Phylogenetic inference of inter-population transmission rates for infectious diseases.

Estimating transmission rates is a challenging yet essential aspect of comprehending and controlling the spread of infectious diseases. Various methods exist for estimating transmission rates, each with distinct assumptions, data needs, and constraints. This study introduces a novel phylogenetic approach called transRate, which integrates genetic information with traditional epidemiological approaches to estimate inter-population transmission rates. The phylogenetic method is statistically consistent as the sample size (i.e. the number of pathogen genomes) approaches infinity under the multi-population susceptible-infected-recovered model. Simulation analyses indicate that transRate can accurately estimate the transmission rate with a sample size of 200 ~ 400 pathogen genomes. Using transRate, we analyzed 40,028 high-quality sequences of SARS-CoV-2 in human hosts during the early pandemic. Our analysis uncovered significant transmission between populations even before widespread travel restrictions were implemented. The development of transRate provides valuable insights for scientists and public health officials to enhance their understanding of the pandemic's progression and aiding in preparedness for future viral outbreaks. As public databases for genomic sequences continue to expand, transRate is increasingly vital for tracking and mitigating the spread of infectious diseases.

M. tuberculosis Infection Attributable to Exposure in Social Networks of Tuberculosis Cases in an Urban African Community.

Background: The persistence of tuberculosis today and its global disparity send a powerful message that effective tuberculosis control must respond to its regional epidemiology. Active case finding through contact investigation is a standard protocol used for tuberculosis control, but its effectiveness has not been established, especially in endemic areas. Methods: To quantify the potential effectiveness of contact investigation in Kampala, Uganda, we used a cross-sectional design to evaluate the social networks of 123 tuberculosis index cases and 124 controls without tuberculosis. Results: Tuberculous infection was present in 515 of 989 tuberculosis case contacts (52.1%) and 396 of 1026 control contacts (38.6%; adjusted prevalence ratio, 1.4; 95% CI, 1.3-1.6). The proportion of infected participants with known exposure within the social network of the tuberculosis case was 35%. The population-attributable fraction was 11.1% for any known exposure, with 7.3% attributable to household exposure and 3.4% attributable to extrahousehold exposure. Conclusions: This low population-attributable fraction indicates that contact tracing in the social networks of index cases will have only a modest effect in reducing tuberculous infection in a community. New approaches to community-level active case finding are needed.

African Centers of Excellence in Bioinformatics and Data Intensive Science: Building Capacity for Enhancing Data Intensive Infectious Diseases Research in Africa.

Africa faces both a disproportionate burden of infectious diseases coupled with unmet needs in bioinformatics and data science capabilities which impacts the ability of African biomedical researchers to vigorously pursue research and partner with institutions in other countries. The African Centers of Excellence in Bioinformatics and Data Intensive Science are collaborating with African academic institutions, industry partners, the Foundation for the National Institutes of Health (FNIH) and the National Institute of Allergy and Infectious Diseases (NIAID) at the National Institutes of Health (NIH) in a public-private partnership to address these challenges through enhancing computational infrastructure, fostering the development of advanced bioinformatics and data science skills among local researchers and students and providing innovative emerging technologies for infectious diseases research.

Contextual Pathways Linking Cumulative Experiences of Racial Discrimination to Black American Men's COVID Vaccine Hesitancy.

The COVID-19 pandemic has revealed and widened racialized health disparities, underscoring the impact of structural inequities and racial discrimination on COVID-19 vaccination uptake. A sizable proportion of Black American men report that they either do not plan to or are unsure about becoming vaccinated against COVID-19. The present study investigated hypotheses regarding the mechanisms by which experiences of racial discrimination are associated with Black American men's COVID-19 vaccine hesitancy. Hypotheses were tested using structural equation modeling with 4 waves of data from 242 Black American men (aged ~ 27) living in resource-poor communities in the rural South. Study findings revealed that racial discrimination was indirectly associated with COVID-19 vaccine hesitancy via increased endorsement of COVID-19 conspiratorial beliefs. Findings also demonstrated that increased levels of ethnic identity strengthen the association between experiences of racial discrimination and COVID-19 conspiratorial beliefs. In contrast, increased levels of social support weakened the association between cumulative experiences of racial discrimination and COVID conspiratorial beliefs. Taken together, these results suggest that racial discrimination may promote conspiratorial beliefs which undermine Black American men's willingness to be vaccinated. Future interventions aimed towards promoting vaccine uptake among Black American men may benefit from the inclusion of targeted efforts to rebuild cultural trust and increase social support.

