A computational quest for identifying potential vaccine candidates against Moraxella lacunata: a multi-pronged approach.

Moraxella lacunata is an emerging gram-negative bacterium that is responsible for multiple nosocomial infections. The bacterium is evolving resistance to several antibiotics, and currently, no effective licensed vaccines are available, which warrants the search for new therapeutics. A multi-epitope-based vaccine has been designed for M. lacunata. The complete proteome of M. lacunata contains 10,110 core proteins. Subcellular localization analysis revealed the presence of five proteins in the extracellular matrix, while 19 proteins were predicted to be located in the outer membrane, and 21 proteins were predicted to be located in the periplasmic region. Only two proteins, the type VI secretion system tube protein (Hcp) and the transporter substrate-binding domain-containing protein, were selected for epitope prediction as they fulfilled all the criteria for being potential vaccine candidates. Shortlisted epitopes from the selected proteins were fused together using "GPGPG" linkers to overcome the limitations of single-epitope vaccines. Next, the cholera toxin-B adjuvant was attached to the peptide epitope using an EAAAK linker. Docking analysis was performed to examine the interaction between the vaccine and immune cell receptors, revealing robust intermolecular interactions and a stable binding conformation. Molecular dynamics simulation findings revealed no drastic changes in the binding conformation of complexes during the simulation period. The net binding free energy of vaccine-receptor complexes was estimated using the molecular mechanics energies combined with the Poisson-Boltzmann and surface area continuum solvation (MM-PBSA) method. The reported values were -586.38 kcal/mol, -283.74 kcal/mol, and -296.88 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. Furthermore, the molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-GBSA) analysis predicted binding free energies of -596.69 kcal/mol, -287.39 kcal/mol, and -298.28 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. The theoretical vaccine design proposed in the study could potentially serve as a powerful therapeutic against targeted pathogens, subject to validation through experimental studies.Communicated by Ramaswamy H. Sarma.

A chemoinformatic-biophysics based approach to identify novel anti-virulent compounds against Pseudomonas aeruginosa disulfide-bond protein A1.

The conventional course of drug discovery is a lengthy, expensive and complex process and often experiences a high failure rate. This in-silico based study screened novel drug molecules against Pseudomonas aeruginosa disulfide-bond protein A1 (PaDsbA1; PDB ID of 4ZL7) using a variety of chemoinformatic and biophysics approaches. The structure-based virtual screening identified three antipseudomonal compounds (BDC_30129064, BDC_20699588 and BDC_25329008) that targeted PaDsbA1 enzyme with a binding energy score of -7.8 kcal/mol, -7.7 kcal/mol and -7.7 kcal/mol, respectively. The compounds revealed deep binding at the enzyme active pocket with close distance hydrogen bond interactions with Thr46, Pro55, Val58, Arg62, His88, and Asp180. The co-crystalized hexaethylene glycol revealed a binding energy of -6.02 kcal/mol. The docked compounds were further subjected to molecular dynamics simulation analysis in order to check the dynamic movements of docked complexes. The complexes reported no drastic changes during simulation time. In the simulation, stable compounds binding and docked conformation were accomplished. The docking and simulation results were validated using free binding energies calculation through molecular mechanics with generalized born surface area solvation and molecular mechanics Poisson Boltzmann surface area (MMGBSA/MMPBSA) approaches. The net binding energy estimated by MMGBSA for BDC_30129064, BDC_20699588 and BDC_25329008 was -75.07 kcal/mol, -77.87 kcal/mol and -59.1 kcal/mol, respectively while that of MMPBSA for the compounds was -72.47 kcal/mol, -78.99 kcal/mol and -60.991 kcal/mol, respectively. The physiochemical properties of the selected compounds indicated them to be physiochemically stable with good absorption, distribution, metabolism and elimination properties. From the above observations and predictions, the compounds can be recommended for further experimental validation in order to decipher their anti-virulence capacity in blocking disulfide bond formation in P. aeruginosa.Communicated by Ramaswamy H. Sarma.

Extending contact screening within a 50-m radius of an index tuberculosis patient using Xpert MTB/RIF in urban Pakistan: Did it impact treatment outcomes?

