB risk determinants. Five hypothetical scenarios were evaluated from 2017 to 2100: 1) maintain current TB prevention and treatment activities (base case); 2) provision of latent TB infection testing and treatment for new legal immigrants; 3) increased uptake of latent TB infection screening and treatment among high-risk populations, including a 3-month isoniazid-rifapentine regimen; 4) improved TB case detection; and 5) improved TB treatment quality. Under the base case, we estimate that by 2050, TB incidence will decline to 14 cases per million, a 52% (95% posterior interval (PI): 35, 67) reduction from 2016, and 82% (95% posterior interval: 78, 86) of incident TB will be among persons born outside of the United States. Intensified TB control could reduce incidence by 77% (95% posterior interval: 66, 85) by 2050. We predict TB may be eliminated in US-born but not non-US-born persons by 2100. Results were sensitive to numbers of people entering the United States with latent or active TB, and were robust to alternative interpretations of epidemiologic evidence. TB elimination in the United States remains a distant goal; however, strengthening TB prevention and treatment could produce important health benefits.

A genotypic and spatial epidemiologic analysis of Massachusetts' Mycobacterium tuberculosis cases from 2012 to 2015

BACKGROUND

Massachusetts had a rate of 2.8 cases of tuberculosis (TB) per 100,000 individuals in 2015. Although TB in Massachusetts is on the decline, the case rate remains far above the 2020 National TB Target of 1.4 per 100,000. To reduce the TB case rate in Massachusetts, it is necessary to understand the local epidemiology and transmission risks.

METHODS

We used an existing TB case database of Massachusetts TB cases in the time frame from 2012 to 2015, which links de-identified patient demographic information with TB genotypes obtained from the United States Centers for Disease Control and Prevention's (CDC) TB Genotyping Information Management System database. Two or more cases with identical genotypes, which were close in space (within 50 km), as determined in a geographic information system (GIS), and time (3 years), were considered TB clusters.

RESULTS

We analyzed 543 genotyped cases. We identified a total of 85 cases that met the TB cluster criteria, and a total of 33 clusters. US-born individuals (p = 0.003), homeless individuals (p = 0.001) and those reporting illicit substance use (p = 0.001) and alcohol use (p = 0.001) were more likely to appear in a TB cluster.

CONCLUSION

Through a combined genotypic and spatial epidemiological approach, we identified populations and individuals more likely to be in a TB cluster. Testing populations identified as at risk for being in a TB cluster, and providing appropriate treatment, may decrease the overall TB case rate and support efforts to achieve national 2020 TB targets.

Clustering and recent transmission of Mycobacterium tuberculosis in a Chinese population

Purpose

The objectives of the present study were to characterize the clinical isolates prevailing in the northeast of Jiangsu and to investigate the mode of transmission. The study also aimed to explore the extent to which Mycobacterium tuberculosis strains contributed to drug resistance and the possible factors related to the recent transmission.

Patients and methods

We consecutively enrolled 912 culture-confirmed pulmonary tuberculosis (TB) cases from 1 January 2013 to 31 December 2014 in Lianyungang City, which is located in the center of China’s vast ocean area and the northeast of Jiangsu province. Isolates were genotyped using 15-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing. The Hunter–Gaston discrimination index (HGDI) was used to estimate the discriminatory power and diversity of molecular markers.

Results

Among 741 successfully genotyped isolates, 144 (19.43%) strains formed 46 clusters, while 597 (80.57%) isolates had the unique MIRU pattern. The total HGDI for all 15 loci was 0.999. The average cluster size was 3 (2–13) patients. The estimated proportion of recent transmission was 13.34%. Patients with unfavorable treatment outcomes were infected with clustered strains at a higher proportion than were those with favorable treatment outcomes (adjusted OR: 1.78, 95% CI: 1.14–2.85, P=0.012).

Conclusion

The probability of recent TB transmission was relatively low in the study site, while the cases mainly arose from the activation of previous infection. Spatial analysis showed that strains forming larger clusters had the characteristics of regional aggregation.

Spatial clusters of latent tuberculous infection, Connecticut, 2010-2014

SETTING

In the United States, tuberculosis (TB) control is increasingly focusing on the identification of persons with latent tuberculous infection (LTBI).

OBJECTIVE

To characterize the local epidemiology of LTBI in Connecticut, USA.

METHODS

We used spatial analyses 1) to identify census tract-level clusters of reported LTBI and TB disease in Connecticut, 2) to compare persons and populations in clusters with those not in clusters, and 3) to compare persons with LTBI to those with TB disease.

RESULTS

Significant census tract-level spatial clusters of LTBI and TB disease were identified. Compared with persons with LTBI in non-clustered census tracts, those in clustered census tracts were more likely to be foreign-born and less likely to be of white non-Hispanic ethnicity. Populations in census tract clusters of high LTBI prevalence had greater crowding, persons living in poverty, and persons lacking health care insurance than populations not in clustered census tracts. Persons with LTBI were less likely than those with TB disease to be of Asian ethnicity, and persons with LTBI were more likely than those with TB disease to reside in a clustered census tract.

CONCLUSIONS

Characterizing fine-scale populations at risk for LTBI supports effective and culturally accessible screening and treatment programs.

Cost-effectiveness of Testing and Treatment for Latent Tuberculosis Infection in Residents Born Outside the United States With and Without Medical Comorbidities in a Simulation Model

IMPORTANCE

Testing for and treating latent tuberculosis infection (LTBI) is among the main strategies to achieve TB elimination in the United States. The best approach to testing among non-US born residents, particularly those with comorbid conditions, is uncertain.

OBJECTIVE

To estimate health outcomes, costs, and cost-effectiveness of LTBI testing and treatment among non-US born residents with and without medical comorbidities.