Prevalence of proximate risk factors of active tuberculosis in latent tuberculosis infection: A cross-sectional study from South India.

The prevalence of proximate risk factors for active tuberculosis (TB) in areas of high prevalence of latent tuberculosis infection (LTBI) is not clearly understood. We aimed at assessing the prevalence of non-communicable multi-morbidity focusing on diabetes mellitus (DM), malnutrition, and hypertension (HTN) as common risk factors of LTBI progressing to active TB. In a cross-sectional study, 2,351 adults (45% male and 55% female) from villages in the Kancheepuram district of South India were enrolled between 2013 and 2020. DM was defined as HbA1c >6.4%, undernutrition was defined as low body mass index (LBMI) <18.5 kg/m2, obesity was classified as BMI ≥25 kg/m2, HTN was reported as systolic pressure >130 mmHg, and LTBI was defined as positive (≥ 0.35 international units/ml) by QuantiFERON Gold In-Tube assay. A total of 1,226 individuals (52%) were positive for LTBI out of 2351 tested individuals. The prevalence of DM and pre-diabetes mellitus (PDM) was 21 and 35%, respectively, HTN was 15% in latent tuberculosis (LTB)-infected individuals. The association of DM [odds ratio (OR)]; adjusted odds ratio (aOR) (OR = 1.26, 95% CI: 1.13-1.65; aOR = 1.19, 95% CI: 1.10-1.58), PDM (OR = 1.11, 95% CI: 1.0-1.35), and HTN (OR = 1.28, 95% CI: 1.11-1.62; aOR = 1.18, 95% CI: 1.0-1.56) poses as risk factors of LTBI progression to active TB. The prevalence of LBMI 9% (OR = 1.07, 95% CI: 0.78-1.48) and obesity 42% (OR = 0.85, 95% CI: 0.70-1.03) did not show any statistically significant association with LTB-infected individuals. The present evidence of a high burden of multi-morbidity suggests that proximate risk factors of active TB in LTBI can be managed by nutrition and lifestyle modification.

Ferrets as a model for tuberculosis transmission.

Even with the COVID-19 pandemic, tuberculosis remains a leading cause of human death due to a single infectious agent. Until successfully treated, infected individuals may continue to transmit Mycobacterium tuberculosis bacilli to contacts. As with other respiratory pathogens, such as SARS-CoV-2, modeling the process of person-to-person transmission will inform efforts to develop vaccines and therapies that specifically impede disease transmission. The ferret (Mustela furo), a relatively inexpensive, small animal has been successfully employed to model transmissibility, pathogenicity, and tropism of influenza and other respiratory disease agents. Ferrets can become naturally infected with Mycobacterium bovis and are closely related to badgers, well known in Great Britain and elsewhere as a natural transmission vehicle for bovine tuberculosis. Herein, we report results of a study demonstrating that within 7 weeks of intratracheal infection with a high dose (>5 x 103 CFU) of M. tuberculosis bacilli, ferrets develop clinical signs and pathological features similar to acute disease reported in larger animals, and ferrets infected with very-high doses (>5 x 104 CFU) develop severe signs within two to four weeks, with loss of body weight as high as 30%. Natural transmission of this pathogen was also examined. Acutely-infected ferrets transmitted M. tuberculosis bacilli to co-housed naïve sentinels; most of the sentinels tested positive for M. tuberculosis in nasal washes, while several developed variable disease symptomologies similar to those reported for humans exposed to an active tuberculosis patient in a closed setting. Transmission was more efficient when the transmitting animal had a well-established acute infection. The findings support further assessment of this model system for tuberculosis transmission including the testing of prevention measures and vaccine efficacy.

Infant BCG vaccination and risk of pulmonary and extrapulmonary tuberculosis throughout the life course: a systematic review and individual participant data meta-analysis.

