SARS-CoV-2 infectivity and antigenic evasion: spotlight on isolated Omicron sub-lineages.

Since the SARS-CoV-2 outbreak in 2019, a diversity of viral genomic variants has emerged and spread globally due to increased transmissibility, pathogenicity, and immune evasion. By the first trimester of 2023 in Chile, as in most countries, BQ and XBB were the predominant circulating sub-lineages of Omicron. The molecular and antigenic characteristics of these variants have been mainly determined using non-authentic spike pseudoviruses, which is often described as a limitation. Additionally, few comparative studies using isolates from recent Omicron sub-lineages have been conducted. In this study, we isolated SARS-CoV-2 variants from clinical samples, including the ancestral B.1.1, Delta, Omicron BA.1, and sub-lineages of BA.2 and BA.5. We assessed their infectivity through cell culture infections and their antibody evasion using neutralization assays. We observed variations in viral plaque size, cell morphology, and cytotoxicity upon infection in Vero E6-TMPRSS2 cells for each variant compared to the ancestral B.1.1 virus. BA.2-derived sub-variants, such as XBB.1.5, showed attenuated viral replication, while BA.5-derived variants, such as BQ.1.1, exhibited replication rates similar to the ancestral SARS-CoV-2 virus. Similar trends were observed in intestinal Caco-2 cells, except for Delta. Antibody neutralization experiments using sera from individuals infected during the first COVID-19 wave (FWI) showed a consistent but moderate reduction in neutralization against Omicron sub-lineages. Interestingly, despite being less prevalent, BQ.1.1 showed a 6.1-fold greater escape from neutralization than XBB.1.5. Neutralization patterns were similar when tested against sera from individuals vaccinated with 3xBNT162b2 (PPP) or Coronavac-Coronavac-BNT162b2 (CCP) schedules. However, CCP sera showed 2.3-fold higher neutralization against XBB.1.5 than FWI and PPP sera. This study provides new insights into the differences between BA.2 and BA.5-derived variants, leading to their eventual outcompetition. Our analysis offers important evidence regarding the balance between infectivity and antigenic escape that drives the evolution of second-generation SARS-CoV-2 variants in the population.

Evaluation of concordance of new QuantiFERON-TB Gold Plus platforms for Mycobacterium tuberculosis infection diagnosis in a prospective cohort of household contacts.

Interferon-gamma (IFN-γ) release assays play a pivotal role in tuberculosis infection (TBI) diagnosis, with QuantiFERON-TB Gold Plus-an enzyme-linked immunosorbent assay (ELISA)-among the most widely utilized. Newer QuantiFERON-TB platforms with shorter turnaround times were recently released. We aimed to evaluate these platforms' agreement in the diagnosis of TBI. Blood samples from a prospective cohort of tuberculosis household contacts were collected at baseline and after 12 weeks of follow-up, and tested with LIAISON, an automated chemiluminescence immunoassay (CLIA) system, QIAreach, a lateral flow (QFT-LF) semi-automated immunoassay, and the ELISA QuantiFERON-TB Gold Plus platform. Test concordances were analyzed. ELISA vs CLIA overall agreement was 83.3% for all tested samples (120/144) [Cohen's kappa coefficient (κ): 0.66 (95% CI: 0.54-0.77)]. Samples positive with CLIA provided consistently higher IFN-γ levels than with ELISA (P < 0.001). Twenty-four (16.7%) discordant pairs were obtained, all CLIA-positive/ELISA-negative: 15 (62.5%) had CLIA IFN-γ levels within borderline values (0.35-0.99 IU/mL) and 9 (37.5%) >0.99 IU/mL. QFT-LF showed only 76.4% (68/89) overall agreement with ELISA [κ: 0.53 (95% CI: 0.37-0.68)] with 21 (23.6%) discordant results obtained, all QFT-LF-positive/ELISA-negative. Overall concordance between ELISA and CLIA platforms was substantial, and only moderate between ELISA and QFT-LF. The CLIA platform yielded higher IFN-γ levels than ELISA, leading to an almost 17% higher positivity rate. The techniques do not seem interchangeable, and validation against other gold standards, such as microbiologically-confirmed tuberculosis disease, is required to determine whether these cases represent true new infections or whether CLIA necessitates a higher cutoff. IMPORTANCE: Tuberculosis is an airborne infectious disease caused by Mycobacterium tuberculosis that affects over 10 million people annually, with over 2 billion people carrying an asymptomatic tuberculosis infection (TBI) worldwide. Currently, TBI diagnosis includes tuberculin skin test and the blood-based interferon-gamma (IFN-γ) release assays, with Qiagen QuantiFERON-TB Gold Plus (QFT) being among those most widely utilized. We evaluated Qiagen's newer QFT platforms commercially available in a prospective cohort of tuberculosis contacts. A substantial agreement was obtained between the current QFT-enzyme-linked immunosorbent assay (ELISA) and the new QFT-chemiluminescence immunoassay (CLIA) platform, although QFT-CLIA provided higher concentrations of IFN-γ, leading to a 16.6% higher positivity rate. We highlight that both platforms may not be directly interchangeable and that further validation is required.

