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Pulmonary fat embolism (PFE) is a recognised complication of long bone fractures. The majority of cases represent microscopic embolism and are not detectable at CT pulmonary arteriography (CTPA). CT can be used to detect macroscopic fat based on Hounsfield attenuation. This case describes a case of macroscopic fat embolism to the pulmonary arteries which was confidently diagnosed at CTPA. Distinction from thromboembolism is important as treatment is supportive and may avoid risks of anticoagulation.

Voriconazole is a broad-spectrum triazole antifungal used to treat invasive fungal infections. It is commonly used prophylactically in immunocompromized patient cohorts, including transplant recipients. Diffuse periostitis is a very rare complication of chronic voriconazole use. It is associated with diffuse bone pain, elevated serum alkaline phosphatase and fluorine levels. Characteristic imaging findings include periosteal thickening with a dense, nodular, irregular and often bilateral pattern. We describe the case of a 71-year-old female who presented with multifocal bone pain six years following double lung transplantation. Her post transplantation course had been complicated by a life threatening episode of sepsis secondary to Scedosporium apiospermum, a rare invasive fungal infection following which lifelong prophylaxis with oral Voriconazole was commenced. We discuss the characteristic clinical and imaging manifestations of this rare condition.

Rigid inflatable gastrostomy (RIG) tubes are widely used in contemporary clinical practice for a variety of indications. Insertion of RIG tubes is associated with a high technical success rate and low incidence of mortality. In this case report, a procedural pitfall associated with intraperitoneal-extragastric malposition is described. Rigorous assessment of abdominal radiographs, as well as awareness of the expected appearance of the RIG tube and gastropexy T-fasteners, allows the abdominal radiologist to detect early RIG position in the early postprocedural period. Abdominal radiography is a widely available and inexpensive technique. The high spatial resolution it provides makes it a valuable tool in determining hardware position.

Introduction: In high tuberculosis (TB) burden countries, the private sector manages a large proportion of initial visits by presumptive patients with TB. In Indonesia, the second largest contributor of TB cases globally, private practitioners (PPs) often do not adhere to national TB guidelines. A district public-private mix programme to mitigate this issue was started in 2019, yet engagement remains low. This study examines what affects the decisions of Indonesian PPs regarding TB management., Methods: We performed semistructured in-depth interviews and focus group discussions (FGDs) with 24 PPs and 6 relevant stakeholders. Data collection and analysis were based on Flottorp's comprehensive and generic checklist on determinants of healthcare professional practice, including seven domains: guideline factors; individual professional barriers; patient factors; professional interactions; incentives and resources; organisational changes capacity and social, legal and political factors. The interviews and FGDs were recorded and transcribed verbatim. Coding and analysis were conducted by using NVivo software., Results: Barriers that influenced PPs adherence to following the national TB guideline were found in all seven domains, including incoherence between national and international TB management guidelines, the complex referral and financing system, limited access to appropriate diagnostics tools and drugs, and patient preferences. This was further exacerbated by perceived lack of trust between PPs and local governmental stakeholders. In this study, in addition to seventh Flottorp's domain, we also found the complex nature of TB disease, which also complicates the decision-making process of PPs in TB management., Conclusion: PPs face several challenges in complying with TB guidelines to enable optimal clinical decision-making., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Infectious disease is the result of interactions between host and pathogen and can depend on genetic variations in both. We conduct a genome-to-genome study of paired human and Mycobacterium tuberculosis genomes from a cohort of 1556 tuberculosis patients in Lima, Peru. We identify an association between a human intronic variant (rs3130660, OR = 10.06, 95%CI: 4.87 - 20.77, P = 7.92 × 10 -8 ) in the FLOT1 gene and a subclavaluee of Mtb Lineage 2. In a human macrophage infection model, we observe hosts with the rs3130660-A allele exhibited stronger interferon gene signatures. The interacting strains have altered redox states due to a thioredoxin reductase mutation. We investigate this association in a 2020 cohort of 699 patients recruited during the COVID-19 pandemic. While the prevalence of the interacting strain almost doubled between 2010 and 2020, its infection is not associated with rs3130660 in this recent cohort. These findings suggest a complex interplay among host, pathogen, and environmental factors in tuberculosis dynamics., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Objectives: Approximately 40% of tuberculosis (TB) cases remain undiagnosed globally. Lower lung field TB (LLF TB) presents atypically and is often misidentified as other lung diseases, leading to diagnostic delays in resource-limited settings. It may contribute to increased TB transmission and mortality. We aimed to identify microbiological determinants of LLF TB and evaluate treatment responses to optimize care., Methods: We conducted an observational cohort study in Lima, Peru, enrolling adults with microbiologically confirmed pulmonary TB (PTB) diagnosed by GeneXpert MTB/RIF assay or sputum culture. Mycobacterium tuberculosis (MTB) lineage was determined using whole-genome sequencing. Due to the delayed chest radiograph changes in LLF TB compared to non-LLF TB, we measured changes in the St. George's Respiratory Questionnaire (SGRQ) score at 2-month treatment mark and evaluated World Health Organization-specified final treatment outcomes. We used logistic regression to evaluate the associations between LLF TB and microbiological determinants and treatment outcomes. We used linear regression to assess whether the change in SGRQ scores over the first 2 months of treatment varied by LLF TB status., Results: Among 1316 PTB patients, 84 (6%) had LLF TB. Compared to non-LLF TB patients, LLF TB patients were more likely to be smear-negative (adjusted odds ratio [aOR] [95% CI] = 2.04 [1.28-3.23], P = 0.002) and to be infected with Lineage 2 (aOR [95% CI] = 1.95 [95% CI: 1.07-3.41; P = 0.024]). People with LLF TB had less improvement in SGRQ scores after 2 months of treatment (adjusted score difference [95% CI] = -6.29 [-10.99 to -1.59], P = 0.009), while they experienced better final outcomes compared to non-LLF TB patients, though this difference did not reach statistical significance (aOR = 0.43 [95% CI: 0.13-1.05], P = 0.103)., Conclusion: Patients with LLF TB are more likely than those with upper lung lesions to be sputum-negative on conventional tests, to be infected with Lineage 2, and to show less clinical improvement after treatment., Competing Interests: Declarations of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this article., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Post-tuberculosis (TB) sequelae present a significant challenge in the management of TB survivors, often leading to persistent health issues even after successful treatment. Identifying risk factors associated with post-TB sequelae is important for improving outcomes and quality of life of TB survivors. This systematic review and meta-analysis aims to identify risk factors associated with long-term physical sequelae among TB survivors., Methods: We systematically searched Medline, Embase, PROQUEST, and Scopus for studies on long-term physical sequelae among TB survivors up to December 12, 2023. The primary outcome of interest was to quantify risk factors of long-term physical sequelae (i.e., respiratory, hepatic, hearing, neurological, visual, renal, and musculoskeletal sequelae). We included all forms of TB patients who experienced long-term physical sequelae. We used narrative synthesis for risk factors reported once and random-effect meta-analysis for primary outcomes with two or more studies. Findings were presented with odds ratios (OR) and 95% confidence intervals (CI). Publication bias was assessed using funnel plots and Egger regression, and heterogeneity was examined with a Galbraith radial plot. The protocol was registered on Prospero (CRD42021250909)., Findings: A total of 73 articles from 28 countries representing 31,553 TB-treated patients were included in the narrative synthesis, with 64 of these studies included in the meta-analysis. Risk factors associated with post-TB lung sequelae include older age (OR = 1.62, 95% CI: 1.07-2.47), previous TB treatment history (OR = 3.43, 95% CI: 2.37-4.97), smoking (OR = 1.41, 95% CI: 1.09-1.83), alcohol consumption (OR = 1.84, 95% CI: 1.04-3.25), smear-positive pulmonary TB diagnosis (OR = 3.11, 95% CI: 1.77-6.44), and the presence of radiographic evidence of pulmonary lesions at the commencement of treatment (OR = 2.04, 95% CI: 1.07-3.87). Risk factors associated with post-TB liver injury included pre-existing hepatitis (OR = 2.41, 95% CI: 1.16-6.08), previous TB treatment (OR = 2.64, 95% CI: 1.22-6.67), hypo-albuminemia (OR = 2.10, 95% CI: 1.53-2.88), HIV co-infection (OR = 2.72, 95% CI: 1.66-4.46), and CD4 count <200 mm 3 in HIV-infected individuals (OR = 2.03, 95%CI: 1.26-3.27). Risk factors associated with post-TB hearing loss include baseline hearing problems (OR = 1.72, 95% CI: 1.30-2.26), and HIV co-infection (OR = 3.02, 95% CI: 1.96-4.64)., Interpretation: This systematic review and meta-analysis found that long-term physical post-TB sequelae including respiratory, hepatic, and hearing impairment were associated with a range of socio-demographic, behavioral, and clinical factors. Identification of these risk factors will help to identify patients who will benefit from interventions to reduce the burden of suffering from post-TB treatment., Funding: Healy Medical Research Raine Foundation, the Australian National Health and Medical Research Council, and Curtin University Higher Degree Research Scholarship fund the study., Competing Interests: All authors declare that they have no conflict of interest., (© 2024 The Authors.)