BACKGROUND: BCG vaccines are given to more than 100 million children every year, but there is considerable debate regarding the effectiveness of BCG vaccination in preventing tuberculosis and death, particularly among older children and adults. We therefore aimed to investigate the age-specific impact of infant BCG vaccination on tuberculosis (pulmonary and extrapulmonary) development and mortality. METHODS: In this systematic review and individual participant data meta-analysis, we searched MEDLINE, Web of Science, BIOSIS, and Embase without language restrictions for case-contact cohort studies of tuberculosis contacts published between Jan 1, 1998, and April 7, 2018. Search terms included "mycobacterium tuberculosis", "TB", "tuberculosis", and "contact". We excluded cohort studies that did not provide information on BCG vaccination or were done in countries that did not recommend BCG vaccination at birth. Individual-level participant data for a prespecified list of variables, including the characteristics of the exposed participant (contact), the index case, and the environment, were requested from authors of all eligible studies. Our primary outcome was a composite of prevalent (diagnosed at or within 90 days of baseline) and incident (diagnosed more than 90 days after baseline) tuberculosis in contacts exposed to tuberculosis. Secondary outcomes were pulmonary tuberculosis, extrapulmonary tuberculosis, and mortality. We derived adjusted odds ratios (aORs) using mixed-effects, binary, multivariable logistic regression analyses with study-level random effects, adjusting for the variable of interest, baseline age, sex, previous tuberculosis, and whether data were collected prospectively or retrospectively. We stratified our results by contact age and Mycobacterium tuberculosis infection status. This study is registered with PROSPERO, CRD42020180512. FINDINGS: We identified 14 927 original records from our database searches. We included participant-level data from 26 cohort studies done in 17 countries in our meta-analysis. Among 68 552 participants, 1782 (2·6%) developed tuberculosis (1309 [2·6%] of 49 686 BCG-vaccinated participants vs 473 [2·5%] of 18 866 unvaccinated participants). The overall effectiveness of BCG vaccination against all tuberculosis was 18% (aOR 0·82, 95% CI 0·74-0·91). When stratified by age, BCG vaccination only significantly protected against all tuberculosis in children younger than 5 years (aOR 0·63, 95% CI 0·49-0·81). Among contacts with a positive tuberculin skin test or IFNγ release assay, BCG vaccination significantly protected against tuberculosis among all participants (aOR 0·81, 95% CI 0·69-0·96), participants younger than 5 years (0·68, 0·47-0·97), and participants aged 5-9 years (0·62, 0·38-0·99). There was no protective effect among those with negative tests, unless they were younger than 5 years (0·54, 0·32-0·90). 14 cohorts reported on whether tuberculosis was pulmonary or extrapulmonary (n=57 421). BCG vaccination significantly protected against pulmonary tuberculosis among all participants (916 [2·2%] in 41 119 vaccinated participants vs 334 [2·1%] in 16 161 unvaccinated participants; aOR 0·81, 0·70-0·94) but not against extrapulmonary tuberculosis (106 [0·3%] in 40 318 vaccinated participants vs 38 [0·2%] in 15 865 unvaccinated participants; 0·96, 0·65-1·41). In the four studies with mortality data, BCG vaccination was significantly protective against death (0·25, 0·13-0·49). INTERPRETATION: Our results suggest that BCG vaccination at birth is effective at preventing tuberculosis in young children but is ineffective in adolescents and adults. Immunoprotection therefore needs to be boosted in older populations. FUNDING: National Institutes of Health.

Seroprevalence of Strongyloides stercoralis infection in a South Indian adult population.

BACKGROUND: The prevalence of Strongyloides stercoralis infection is estimated to be 30-100 million worldwide, although this an underestimate. Most cases remain undiagnosed due to the asymptomatic nature of the infection. We wanted to estimate the seroprevalence of S. stercoralis infection in a South Indian adult population. METHODS: To this end, we performed community-based screening of 2351 individuals (aged 18-65) in Kanchipuram District of Tamil Nadu between 2013 and 2020. Serological testing for S. stercoralis was performed using the NIE ELISA. RESULTS: Our data shows a seroprevalence of 33% (768/2351) for S. stercoralis infection which had a higher prevalence among males 36% (386/1069) than among females 29.8% (382/1282). Adults aged ≥55 (aOR = 1.65, 95% CI: 1.25-2.18) showed higher adjusted odds of association compared with other age groups. Eosinophil levels (39%) (aOR = 1.43, 95% CI: 1.19-1.74) and hemoglobin levels (24%) (aOR = 1.25, 95% CI: 1.11-1.53) were significantly associated with S. stercoralis infection. In contrast, low BMI (aOR = 1.15, 95% CI: 0.82-1.61) or the presence of diabetes mellitus (OR = 1.18, 95% CI: 0.83-1.69) was not associated with S. stercoralis seropositivity. CONCLUSIONS: Our study provides evidence for a very high baseline prevalence of S. stercoralis infection in South Indian communities and this information could provide realistic and concrete planning of control measures.

