Biology subjects

Jubair, M.

Publications and source records attributed to Jubair, M..

3 recordsLinked to original sources

bioRxiv2026

Genomic Surveillance of Respiratory Syncytial Virus among Patients with Acute Respiratory Infection through Hospital-Based Influenza Surveillance Platforms in Bangladesh, August 2024-December 2025

BackgroundRSV is one of the major contributing factors of acute lower respiratory tract infection among younger children who are below five years old; over 95% of the burden falls on low- and middle-income countries. Bangladesh faces a substantial pediatric RSV burden yet lacks post-pandemic whole-genome data. Approval of nirsevimab and maternal vaccines (Arexvy, Abrysvo), underscores the need for region-specific genomic surveillance to inform prevention and control strategies. ObjectivesTo conduct the whole-genome sequencing (WGS) study of RSV in Bangladeshi population, characterizing viral genotypic diversity, phylogenetics, F and G protein mutations, glycosylation dynamics, while generating and depositing complete genomes in GISAID. MethodsBetween August 2024 and December 2025, of 1,390 RSV-positive specimens (Ct [≤]35), 59 high-viral-load samples (Ct [≤]25) were selected for whole-genome sequencing using Oxford Nanopore Technology (ARTIC primers), assembled with MIRA v2.0.0, and analyzed via Augur/Nextstrain, Nextclade, and NetNGlyc/NetOGlyc 4.0. ResultsOf 11,874 patients, 1,390 (11.7%) were RSV-positive (RSV-A 94.6%). From selected 59 RSV-positive cases, 49 high-quality genomes were generated (83.1% pass; 94.7% completeness; median depth 1,500x, range 443-4,948): 43 RSV-A (ON1; A.D.3.7 63%, A.D.3 19%, A.D.3.12 9%, A.D.3.1 7%, A.D.1.11 2%) and 6 RSV-B (BA9/B.D.E.1). S276N at antigenic site II (34.9% RSV-A) and S389P in all RSV-B were detected; neither confers resistance to nirsevimab or palivizumab. An F protein N75 N-glycosylation site was fixed in all RSV-A; RSV-B acquired HVR2 N256 glycan in 67%. All 49 genomes were deposited in GISAID. ConclusionThis WGS study of RSV in the Bangladeshi population confirms LMIC nanopore surveillance feasibility, multi-lineage co-circulation, and intact conservation of all vaccine and antibody targets. Progressive glycan remodeling warrants monitoring. These findings establish a genomic baseline to guide nirsevimab and maternal vaccine deployment in Bangladesh, with direct relevance for RSV surveillance programs across South Asia.

evolutionary biology↗

bioRxiv2024

Pathogens and Antimicrobial Resistance Genes in Household Environments: A Study of Soil Floors and Cow Dung in Rural Bangladesh

In low- and middle-income countries, living in homes with soil floors and animal cohabitation may expose children to fecal organisms, increasing risk of enteric and antimicrobial-resistant infections. Our objective was to understand whether cow cohabitation in homes with soil floors in rural Bangladesh contributed to the presence and diversity of potential pathogens and antimicrobial resistance genes (ARGs) in the home. In 10 randomly selected households in rural Sirajganj District, we sampled floor soil and cow dung, which is commonly used as sealant in soil floors. We extracted DNA and performed shotgun metagenomic sequencing to explore potential pathogens and ARGs in each sample type. We detected 6 potential pathogens in soil only, 49 pathogens in cow dung only, and 167 pathogens in both soil and cow dung. Pathogen species with relative abundances >5% in both soil floors and cow dung from the same households included E. coli (N=8 households), Salmonella enterica (N=6), Klebsiella pneumoniae (N=2), and Pseudomonas aeruginosa (N=1). Cow dung exhibited modestly higher pathogen genus richness compared to soil floors (Wilcoxon signed-rank test p=0.002). Using Bray-Curtis dissimilarity, pathogen species community composition differed between floors and cow dung (PERMANOVA p<0.001). All soil floors and cow dung samples contained ARGs against antibiotic classes including sulfonamides, rifamycin, aminoglycosides, lincosamides, and tetracycline. Paired floor and cow dung samples shared ARGs against rifamycin. Our findings support the development of interventions to reduce soil and animal feces exposure in rural, low-income settings. ImportanceIn low-income countries, inadequate housing materials and animal cohabitation can lead to fecal contamination of rural homes. Contaminated soil floors are difficult to clean and may harbor organisms causing illness and antibiotic resistance, especially in young children, who frequently ingest soil. We sequenced soil floor and cow dung samples from households in Sirajganj district, Bangladesh and identified pathogens and antibiotic resistance genes. We detected 167 pathogens in both soil and cow dung; pathogens present in both sample types at the highest relative abundances were E. coli, Salmonella enterica, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Antibiotic resistance genes were found in all samples. In cow dung, the most common genes conferred resistance to the antibiotics lincosamide, rifamycin, cephamycin, and tetracycline. In soil floors, the most common genes conferred resistance to rifamycin, sulfonamides, and aminoglycosides. Household soil and cow dung may be important reservoirs of pathogens and antimicrobial resistance in low-income countries.

microbiology↗

bioRxiv2024

Natural Bacteriocins as Potential Drug Candidates Targeting Core Proteins in Mastitis Pathogens of Dairy Cattle

Mastitis poses a major challenge in the dairy industry, with rising antibiotic-resistant strains underscoring the urgent need for alternative antimicrobial strategies. This study aimed to (i) identify essential core proteins in clinical mastitis (CM)-causing pathogens using genomic approach, and (ii) assess the efficacy of natural antimicrobial peptides as novel therapeutic agents targeting the selected core proteins for the rational management of mastitis in dairy cows. Through a core genomic analysis of 16 CM-causing pathogens, including strains of Staphylococcus aureus, S. warneri, Streptococcus agalactiae, S. uberis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, P. putida, and P. asiatica, we identified 65 core proteins shared among these pathogens. Among them, ten proteins including PhoH, TrpB, FtsZ, HslV, HupB, RibH, InfA, MurA, GlxK, and Rho were found to be essential for the survival and virulence of these pathogens. Importantly, further novelty, resistance, and virulence assessments identified Rho and HupB as potential therapeutic targets. A comprehensive screening of 70 bacteriocin peptides (BPs) revealed 14 BPs that effectively interacted with both Rho and HupB proteins. Further analysis showed that BP8 and BP32 disrupt Rho protein function by blocking transcription termination process, while BP8, BP39, and BP40 prevent HupB from binding to DNA. These findings confirm the promising stability and efficacy of BP8 against both target proteins in CM-pathogens, highlighting it as a promising broad-spectrum therapeutic agent. Our computational study identified Rho and HupB as key proteins in CM-causing pathogens, which can be targeted by natural bacteriocins like BP8, suggesting its potential for developing effective and sustainable therapeutics against mastitis in dairy cattle. Author SummaryMastitis poses a significant threat to the global dairy industry, with rising antibiotic resistance necessitating alternative therapeutic strategies. This study identified essential core proteins in clinical mastitis-causing pathogens through a genomic approach and evaluated natural antimicrobial peptides (bacteriocins) as novel therapeutic agents. Through a core-genomic analysis, Rho and HupB were identified as key therapeutic targets. Bacteriocin peptides such as BP8 demonstrated promising efficacy by disrupting regular transcription termination process and DNA replication, offering a promising solution for next-generation mastitis therapies. The findings underscore the potential of BP8 as a sustainable, broad-spectrum antimicrobial agent, contributing to the rational management of mastitis in dairy cattle.

bioinformatics↗