DESIGN, SETTING, AND PARTICIPANTS

Decision analytic tree and Markov cohort simulation model among non-US born residents with no comorbidities, with diabetes, with HIV infection, or with end-stage renal disease (ESRD) using a health care sector perspective with 3% annual discounting. Strategies compared included no testing, tuberculin skin test (TST), interferon gamma release assay (IGRA), confirm positive (initial TST, IGRA only for TST-positive results; both tests positive indicates LTBI), and confirm negative (initial IGRA, then TST for IGRA-negative; any test positive indicates LTBI). All strategies were coupled to treatment with 3 months of self-administered rifapentine and isoniazid.

MAIN OUTCOMES AND MEASURES

Number needed to test and treat to prevent 1 case of TB reactivation, discounted quality-adjusted life-years (QALYs), discounted lifetime medical costs, and incremental cost-effectiveness ratios (ICERs).

RESULTS

Improving health outcomes increased costs, with choice of test dependent on willingness to pay. Strategies ranked by ascending costs and benefits: no testing, confirm positive, TST, IGRA, and confirm negative. The ICERs varied by non-US born patient risk group: patients with no comorbidities, IGRA was likely cost-effective at $83 000/QALY; patients with diabetes, both confirm positive ($53 000/QALY) and IGRA ($120 000/QALY) were likely cost-effective; patients with HIV, confirm negative was clearly preferred ($63 000/QALY); and patients with ESRD, no testing was cost-effective. Increased LTBI prevalence and reduced return for TST reading improved IGRA's relative performance. In 10 000 probabilistic simulations among non-US born patients with no comorbidities, with diabetes, and with HIV, some form of testing was virtually always cost-effective. These simulations highlight the uncertainty of test choice for non-US born patients with no comorbidities and non-US born patients with diabetes, but strategies including IGRA were preferred in over 60% of simulations for all non-US born populations except those with ESRD.

CONCLUSIONS AND RELEVANCE

Testing for and treating LTBI among non-US born residents with and without selected comorbidities is likely cost-effective except among those with ESRD in whom competing risks of death limit benefits. Strategies including IGRA fell below a $100 000/QALY willingness-to-pay threshold for non-US born patients with no comorbidities, patients with diabetes, and patients with HIV.

Comparing Drivers and Dynamics of Tuberculosis in California, Florida, New York, and Texas

RATIONALE

There is substantial state-to-state heterogeneity in tuberculosis (TB) in the United States; better understanding this heterogeneity can inform effective response to TB at the state level, the level at which most TB control efforts are coordinated.

OBJECTIVES

To characterize drivers of state-level heterogeneity in TB epidemiology in the four U.S. states that bear half the country's TB burden: California, Florida, New York, and Texas.

METHODS

We constructed an individual-based model of TB in the four U.S. states and calibrated the model to state-specific demographic and age- and nativity-stratified TB incidence data. We used the model to infer differences in natural history of TB and in future projections of TB.

MEASUREMENTS AND MAIN RESULTS

We found that differences in both demographic makeup (particularly the size and composition of the foreign-born population) and TB transmission dynamics contribute to state-level differences in TB epidemiology. The projected median annual rate of decline in TB incidence in the next decade was substantially higher in Texas (3.3%; 95% range, -5.6 to 10.9) than in California (1.7%; 95% range, -3.8 to 7.1), Florida (1.5%; 95% range, -7.4 to 14), and New York (1.9%; 95% range, -6.4 to 9.8). All scenarios projected a flattening of the decline in TB incidence by 2025 without additional resources or interventions.

CONCLUSIONS

There is substantial state-level heterogeneity in TB epidemiology in the four states, which reflect both demographic factors and potential differences in the natural history of TB. These differences may inform resource allocation decisions in these states.

Assessment of tuberculosis spatial hotspot areas in Antananarivo, Madagascar, by combining spatial analysis and genotyping

Background

Tuberculosis (TB) remains a public health problem in Madagascar. A crucial element of TB control is the development of an easy and rapid method for the orientation of TB control strategies in the country. Our main objective was to develop a TB spatial hotspot identification method by combining spatial analysis and TB genotyping method in Antananarivo.

Methods

Sputa of new pulmonary TB cases from 20 TB diagnosis and treatment centers (DTCs) in Antananarivo were collected from August 2013 to May 2014 for culture. Mycobacterium tuberculosis complex (MTBC) clinical isolates were typed by spoligotyping on a Luminex® 200 platform. All TB patients were respectively localized according to their neighborhood residence and the spatial distribution of all pulmonary TB patients and patients with genotypic clustered isolates were scanned respectively by the Kulldorff spatial scanning method for identification of significant spatial clustering. Areas exhibiting spatial clustering of patients with genotypic clustered isolates were considered as hotspot TB areas for transmission.

Results

Overall, 467 new cases were included in the study, and 394 spoligotypes were obtained (84.4%). New TB cases were distributed in 133 of the 192 Fokontany (administrative neighborhoods) of Antananarivo (1 to 15 clinical patients per Fokontany) and patients with genotypic clustered isolates were distributed in 127 of the 192 Fokontany (1 to 13 per Fokontany). A single spatial focal point of epidemics was detected when ignoring genotypic data (p = 0.039). One Fokontany of this focal point and three additional ones were detected to be spatially clustered when taking genotypes into account (p < 0.05). These four areas were declared potential TB transmission hotspots in Antananarivo and will be considered as priority targets for surveillance in the future.

Conclusion

This method, combining spatial analysis and TB genotyping will now be used for further focused clinical and epidemiological studies in Madagascar and will allow better TB control strategies by public health authorities.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-017-2653-9) contains supplementary material, which is available to authorized users.

