Khalid, K. | Search bioRxiv

bioRxiv2022

In-silico design and assessment of OprD-based multi-epitope vaccine against Acinetobacter baumannii

Gram-negative, opportunist pathogen Acinetobacter baumannii is notorious for causing a plethora of nosocomial infections predominantly respiratory diseases and blood-stream infections. Due to resistance development towards last-resort antibiotics, its treatment is becoming increasingly difficult. Despite numerous therapeutic developments, no vaccine is available against this ubiquitous pathogen. It is therefore apropos to formulate a rational vaccine plan to get rid of the super-bug. Considering the importance of Outer Membrane Porin D (OprD) as a potential vaccine candidate, we methodically combined the most persistent epitopes present in the A. baumannii strains with the help of different immunoinformatic approaches to envisage a systematic multi-epitope vaccine. The proposed vaccine contains highly immunogenic stretches of linear B-cells, cytotoxic T lymphocyte epitopes, and helper T lymphocyte epitopes of outer membrane porin OprD. The finalized epitopes proved to be significant as they are conserved in A. baumannii strains. The final 3D structure of the construct was projected, refined, and verified by employing several in silico approaches. Apt binding of the protein and adjuvant with the TLR4 suggested significantly high immunogenic potential of our designed vaccine. MD simulations showed highly stable composition of the protein. Immune simulations disclosed a prominent increase in the levels of the immune response. The proposed vaccine model is proposed to be thermostable, immunogenic, water-soluble, and non-allergenic. However, this study is purely computational and needs to be validated by follow-up wet laboratory studies to confirm the safety and immunogenicity of our multi-epitope vaccine.

bioinformatics↗

bioRxiv2018

Initial Sequencing and Characterization of Gastrointestinal and Oral Microbiota in Urban Pakistani Adults Reveals Abnormally High Levels of Potentially Starch Metabolizing Bacteria in the General Population

We describe the characterization of the gastrointestinal tract (gut) and oral microbiota (bacteria) in 32 urban Pakistani adults representing seven major geographies and six ethnicities in the country. Study participants were between ages 18 and 40, had body mass index between 18 and 25 Kg/m2, and were early-career students or professionals belonging to 25 major cities of the country. These individuals donated a total of 61 samples (32 gut and 29 oral) that were subjected to 16S ribosomal RNA (rRNA) gene sequencing. Microbiome composition of Pakistani individuals was compared against the uBiome database of selected individuals who self-reported to be in excellent health. Using the crude measure of percentage overlap or similarity between the gut microbiota profile of Pakistani and uBiome dataset as proxy for health, our sequencing indicated that the Pakistani gut microbiota was moderately healthy relative to the uBiome dataset and Pakistani women appeared healthier relative to men. The Pakistani gut microbiome seemed susceptible to obesity and weight gain, levels of probiotics was very high likely due to the popularity of milk-based and fermented foods in the Pakistani diet, and bacteria that metabolize starch and carbohydrates (typically seen in the gut microbiota of honey bee) were abnormally enriched in the gut of Pakistani men. Our investigations reveal serious issues with the dietary habits and lifestyle of Pakistani individuals of consuming food enriched in high carbohydrates and fats, overcooked in oil and spices, following a sedentary lifestyle, little or no daily intake of fresh fruits, over-consumption of antibiotics from a very early age, and health and hygiene standards that do not meet international standards. Our sequencing is the first step towards generating a country-wide understanding of the impact of the local diet and lifestyle on Pakistani gut microbiota and can help understand its overall association with health and wellness.

microbiology↗