Factors associated with tuberculosis treatment initiation among bacteriologically negative individuals evaluated for tuberculosis: an individual patient data meta-analysis.

Background: Globally, over one-third of pulmonary tuberculosis (TB) disease diagnoses are made based on clinical criteria after a negative diagnostic test result. Understanding factors associated with clinicians' decisions to initiate treatment for individuals with negative test results is critical for predicting the potential impact of new diagnostics. Methods: We performed a systematic review and individual patient data meta-analysis using studies conducted between January/2010 and December/2022 (PROSPERO: CRD42022287613). We included trials or cohort studies that enrolled individuals evaluated for TB in routine settings. In these studies participants were evaluated based on clinical examination and routinely-used diagnostics, and were followed for ≥1 week after the initial test result. We used hierarchical Bayesian logistic regression to identify factors associated with treatment initiation following a negative result on an initial bacteriological test (e.g., sputum smear microscopy, Xpert MTB/RIF). Findings: Multiple factors were positively associated with treatment initiation: male sex [adjusted Odds Ratio (aOR) 1.61 (1.31-1.95)], history of prior TB [aOR 1.36 (1.06-1.73)], reported cough [aOR 4.62 (3.42-6.27)], reported night sweats [aOR 1.50 (1.21-1.90)], and having HIV infection but not on ART [aOR 1.68 (1.23-2.32)]. Treatment initiation was substantially less likely for individuals testing negative with Xpert [aOR 0.77 (0.62-0.96)] compared to smear microscopy and declined in more recent years. Interpretation: Multiple factors influenced decisions to initiate TB treatment despite negative test results. Clinicians were substantially less likely to treat in the absence of a positive test result when using more sensitive, PCR-based diagnostics.

Intra-amniotic Candida albicans Infection Treated With Liposomal Amphotericin B With a Successful Neonatal Outcome.

Intra-amniotic infection with Candida species is an uncommon but severe condition with high fetal morbimortality and no established clinical guidelines for its management. We report a Candida albicans intra-amniotic infection diagnosed in a 25-week pregnant woman, successfully treated with high-dose liposomal amphotericin B. Pregnancy was prolonged until 30 weeks, and despite persistently positive Candida cultures in amniotic fluid, a healthy newborn was delivered without evidence of systemic infection. Amphotericin concentration was determined at birth, revealing levels over 30 times higher in mother's and cord blood than in the amniotic fluid, probably explaining the clinical protection despite failure in obtaining fungal clearance.

Differential levels of anti-Mycobacterium tuberculosis-specific IgAs in saliva of household contacts with latent tuberculosis infection.