Ferroptosis is an iron-dependent cell death mechanism that may be important to prevent tumor formation and useful as a target for new cancer therapies. Transcriptional networks play a crucial role in shaping ferroptosis sensitivity by regulating the expression of transporters, metabolic enzymes, and other proteins. The Cap'n'collar (CNC) protein NFE2 like bZIP transcription factor 2 (NFE2L2, also known as NRF2) is a key regulator of ferroptosis in many cells and contexts. Emerging evidence indicates that the related CNC family members, BTB domain and CNC homolog 1 (BACH1) and NFE2 like bZIP transcription factor 1 (NFE2L1), also have roles in ferroptosis regulation. Here, we comprehensively review the role of CNC transcription factors in governing cellular sensitivity to ferroptosis. We describe how CNC family members regulate ferroptosis sensitivity through modulation of iron, lipid, and redox metabolism. We also use examples of ferroptosis regulation by CNC proteins to illustrate the flexible and highly context-dependent nature of the ferroptosis mechanism in different cells and conditions., Competing Interests: Conflict of interest S. J. D. is an inventor on patents related to ferroptosis. The other author declares that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Rationale: The persistent burden of tuberculosis (TB) disease emphasizes the need to identify individuals with TB for treatment and those at a high risk of incident TB for prevention. Targeting interventions toward those at high risk of developing and transmitting TB is a public health priority. Objectives: We aimed to identify characteristics of individuals involved in TB transmission in a community setting, which may guide the prioritization of targeted interventions. Methods: We collected clinical and sociodemographic data from a cohort of patients with TB in Lima, Peru. We used whole-genome sequencing data to assess the genetic distance between all possible pairs of patients; we considered pairs to be the result of a direct transmission event if they differed by three or fewer SNPs, and we assumed that the first diagnosed patient in a pair was the transmitter and the second was the recipient. We used logistic regression to examine the association between host factors and the likelihood of direct TB transmission. Measurements and Main Results: Analyzing data from 2,518 index patients with TB, we identified 1,447 direct transmission pairs. Regardless of recipient attributes, individuals less than 34 years old, males, and those with a history of incarceration had a higher likelihood of being transmitters in direct transmission pairs. Direct transmission was more likely when both patients were drinkers or smokers. Conclusions: This study identifies men, young adults, former prisoners, alcohol consumers, and smokers as priority groups for targeted interventions. Innovative strategies are needed to extend TB screening to social groups such as young adults and prisoners with limited access to routine preventive care.

