RANTES/CCL5 and risk for coronary events: Results from the MONICA/KORA Augsburg case-cohort, Athero-express and CARDIoGRAM studies

Background: The chemokine RANTES (regulated on activation, normal T-cell expressed and secreted)/CCL5 is involved in the pathogenesis of cardiovascular disease in mice, whereas less is known in humans. We hypothesised that its relevance for atherosclerosis should be reflected by associations between CCL5 gene variants, RANTES serum concentrations and protein levels in atherosclerotic plaques and risk for coronary events. Methods and Findings: We conducted a case-cohort study within the population-based MONICA/KORA Augsburg studies. Baseline RANTES serum levels were measured in 363 individuals with incident coronary events and 1,908 non-cases (mean follow-up: 10.2±

TB/HIV: an orphan disease?

No abstract available

Adherence in the treatment of patients with extensively drug-resistant tuberculosis and HIV in South Africa: a prospective cohort study.

CAPRISA, 2014.Abstract available in pdf

Population-level emergence of bedaquiline and clofazimine resistance-associated variants among patients with drug-resistant tuberculosis in southern Africa: a phenotypic and phylogenetic analysis.

BACKGROUND: Bedaquiline and clofazimine are important drugs in the treatment of drug-resistant tuberculosis and are commonly used across southern Africa, although drug susceptibility testing is not routinely performed. In this study, we did a genotypic and phenotypic analysis of drug-resistant Mycobacterium tuberculosis isolates from cohort studies in hospitals in KwaZulu-Natal, South Africa, to identify resistance-associated variants (RAVs) and assess the extent of clofazimine and bedaquiline cross-resistance. We also used a comprehensive dataset of whole-genome sequences to investigate the phylogenetic and geographical distribution of bedaquiline and clofazimine RAVs in southern Africa. METHODS: In this study, we included M tuberculosis isolates reported from the PRAXIS study of patients with drug-resistant tuberculosis treated with bedaquiline (King Dinuzulu Hospital, Durban) and three other cohort studies of drug-resistant tuberculosis in other KwaZulu-Natal hospitals, and sequential isolates from six persistently culture-positive patients with extensively drug-resistant tuberculosis at the KwaZulu-Natal provincial referral laboratory. Samples were collected between 2013 and 2019. Microbiological cultures were done as part of all parent studies. We sequenced whole genomes of included isolates and measured bedaquiline and clofazimine minimum inhibitory concentrations (MICs) for isolates identified as carrying any Rv0678 variant or previously published atpE, pepQ, and Rv1979c RAVs, which were the subject of the phenotypic study. We combined all whole-genome sequences of M tuberculosis obtained in this study with publicly available sequence data from other tuberculosis studies in southern Africa (defined as the countries of the Southern African Development Community), including isolates with Rv0678 variants identified by screening public genomic databases. We used this extended dataset to reconstruct phylogenetic relationships across lineage 2 and 4 M tuberculosis isolates. FINDINGS: We sequenced the whole genome of 648 isolates from 385 patients with drug-resistant tuberculosis recruited into cohort studies in KwaZulu-Natal, and 28 isolates from six patients from the KwaZulu-Natal referral laboratory. We identified 30 isolates with Rv0678 RAVs from 16 (4%) of 391 patients. We did not identify any atpE, pepQ, or Rv1979c RAVs. MICs were measured for 21 isolates with Rv0678 RAVs. MICs were above the critical concentration for bedaquiline resistance in nine (43%) of 21 isolates, in the intermediate category in nine (43%) isolates, and within the wild-type range in three (14%) isolates. Clofazimine MICs in genetically wild-type isolates ranged from 0·12-0·5 μg/mL, and in isolates with RAVs from 0·25-4·0 μg/mL. Phylogenetic analysis of the extended dataset including M tuberculosis isolates from southern Africa resolved multiple emergences of Rv0678 variants in lineages 2 and 4, documented two likely nosocomial transmission events, and identified the spread of a possibly bedaquiline and clofazimine cross-resistant clone in eSwatini. We also identified four patients with pepQ frameshift mutations that may confer resistance. INTERPRETATION: Bedaquiline and clofazimine cross-resistance in southern Africa is emerging repeatedly, with evidence of onward transmission largely due to Rv0678 mutations in M tuberculosis. Roll-out of bedaquiline and clofazimine treatment in the setting of limited drug susceptibility testing could allow further spread of resistance. Designing strong regimens would help reduce the emergence of resistance. Drug susceptibility testing is required to identify where resistance does emerge. FUNDING: Wellcome Trust, National Institute of Allergy and Infectious Diseases and National Center for Advancing Translational Sciences of the National Institutes of Health

Clofazimine in the treatment of extensively drug-resistant tuberculosis with HIV coinfection in South Africa: a retrospective cohort study.

CAPRISA, 2014.Abstract available in pdf

Preferential adherence to antiretroviral therapy over tuberculosis treatment: a qualitative study of drug-resistant TB/HIV co-infected patients in South Africa.