Recent TB transmission, clustering and predictors of large clusters in London, 2010-2012: results from first 3 years of universal MIRU-VNTR strain typing

Background

The incidence of TB has doubled in the last 20 years in London. A better understanding of risk groups for recent transmission is required to effectively target interventions. We investigated the molecular epidemiological characteristics of TB cases to estimate the proportion of cases due to recent transmission, and identify predictors for belonging to a cluster.

Methods

The study population included all culture-positive TB cases in London residents, notified between January 2010 and December 2012, strain typed using 24-loci multiple interspersed repetitive units-variable number tandem repeats. Multivariable logistic regression analysis was performed to assess the risk factors for clustering using sociodemographic and clinical characteristics of cases and for cluster size based on the characteristics of the first two cases.

Results

There were 10 147 cases of which 5728 (57%) were culture confirmed and 4790 isolates (84%) were typed. 2194 (46%) were clustered in 570 clusters, and the estimated proportion attributable to recent transmission was 34%. Clustered cases were more likely to be UK born, have pulmonary TB, a previous diagnosis, a history of substance abuse or alcohol abuse and imprisonment, be of white, Indian, black-African or Caribbean ethnicity. The time between notification of the first two cases was more likely to be <90 days in large clusters.

Conclusions

Up to a third of TB cases in London may be due to recent transmission. Resources should be directed to the timely investigation of clusters involving cases with risk factors, particularly those with a short period between the first two cases, to interrupt onward transmission of TB.

[Identification of the Mycobacterium tuberculosis Beijing lineage in Ecuador]

INTRODUCTION

Mycobacterium tuberculosis Beijing lineage isolates are considered to be especially virulent, transmissible and prone to acquire resistances. Beijing strains have been reported worldwide, but studies in Latin America are still scarce. The only multinational study performed in the region indicated a heterogeneous distribution for this lineage, which was absent in Chile, Colombia and Ecuador, although further studies found the lineage in Chile and Colombia.

OBJECTIVE

To search for the presence of the Beijing lineage in Ecuador, the only country in the region where it remains unreported.

MATERIALS AND METHODS

We obtained a convenience sample (2006-2012) from two hospitals covering different populations. The isolates were genotyped using 24-MIRU-VNTR. Lineages were assigned by comparing their patterns to those in the MIRU-VNTRplus platform. Isolates belonging to the Beijing lineage were confirmed by allele-specific PCR.

RESULTS

We identified the first Beijing isolate in Ecuador in an unexpected epidemiological scenario: A patient was infected in the Andean region, in a population with low mobility and far from the borders of the neighboring countries where Beijing strains had been previously reported.

CONCLUSION

This is the first report of the presence of the Beijing lineage in Ecuador in an unusual epidemiological context that deserves special attention.

Individual- and neighborhood-level contextual factors are associated with Mycobacterium tuberculosis transmission: genotypic clustering of cases in Michigan, 2004-2012

PURPOSE

Using genotyping data of Mycobacterium tuberculosis isolates from new cases reported to the tuberculosis (TB) surveillance program, we evaluated risk factors for recent TB transmission at both the individual- and neighborhood- levels among U.S.-born and foreign-born populations.

METHODS

TB cases (N = 1236) reported in Michigan during 2004 to 2012 were analyzed using multivariable Poisson regression models to examine risk factors for recent transmission cross-sectionally for U.S.-born and foreign-born populations separately. Recent transmission was defined based on spoligotype and 12-locus-mycobacterial interspersed repetitive unit-variable number tandem repeat typing matches of bacteria from cases that were diagnosed within 1 year of each other. Four classes of predictor variables were examined: demographic factors, known TB risk factors, clinical characteristics, and neighborhood-level factors.

RESULTS

Overall, 22% of the foreign-born cases resulted from recent transmission. Among the foreign-born, race and being a contact of an infectious TB case were significant predictors of recent transmission. More than half (52%) of U.S.-born cases resulted from recent transmission. Among the U.S.-born, recent transmission was predicted by both individual- and neighborhood-level sociodemographic characteristics.

CONCLUSIONS

Interventions aimed at reducing TB incidence among foreign-born should focus on reducing reactivation of latent infection. However, reducing TB incidence among the U.S.-born will require decreasing transmission among socially disadvantaged groups at the individual- and neighborhood- levels. This report fills an important knowledge gap regarding the contemporary social context of TB in the United States, thereby providing a foundation for future studies of public health policies that can lead to the development of more targeted, effective TB control.

Evaluation of 24-locus MIRU-VNTR genotyping in Mycobacterium tuberculosis cluster investigations in four jurisdictions in the United States, 2006-2010

The U.S. Centers for Disease Control and Prevention (CDC) uses a combination of spacer oligonucleotide typing (spoligotyping) and mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) analyses as part of the National TB Genotyping Service (NTGS). The NTGS expansion from 12-locus MIRU-VNTR (MIRU12) to 24-locus MIRU-VNTR (MIRU24) in 2009 enhanced the ability to discriminate Mycobacterium tuberculosis strains. In the current study, we investigated the MIRU24 concordance among epidemiologic-linked tuberculosis (TB) patients in four U.S. health jurisdictions. We also evaluated the programmatic benefits of combining MIRU24 and spoligotyping with epidemiologic evidence in identifying potential recent TB transmission. We examined 342 TB patients in 42 spoligotype/MIRU12 (PCRType) clusters (equivalent to 46 spoligotype/MIRU24 [GENType] clusters) to identify epidemiologic links among cases. GENType clusters, when compared to PCRType clusters, had 12 times higher odds of epidemiologic links being identified if patients were younger than 25 years and 3 times higher odds if patients resided in the same zip code, or had HIV infection. Sixty (18%) fewer PCRType-clustered patients would need investigations if clusters are defined using GENType instead of PCRType. An important advantage of defining clusters by MIRU24 is resource savings related to the reduced number of clustered cases needing investigation.