Introduction: Mucosal immunity is strongly elicited in early stages of many respiratory and enteric infections; however, its role in tuberculosis pathogenesis has been scarcely explored. We aimed to investigate Mycobacterium tuberculosis (Mtb) specific IgA levels in saliva in different stages of latent Tuberculosis Infection (TBI). Methodology: A multiplex bead-based Luminex immunoassay was developed to detect specific IgA against 12 highly immunogenic Mtb antigens. A prospective cohort of household contacts (>14 years) of pulmonary TB cases was established in Santiago, Chile. Contacts were classified as Mtb-infected or not depending on serial interferon-γ release assay results. Saliva samples were collected and tested at baseline and at a 12-week follow-up. Results: Mtb-specific IgA was detectable at all visits in all participants (n = 168), including the "non-Mtb infected" (n = 64). Significantly higher median levels of IgA were found in the "Mtb infected" compared to the uninfected for anti-lipoarabinomannan (LAM) (110 vs. 84.8 arbitrary units (AU), p < 0.001), anti-PstS1 (117 vs. 83 AU, p < 0.001), anti-Cell Membrane Fraction (CMF) (140 vs. 103 AU, p < 0.001) and anti-Culture Filtrate Proteins (CFP) (median 125 vs. 96 AU, p < 0.001), respectively. Nonetheless, the discriminatory performance of these specific mucosal IgA for TBI diagnosis was low. Conclusion: Saliva holds Mtb-specific IgA against several antigens with increased levels for anti-LAM, anti-PstS1, anti-CMF and anti-CFP found in household contacts with an established TBI. The role of these mucosal antibodies in TB pathogenesis, and their kinetics in different stages of Mtb infection merits further exploring.

Primer Consenso Chileno de Grupo de Estudio de Tuberculosis Ocular / First Chilean Consensus Document of the Ocular Tuberculosis Study Group

INTRODUCCIÓN: El tratamiento de la tuberculosis (TB) ocular es un tema que genera controversia en el mundo. Para el correcto manejo de estos pacientes, es necesario el desarrollo de guías que consideren la epidemiología de la TB ocular en cada nación. El objetivo de este consenso fue discutir de forma interdisciplinaria la epidemiología, fisiopatología, clínica, diagnóstico, estudio y tratamiento de los pacientes con TB ocular, para establecer un algoritmo de tratamiento y proponer qué pacientes deben ser tratados en Chile y con qué tratamiento. Además, se establecieron acuerdos para efectuar quimioprofilaxis de los pacientes con TB latente que tienen indicación de tratamiento inmunosupresor por enfermedades inflamatorias oculares.

The treatment of ocular tuberculosis (TB) remains controversial worldwide. The development of guidelines for ocular TB can facilitate the approach and management of these patients. These guidelines should be developed regionally, considering the local TB epidemiology. The objectives of this consensus are: to initiate an interdisciplinary discussion about the epidemiology, pathophysiology, clinical presentation, diagnosis, workup and treatment of patients with ocular TB, to establish a treatment algorithm and define which patients should be treated in Chile and how and, to analyze and discuss the published data regarding chemoprophylaxis for patients with latent TB who need to start immunosuppressive treatment due to inflammatory ocular conditions.

Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection.

The upper respiratory tract is an obliged pathway for respiratory pathogens and a healthy microbiota may support the host's mucosal immunity preventing infection. We analyzed the nasopharyngeal microbiome in tuberculosis household contacts (HHCs) and its association with latent tuberculosis infection (TBI). A prospective cohort of HHCs was established and latent TBI status was assessed by serial interferon-γ release assay (IGRA). Nasopharyngeal swabs collected at baseline were processed for 16S rRNA gene sequencing. The 82 participants included in the analysis were classified as: (a) non-TBI [IGRA negative at baseline and follow-up, no active TB (n = 31)], (b) pre-TBI [IGRA negative at baseline but converted to IGRA positive or developed active TB at follow-up (n = 16)], and (c) TBI [IGRA positive at enrollment (n = 35)]. Predominant phyla were Actinobacteriota, Proteobacteria, Firmicutes and Bacteroidota. TBI group had a lower alpha diversity compared to non-TBI (padj = 0.04) and pre-TBI (padj = 0.04). Only TBI and non-TBI had beta diversity differences (padj = 0.035). Core microbiomes' had unique genera, and genus showed differential abundance among groups. HHCs with established latent TBI showed reduced nasopharyngeal microbial diversity with distinctive taxonomical composition. Whether a pre-existing microbiome feature favors, are a consequence, or protects against Mycobacterium tuberculosis needs further investigation.