CAPRISA, 2014.Abstract available in pdf

Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis

BACKGROUND: Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. METHODS: We compiled a dataset of 3682 Mtb genomes, including 180 carrying variants in mmpR5, and its immediate background (i.e. mmpR5 promoter and adjacent mmpL5 gene), that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We characterised the occurrence of all nonsynonymous mutations in mmpR5 in this dataset and estimated, using time-resolved phylogenetic methods, the age of their emergence. RESULTS: We identified eight cases where RAVs were present in the genomes of strains collected prior to the use of bedaquiline in TB treatment regimes. Phylogenetic reconstruction points to multiple emergence events and circulation of RAVs in mmpR5, some estimated to predate the introduction of bedaquiline. However, epistatic interactions can complicate bedaquiline drug-susceptibility prediction from genetic sequence data. Indeed, in one clade, Ile67fs (a RAV when considered in isolation) was estimated to have emerged prior to the antibiotic era, together with a resistance reverting mmpL5 mutation. CONCLUSIONS: The presence of a pre-existing reservoir of Mtb strains carrying bedaquiline RAVs prior to its clinical use augments the need for rapid drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in TB care and control

Derivation and external validation of community-acquired pneumonia subphenotypes in Southeast Asia: a secondary analysis of prospective cohort studies

BackgroundIdentifying pneumonia subphenotypes in understudied populations can advance equitable personalized medicine for pneumonia care. We aimed to derive and validate subphenotypes of patients presenting with community-acquired pneumonia (CAP) in Southeast Asia.MethodsThis secondary analysis included three prospective cohorts conducted between March 2013 and April 2020. First, we performed latent class analysis to identify subphenotypes using clinical and laboratory variables in a prospective cohort of adults hospitalized with CAP in northeastern Thailand. Next, we compared clinical and biological features between the subphenotypes and then developed a parsimonious classifier model (PCM) for accurate subphenotype assignment. We then validated the accuracy of PCM subphenotype assignment in an external, multinational prospective cohort of patients hospitalized with CAP in Southeast Asia. Finally, in an exploratory analysis, we used the PCM to assign pneumonia subphenotypes in a prospective cohort of patients hospitalized with COVID-19 in the United States of America and evaluated a heterogeneity of treatment effect with corticosteroids.FindingsAmong 953 CAP patients in the Thai derivation cohort, we identified two subphenotypes: CAP1 (141, 15%) and CAP2 (812, 85%). We observed greater respiratory failure, 28-day mortality, inflammatory cytokines and metabolic derangements among CAP1 patients. A four-variable PCM discriminated subphenotype assignment in bootstrap internal validation (optimism-corrected C-statistic 0.97). In the Southeast Asian external validation cohort, CAP1 and CAP2 subphenotypes assigned by the PCM shared similar differential clinical features and outcomes with the Thai derivation cohort. In the cohort of patients with COVID-19, CAP1 and CAP2 subphenotypes assigned by the PCM differed by key clinical characteristics and revealed an interaction between corticosteroid treatment and mortality (P = 0.002).InterpretationIn Southeast Asia, CAP subphenotypes are associated with distinct outcomes, inflammatory profiles, and metabolomic signatures. These subphenotypes may represent unique targets for future CAP interventional trials.FundingSupported by US NIH awards T32HL007287, F32HL168809, K08HL157562, U01AI115520, R01AI137111, R01GM114029, R21AI173435, R01HL113382, the Wellcome Trust grants 090219/Z/09/Z, 101103/Z/13/Z, 106680/B/14/Z, and 106698/B/14/Z, the US National Cancer Institute, National Institutes of Health HHSN261200800001E, and Firland Foundation award 20220012. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission

Racial and ethnic disparities in aortic stenosis within a universal healthcare system characterized by natural language processing for targeted intervention

AIMS: Aortic stenosis (AS) is a condition marked by high morbidity and mortality in severe, symptomatic cases without intervention via transcatheter aortic valve implantation (TAVI) or surgical aortic valve replacement (SAVR). Racial and ethnic disparities in access to these treatments have been documented, particularly in North America, where socioeconomic factors such as health insurance confound analyses. This study evaluates disparities in AS management across racial and ethnic groups, accounting for socioeconomic deprivation, using an artificial intelligence (AI) framework.METHODS AND RESULTS: We conducted a retrospective cohort study using a natural language processing pipeline to analyse both structured and unstructured data from &gt; 1 million patients at a London hospital. Key variables included age, sex, self-reported race and ethnicity, AS severity, and socioeconomic status. The primary outcomes were rates of valvular intervention and all-cause mortality. Among 6967 patients with AS, Black patients were younger, more symptomatic, and more comorbid than White patients. Black patients with objective evidence of AS on echocardiography were less likely to receive a clinical diagnosis than White patients. In severe AS, TAVI and SAVR procedures were performed at lower rates among Black patients than among White patients, with a longer time to SAVR. In multivariate analysis of severe AS, controlling for socioeconomic status, Black patients experienced higher mortality (hazard ratio = 1.42, 95% confidence interval = 1.05-1.92, P = 0.02). CONCLUSION: An AI framework characterizes racial and ethnic disparities in AS management, which persist in a universal healthcare system, highlighting targets for future healthcare interventions.</p