Strains of Mycobacterium tuberculosis transmitting infection in Brazilian households and those associated with community transmission of tuberculosis

Molecular epidemiologic studies have shown that the dynamics of tuberculosis transmission varies geographically. We sought to determine which strains of Mycobacterium tuberculosis (MTB) were infecting household contacts (HHC), and which were causing clusters of tuberculosis (TB) disease in Vitoria-ES, Brazil. A total of 741 households contacts (445 TST +) and 139 index cases were characterized according to the proportion of contacts in each household that had a tuberculin skin test positive: low (LT) (≤40% TST+), high (HT) (≥70% TST+) and (40-70% TST+) intermediate (IT) transmission. IS6110-RFLP and spoligotyping analysis were performed only 139 MTB isolates from index cases and 841 community isolates. Clustering occurred in 45% of the entire study population. There was no statistically significant association between MTB household transmission category and clustering. Within the household study population, the proportion of clusters in HT and LT groups was similar (31% and 36%, respectively; p = 0.82). Among index cases isolates associated with households demonstrating TST conversion, the frequency of unique pattern genotypes was higher for index cases of the LT compared to HT households (p = 0.03). We concluded that clusters and lineages associated with MTB infection in HT households had no proclivity for increased transmission of TB in the community.

Use of Activity Space in a Tuberculosis Outbreak: Bringing Homeless Persons Into Spatial Analyses

BACKGROUND

Tuberculosis (TB) causes significant morbidity and mortality in US cities, particularly in poor, transient populations. During a TB outbreak in Fulton County, Atlanta, GA, we aimed to determine whether local maps created from multiple locations of personal activity per case would differ significantly from traditional maps created from single residential address.

METHODS

Data were abstracted for patients with TB disease diagnosed in 2008-2014 and receiving care at the Fulton County Health Department. Clinical and activity location data were abstracted from charts. Kernel density methods, activity space analysis, and overlay with homeless shelter locations were used to characterize case spatial distribution when using single versus multiple addresses.

RESULTS

Data were collected for 198 TB cases, with over 30% homeless US-born cases included. Greater spatial dispersion of cases was found when utilizing multiple versus single addresses per case. Activity spaces of homeless and isoniazid (INH)-resistant cases were more spatially congruent with one another than non-homeless and INH-susceptible cases (P < .0001 and P < .0001, respectively).

CONCLUSIONS

Innovative spatial methods allowed us to more comprehensively capture the geography of TB-infected homeless persons, who made up a large portion of the Fulton County outbreak. We demonstrate how activity space analysis, prominent in exposure science and chronic disease, supports that routine capture of multiple location TB data may facilitate spatially different public health interventions than traditional surveillance maps.

Tuberculosis Caused by Mycobacterium africanum, United States, 2004-2013

Mycobacterium africanum is endemic to West Africa and causes tuberculosis (TB). We reviewed reported cases of TB in the United States during 2004-2013 that had lineage assigned by genotype (spoligotype and mycobacterial interspersed repetitive unit variable number tandem repeats). M. africanum caused 315 (0.4%) of 73,290 TB cases with lineage assigned by genotype. TB caused by M. africanum was associated more with persons from West Africa (adjusted odds ratio [aOR] 253.8, 95% CI 59.9-1,076.1) and US-born black persons (aOR 5.7, 95% CI 1.2-25.9) than with US-born white persons. TB caused by M. africanum did not show differences in clinical characteristics when compared with TB caused by M. tuberculosis. Clustered cases defined as >2 cases in a county with identical 24-locus mycobacterial interspersed repetitive unit genotypes, were less likely for M. africanum (aOR 0.1, 95% CI 0.1-0.4), which suggests that M. africanum is not commonly transmitted in the United States.

Validation of genotype cluster investigations for Mycobacterium tuberculosis: application results for 44 clusters from four heterogeneous United States jurisdictions

BACKGROUND

Tracking the dissemination of specific Mycobacterium tuberculosis (Mtb) strains using genotyped Mtb isolates from tuberculosis patients is a routine public health practice in the United States. The present study proposes a standardized cluster investigation method to identify epidemiologic-linked patients in Mtb genotype clusters. The study also attempts to determine the proportion of epidemiologic-linked patients the proposed method would identify beyond the outcome of the conventional contact investigation.

METHODS

The study population included Mtb culture positive patients from Georgia, Maryland, Massachusetts and Houston, Texas. Mtb isolates were genotyped by CDC's National TB Genotyping Service (NTGS) from January 2006 to October 2010. Mtb cluster investigations (CLIs) were conducted for patients whose isolates matched exactly by spoligotyping and 12-locus MIRU-VNTR. CLIs were carried out in four sequential steps: (1) Public Health Worker (PHW) Interview, (2) Contact Investigation (CI) Evaluation, (3) Public Health Records Review, and (4) CLI TB Patient Interviews. Comparison between patients whose links were identified through the study's CLI interviews (Step 4) and patients whose links were identified earlier in CLI (Steps 1-3) was conducted using logistic regression.

RESULTS

Forty-four clusters were randomly selected from the four study sites (401 patients in total). Epidemiologic links were identified for 189/401 (47 %) study patients in a total of 201 linked patient-pairs. The numbers of linked patients identified in each CLI steps were: Step 1 - 105/401 (26.2 %), Step 2 - 15/388 (3.9 %), Step 3 - 41/281 (14.6 %), and Step 4 - 28/119 (30 %). Among the 189 linked patients, 28 (14.8 %) were not identified in previous CI. No epidemiologic links were identified in 13/44 (30 %) clusters.

