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TB is a priority pathogen for the application of whole-genome sequencing (WGS) into routine public health practice. In low-incidence settings, a growing number of services have begun to incorporate routine WGS into standard practice. The increasing availability of real-time genomic information supports a variety of aspects of the public health response, including the detection of drug resistance, monitoring of laboratory and clinical practices, contact tracing investigations and active case finding. Optimal structures and approaches are needed to support the rapid translation of genomic information into practice and to evaluate outcomes and impact. In this consensus paper, we outline the elements needed to systemically incorporate routine WGS into the TB public health response, including the sustainability of services, multidisciplinary team models and monitoring and evaluation frameworks. If integrated in an efficient and thoughtful manner, routine WGS has the potential to significantly improve clinical TB care for individuals and the overall public health response., Competing Interests: Conflicts of interest: none declared., (© 2024 The Authors.)

Several human-adapted Mycobacterium tuberculosis complex (Mtbc) lineages exhibit a restricted geographical distribution globally. These lineages are hypothesized to transmit more effectively among sympatric hosts, that is, those that share the same geographical area, though this is yet to be confirmed while controlling for exposure, social networks and disease risk after exposure. Using pathogen genomic and contact tracing data from 2,279 tuberculosis cases linked to 12,749 contacts from three low-incidence cities, we show that geographically restricted Mtbc lineages were less transmissible than lineages that have a widespread global distribution. Allopatric host-pathogen exposure, in which the restricted pathogen and host are from non-overlapping areas, had a 38% decrease in the odds of infection among contacts compared with sympatric exposures. We measure tenfold lower uptake of geographically restricted lineage 6 strains compared with widespread lineage 4 strains in allopatric macrophage infections. We conclude that Mtbc strain-human long-term coexistence has resulted in differential transmissibility of Mtbc lineages and that this differs by human population., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Severe mpox has been observed in people with advanced human immunodeficiency virus (HIV). We describe clinical outcomes of 13 patients with advanced HIV (CD4 <200 cells/μL), severe mpox, and multiorgan involvement. Despite extended tecovirimat courses and additional agents, including vaccinia immune globulin, cidofovir, and brincidofovir, this group experienced prolonged hospitalizations and high mortality., Competing Interests: Potential conflicts of interest. E. A. G. has received consulting fees from the American Society of Health-System Pharmacists and has received honoraria for lectures, presentations, speakers’ bureaus, manuscript writing, or educational events from Southeast AIDS Education and Training Center (AETC). O. M. has received consulting fees from The Public Theatre and from Primary Care Development Corporation and has received payment or honoraria for lectures, presentations, speakers’ bureaus, manuscript writing, or educational events from Northeast Caribbean AETC, Infectious Diseases Society of New York, Columbia School of Social Work, Physicians’ Research Network, and State University of New York Downstate. J. Z. has received honoraria for lectures, presentations, speakers’ bureaus, manuscript writing, or educational events from Rutgers New Jersey Medical School, Albany Medical Center, International Antiviral Society–USA, University of Rochester, Nassau University Medical Center, Memorial Sloan Kettering, East Tennessee Children's Hospital, and Stony Brook Medical Center. M. A. D. previously held stock with Gilead Sciences that was sold prior to starting work on this manuscript. All other authors report no potential conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Competing Interests: All authors declare that they have no competing interests in this manuscript and its publication.

BACKGROUND: We have updated the epidemiology of tuberculosis (TB) among healthcare personnel (HCP) in New York City (NYC), USA, during a period of declining TB burden. METHODS: Using routinely collected Health Department data for NYC TB cases from 2001 to 2014, we conducted a retrospective descriptive analysis. P values were calculated using Pearson's χ² or Fisher's exact test for categorical data; Wilcoxon rank-sum test was used to compare medians. We used the Cochran-Armitage test for trend and linear regression for trend analyses. RESULTS: HCP accounted for 6% of adults with TB throughout the study period and were more likely than other adults to be female (68% vs. 37%, P ≤ 0.0001), have extrapulmonary-only disease (31% vs. 23%, P ≤ 0.0001), have an isolate with multidrug resistance (4% vs. 2%, P = 0.0211), and report a previous history of latent TB infection (LTBI) (51% vs. 23%, P ≤ 0.0001). Compared to non-US-born HCP, US-born HCP were more likely to have HIV infection (18% vs. 8%, P = 0.0011) or a genotypically clustered isolate (67% vs. 37%, P ≤ 0.0001) and less likely to report history of prior LTBI (43% vs. 54%, P = 0.0128). CONCLUSIONS: Further research is needed to explore transmission and occupational risk among HCP. New approaches are needed to optimize completion of prophylaxis for HCP with LTBI.