The World Health Organization's end TB strategy promotes the use of symptom and chest radiograph screening for tuberculosis (TB) disease. However, asymptomatic early states of TB beyond latent TB infection and active disease can go unrecognized using current screening criteria. We conducted a longitudinal cohort study enrolling household contacts initially free of TB disease and followed them for the occurrence of incident TB over 1 year. Among 1,747 screened contacts, 27 (52%) of the 52 persons in whom TB subsequently developed during follow-up had a baseline abnormal radiograph. Of contacts without TB symptoms, persons with an abnormal radiograph were at higher risk for subsequent TB than persons with an unremarkable radiograph (adjusted hazard ratio 15.62 [95% CI 7.74-31.54]). In young adults, we found a strong linear relationship between radiograph severity and time to TB diagnosis. Our findings suggest chest radiograph screening can extend to detecting early TB states, thereby enabling timely intervention.

Objective: Mathematical models are vital tools to understand transmission dynamics and assess the impact of interventions to mitigate COVID-19. However, historically, their use in Africa has been limited. In this scoping review, we assess how mathematical models were used to study COVID-19 vaccination to potentially inform pandemic planning and response in Africa., Methods: We searched six electronic databases: MEDLINE, Embase, Web of Science, Global Health, MathSciNet and Africa-Wide NiPAD, using keywords to identify articles focused on the use of mathematical modelling studies of COVID-19 vaccination in Africa that were published as of October 2022. We extracted the details on the country, author affiliation, characteristics of models, policy intent and heterogeneity factors. We assessed quality using 21-point scale criteria on model characteristics and content of the studies., Results: The literature search yielded 462 articles, of which 32 were included based on the eligibility criteria. Nineteen (59%) studies had a first author affiliated with an African country. Of the 32 included studies, 30 (94%) were compartmental models. By country, most studies were about or included South Africa (n = 12, 37%), followed by Morocco (n = 6, 19%) and Ethiopia (n = 5, 16%). Most studies (n = 19, 59%) assessed the impact of increasing vaccination coverage on COVID-19 burden. Half (n = 16, 50%) had policy intent: prioritising or selecting interventions, pandemic planning and response, vaccine distribution and optimisation strategies and understanding transmission dynamics of COVID-19. Fourteen studies (44%) were of medium quality and eight (25%) were of high quality., Conclusions: While decision-makers could draw vital insights from the evidence generated from mathematical modelling to inform policy, we found that there was limited use of such models exploring vaccination impacts for COVID-19 in Africa. The disparity can be addressed by scaling up mathematical modelling training, increasing collaborative opportunities between modellers and policymakers, and increasing access to funding., (© 2024 The Authors Tropical Medicine & International Health Published by John Wiley & Sons Ltd.)

We explored the utility of brief Mycobacterium tuberculosis whole-genome sequencing (WGS) "snapshots" at a sentinel site within Lima, Peru, for evaluating local transmission dynamics over time. Within a 17-km2 area, 15 of 70 (21%) isolates with WGS collected during 2011-2012 and 22 of 81 (27%) collected during 2020-2021 were clustered (P = .414), and additional isolates clustered with those from outside the area. Isolates from the later period were disproportionately related to large historic clusters in Lima from the earlier period. WGS snapshots at a sentinel site may not be useful for monitoring transmission, but monitoring the persistence of large transmission clusters might be., Competing Interests: Potential conflicts of interest. The authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Mathematical modeling of infectious diseases is an important decision-making tool for outbreak control. However, in Africa, limited expertise reduces the use and impact of these tools on policy. Therefore, there is a need to build capacity in Africa for the use of mathematical modeling to inform policy. Here we describe our experience implementing a mathematical modeling training program for public health professionals in East Africa., Methods: We used a deliverable-driven and learning-by-doing model to introduce trainees to the mathematical modeling of infectious diseases. The training comprised two two-week in-person sessions and a practicum where trainees received intensive mentorship. Trainees evaluated the content and structure of the course at the end of each week, and this feedback informed the strategy for subsequent weeks., Findings: Out of 875 applications from 38 countries, we selected ten trainees from three countries - Rwanda (6), Kenya (2), and Uganda (2) - with guidance from an advisory committee. Nine trainees were based at government institutions and one at an academic organization. Participants gained skills in developing models to answer questions of interest and critically appraising modeling studies. At the end of the training, trainees prepared policy briefs summarizing their modeling study findings. These were presented at a dissemination event to policymakers, researchers, and program managers. All trainees indicated they would recommend the course to colleagues and rated the quality of the training with a median score of 9/10., Conclusions: Mathematical modeling training programs for public health professionals in Africa can be an effective tool for research capacity building and policy support to mitigate infectious disease burden and forecast resources. Overall, the course was successful, owing to a combination of factors, including institutional support, trainees' commitment, intensive mentorship, a diverse trainee pool, and regular evaluations., Competing Interests: The authors have no competing interests to declare., (Copyright: © 2024 The Author(s).)