Barreras para las actividades de investigación en los programas de residencia: estudio de métodos mixtos / Barriers for research activities in residency programs: A mix-methods study

Introducción Las actividades de investigación tienen un impacto positivo en el rendimiento de los médicos residentes. Falta información sobre investigaciones desarrolladas por residentes de países en vías de desarrollo. Nuestro objetivo fue evaluar las barreras y facilitadores para la investigación en programas de residencia en una Facultad de Medicina de América Latina. Métodos Se llevó a cabo un diseño de estudio de metodología mixta. Utilizamos un enfoque de teoría fundamentada para la fase cualitativa, recopilando los datos a través de entrevistas semiestructuradas y grupos focales con profesores y residentes. Para la fase cuantitativa, se administraron encuestas a residentes y profesores. Para evaluar las propiedades psicométricas de las encuestas utilizamos análisis factorial y scree plot (validez); alfa de Cronbach y coeficiente de Correlación Intraclase (confiabilidad). Resultados Se realizaron grupos focales que incluyeron diez profesores y quince residentes, y se identificaron los siguientes dominios: a) facilitadores para la participación de los residentes, b) barreras, c) estrategias para introducir la investigación en el currículo, d) argumentos que respaldan las actividades de investigación durante la residencia, y e) perfil de los residentes motivados en la investigación. Tanto los residentes como el profesorado identificaron la falta de tiempo protegido y la ausencia de tutoría adecuada como las principales barreras. Se encontró una brecha de género relacionada con las publicaciones internacionales (34% vs 66% mujeres/hombres), las mujeres percibieron que las actividades de investigación 'compiten con otras actividades' (OR: 2.04, IC 95% 1.03 a 4.07). Conclusiones Los residentes y profesores de una universidad latinoamericana de alta productividad valoran mucho la investigación. La presencia de brecha de género, la falta de tiempo protegido y de tutorías destacan como las principales barreras. Las estrategias propuestas para mejorar la investigación dentro de los programas de residencia son: establecer un programa de tutoría interdisciplinario entre residentes e investigadores; promover las rotaciones electivas; y premiar propuestas que consideren la equidad de género.

Introduction Research activities have a positive impact on the performance of residents. However, information on research conducted by residents from developing countries is scarce. Our study sought to identify the barriers and facilitators for developing research in medical residency programs in a Latin-American faculty of medicine. Methods A mixed methodology study design was carried out. We used a grounded theory approach for the qualitative phase, collecting data through semi-structured interviews and focus groups with faculty and residents. For the quantitative phase, surveys were administered to residents and teachers. We used factor analysis and scree plot (validity), Cronbach's alpha, and Intraclass correlation coefficient (reliability) to evaluate the surveys' psychometric properties. Results Focus groups involving ten faculty members and 15 residents were conducted, and the following domains were identified: a) facilitators for resident participation, b) barriers, c) strategies for introducing research into the curriculum, d) arguments supporting research activities throughout medical residency, and e) profile of research-motivated residents. Both residents and faculty members identified a lack of protected time and adequate mentoring as the major barriers. A gender gap was found related to international publications (34% vs. 66% women/men); women perceived that research activities 'compete with other activities' (OR: 2.04, 95% CI 1.03 to 4.07). Conclusions Research is highly valued by both residents and faculty members at a Latin-American university with a strong academic output. Major barriers to promoting research in this context include lack of protected time and effective mentoring, and gender gaps. Strategies proposed to improve research within medical residency programs include: establishing an interdisciplinary mentoring program between residents and researchers, promoting elective rotations, and rewarding proposals that consider gender equity.

Vitamin D and cathelicidin levels and susceptibility to Mycobacterium tuberculosis infection acquisition in household contacts.