CONCLUSIONS

We validated a standardized and practical method to systematically identify epidemiologic links among patients in Mtb genotype clusters, which can be integrated into the TB control and prevention programs in public health settings. The CLI interview identified additional epidemiologic links that were not identified in previous CI. One-third of the clusters showed no epidemiologic links despite being extensively investigated, suggesting that some improvement in the interviewing methods is still needed.

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.

The Prevalence of Latent Tuberculosis Infection in the United States

RATIONALE

Individuals with latent tuberculosis infection (LTBI) represent a reservoir of infection, many of whom will progress to tuberculosis (TB) disease. A central pillar of TB control in the United States is reducing this reservoir through targeted testing and treatment.

OBJECTIVES

To estimate the prevalence of LTBI in the United States using the tuberculin skin test (TST) and an IFN-γ release assay.

METHODS

We used nationally representative data from the 2011-2012 National Health and Nutrition Examination Survey (n = 6,083 aged ≥6 yr). LTBI was measured by both the TST and QuantiFERON-TB Gold In-Tube test (QFT-GIT). Weighted population, prevalence, and multiple logistic regression were used.

MEASUREMENTS AND MAIN RESULTS

The estimated prevalence of LTBI in 2011-2012 was 4.4% as measured by the TST and 4.8% by QFT-GIT, corresponding to 12,398,000 and 13,628,000 individuals, respectively. Prevalence declined slightly since 2000 among the U.S. born but remained constant among the foreign born. Earlier birth cohorts consistently had higher prevalence than more recent ones. Higher risk groups included the foreign born, close contact with a case of TB disease, and certain racial/ethnic groups.

CONCLUSIONS

After years of decline, the prevalence of LTBI remained relatively constant between 2000 and 2011. A large reservoir of 12.4 million still exists, with foreign-born persons representing an increasingly larger proportion of this reservoir (73%). Estimates and risk factors for LTBI were generally similar between the TST and QFT-GIT. The updated estimates of LTBI and associated risk groups can help improve targeted testing and treatment in the United States.

Protocol for a population-based molecular epidemiology study of tuberculosis transmission in a high HIV-burden setting: the Botswana Kopanyo study

INTRODUCTION

Mycobacterium tuberculosis (Mtb) is transmitted from person to person via airborne droplet nuclei. At the community level, Mtb transmission depends on the exposure venue, infectiousness of the tuberculosis (TB) index case and the susceptibility of the index case's social network. People living with HIV infection are at high risk of TB, yet the factors associated with TB transmission within communities with high rates of TB and HIV are largely undocumented. The primary aim of the Kopanyo study is to better understand the demographic, clinical, social and geospatial factors associated with TB and multidrug-resistant TB transmission in 2 communities in Botswana, a country where 60% of all patients with TB are also infected with HIV. This manuscript describes the methods used in the Kopanyo study.

METHODS AND ANALYSIS

The study will be conducted in greater Gaborone, which has high rates of HIV and a mobile population; and in Ghanzi, a rural community with lower prevalence of HIV infection and home to the native San population. Kopanyo aims to enrol all persons diagnosed with TB during a 4-year study period. From each participant, sputum will be cultured, and for all Mtb isolates, molecular genotyping (24-locus mycobacterial interspersed repetitive units-variable number of tandem repeats) will be performed. Patients with matching genotype results will be considered members of a genotype cluster, a proxy for recent transmission. Demographic, behavioural, clinical and social information will be collected by interview. Participant residence, work place, healthcare facilities visited and social gathering venues will be geocoded. We will assess relationships between these factors and cluster involvement to better plan interventions for reducing TB transmission.

ETHICS

Ethical approval from the Independent Review Boards at the University of Pennsylvania, US Centers for Disease Control and Prevention, Botswana Ministry of Health and University of Botswana has been obtained.

Spatiotemporal Clustering of Mycobacterium tuberculosis Complex Genotypes in Florida: Genetic Diversity Segregated by Country of Birth

Background

Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). Although the MTBC is highly clonal, between-strain genetic diversity has been observed. In low TB incidence settings, immigration may facilitate the importation of MTBC strains with a potential to complicate TB control efforts.

Methods

We investigated the genetic diversity and spatiotemporal clustering of 2,510 MTBC strains isolated in Florida, United States, between 2009 and 2013 and genotyped using spoligotyping and 24-locus MIRU-VNTR. We mapped the genetic diversity to the centroid of patient residential zip codes using a geographic information system (GIS). We assessed transmission dynamics and the influence of immigration on genotype clustering using space-time permutation models adjusted for foreign-born population density and county-level HIV risk and multinomial models stratified by country of birth and timing of immigration in SaTScan.

Principal Findings

Among the 2,510 strains, 1,245 were reported among foreign-born persons; including 408 recent immigrants (<5 years). Strain allelic diversity (h) ranged from low to medium in most locations and was most diverse in urban centers where foreign-born population density was also high. Overall, 21.5% of cases among U.S.-born persons and 4.6% among foreign-born persons clustered genotypically and spatiotemporally and involved strains of the Haarlem family. One Haarlem space-time cluster identified in the mostly rural northern region of Florida included US/Canada-born individuals incarcerated at the time of diagnosis; two clusters in the mostly urban southern region of Florida were composed predominantly of foreign-born persons. Both groups had HIV prevalence above twenty percent.

Conclusions/Significance

Almost five percent of TB cases reported in Florida during 2009–2013 were potentially due to recent transmission. Improvements to TB screening practices among the prison population and recent immigrants are likely to impact TB control. Due to the monomorphic nature of available markers, whole genome sequencing is needed to conclusively delineate recent transmission events between U.S. and foreign-born persons.