Background: Tuberculosis (TB) remains a global public health challenge, causing substantial mortality and morbidity. While TB treatment has made significant progress, it often leaves survivors with post-TB sequelae, resulting in long-term health issues. Current healthcare systems and guidelines lack comprehensive strategies to address post-TB sequelae, primarily due to insufficient evidence. This systematic review and meta-analysis aimed to identify effective interventions for preventing post-TB sequelae., Methods: A systematic search was conducted across four databases including PubMed, SCOPUS, Web of Science, and Cochrane Central Register of Controlled Trials from inception to September 22, 2023. Eligible studies reported interventions designed to prevent post-TB sequelae were included. A random effect meta-analysis was conducted where applicable, and heterogeneity between studies was evaluated visually using forest plots and quantitatively using an index of heterogeneity (I 2 ). This study is registered with PROSPERO (CRD42023464392)., Findings: From the 2525 unique records screened, 25 studies involving 10,592 participants were included. Different interventions were evaluated for different outcomes. However, only a few interventions were effective in preventing post-TB sequelae. Rehabilitation programs significantly improved lung function (Hedges's g = 0.21; 95% confidence interval (CI): 0.03, 0.39) and prevented neurological sequelae (relative risk (RR) = 0.10; 95% CI: 0.02, 0.42). Comprehensive interventions and cognitive-behavioural therapy significantly reduced the risk of mental health disorders among TB survivors (Hedges's g = -1.89; 95% CI: -3.77, -0.01). In contrast, interventions targeting post-TB liver sequelae, such as vitamin A and vitamin D supplementation and hepatoprotective agents, did not show significant reductions in sequelae (RR = 0.90; 95% CI: 0.52, 1.57). Moreover, adjunctive therapies did not show a significant effect in preventing post-TB neurological sequelae (RR = 0.62, 95% CI: 0.31, 1.24)., Interpretation: Rehabilitation programs prevented post-TB lung, neurologic and mental health sequelae, while adjuvant therapies and other interventions require further investigation., Funding: Healy Medical Research Raine Foundation, Curtin School of Population Health and the Australian National Health and Medical Research Council., Competing Interests: The authors have no conflicts of interest to declare., (© 2024 The Author(s).)

The COVID-19 pandemic brought about significant life disruptions among healthcare workers (HCWs), including changes in weight, eating habits, and physical activity. This qualitative study sought to evaluate the initial and longitudinal effects of health habits among HCWs throughout the pandemic. Data were collected through Qualtrics surveys at three points over a 2-year period with questions asking participants ( n = 234) to describe whether they experienced changes in weight, eating behaviors, and physical activity and why they believe these changes occurred. The open-ended responses were analyzed following the summative content analysis approach. Four key themes emerged: (1) problematic eating patterns and habits, (2) disruptions in physical activity, (3) alterations in work environment and schedule, and (4) declines in mental health. Respondent reflections highlight the immediate and long-term pandemic-related effects on weight status for some, attributed to alterations in routines and health habits. Other HCWs reported a "reset" or indicated their habits may have been initially disrupted but normalized or improved over the 2-year time span. Findings underscore the need for strategies that support the physical and mental health of healthcare workers.

Mammalian cells can die by apoptosis or by one of several non-apoptotic mechanisms, such as ferroptosis. Here, we present a protocol to distinguish ferroptosis from other cell death mechanisms in cultured cells. We describe steps for seeding cells, administering mechanism-specific cell death inducers and inhibitors, and measuring cell death and viability. We then detail the use of molecular markers to verify mechanisms of cell death. This protocol can be used to identify and distinguish ferroptosis in 2D and 3D cultures. For complete details on the use and execution of this protocol, please refer to Ko, et al. (2019), 1 Magtanong, et al. (2022), 2 and Armenta, et al. (2022). 3 ., Competing Interests: Declaration of interests S.J.D. is a co-founder of Prothegen Inc and a member of the scientific advisory board for Hillstream BioPharma. S.J.D. holds patents related to ferroptosis., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background: Although previous studies have shown that vitamin A deficiency is associated with incident tuberculosis (TB) disease, the direction of the association has not been established. We investigated the impact of vitamin A deficiency on TB disease progression., Methods: We conducted a longitudinal cohort study nested within a randomized clinical trial among HIV-infected patients in Haiti. We compared serial vitamin A levels in individuals who developed TB disease to controls matched on age, gender, follow-up time, and time to antiretroviral therapy initiation. We also evaluated histopathology, bacterial load, and immune outcomes in TB infection in a guinea pig model of dietary vitamin A deficiency., Results: Among 773 participants, 96 developed incident TB during follow-up, 62.5% (60) of whom had stored serum samples obtained 90-365 days before TB diagnosis. In age- and sex- adjusted and multivariate analyses, respectively, incident TB cases were 3.99 times (95% confidence interval [CI], 2.41 to 6.60) and 3.59 times (95% CI, 2.05 to 6.29) more likely to have been vitamin A deficient than matched controls. Vitamin A-deficient guinea pigs manifested more extensive pulmonary pathology, atypical granuloma morphology, and increased bacterial growth after experimental TB infection. Reintroduction of dietary vitamin A to deficient guinea pigs after established TB disease successfully abrogated severe disease manifestations and altered cellular immune profiles., Conclusions: Human and animal studies support the role of baseline vitamin A deficiency as a determinant of future TB disease progression., Competing Interests: Potential conflicts of interest. The authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Spatially targeted interventions may be effective alternatives to individual or population-based prevention strategies against tuberculosis (TB). However, their efficacy may depend on the mechanisms that lead to geographically constrained hotspots. Local TB incidence may reflect high levels of local transmission; conversely, they may point to frequent travel of community members to high-risk areas. We used whole-genome sequencing to explore patterns of TB incidence and transmission in Lima, Peru. Between 2009 and 2012, we recruited incident pulmonary TB patients and their household contacts, whom we followed for the occurrence of TB disease. We used whole-genome sequences of 2,712 Mycobacterial tuberculosis isolates from 2,440 patients to estimate pariwise genomic distances and compared these to the spatial distance between patients' residences. Genomic distances increased rapidly as spatial distances increased and remained high beyond 2 km of separation. Next, we divided the study catchment area into 1 × 1 km grid-cell surface units and used household spatial coordinates to locate each TB patient to a specific cell. We estimated cell-specific transmission by calculating the proportion of patients in each cell with a pairwise genomic distance of 10 or fewer single-nucleotide polymorphisms. We found that cell-specific TB incidence and local transmission varied widely but that cell-specific TB incidence did not correlate closely with our estimates of local transmission (Cohen's k = 0.27). These findings indicate that an understanding of the spatial heterogeneity in the relative proportion of TB due to local transmission may help guide the implementation of spatially targeted interventions.