INTRODUCTION: Vitamin D deficiency has been proposed to confer susceptibility to acquiring tuberculosis infection by impairing the innate immune response. METHODS: In an exploratory study, we examined whether the levels of 25-hydroxyvitamin D3 (25(OH)D3) in serum, and cathelicidin - an antimicrobial peptide-induced under calcitriol - in the nasal fluid, would associate with the risk of acquiring tuberculosis infection. RESULTS: Within a prospective cohort of 231 tuberculosis household contacts tested with repeated interferon-gamma release assays, we serially analyzed all the uninfected contacts acquiring tuberculosis infection at follow-up ("converters", n=18), and an age and sex-matched control group of contacts not acquiring tuberculosis infection ("non-converters", n=36). The median levels of serum 25(OH)D3 did not differ between convertors and non-converters at baseline (14.9 vs. 13.2 ng/ml, p=0.41), nor at follow-up (19.0 vs 18.6ng/ml, p=0.83). Similarly, cathelicidin levels did not differ between both groups. CONCLUSION: These data argue against a major role for hypovitaminosis D in tuberculosis infection susceptibility.

Barriers for research activities in residency programs: A mix-methods study.

Introduction: Research activities have a positive impact on the performance of residents. However, information on research conducted by residents from developing countries is scarce. Our study sought to identify the barriers and facilitators for developing research in medical residency programs in a Latin-American faculty of medicine. Methods: A mixed methodology study design was carried out. We used a grounded theory approach for the qualitative phase, collecting data through semi-structured interviews and focus groups with faculty and residents. For the quantitative phase, surveys were administered to residents and teachers. We used factor analysis and scree plot (validity), Cronbach's alpha, and Intraclass correlation coefficient (reliability) to evaluate the surveys' psychometric properties. Results: Focus groups involving ten faculty members and 15 residents were conducted, and the following domains were identified: a) facilitators for resident participation, b) barriers, c) strategies for introducing research into the curriculum, d) arguments supporting research activities throughout medical residency, and e) profile of research-motivated residents. Both residents and faculty members identified a lack of protected time and adequate mentoring as the major barriers. A gender gap was found related to international publications (34% vs. 66% women/men); women perceived that research activities 'compete with other activities' (OR: 2.04, 95% CI 1.03 to 4.07). Conclusions: Research is highly valued by both residents and faculty members at a Latin-American university with a strong academic output. Major barriers to promoting research in this context include lack of protected time and effective mentoring, and gender gaps. Strategies proposed to improve research within medical residency programs include: establishing an interdisciplinary mentoring program between residents and researchers, promoting elective rotations, and rewarding proposals that consider gender equity.

Introducción: Las actividades de investigación tienen un impacto positivo en el rendimiento de los médicos residentes. Falta información sobre investigaciones desarrolladas por residentes de países en vías de desarrollo. Nuestro objetivo fue evaluar las barreras y facilitadores para la investigación en programas de residencia en una Facultad de Medicina de América Latina. Métodos: Se llevó a cabo un diseño de estudio de metodología mixta. Utilizamos un enfoque de teoría fundamentada para la fase cualitativa, recopilando los datos a través de entrevistas semiestructuradas y grupos focales con profesores y residentes. Para la fase cuantitativa, se administraron encuestas a residentes y profesores. Para evaluar las propiedades psicométricas de las encuestas utilizamos análisis factorial y scree plot (validez); alfa de Cronbach y coeficiente de Correlación Intraclase (confiabilidad). Resultados: Se realizaron grupos focales que incluyeron diez profesores y quince residentes, y se identificaron los siguientes dominios: a) facilitadores para la participación de los residentes, b) barreras, c) estrategias para introducir la investigación en el currículo, d) argumentos que respaldan las actividades de investigación durante la residencia, y e) perfil de los residentes motivados en la investigación. Tanto los residentes como el profesorado identificaron la falta de tiempo protegido y la ausencia de tutoría adecuada como las principales barreras. Se encontró una brecha de género relacionada con las publicaciones internacionales (34% vs 66% mujeres/hombres), las mujeres percibieron que las actividades de investigación 'compiten con otras actividades' (OR: 2.04, IC 95% 1.03 a 4.07). Conclusiones: Los residentes y profesores de una universidad latinoamericana de alta productividad valoran mucho la investigación. La presencia de brecha de género, la falta de tiempo protegido y de tutorías destacan como las principales barreras. Las estrategias propuestas para mejorar la investigación dentro de los programas de residencia son: establecer un programa de tutoría interdisciplinario entre residentes e investigadores; promover las rotaciones electivas; y premiar propuestas que consideren la equidad de género.