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.

A Novel Tool Improves Existing Estimates of Recent Tuberculosis Transmission in Settings of Sparse Data Collection

In any setting, a proportion of incident active tuberculosis (TB) reflects recent transmission (“recent transmission proportion”), whereas the remainder represents reactivation. Appropriately estimating the recent transmission proportion has important implications for local TB control, but existing approaches have known biases, especially where data are incomplete. We constructed a stochastic individual-based model of a TB epidemic and designed a set of simulations (derivation set) to develop two regression-based tools for estimating the recent transmission proportion from five inputs: underlying TB incidence, sampling coverage, study duration, clustered proportion of observed cases, and proportion of observed clusters in the sample. We tested these tools on a set of unrelated simulations (validation set), and compared their performance against that of the traditional ‘n-1’ approach. In the validation set, the regression tools reduced the absolute estimation bias (difference between estimated and true recent transmission proportion) in the ‘n-1’ technique by a median [interquartile range] of 60% [9%, 82%] and 69% [30%, 87%]. The bias in the ‘n-1’ model was highly sensitive to underlying levels of study coverage and duration, and substantially underestimated the recent transmission proportion in settings of incomplete data coverage. By contrast, the regression models’ performance was more consistent across different epidemiological settings and study characteristics. We provide one of these regression models as a user-friendly, web-based tool. Novel tools can improve our ability to estimate the recent TB transmission proportion from data that are observable (or estimable) by public health practitioners with limited available molecular data.

Data for action: collection and use of local data to end tuberculosis

Accelerating progress in the fight against tuberculosis will require a drastic shift from a strategy focused on control to one focused on elimination. Successful disease elimination campaigns are characterised by locally tailored responses that are informed by appropriate data. To develop such a response to tuberculosis, we suggest a three-step process that includes improved collection and use of existing programmatic data, collection of additional data (eg, geographic information, drug resistance, and risk factors) to inform tailored responses, and targeted collection of novel data (eg, sequencing data, targeted surveys, and contact investigations) to improve understanding of tuberculosis transmission dynamics. Development of a locally targeted response for tuberculosis will require substantial investment to reconfigure existing systems, coupled with additional empirical data to evaluate the effectiveness of specific approaches. Without adoption of an elimination strategy that uses local data to target hotspots of transmission, ambitious targets to end tuberculosis will almost certainly remain unmet.

Characterizing tuberculosis genotype clusters along the United States-Mexico border

We examined the growth of tuberculosis (TB) genotype clusters during 2005-2010 in the United States, categorized by country of origin and ethnicity of the index case and geographic proximity to the US-Mexico border at the time of TB diagnosis. Nationwide, 38.9% of cases subsequent to Mexico-born index cases were US-born. Among clusters following US-born Hispanic and US-born non-Hispanic index cases, respectively 29.2% and 5.3% of subsequent cluster members were Mexico-born. In border areas, the majority of subsequent cases were Mexico-born following US-born Hispanic (56.4%) and US-born non-Hispanic (55.6%) index cases. These findings suggest that TB transmission commonly occurs between US-born and Mexico-born persons. Along the US-Mexico border, prioritizing TB genotype clusters following US-born index cases for investigation may prevent subsequent cases among both US-born and Mexico-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.

Using tuberculosis patient characteristics to predict future cases with matching genotype results

SETTING

United States.

BACKGROUND

It is unknown whether tuberculosis (TB) case or patient characteristics can predict the likelihood of future related TB cases.

OBJECTIVE

To estimate the likelihood for future related cases, i.e., cases with matching TB genotypes within the same county diagnosed within the 2 years following the year of reporting of each included case.

DESIGN

We considered all TB cases with genotyping results reported in the United States during 2004-2010. Predictive scores were calculated based on patient characteristics by dividing the number of patients who were not the last case in a county-level TB genotype cluster by the total number of patients.

RESULTS

Overall, there was a 30.8% chance that a future related case would be detected during the 2 years following the report year of any given case. Future related cases were detected in 34.7% of instances following the diagnosis of smear-positive cases, 51.9% of instances following the diagnosis of a homeless patient and 45.2% of instances following the diagnosis of a patient who reported substance abuse. Predictive scores ranged by race (White 13.9%, Native Hawaiian 43.8%) and age group (⩾65 years 13.1%, 0-4 years 43%), and were higher for US-born patients.

CONCLUSIONS

Behavioral and sociodemographic factors can help predict the likelihood of future related cases and can be used to prioritize contact investigations.

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.

Mycobacterium tuberculosis complex transmission is not associated with recent immigration (≤5 years) in Florida

As tuberculosis (TB) incidence decreases in the US, foreign-born persons continue to account for a larger proportion of the burden. In these cross-sectional analyses of 1149 culture-confirmed TB cases genotyped using spoligotyping and 24-locus MIRU, we show that over a quarter of cases among the foreign-born population in Florida resulted from recent transmission of the Mycobacterium tuberculosis complex. In addition, over a third of these cases occurred among persons who had immigrated 5 years or less prior to their diagnosis. Although recent immigration was not a significant predictor of TB transmission, younger age, birthplace in the Americas, homelessness, drug use and TB lineage are risk factors for TB transmission among the foreign-born population in Florida. These data provide actionable insights into TB transmission among the foreign-born population in Florida.

Preventing Infectious Pulmonary Tuberculosis Among Foreign-Born Residents of the United States

OBJECTIVES

We described risk factors associated with infectious tuberculosis (TB) and missed TB-prevention opportunities in foreign-born US residents, who account for almost two thirds of the nation's TB patients.