We investigated whether ancestry-specific genetic factors affect tuberculosis (TB) progression risk in a cohort of admixed Peruvians. We genotyped 2,105 patients with TB and 1,320 household contacts (HHCs) who were infected with Mycobacterium tuberculosis ( M. tb ) but did not develop TB and inferred each individual's proportion of native Peruvian genetic ancestry. Our HHC study design and our data on potential confounders allowed us to demonstrate increased risk independent of socioeconomic factors. A 10% increase in individual-level native Peruvian genetic ancestry proportion corresponded to a 25% increased TB progression risk. This corresponds to a 3-fold increased risk for individuals in the highest decile of native Peruvian genetic ancestry versus the lowest decile, making native Peruvian genetic ancestry comparable in effect to clinical factors such as diabetes. Our results suggest that genetic ancestry is a major contributor to TB progression risk and highlight the value of including diverse populations in host genetic studies., Competing Interests: DECLARATION OF INTERESTS The authors have no conflict of interests.

Importance: The management of multidrug-resistant tuberculosis (MDR-TB) during pregnancy is challenging, yet no systematic synthesis of evidence has accurately measured treatment outcomes., Objective: To systematically synthesize treatment outcomes and adverse events among pregnant patients with MDR-TB., Data Sources: PubMed, Scopus, Web of Science, and ProQuest were searched from the inception of each database through August 31, 2021., Study Selection: Studies containing cohorts of pregnant patients with a defined treatment outcome were eligible., Data Extraction and Synthesis: Independent reviewers screened studies and assessed the risk of bias. The study followed the Preferring Reporting Items for Systematic Review and Meta-analyses reporting guideline. Meta-analysis was performed using random-effects models. The sources of heterogeneity were explored through metaregression., Main Outcomes and Measures: The primary outcome was the proportion of patients with each treatment outcome (including treatment success, death, loss to follow-up, and treatment failure), and the secondary outcomes included the proportion of patients experiencing adverse events during pregnancy., Results: In this systematic review and meta-analysis, 10 studies containing 275 pregnant patients with available data on treatment outcomes were included. The pooled estimate was 72.5% (95% CI, 63.3%-81.0%) for treatment success, 6.8% (95% CI, 2.6%-12.4%) for death, 18.4% (95% CI, 13.1%-24.2%) for loss to follow-up, and 0.6% (95% CI, 0.0%-2.9%) for treatment failure. Treatment success was significantly higher in studies in which the proportion of patients taking linezolid was greater than the median (20.1%) compared with studies in which this proportion was lower than the median (odds ratio, 1.22; 95% CI, 1.05-1.42). More than half of the pregnant patients (54.7%; 95% CI, 43.5%-65.4%) experienced at least 1 type of adverse event, most commonly liver function impairment (30.4%; 95% CI, 17.7%-45.7%), kidney function impairment (14.9%; 95% CI, 6.2%-28.3%), hypokalemia (11.9%; 95% CI, 3.9%-25.6%), hearing loss (11.8%; 95% CI, 5.5%-21.3%), gastrointestinal disorders (11.8%; 95% CI, 5.2%-21.8%), psychiatric disorders (9.1%; 95% CI, 2.5%-21.6%), or anemia (8.9%; 95% CI, 3.6%-17.4%). The pooled proportion of favorable pregnancy outcomes was 73.2% (95% CI, 49.4%-92.1%). The most common types of adverse pregnancy outcomes were preterm birth (9.5%; 95% CI, 0.0%-29.0%), pregnancy loss (6.0%; 95% CI, 1.3%-12.9%), low birth weight (3.9%; 95% CI, 0.0%-18.7%), and stillbirth (1.9%; 95% CI, 0.1%-5.1%). Most of the studies had low-quality (3 studies) or medium-quality (4 studies) scores., Conclusions and Relevance: In this systematic review and meta-analysis, high treatment success and favorable pregnancy outcomes were reported among pregnant patients with MDR-TB. Further research is needed to design shorter, more effective, and safer treatment regimens for pregnant patients with MDR-TB.

Non-coding genetic variants may cause disease by modulating gene expression. However, identifying these expression quantitative trait loci (eQTLs) is complicated by differences in gene regulation across fluid functional cell states within cell types. These states-for example, neurotransmitter-driven programs in astrocytes or perivascular fibroblast differentiation-are obscured in eQTL studies that aggregate cells 1,2 . Here we modelled eQTLs at single-cell resolution in one complex cell type: memory T cells. Using more than 500,000 unstimulated memory T cells from 259 Peruvian individuals, we show that around one-third of 6,511 cis-eQTLs had effects that were mediated by continuous multimodally defined cell states, such as cytotoxicity and regulatory capacity. In some loci, independent eQTL variants had opposing cell-state relationships. Autoimmune variants were enriched in cell-state-dependent eQTLs, including risk variants for rheumatoid arthritis near ORMDL3 and CTLA4; this indicates that cell-state context is crucial to understanding potential eQTL pathogenicity. Moreover, continuous cell states explained more variation in eQTLs than did conventional discrete categories, such as CD4 + versus CD8 + , suggesting that modelling eQTLs and cell states at single-cell resolution can expand insight into gene regulation in functionally heterogeneous cell types., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant TCRα-chain that uses T cell receptor α-variable 1-2 (TRAV1-2) joined to TRAJ33/20/12 and recognizes metabolites from bacterial riboflavin synthesis bound to the Ag-presenting molecule MHC class I related (MR1). Our attempts to identify alternative MR1-presented Ags led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered Ag specificity likely alters affinity for the most potent known Ag, 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU), we performed bulk TCRα- and TCRβ-chain sequencing and single-cell-based paired TCR sequencing on T cells that bound the MR1-5-OP-RU tetramer with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramer low cells. Although we initially interpreted these as diverse MR1-restricted TCRs, single-cell TCR sequencing revealed that cells expressing atypical TCRα-chains also coexpressed an invariant MAIT TCRα-chain. Transfection of each non-TRAV1-2 TCRα-chain with the TCRβ-chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRα-chain expression in human T cells and competition for the endogenous β-chain explains the existence of some MR1-5-OP-RU tetramer low T cells. The discovery of simultaneous expression of canonical and noncanonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of Ag specificity., (Copyright © 2022 by The American Association of Immunologists, Inc.)