Ethical, Legal, and Sociocultural Issues in the Use of Mobile Technologies and Call Detail Records Data for Public Health in the East African Region: Scoping Review.

BACKGROUND: The exponential scale and pace of real-time data generated from mobile phones present opportunities for new insights and challenges across multiple sectors, including health care delivery and public health research. However, little attention has been given to the new ethical, social, and legal concerns related to using these mobile technologies and the data they generate in Africa. OBJECTIVE: The objective of this scoping review was to explore the ethical and related concerns that arise from the use of data from call detail records and mobile technology interventions for public health in the context of East Africa. METHODS: We searched the PubMed database for published studies describing ethical challenges while using mobile technologies and related data in public health research between 2000 and 2020. A predefined search strategy was used as inclusion criteria with search terms such as "East Africa," "mHealth," "mobile phone data," "public health," "ethics," or "privacy." We screened studies using prespecified eligibility criteria through a two-stage process by two independent reviewers. Studies were included if they were (1) related to mobile technology use and health, (2) published in English from 2000 to 2020, (3) available in full text, and (4) conducted in the East African region. We excluded articles that (1) were conference proceedings, (2) studies presenting an abstract only, (3) systematic and literature reviews, (4) research protocols, and (5) reports of mobile technology in animal subjects. We followed the five stages of a published framework for scoping reviews recommended by Arksey and O'Malley. Data extracted included title, publication year, target population, geographic region, setting, and relevance to mobile health (mHealth) and ethics. Additionally, we used the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) Extension for Scoping Reviews checklist to guide the presentation of this scoping review. The rationale for focusing on the five countries in East Africa was their geographic proximity, which lends itself to similarities in technology infrastructure development. RESULTS: Of the 94 studies identified from PubMed, 33 met the review inclusion criteria for the final scoping review. The 33 articles retained in the final scoping review represent studies conducted in three out of five East African countries: 14 (42%) from Uganda, 13 (39%) from Kenya, and 5 (16%) from Tanzania. Three main categories of concerns related to the use of mHealth technologies and mobile phone data can be conceptualized as (1) ethical issues (adequate informed consent, privacy and confidentiality, data security and protection), (2) sociocultural issues, and (3) regulatory/legal issues. CONCLUSIONS: This scoping review identified major cross-cutting ethical, regulatory, and sociocultural concerns related to using data from mobile technologies in the East African region. A comprehensive framework that accounts for the critical concerns raised would be valuable for guiding the safe use of mobile technology data for public health research purposes.

Fossil coleoid cephalopod from the Mississippian Bear Gulch Lagerstätte sheds light on early vampyropod evolution.

We describe an exceptionally well-preserved vampyropod, Syllipsimopodi bideni gen. et sp. nov., from the Carboniferous (Mississippian) Bear Gulch Lagerstätte of Montana, USA. The specimen possesses a gladius and ten robust arms bearing biserial rows of suckers; it is the only known vampyropod to retain the ancestral ten-arm condition. Syllipsimopodi is the oldest definitive vampyropod and crown coleoid, pushing back the fossil record of this group by ~81.9 million years, corroborating molecular clock estimates. Using a Bayesian tip-dated phylogeny of fossil neocoleoid cephalopods, we demonstrate that Syllipsimopodi is the earliest-diverging known vampyropod. This strongly challenges the common hypothesis that vampyropods descended from a Triassic phragmoteuthid belemnoid. As early as the Mississippian, vampyropods were evidently characterized by the loss of the chambered phragmocone and primordial rostrum-traits retained in belemnoids and many extant decabrachians. A pair of arms may have been elongated, which when combined with the long gladius and terminal fins, indicates that the morphology of the earliest vampyropods superficially resembled extant squids.

Characterization of the Proportion of Clustered Tuberculosis Cases in Guatemala: Insights from a Molecular Epidemiology Study, 2010-2014.