The determination of lineages from strain-based molecular genotyping information is an important problem in tuberculosis. Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is a commonly used molecular genotyping approach that uses counts of the number of times pre-specified loci repeat in a strain. There are three main approaches for determining lineage based on MIRU-VNTR data - one based on a direct comparison to the strains in a curated database, and two others, on machine learning algorithms trained on a large collection of labeled data. All existing methods have limitations. The direct approach imposes an arbitrary threshold on how much a database strain can differ from a given one to be informative. On the other hand, the machine learning-based approaches require a substantial amount of labeled data. Notably, all three methods exhibit suboptimal classification accuracy without additional data. We explore several computational approaches to address these limitations. First, we show that eliminating the arbitrary threshold improves the performance of the direct approach. Second, we introduce RuleTB, an alternative direct method that proposes a concise set of rules for determining lineages. Lastly, we propose StackTB, a machine learning approach that requires only a fraction of the training data to outperform the accuracy of both existing machine learning methods. Our approaches demonstrate superior performance on a training dataset collected in New York City over 10 years, and the improvement in performance translates to a held-out testing set. We conclude that our methods provide opportunities for improving the determination of pathogenic lineages based on MIRU-VNTR data., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

Setting: Tuberculosis (TB) has decreased substantially in New York City (NYC), but progress has slowed in recent years. Continued declines will require novel approaches tailored to foreign-born populations., Objective: To describe TB epidemiology among the Mexico-born population of NYC to inform interventions in this community., Design: The study included NYC patients with TB disease identified from 2001 to 2014. Incidence rates were compared by country of birth groupings. Demographic and patient characteristics were analyzed for all Mexico-born TB patients. Patients were compared by Mycobacterium bovis vs. non-M. bovis TB strain. Culture-confirmed patients were compared by genotype clustering status., Results: From 2001 to 2014, 621 Mexico-born TB patients were identified in NYC. TB rates were significantly higher among Mexico-born vs. US-born persons every year. Mexico-born patients had lived in the United States for a median 7 years at diagnosis. The geographic distribution of Mexico-born TB patients was similar to that of the total Mexico-born population. Overall, 71% of patients reported previous employment; 52% of non-M. bovis patients were clustered based on genotyping results., Conclusions: Our results provide a foundation to inform future interventions in the Mexico-born population. Additional work is needed to explore possible local TB transmission and health care-seeking practices.

Background: Patients with prior positive tuberculin skin test (TST) results may benefit from prophylaxis after repeat exposure to infectious tuberculosis (TB)., Objective: To evaluate factors associated with active TB disease among persons with prior positive TST results named as contacts of persons with infectious TB., Design: Population-based retrospective cohort study., Participants: A total of 2,933 contacts with prior positive TST results recently exposed to infectious TB identified in New York City's TB registry during the period from January 1, 1997 through December 31, 2003., Main Measurements: Contacts developing active TB disease ≤ 4 years after exposure were identified and compared with those who did not, using Poisson regression analysis. Genotyping was performed on selected Mycobacterium tuberculosis-positive isolates., Key Results: Among contacts with prior positive TST results, 39 (1.3 %) developed active TB disease ≤ 4 years after exposure (≤ 2 years: 34). Risk factors for contacts that were independently associated with TB were age < 5 years (adjusted prevalence ratio [aPR] = 19.48; 95 % confidence interval [CI] = 7.15-53.09), household exposure (aPR = 2.60;CI = 1.30-5.21), exposure to infectious patients (i.e., cavities on chest radiograph, acid-fast bacilli on sputum smear; aPR = 1.9 3; CI = 1.01-3.71), and exposure to a U.S.-born index patient (aPR = 4.04; CI = 1.95-8.38). Receipt of more than 1 month of treatment for latent TB infection following the current contact investigation was found to be protective (aPR = 0.27; CI =  .08-0.93). Genotype results were concordant with the index patients among 14 of 15 contacts who developed active TB disease and had genotyping results available., Conclusions: Concordant genotype results and a high proportion of contacts developing active TB disease within 2 years of exposure indicate that those with prior positive TST results likely developed active TB disease from recent rather than remote infection. Healthcare providers should consider prophylaxis for contacts with prior TB infection, especially young children and close contacts of TB patients (e.g., those with household exposure).

Genotyping results and epidemiologic investigation were used to confirm tuberculosis transmission from a cadaver to an embalmer. This investigation highlights the utility of genotyping in identifying unsuspected epidemiologic links and unusual transmission settings. In addition, the investigation provides additional evidence for the occupational risk of tuberculosis among funeral service workers and indicates a need for education about tuberculosis risk and the importance of adhering to appropriate infection control measures among funeral service workers., (Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.)

We have examined the relations among three common treatment outcome measures in irritable bowel syndrome (IBS): end of treatment global ratings by a physician, end of treatment patient global ratings, and measures derived from a daily symptom diary completed by the patient. Eighty-four IBS patients (53 female, 31 male) participated in a randomized controlled evaluation of three psychological treatment conditions for IBS. Treatment outcome measures from this trial (Blanchard et al., 1992) were used in the present methodological study. Physician global ratings were significantly correlated with patient global ratings (r = .45, p < .01). Both of these global ratings also correlated significantly with a composite score from patient diary ratings. Multiple regression analyses revealed that reductions in bloating and constipation account for 18% of the variance in patient global ratings. Global ratings at end of treatment by either patient or physician were only partially related to symptom relief as measured by a daily diary.