As single-cell datasets grow in sample size, there is a critical need to characterize cell states that vary across samples and associate with sample attributes, such as clinical phenotypes. Current statistical approaches typically map cells to clusters and then assess differences in cluster abundance. Here we present co-varying neighborhood analysis (CNA), an unbiased method to identify associated cell populations with greater flexibility than cluster-based approaches. CNA characterizes dominant axes of variation across samples by identifying groups of small regions in transcriptional space-termed neighborhoods-that co-vary in abundance across samples, suggesting shared function or regulation. CNA performs statistical testing for associations between any sample-level attribute and the abundances of these co-varying neighborhood groups. Simulations show that CNA enables more sensitive and accurate identification of disease-associated cell states than a cluster-based approach. When applied to published datasets, CNA captures a Notch activation signature in rheumatoid arthritis, identifies monocyte populations expanded in sepsis and identifies a novel T cell population associated with progression to active tuberculosis., (© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Background: There is a dearth of research to understand which children, among those who are exposed at home to tuberculosis (TB), are at the highest risk of TB disease, to tailor care. We sought to identify predictors of TB progression in children., Methods: We conducted a prospective cohort study of children living with adults with pulmonary TB in Lima, Peru (2009-2012). We applied classification and regression tree analysis to examine potential predictors of incident TB disease during 12 months in 3 age groups (0-4, 5-9, and 10-14 years). We calculated the relative risk (RR) for top predictors in each age group., Results: Among 4545 children 0-14 years old, 156 (3.4%) were diagnosed with TB within 1 year of household exposure to TB (3.4%, 2.3%, and 4.7% in children 0-4, 5-9, and 10-14 years old, respectively). The most important predictor of TB was having a positive tuberculin skin test (TST) result, with RRs of 6.6 (95% CI, 4.0-10.7), 6.6 (95% CI, 3.2-13.6), and 5.2 (95% CI, 3.0-9.0) in the age groups 0-4, 5-9, and 10-14 years, respectively. In young children with a positive TST, not using isoniazid preventive treatment further increased risk of disease (RR, 12.2 [95% CI, 3.8-39.2])., Conclusions: We present a tool that identifies child household contacts at high risk of TB disease progression based on data collected during contact tracing. In addition to the use of TB preventive therapy for all children exposed at home to TB, those children at highest risk of progressing to TB disease may benefit from more frequent follow-up., (© The Author(s) 2021. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Background: While previous studies have shown that cigarette smoking increases the infectiousness of tuberculosis patients, the impact of smoking cessation on tuberculosis transmissibility has not been evaluated., Methods: Between 2009 and 2012, we enrolled 4500 tuberculosis patients and followed 14 044 household contacts in Lima, Peru. Tuberculosis patients were classified into 4 categories: never smoked, quit in the distant past (stopped smoking >2 months prior to time of diagnosis), recently quit (stopped smoking ≤2 months prior to time of diagnosis), and active smokers. We used a modified Poisson generalized estimating equation to assess the risk of tuberculosis infection of child contacts at enrollment and by 6 months of follow-up., Results: In total, 1371 (76.8%) child contacts were exposed to patients who had never smoked, 211 (11.8%) were exposed to distant quitters, 155 (8.7%) were exposed to recent quitters, and 49 (2.7%) were exposed to active smokers. Compared with child contacts of index patients who had never smoked, child contacts of recent quitters had a similar risk of tuberculosis infection at enrollment (adjusted risk ratio, 95% confidence intervals [0.81, 0.50-1.32]) and by six months of follow-up (0.76, 0.51-1.13); and by 6 months of follow-up (aRR, 0.76; 95% CI, .51-1.13); child contacts of recent quitters had a significantly reduced risk of tuberculosis infection compared with contacts of active smokers (enrollment 0.45, 0.24-0.87; 6-month follow-up 0.48, 0.29-0.79)., Conclusions: Our results show that the adverse effects of smoking on the transmissibility of tuberculosis are significantly reduced shortly after quitting smoking, reinforcing the importance of smoking cessation interventions in tuberculosis control., (© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)

An estimated 15-20% of patients who are treated for pulmonary tuberculosis (TB) are culture-negative at the time of diagnosis. Recent work has focused on the existence of differentially detectable Mycobacterium tuberculosis ( Mtb ) bacilli that do not grow under routine solid culture conditions without the addition of supplementary stimuli. We identified a cohort of TB patients in Lima, Peru, in whom acid-fast bacilli could be detected by sputum smear microscopy, but from whom Mtb could not be grown in standard solid culture media. When we attempted to re-grow Mtb from the frozen sputum samples of these patients, we found that 10 out of 15 could be grown in a glycerol-poor/lipid-rich medium. These fell into the following two groups: a subset that could be regrown in glycerol after "lipid-resuscitation", and a group that displayed a heritable glycerol-sensitive phenotype that were unable to grow in the presence of this carbon source. Notably, all of the glycerol-sensitive strains were found to be multidrug resistant. Although whole-genome sequencing of the lipid-resuscitated strains identified 20 unique mutations compared to closely related strains, no single genetic lesion could be associated with this phenotype. In summary, we found that lipid-based media effectively fostered the growth of Mtb from a series of sputum smear-positive samples that were not culturable in glycerol-based Lowenstein-Jensen or 7H9 media, which is consistent with Mtb 's known preference for non-glycolytic sources during infection. Analysis of the recovered strains demonstrated that both genetic and non-genetic mechanisms contribute to the observed differential capturability, and suggested that this phenotype may be associated with drug resistance.