METHODS

In a cross-sectional study at 20 US sites of foreign-born persons diagnosed with TB in 2005 through 2006, we collected results of sputum smear microscopy for acid-fast bacilli (a marker for infectiousness) and data on visa status, sociodemographics, TB-related care seeking, and latent TB infection (LTBI) diagnosis opportunities.

RESULTS

Among 980 persons with pulmonary TB who reported their visa status, 601 (61%) were legal permanent residents, 131 (13.4%) had temporary visas, and 248 (25.3%) were undocumented. Undocumented persons were more likely than permanent residents to have acid-fast bacilli-positive smears at diagnosis (risk ratio = 1.3; 95% confidence interval = 1.2, 1.4). Of those diagnosed 1 year or more after arrival, 57.3% reported LTBI screening opportunities; fewer than 25% actually were. Undocumented persons reported fewer LTBI screening opportunities and were less likely to be tested.

CONCLUSIONS

Progress toward TB elimination in the United States depends upon expanding opportunities for regular medical care and promotion of LTBI screening and treatment among foreign-born persons.

Towards tuberculosis elimination: an action framework for low-incidence countries

This paper describes an action framework for countries with low tuberculosis (TB) incidence (<100 TB cases per million population) that are striving for TB elimination. The framework sets out priority interventions required for these countries to progress first towards "pre-elimination" (<10 cases per million) and eventually the elimination of TB as a public health problem (less than one case per million). TB epidemiology in most low-incidence countries is characterised by a low rate of transmission in the general population, occasional outbreaks, a majority of TB cases generated from progression of latent TB infection (LTBI) rather than local transmission, concentration to certain vulnerable and hard-to-reach risk groups, and challenges posed by cross-border migration. Common health system challenges are that political commitment, funding, clinical expertise and general awareness of TB diminishes as TB incidence falls. The framework presents a tailored response to these challenges, grouped into eight priority action areas: 1) ensure political commitment, funding and stewardship for planning and essential services; 2) address the most vulnerable and hard-to-reach groups; 3) address special needs of migrants and cross-border issues; 4) undertake screening for active TB and LTBI in TB contacts and selected high-risk groups, and provide appropriate treatment; 5) optimise the prevention and care of drug-resistant TB; 6) ensure continued surveillance, programme monitoring and evaluation and case-based data management; 7) invest in research and new tools; and 8) support global TB prevention, care and control. The overall approach needs to be multisectorial, focusing on equitable access to high-quality diagnosis and care, and on addressing the social determinants of TB. Because of increasing globalisation and population mobility, the response needs to have both national and global dimensions.

Increased risk of tuberculosis among foreign-born persons with diabetes in California, 2010-2012

Background

Diabetes increases the risk of tuberculosis. We sought to identify populations of persons with diabetes in California at further increased risk for tuberculosis to target tuberculosis infection screening and treatment efforts.

Methods

We performed a retrospective population-based analysis of adult (aged ≥18 years) tuberculosis cases reported in California during 2010–2012. Tuberculosis cases with and without diabetes were grouped into regions of birth and stratified by age category. Population estimates were calculated using 2011–2012 California Health Interview Survey data. We calculated tuberculosis disease rate and relative risk of tuberculosis among persons with diabetes stratified by birth location and age group; and the number needed to screen and, if positive, treat for tuberculosis infection to prevent one case of active tuberculosis over 5 years (NNS).

Results

During 2010–2012, among 6,050 adults with active tuberculosis in California, 82% were foreign-born and 24% had diabetes. The overall relative risk for tuberculosis among persons with diabetes was 3.5 (95% confidence interval, 3.3–3.7) with a rate of 21 per 100,000 persons with diabetes. The rate among foreign-born persons with diabetes (141.5/100,000) was almost 12 times greater than among nonforeign-born persons with diabetes (12.0/100,000). The NNS was 7,930 among all adults, 2,740 among adults with diabetes, 1,526 among all foreign-born adults, and 596 among foreign-born adults with diabetes.

Conclusions

In California, foreign-born persons with diabetes had significantly elevated rates of active tuberculosis. Focusing tuberculosis infection screening and treatment efforts on foreign-born persons with diabetes may be a feasible and efficient way to make progress toward tuberculosis elimination in California.

Electronic supplementary material

The online version of this article (doi:10.1186/s12889-015-1600-1) contains supplementary material, which is available to authorized users.

Tuberculosis and excess alcohol use in the United States, 1997-2012

BACKGROUND

Excess alcohol use among tuberculosis (TB) patients complicates TB control strategies.

OBJECTIVES

To characterize the role of excess alcohol use in TB control, we describe the epidemiology of excess alcohol use and TB in the United States among those aged ⩾15 years.

DESIGN

Using data reported to the National Tuberculosis Surveillance System, 1997-2012, we examined associations between excess alcohol use and TB treatment outcomes and markers for increased transmission (involvement in a local genotype cluster of cases) using multivariate logistic regression. We used Cox proportional hazards regression analysis to examine the relationship between excess alcohol use and the rate of conversion from positive to negative in sputum culture results.

RESULTS

Excess alcohol use was documented for 31 207 (15.1%) of 207 307 patients. Prevalence of excess alcohol use was greater among male patients (20.6%) and US-born patients (24.6%). Excess alcohol use was associated with a positive sputum smear result (aOR 1.23, 95%CI 1.18-1.28) and death during treatment (vs. completion of treatment) (aOR 1.16, 95%CI 1.10-1.22). The rate of culture conversion was higher among patients without excess alcohol use (adjusted hazard ratio 1.20, 95%CI 1.18-1.23).

CONCLUSIONS

Excess alcohol use was common among patients with TB, and was associated with TB transmission, lower rates of sputum culture conversion, and greater mortality.