BACKGROUND: Pakistan implemented initiatives to detect tuberculosis (TB) patients through extended contact screening (ECS); it improved case detection but treatment outcomes need assessment. OBJECTIVES: To compare treatment outcomes of pulmonary TB (PTB) patients detected by ECS with those detected by routine passive case finding (PCF). METHODS: A cohort study using secondary program data conducted in Lahore, Faisalabad and Rawalpindi districts and Islamabad in 2013-15. We used log binomial regression models to assess if ECS was associated with unfavorable treatment outcomes (death, loss-to-follow-up, failure, not evaluated) after adjusting for potential confounders. RESULTS: We included 79,431 people with PTB; 4604 (5.8%) were detected by ECS with 4052 (88%) bacteriologically confirmed. In all PTB patients the proportion with unfavorable outcomes was not significantly different in ECS group (9.6%) compared to PCF (9.9%), however, among bacteriologically confirmed patients unfavorable outcomes were significantly lower in ECS (9.9%) than PCF group (11.6%, P = 0.001). ECS was associated with a lower risk of unfavorable outcomes (adjusted relative risk (aRR) 0.90; 95% CI 0.82-0.99) among 'all PTB' patients and bacteriologically confirmed PTB patients (aRR 0.91; 95% CI 0.82-1.00). CONCLUSION: In PTB patients detected by ECS the treatment outcomes were not inferior to those detected by PCF.

Did diabetes mellitus affect treatment outcome in drug-resistant tuberculosis patients in Pakistan from 2010 to 2014?

Settings: All hospitals managing drug-resistant tuberculosis (DR-TB) according to national guidelines in Pakistan. Objectives: To assess the effect of diabetes mellitus (DM) and factors associated with unfavourable outcomes in DR-TB. Methods: A cross-sectional study based on a retrospective record review of patients enrolled on DR-TB treatment from 2010 to 2014 in Pakistan. DR-TB data reported to Pakistan's National TB Control Programme on a monthly basis were used for the study. Result: Among 5811 patients enrolled on second-line drugs, 8.8% had DM. Overall, 68.9% had favourable outcomes. No association was found between DM and DR-TB treatment outcomes (risk ratio 0.90, 95%CI 0.74-1.05). Unfavourable outcomes were more frequent among DR-TB patients with human immunodeficiency virus (HIV) co-infection (OR 11.58, 95%CI 2.20-60.72), extensively drug-resistant TB patients (OR 5.36, 95%CI 1.00-28.72), patients with exposure to both first-line and second-line anti-tuberculosis drugs (OR 2.45, 95%CI 1.21-4.97) and those with a previous history of treatment in the private sector (OR 1.53, 95%CI 1.16-2.02). Conclusion: Although there were limitations to correctly measuring DM and its management, DM appears not to be a risk factor for unfavourable outcomes in DR-TB patients in our study. DR-TB and HIV co-infection, second-line drug resistance and history of treatment in the private sector were nevertheless more frequently associated with adverse outcomes.

Contexte : Tous les hôpitaux prenant en charge la tuberculose pharmacorésistante (TB-DR) selon les directives nationales du Pakistan.Objectif : Evaluer l'effet du diabète (DM) et les facteurs associés à un résultat défavorable du traitement de la TB-DR.Méthode : Etude transversale basée sur une revue rétrospective de dossiers de patients enrôlés dans un traitement de TB-DR de 2010 à 2014 au Pakistan. Les registres de TB-DR envoyés au programme national de lutte contre la TB chaque mois ont été utilisés pour l'étude.Résultats : Parmi 5811 patients enrôlés dans un traitement par médicaments de deuxième ligne, 8,8% avaient un DM. Dans l'ensemble, 68,9% ont eu des résultats favorables. Il n'a pas été trouvé d'association entre le DM et le résultat du traitement de la TB-DR (ratio de risque 0,90 ; IC95% 0,74­1,05). Les facteurs associés à des résultats défavorables sont la coinfection par TB-DR et le virus de l'immunodéficience humaine (VIH) (OR 11,58 ; IC95% 2,20­60,72), la TB ultrarésistante (OR 5,36 ; IC95% 1,00­28,72), l'exposition à la fois aux médicaments de première ligne et de deuxième ligne (OR 2,45 ; IC95% 1,21­4,97) et des antécédents de traitement dans le secteur privé (OR 1,53 ; IC95% 1,16­2,02).Conclusion : Dans notre étude, avec ses limites en termes de mesures correctes du DM et de sa prise en charge, le DM ne semble pas être un facteur de risque de résultat défavorable pour les patients TB-DR. Par contre, la coinfection TB-DR et VIH, la résistance aux médicaments de deuxième ligne et les antécédents de traitement dans le secteur privé ont été associés à des résultats médiocres.