There is little information about the amount of recent tuberculosis transmission in low-income settings. Genetic clustering can help identify ongoing transmission events. A retrospective observational study was performed on Mycobacterium tuberculosis isolates from persons living with HIV (PLHIV) and HIV-seronegative participants who submitted samples to a referral tuberculosis laboratory in Guatemala City, Guatemala from 2010 to 2014. Genotyping results were classified according to the international spoligotyping database, SITVIT2. Spoligotype patterns were categorized as clustered or nonclustered depending on their genotype. The proportion of clustering and the index of recent transmission index (RTIn-1) were estimated. In the RTIn-1 method, clustered cases represent recent transmission, whereas nonclustered cases represent reactivation of older tuberculosis infections. As a secondary aim, the potential risk factors associated with clustering in isolates from the subset of participants living with HIV were explored. From 2010 to 2014, a total of 479 study participants were confirmed as culture-positive tuberculosis cases. Among the 400 available isolates, 71 spoligotype patterns were identified. Overall, the most frequent spoligotyping families were Latin American-Mediterranean (LAM) (39%), followed by T (22%) and Haarlem (14%). Out of the 400 isolates, 365 were grouped in 36 clusters (range of cluster size: 2-92). Thus, the proportion of clustering was 91% and the RTIn-1 was 82%. Among PLHIV, pulmonary tuberculosis was associated with clustering (OR = 4.3, 95% CI 1.0-17.7). Our findings suggest high levels of ongoing transmission of M. tuberculosis in Guatemala as revealed by the high proportion of isolates falling into genomic clusters.

Establishing a centralized data mart from the Rakai community cohort study to improve HIV research in Rakai, Uganda.

To improve timely access to quality HIV research data, the Rakai Health Sciences Program (RHSP) Data Mart was developed to store cohort study data from a legacy database platform in a modernized system using standard data management processes. The RHSP Data Mart was developed on a Microsoft SQL Server platform using Microsoft SQL Server Integration Services with custom data mappings and queries. The data mart stores 20+ years of longitudinal HIV research data and includes standard processes for managing data, data dictionary, training materials, and a library of queries to fulfill data requests and load new data from completed survey rounds. The RHSP Data Mart enables efficient querying and analysis of multidimensional research data by simplifying data integration and processing. A sustainable database platform with well-defined data management processes promotes data accessibility and reproducibility, enabling researchers to advance their understanding and management of infectious diseases.

Bioinformatics mentorship in a resource limited setting.

BACKGROUND: The two recent simultaneous developments of high-throughput sequencing and increased computational power have brought bioinformatics to the forefront as an important tool for effective and efficient biomedical research. Consequently, there have been multiple approaches to developing bioinformatics skills. In resource rich environments, it has been possible to develop and implement formal fully accredited graduate degree training programs in bioinformatics. In resource limited settings with a paucity of expert bioinformaticians, infrastructure and financial resources, the task has been approached by delivering short courses on bioinformatics-lasting only a few days to a couple of weeks. Alternatively, courses are offered online, usually over a period of a few months. These approaches are limited by both the lack of sustained in-person trainer-trainee interactions, which is a key part of quality mentorships and short durations which constrain the amount of learning that can be achieved. METHODS: Here, we pioneered and tested a bioinformatics training/mentorship model that effectively uses the available expertise and computational infrastructure to deliver an in-person hands-on skills training experience. This is done through a few physical lecture hours each week, guided personal coursework over the rest of the week, group discussions and continuous close mentorship and assessment of trainees over a period of 1 year. RESULTS: This model has now completed its third iteration at Makerere University and has successfully mentored trainees, who have progressed to a variety of viable career paths. CONCLUSIONS: One-year (intermediate) skills based in-person bioinformatics training and mentorships are viable, effective and particularly appropriate for resource limited settings.

Association between tuberculosis in men and social network structure in Kampala, Uganda.

BACKGROUND: Globally, tuberculosis disease (TB) is more common among males than females. Recent research proposes that differences in social mixing by sex could alter infection patterns in TB. We examine evidence for two mechanisms by which social-mixing could increase men's contact rates with TB cases. First, men could be positioned in social networks such that they contact more people or social groups. Second, preferential mixing by sex could prime men to have more exposure to TB cases. METHODS: We compared the networks of male and female TB cases and healthy matched controls living in Kampala, Uganda. Specifically, we estimated their positions in social networks (network distance to TB cases, degree, betweenness, and closeness) and assortativity patterns (mixing with adult men, women, and children inside and outside the household). RESULTS: The observed network consisted of 11,840 individuals. There were few differences in estimates of node position by sex. We found distinct mixing patterns by sex and TB disease status including that TB cases have proportionally more adult male contacts and fewer contacts with children. CONCLUSIONS: This analysis used a network approach to study how social mixing patterns are associated with TB disease. Understanding these mechanisms may have implications for designing targeted intervention strategies in high-burden populations.