Evaluation of large genotypic Mycobacterium tuberculosis clusters: contributions from remote and recent transmission

Tuberculosis genotypic clustering is used as a proxy for recent transmission. The association between clustering and recent transmission becomes problematic when the genotyping method lacks specificity in defining a cluster, as well as for clusters with extensive jurisdictional histories and/or common genotypes. We investigated the four largest spoligotype/12 loci MIRU-VNTR-defined clusters in Harris County, Texas from 2006-2012 to determine their historical contribution to tuberculosis morbidity, estimate the contributions from recent and remote transmission, and determine the impact of secondary genotyping on cluster definition. The clusters contained 189, 64, 51 and 38 cases. Each cluster was linked to cluster(s) previously identified by Houston Tuberculosis Initiative; 3 since 1995 and the fourth in 2002. Among cases for which timing of Mycobacterium tuberculosis transmission relative to tuberculosis disease could be ascertained, nearly equal proportions were associated with recent and remote transmission. The extent to which genotyping with an additional 12 MIRU-VNTR loci modified the cluster definition varied from little or no impact for the two smaller clusters to moderate impact for the larger clusters. Tuberculosis control measures to reduce morbidity associated with large clusters must involve strategies to identify and treat individuals who recently acquired infection, as well as persons infected for years.

Tuberculosis among the homeless, United States, 1994-2010

OBJECTIVES

1) To describe homeless persons diagnosed with tuberculosis (TB) during the period 1994-2010, and 2) to estimate a TB incidence rate among homeless persons in the United States.

METHODS

TB cases reported to the National Tuberculosis Surveillance System were analyzed by origin of birth. Incidence rates were calculated using the US Department of Housing and Urban Development homeless population estimates. Analysis of genotyping results identified clustering as a marker for transmission among homeless TB patients.

RESULTS

Of 270,948 reported TB cases, 16,527 (6%) were homeless. The TB incidence rate among homeless persons ranged from 36 to 47 cases per 100,000 population in 2006-2010. Homeless TB patients had over twice the odds of not completing treatment and of belonging to a genotype cluster. US- and foreign-born homeless TB patients had respectively 8 and 12 times the odds of substance abuse.

CONCLUSIONS

Compared to the general population, homeless persons had an approximately 10-fold increase in TB incidence, were less likely to complete treatment and more likely to abuse substances. Public health outreach should target homeless populations to reduce the excess burden of TB in this population.

Decline in tuberculosis among Mexico-born persons in the United States, 2000-2010

BACKGROUND

In 2010, Mexico was the most common (22.9%) country of origin for foreign-born persons with tuberculosis in the United States, and overall trends in tuberculosis morbidity are substantially influenced by the Mexico-born population.

OBJECTIVES

To determine the risk of tuberculosis disease among Mexico-born persons living in the United States.

METHODS

Using data from the U.S. National Tuberculosis Surveillance System and the American Community Survey, we examined tuberculosis case counts and case rates stratified by years since entry into the United States and geographic proximity to the United States-Mexico border. We calculated trends in case rates over time measured by average annual percent change.

RESULTS

The total tuberculosis case count (-14.5%) and annual tuberculosis case rate (average annual percent change -5.1%) declined among Mexico-born persons. Among those diagnosed with tuberculosis less than 1 year since entry into the United States (newly arrived persons), there was a decrease in tuberculosis cases (-60.4%), no change in tuberculosis case rate (average annual percent change of 0.0%), and a decrease in population (-60.7%). Among those living in the United States for more than 5 years (non-recently arrived persons), there was an increase in tuberculosis cases (+3.4%), a decrease in tuberculosis case rate (average annual percent change of -4.9%), and an increase in population (+62.7%). In 2010, 66.7% of Mexico-born cases were among non-recently arrived persons, compared with 51.1% in 2000. Although border states reported the highest proportions (>15%) of tuberculosis cases that were Mexico-born, the highest Mexico-born-specific tuberculosis case rates (>20/100,000 population) were in states in the eastern and southeastern regions of the United States.

CONCLUSIONS

The decline in tuberculosis morbidity among Mexico-born persons may be attributed to fewer newly arrived persons from Mexico and lower tuberculosis case rates among non-recently arrived Mexico-born persons. The extent of the decline was dampened by an unchanged tuberculosis case rate among newly arrived persons from Mexico and a large increase in the non-recently arrived Mexico-born population. If current trends continue, tuberculosis morbidity among Mexico-born persons will be increasingly driven by those who have been living in the United States for more than 5 years.

Neighborhood socioeconomic position and tuberculosis transmission: a retrospective cohort study

Background

Current understanding of tuberculosis (TB) genotype clustering in the US is based on individual risk factors. This study sought to identify whether area-based socioeconomic status (SES) was associated with genotypic clustering among culture-confirmed TB cases.

Methods

A retrospective cohort analysis was performed on data collected on persons with incident TB in King County, Washington, 2004–2008. Multilevel models were used to identify the relationship between area-level SES at the block group level and clustering utilizing a socioeconomic position index (SEP).

Results

Of 519 patients with a known genotyping result and block group, 212 (41%) of isolates clustered genotypically. Analyses suggested an association between lower area-based SES and increased recent TB transmission, particularly among US-born populations. Models in which community characteristics were measured at the block group level demonstrated that lower area-based SEP was positively associated with genotypic clustering after controlling for individual covariates. However, the trend in higher clustering odds with lower SEP index quartile diminished when additional block-group covariates.

Conclusions

Results stress the need for TB control interventions that take area-based measures into account, with particular focus on poor neighborhoods. Interventions based on area-based characteristics, such as improving case finding strategies, utilizing location-based screening and addressing social inequalities, could reduce recent rates of transmission.