There are many outstanding questions about how to control the global COVID-19 pandemic. The information void has been especially stark in the World Health Organization Africa Region, which has low per capita reported cases, low testing rates, low access to therapeutic drugs, and has the longest wait for vaccines. As with all disease, the central challenge in responding to COVID-19 is that it requires integrating complex health systems that incorporate prevention, testing, front line health care, and reliable data to inform policies and their implementation within a relevant timeframe. It requires that the population can rely on the health system, and decision-makers can rely on the data. To understand the process and challenges of such an integrated response in an under-resourced rural African setting, we present the COVID-19 strategy in Ifanadiana District, where a partnership between Malagasy Ministry of Public Health (MoPH) and non-governmental organizations integrates prevention, diagnosis, surveillance, and treatment, in the context of a model health system. These efforts touch every level of the health system in the district-community, primary care centers, hospital-including the establishment of the only RT-PCR lab for SARS-CoV-2 testing outside of the capital. Starting in March of 2021, a second wave of COVID-19 occurred in Madagascar, but there remain fewer cases in Ifanadiana than for many other diseases (e.g., malaria). At the Ifanadiana District Hospital, there have been two deaths that are officially attributed to COVID-19. Here, we describe the main components and challenges of this integrated response, the broad epidemiological contours of the epidemic, and how complex data sources can be developed to address many questions of COVID-19 science. Because of data limitations, it still remains unclear how this epidemic will affect rural areas of Madagascar and other developing countries where health system utilization is relatively low and there is limited capacity to diagnose and treat COVID-19 patients. Widespread population based seroprevalence studies are being implemented in Ifanadiana to inform the COVID-19 response strategy as health systems must simultaneously manage perennial and endemic disease threats., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer SN declared a shared affiliation, with no collaboration, with one of the authors AG, to the handling editor at the time of the review., (Copyright © 2021 Rakotonanahary, Andriambolamanana, Razafinjato, Raza-Fanomezanjanahary, Ramanandraitsiory, Ralaivavikoa, Tsirinomen'ny Aina, Rahajatiana, Rakotonirina, Haruna, Cordier, Murray, Cowley, Jordan, Krasnow, Wright, Gillespie, Docherty, Loyd, Evans, Drake, Ngonghala, Rich, Popper, Miller, Ihantamalala, Randrianambinina, Ramiandrisoa, Rakotozafy, Rasolofomanana, Rakotozafy, Andriamahatana Vololoniaina, Andriamihaja, Garchitorena, Rakotonirina, Mayfield, Finnegan and Bonds.)

Multimodal T cell profiling can enable more precise characterization of elusive cell states underlying disease. Here, we integrated single-cell RNA and surface protein data from 500,089 memory T cells to define 31 cell states from 259 individuals in a Peruvian tuberculosis (TB) progression cohort. At immune steady state >4 years after infection and disease resolution, we found that, after accounting for significant effects of age, sex, season and genetic ancestry on T cell composition, a polyfunctional type 17 helper T (T H 17) cell-like effector state was reduced in abundance and function in individuals who previously progressed from Mycobacterium tuberculosis (M.tb) infection to active TB disease. These cells are capable of responding to M.tb peptides. Deconvoluting this state-uniquely identifiable with multimodal analysis-from public data demonstrated that its depletion may precede and persist beyond active disease. Our study demonstrates the power of integrative multimodal single-cell profiling to define cell states relevant to disease and other traits.

The African region was predicted to have worse COVID-19 infection and death rates due to challenging health systems and social determinants of health. However, in the 10 months after its first case, Rwanda recorded 10316 cases and 133 COVID-19-related deaths translating to a case fatality rate (CFR) of 1.3%, which raised the question: why does Rwanda have a low COVID-19 CFR? Here we analysed COVID-19 data and explored possible explanations to better understand the disease burden in the context of Rwanda's infection control strategies.We investigated whether the age distribution plays a role in the observed low CFR in Rwanda by comparing the expected number of deaths for 10-year age bands based on the CFR reported in other countries with the observed number of deaths for each age group. We found that the age-specific CFRs in Rwanda are similar to or, in some older age groups, slightly higher than those in other countries, suggesting that the lower population level CFR reflects the younger age structure in Rwanda, rather than a lower risk of death conditional on age. We also accounted for Rwanda's comprehensive SARS-CoV-2 testing strategies and reliable documentation of COVID-19-related deaths and deduced that these measures may have allowed them to likely identify more asymptomatic or mild cases than other countries and reduced their reported CFR.Overall, the observed low COVID-19 deaths in Rwanda is likely influenced by the combination of effective infection control strategies, reliable identification of cases and reporting of deaths, and the population's young age structure., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

The cell wall of Mycobacterium tuberculosis is composed of diverse glycolipids which potentially interact with the human immune system. To overcome difficulties in obtaining pure compounds from bacterial extracts, we recently synthesized three forms of mycobacterial diacyltrehalose (DAT) that differ in their fatty acid composition, DAT 1 , DAT 2 , and DAT 3 . To study the potential recognition of DATs by human T cells, we treated the lipid-binding antigen presenting molecule CD1b with synthetic DATs and looked for T cells that bound the complex. DAT 1 - and DAT 2 -treated CD1b tetramers were recognized by T cells, but DAT 3 -treated CD1b tetramers were not. A T cell line derived using CD1b-DAT 2 tetramers showed that there is no cross-reactivity between DATs in an IFN-γ release assay, suggesting that the chemical structure of the fatty acid at the 3-position determines recognition by T cells. In contrast with the lack of recognition of DAT 3 by human T cells, DAT 3, but not DAT 1 or DAT 2 , activates Mincle. Thus, we show that the mycobacterial lipid DAT can be both an antigen for T cells and an agonist for the innate Mincle receptor, and that small chemical differences determine recognition by different parts of the immune system.