Marco de referencia: Todos los hospitales que suministran tratamiento contra la tuberculosis farmacorresistente (TB-DR) en el marco de las directrices nacionales de Pakistán.Objetivo: Evaluar el efecto de la diabetes (DM) sobre el desenlace de la TB-DR y los factores que se asocian con los desenlaces desfavorables.Método: Un estudio transversal realizado a partir del examen retrospectivo de las historias clínicas de los pacientes que iniciaron tratamiento por TB-DR del 2010 al 2014 en el Pakistán.Métodos: En el presente estudio se consultaron los registros de los casos de TB-DR que se notifican mensualmente al Programa Nacional de control de la Tuberculosis.Resultados: De los 5811 pacientes que iniciaron tratamiento con medicamentos de segunda línea, el 8,8% sufría DM. En general, el 68,9% de los casos alcanzó desenlaces favorables. No se observó ninguna asociación entre la presencia de DM y el desenlace terapéutico de la TB-DR (riesgo relativo 0,90; IC95% 0,74­1,05). Los factores que se asociaron con desenlaces desfavorables fueron la coinfección por el virus de la inmunodeficiencia humana (VIH) y la TB-DR (OR 11,58; IC95% 2,20­60,72), la TB ultrarresistente (OR 5,36; IC95% 1,00­28,72), la exposición a los dos tipos de fármacos, de primera y de segunda línea (OR 2,45; IC95% 1,21­4,97) y el antecedente de tratamiento antituberculoso en el sector privado (OR 1,53; IC95% 1,16­2,02).Conclusión: Según los resultados del presente estudio, pese a algunas limitaciones en la evaluación correcta de la DM y su tratamiento, no pareciera que la presencia de DM fuese un factor de riesgo de resultados desfavorables del tratamiento de pacientes con TB-DR. Sin embargo, la coinfección por el VIH y la TB-DR, la resistencia a fármacos de segunda línea y el antecedente de tratamiento antituberculoso en el sector privado se asociaron con desenlaces desfavorables.

Population Based National Tuberculosis Prevalence Survey among Adults (>15 Years) in Pakistan, 2010-2011.

BACKGROUND: We aimed to determine the prevalence of pulmonary tuberculosis (TB) amongst the adult population in 2010-2011 in Pakistan. METHOD: A nationwide cross-sectional survey with multistage cluster sampling was conducted among adults (≥15 years) in 95 clusters in 2010-2011. All consenting participants were screened for cough and by chest X-ray. Participants with presumptive TB submitted two sputum samples for smear microscopy, culture, and molecular testing if needed. The TB prevalence estimates were adjusted for missing data and the cluster design. RESULT: Of 131,329 eligible individuals, 105,913 (81%) participated in the survey, of whom 10,471 (9.9%) were eligible for sputum examination. We found 341 bacteriologically positive TB cases of whom 233 had sputum smear-positive TB. The adjusted prevalence estimates for smear and bacteriologically positive TB were 270/100,000 (95% confidence interval (CI) 217-323), and 398/100,000 (95% CI 333-463), respectively. Only 61% of the diagnosed TB cases screened positive on symptoms (cough >2wks), whereas the other TB cases were detected based on X-ray abnormalities. The TB prevalence increased with age and was 1.8 times higher among men than women. The prevalence-to-notification ratio of smear-positive TB was 3.1 (95% CI 2.5-3.7), was higher among men than women, and increased with age. CONCLUSION: Our data suggest that there is under-detection and/or -notification of TB, especially among men and elderly. TB control should be strengthened specifically in these risk groups. X-ray examination should be combined with symptom screening to enhance case detection.