Community drivers of tuberculosis diagnostic delay in Kampala, Uganda: a retrospective cohort study.

BACKGROUND: Recent approaches to TB control have focused on identifying and treating active cases to halt further transmission. Patients with TB symptoms often delay to seek care, get appropriate diagnosis, and initiate effective treatment. These delays are partly influenced by whom the patients contact within their community network. We aimed to evaluate the community drivers of diagnostic delay in an urban setting in Uganda. METHODS: In this study we analyze data from a retrospective cohort of 194 TB patients in Kampala, Uganda. We characterized the patterns of contacts made by patients seeking care for TB symptoms. The main outcome of interest was total community contact delay, defined as the time patients spent seeking care before visiting a provider capable of diagnosing TB. RESULTS: Visits to health providers without access to appropriate diagnostic services accounted for 56% of contacts made by cohort members, and were significantly associated with community contact delay, as were symptoms common to other prevalent illnesses, such as bone and joint pain. CONCLUSIONS: Education programs aimed at primary care providers, as well as other community members, may benefit case identification, by informing them of rarer symptoms of TB, potential for co-infections of TB and other prevalent diseases, and the availability of diagnostic services.

Heme oxygenase-1 and neopterin plasma/serum levels and their role in diagnosing active and latent TB among HIV/TB co-infected patients: a cross sectional study.

BACKGROUND: Tuberculosis (TB) diagnosis in the context of HIV co-infection remains challenging. Heme oxygenase 1 (HO-1) and neopterin have been validated as potential biomarkers for TB diagnosis. Latent TB infection (LTBI) is diagnosed using tuberculin skin test (TST) and interferon gamma release assays (T-Spot and QuantiFERON TB gold tests, respectively). However, these tests have shown challenges and yet diagnosing LTBI is important for the overall control of TB. This study was conducted to determine the levels of H0-1 and neopterin, and their role in the diagnosis of TB among individuals enrolled in the Community Health and Social Network of Tuberculosis (COHSONET) study and the Kampala TB Drug Resistance Survey (KDRS). METHODS: This was a nested cross-sectional study. Plasma and serum samples collected from 140 patients at Mulago National Referral Hospital, Kampala Uganda were used. M.tb culture was performed on sputum to confirm active TB(ATB) and QuantiFERON TB gold test to confirm latent TB infection (LTBI). ELISAs were performed to determine the levels of HO-1 and neopterin. Data analysis was done using t-test and Receiver Operating Characteristic curves to determine the diagnostic accuracy. RESULTS: HO-1 levels among active tuberculosis (ATB)/HIV-infected patients and LTBI/HIV-infected patients were 10.7 ng/ml (IQR: 7.3-12.7 ng/ml) and 7.5 ng/ml (IQR: 5.4-14.1 ng/ml) respectively. Neopterin levels among ATB/HIV-positive patients and LTBI/HIV-positive patients were 11.7 ng/ml (IQR: 5.2.4 ng/ml) and 8.8 ng/ml (IQR: 2.4-19.8 ng/ml), respectively. HO-1 showed a sensitivity of 58.57% and a specificity of 67.14% with area under the curve (AUC) of 0.57 when used to discriminate between ATB and LTB. Neopterin showed an AUC of 0.62 with a sensitivity of 57.14% and a specificity of 60.0% when used to distinguish ATB from LTB. CONCLUSION: There was no in significant difference in HO-1 concentration levels of ATB individuals compared to LTB individuals. There was a significant difference in neopterin concentrations levels of ATB individuals compared to latently infected individuals. Findings from this study, show that HO-1 and neopterin have poor ability to distinguish between ATB and LTB.

Assessing a transmission network of Mycobacterium tuberculosis in an African city using single nucleotide polymorphism threshold analysis.