Introduction: Despite renewed commitment to universal health coverage and health system strengthening (HSS) to improve access to primary care, there is insufficient evidence to guide their design and implementation. To address this, we conducted an impact evaluation of an ongoing HSS initiative in rural Madagascar, combining data from a longitudinal cohort and primary health centres., Methods: We carried out a district representative household survey at the start of the HSS intervention in 2014 in over 1500 households in Ifanadiana district, and conducted follow-up surveys at 2 and 4 years. At each time point, we estimated maternal, newborn and child health coverage; economic and geographical inequalities in coverage; and child mortality rates; both in the HSS intervention and control catchments. We used logistic regression models to evaluate changes associated with exposure to the HSS intervention. We also estimated changes in health centre per capita utilisation during 2013 to 2018., Results: Child mortality rates decreased faster in the HSS than in the control catchment. We observed significant improvements in care seeking for children under 5 years of age (OR 1.23; 95% CI 1.05 to 1.44) and individuals of all ages (OR 1.37, 95% CI 1.19 to 1.58), but no significant differences in maternal care coverage. Economic inequalities in most coverage indicators were reduced, while geographical inequalities worsened in nearly half of the indicators., Conclusion: The results demonstrate improvements in care seeking and economic inequalities linked to the early stages of a HSS intervention in rural Madagascar. Additional improvements in this context of persistent geographical inequalities will require a stronger focus on community health., Competing Interests: Competing interests: Some authors are current or former employees of institutions discussed in this article, including the non-governmental organisation PIVOT and the Government of Madagascar. These affiliations are explicitly listed in the article., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Efficient contact investigation strategies are needed for the early diagnosis of tuberculosis (TB) disease and treatment of latent TB infections., Methods: Between September 2009 and August 2012, we conducted a prospective cohort study in Lima, Peru, in which we enrolled and followed 14 044 household contacts of adults with pulmonary TB. We used information from a subset of this cohort to derive 2 clinical prediction tools that identify contacts of TB patients at elevated risk of progressing to active disease by training multivariable models that predict (1) coprevalent TB among all household contacts and (2) 1-year incident TB among adult contacts. We validated the models in a geographically distinct subcohort and compared the relative utilities of clinical decisions based on these tools to existing strategies., Results: In our cohort, 296 (2.1%) household contacts had coprevalent TB and 145 (1.9%) adult contacts developed incident TB within 1 year of index patient diagnosis. We predicted coprevalent disease using information that could be readily obtained at the time an index patient was diagnosed and predicted 1-year incident TB by including additional contact-specific characteristics. The area under the receiver operating characteristic curves for coprevalent TB and incident TB were 0.86 (95% confidence interval [CI], .83-.89]) and 0.72 (95% CI, .67-.77), respectively. These clinical tools give 5%-10% higher relative utilities than existing methods., Conclusions: We present 2 tools that identify household contacts at high risk for TB disease based on reportable information from patient and contacts alone. The performance of these tools is comparable to biomarkers that are both more costly and less feasible than this approach., (© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America.)

We examined Mycobacterium tuberculosis DNA detection from buccal swab samples collected from children in Lima, Peru. DNA was extracted and amplified via real-time polymerase chain reaction. Sensitivity was 21% (95% confidence interval [CI]: 7%-42%) in 24 culture-confirmed tuberculosis cases and 4.6% (95% CI: 1%-13%) in 65 clinically diagnosed unconfirmed cases. Sensitivity was highest for smear-positive tuberculosis. Specificity was 99% in the 199 controls (95% CI: 96%-100%).

Background: Identifying hotspots of tuberculosis transmission can inform spatially targeted active case-finding interventions. While national tuberculosis programs maintain notification registers which represent a potential source of data to investigate transmission patterns, high local tuberculosis incidence may not provide a reliable signal for transmission because the population distribution of covariates affecting susceptibility and disease progression may confound the relationship between tuberculosis incidence and transmission. Child cases of tuberculosis and other endemic infectious disease have been observed to provide a signal of their transmission intensity. We assessed whether local overrepresentation of child cases in tuberculosis notification data corresponds to areas where recent transmission events are concentrated., Methods: We visualized spatial clustering of children < 5 years old notified to Peru's National Tuberculosis Program from two districts of Lima, Peru, from 2005 to 2007 using a log-Gaussian Cox process to model the intensity of the point-referenced child cases. To identify where clustering of child cases was more extreme than expected by chance alone, we mapped all cases from the notification data onto a grid and used a hierarchical Bayesian spatial model to identify grid cells where the proportion of cases among children < 5 years old is greater than expected. Modeling the proportion of child cases allowed us to use the spatial distribution of adult cases to control for unobserved factors that may explain the spatial variability in the distribution of child cases. We compare where young children are overrepresented in case notification data to areas identified as transmission hotspots using molecular epidemiological methods during a prospective study of tuberculosis transmission conducted from 2009 to 2012 in the same setting., Results: Areas in which childhood tuberculosis cases are overrepresented align with areas of spatial concentration of transmission revealed by molecular epidemiologic methods., Conclusions: Age-disaggregated notification data can be used to identify hotspots of tuberculosis transmission and suggest local force of infection, providing an easily accessible source of data to target active case-finding intervention.

On average, Peruvian individuals are among the shortest in the world 1 . Here we show that Native American ancestry is associated with reduced height in an ethnically diverse group of Peruvian individuals, and identify a population-specific, missense variant in the FBN1 gene (E1297G) that is significantly associated with lower height. Each copy of the minor allele (frequency of 4.7%) reduces height by 2.2 cm (4.4 cm in homozygous individuals). To our knowledge, this is the largest effect size known for a common height-associated variant. FBN1 encodes the extracellular matrix protein fibrillin 1, which is a major structural component of microfibrils. We observed less densely packed fibrillin-1-rich microfibrils with irregular edges in the skin of individuals who were homozygous for G1297 compared with individuals who were homozygous for E1297. Moreover, we show that the E1297G locus is under positive selection in non-African populations, and that the E1297 variant shows subtle evidence of positive selection specifically within the Peruvian population. This variant is also significantly more frequent in coastal Peruvian populations than in populations from the Andes or the Amazon, which suggests that short stature might be the result of adaptation to factors that are associated with the coastal environment in Peru.