Biology subjects

Lawal, O. U.

Publications and source records attributed to Lawal, O. U..

3 recordsLinked to original sources

bioRxiv2024

TSPDB: A curated resource of tailspike proteins with potential applications in phage research

Phages are ubiquitous viruses that drive bacterial evolution through infection and replication within host bacteria. Phage tailspike proteins (TSPs) are key components of phage tail structures, exhibiting polysaccharide depolymerase activity and host specificity. Despite their potential as novel antimicrobials, few TSPs have been fully characterized due to laborious detection techniques. To address this, we present TSPDB, a curated resource for rapid detection of TSPs in genomics and metagenomics sequence data. We mined public databases, obtaining 17,211 TSP sequences, which were filtered to exclude duplicates and partial sequences, resulting in 8,099 unique TSP sequences. TSPDB contains TSPs from over 400 bacterial genera, with significant diversity among them as revealed by the phylogenetic analysis. The top 13 genera represented were Gram-positive, with Bacillus, Streptococcus, and Clostridium being the most common. Of note, Phage TSPs in Gram-positive bacteria were on average 1 Kbp larger than those in Gram-negative bacteria. TSPDB has been applied in a recent study to screen phage genomes, demonstrating its potential for functional annotation. TSPDB serves as a comprehensive repository and a resource for researchers in phage biology, particularly in phage associated therapy and antimicrobial or biocontrol applications. TSPDB is compatible with bioinformatics tools for in silico detection of TSPs in genomics and metagenomic data, and is freely accessible on GitHub and Figshare, providing a valuable resource for the scientific community.

genomics↗

bioRxiv2024

Phylogenomics of novel clones of Aeromonas veronii recovered from a freshwater lake reveals unique biosynthetic gene clusters

Aquatic ecosystems are important reservoirs for clinically relevant pathogens and antimicrobial resistance genes, thus present a significant risk to global health. Here, we assessed the phylogenomics of Aeromonas veronii (A. veronii) recovered from Lake Wilcox in Ontario using a combination of morphological, biochemical, and whole-genome sequencing (WGS) techniques. Eleven distinct bacterial colonies were isolated and identified as A. veronii (n=9), and two other Aeromonas species (A. caviae and A. allosaccharophila), with significant discrepancies noted between biochemical and WGS identification methods. Of note, 67% (n=6/9) of A. veronii isolates were human pathogens (Pathogenicity score [≥] 0.50). The genomic analysis revealed high genetic diversity among the A. veronii isolates, including the discovery of 41 novel alleles and seven new sequence types (ST) suggesting the lake as a reservoir for multiple human pathogenic clones of this bacterium. The comparison of the newly isolated and sequenced A. veronii with 214 A. veronii genomes revealed significant genetic diversity and suggests potential broad geographical dissemination of strains. Chromosomal genes (OXA-912 and cphA [cphA3, cphA4, cphA7]) genes encoding resistance to {beta}-lactamases were detected in all isolates. Human and non-human pathogenic strains of A. veronii differed in their virulence gene content, with type III secretion systems being associated with human pathogenic isolates. Mobilome analysis revealed the absence of plasmids in A. veronii isolates and the presence of 13 intact the great majority of which were P22-like (Peduoviridae) phages, and nine different insertion sequence families. Novel biosynthetic gene clusters were identified and characterized, indicating the potential for unique secondary metabolite production in A. veronii with different pathogenic potential. Overall, this study underscores the importance of continuous surveillance of aquatic ecosystems for the presence of pathogens, contributing to our understanding of their evolution, potential for human pathogenicity, and the ecological roles of their genetic elements.

microbiology↗

bioRxiv2024

Enable, Empower, Succeed: Harnessing Open Science for Antimicrobial Resistance Containment

Antimicrobial resistance (AMR) poses a significant threat to global health, particularly in Western sub-Saharan Africa where 27.3 deaths per 100,000 lives are affected, and surveillance and control measures are often limited. Genomics research plays a crucial role in understanding the emergence, spread and containment measures of AMR. However, its implementation in such settings is particularly challenging due to limited human capacity. This manuscript outlines a three-day bioinformatics workshop in Cameroon, highlighting efforts to build human capacity for genomics research to support AMR surveillance using readily accessible and user-friendly web-based tools. The workshop introduced participants to basic next-generation sequencing concepts, data file formats used in bacterial genomics, data sharing procedures and considerations, as well as the use of web-based bioinformatics software to analyse genomic data, including in silico prediction of AMR, phylogenetics analyses, and a quick introduction to Linux(C) command line. We provide a detailed description of the relevant training approaches used, including workshop structure, the selection and planning, and utilization of freely available web-based tools, and the evaluation methods employed. Our approach aimed to overcome limitations such as inadequate infrastructure, limited access to computational resources, and scarcity of expertise. By leveraging the power of freely available web-based tools, we demonstrated how participants can acquire fundamental bioinformatics skills, enhance their understanding of biological data analysis, and contribute to the field, even in an underprivileged environment. Our findings highlight the effectiveness of this training approach in empowering local researchers and bridging the bioinformatics gap in genomics surveillance of AMR in resource-constrained settings. Building human capacity for genomics research globally, and especially in resource-constrained settings, is imperative for ensuring global health and sustainable containment of AMR. Data summaryThe authors confirm that all supporting data, code and protocols have been provided within the article or through supplementary data files. Impact StatementAntimicrobial resistance (AMR) is a major global health threat, especially in Western sub-Saharan Africa, where 27.3 deaths per 100,000 lives occur. Genomics research play an instrumental role for understanding AMRs emergence, spread, and containment measures. However, its implementation in these settings is challenging due to limited human capacity. A three-day bioinformatics workshop in Cameroon aimed to build human capacity for genomics research using web-based tools. Participants were introduced to next-generation sequencing concepts, data file formats, data sharing procedures, and web-based bioinformatics software for analysing genomic data. The workshop aimed to overcome limitations like inadequate infrastructure, computational resources, and expertise scarcity. The findings show the effectiveness of this training approach in empowering local researchers and bridging the bioinformatics gap in genomics surveillance of AMR in resource-constrained settings.

scientific communication and education↗