Tuberculosis (TB) is the leading cause of death in humans by a single infectious agent worldwide with approximately two billion humans latently infected with the bacterium Mycobacterium tuberculosis. Currently, the accepted method for controlling the disease is Tuberculosis Directly Observed Treatment Shortcourse (TB-DOTS). This program is not preventative and individuals may transmit disease before diagnosis, thus better understanding of disease transmission is essential. Using whole-genome sequencing and single nucleotide polymorphism analysis, we analyzed genomes of 145 M. tuberculosis clinical isolates from active TB cases from the Rubaga Division of Kampala, Uganda. We established that these isolates grouped into M. tuberculosis complex (MTBC) lineages 1, 2, 3, and 4, with the most isolates grouping into lineage 4. Possible transmission pairs containing ≤12 SNPs were identified in lineages 1, 3, and 4 with the prevailing transmission in lineages 3 and 4. Furthermore, investigating DNA codon changes as a result of specific SNPs in prominent virulence genes including plcA and plcB could indicate potentially important modifications in protein function. Incorporating this analysis with corresponding epidemiological data may provide a blueprint for the integration of public health interventions to decrease TB transmission in a region.

Defining an intermediate category of tuberculin skin test: A mixture model analysis of two high-risk populations from Kampala, Uganda.

One principle of tuberculosis control is to prevent the development of tuberculosis disease by treating individuals with latent tuberculosis infection. The diagnosis of latent infection using the tuberculin skin test is not straightforward because of concerns about immunologic cross reactivity with the Bacille Calmette-Guerin (BCG) vaccine and environmental mycobacteria. To parse the effects of BCG vaccine and environmental mycobacteria on the tuberculin skin test, we estimated the frequency distribution of skin test results in two divisions of Kampala, Uganda, ten years apart. We then used mixture models to estimate parameters for underlying distributions and defined clinically meaningful criteria for latent infection, including an indeterminate category. Using percentiles of two underlying normal distributions, we defined two skin test readings to demarcate three ranges. Values of 10 mm or greater contained 90% of individuals with latent infection; values less than 7.2 mm contained 80% of individuals without infection. Contacts with values between 7.2 and 10 mm fell into an indeterminate zone where it was not possible to assign infection. We conclude that systematic tuberculin skin test surveys within populations at risk, combined with mixture model analysis, may be a reproducible, evidence-based approach to define meaningful criteria for latent tuberculosis infection.

Neuraxial Anesthesia Is Associated With Decreased Pain Scores and Post-Anesthesia Care Unit Opioid Requirement Compared With General Anesthesia in Hip Arthroscopy.

PURPOSE: We sought to identify the immediate postoperative differences in opioid use, pain scores, and post-anesthesia care unit (PACU) length of stay (LOS) after hip arthroscopy related to the type of anesthesia used for the surgical procedure. METHODS: Patients undergoing hip arthroscopy for femoroacetabular impingement syndrome with labral tears by a single surgeon at an academic center between October 2017 and July 2019 were reviewed retrospectively. The primary outcome was PACU opioid administration, measured by morphine equivalents. Secondary parameters included total LOS, postincision LOS, PACU LOS, and PACU arrival/discharge pain scores. Analyses conducted were t tests, Wilcoxon rank sum tests, or χ2 tests. RESULTS: A total of 129 patients met inclusion criteria for this study; 54 male and 75 female, with an average age of 28 (±10.1) years. In total, 52 (40.3%) had general anesthesia and 77 (59.7%) had neuraxial anesthesia, including spinal, epidural, and combined spinal-epidural anesthesia, which were intermixed throughout the study period. Intraoperative and PACU opioid administration demonstrated a significant difference in medians. Neuraxial methods required a lower morphine equivalents in both the operating room (30.0 vs 53.9, P = .001) and PACU (18.2 vs 31.2, P = 0.002). Neuraxial anesthesia had lower median PACU arrival and discharge pain scores (0.0 vs. 5.0, P = .001, 3.0 vs. 4.0, P = .013). There was no statistically significant difference in postincision LOS or traction time. General anesthesia was associated with a longer PACU phase 1 time (1.0 vs 1.3 hours, P = .005). No major adverse events such as death, disability, or prolonged hospitalization occurred in either group. CONCLUSIONS: Neuraxial anesthesia use in routine hip arthroscopy was associated with lower immediate postoperative pain scores, lower intraoperative and immediate postoperative opioid requirements, and may be associated with shorter anesthesia recovery time without any major adverse events when compared with general anesthesia. LEVEL OF EVIDENCE: III, Retrospective Comparative Study.