Biology subjects

Dada, R. A.

Publications and source records attributed to Dada, R. A..

4 recordsLinked to original sources

bioRxiv2026

Enteroaggregative Escherichia clade I from Nigeria

Escherichia coli, the Escherichia type species, is present in mammalian and avian intestinal microbiota, and includes both commensals and pathogens. Other Escherichia species are understudied because they are less commonly associated with human disease and because of paucity of tools that can correctly delineate them from E. coli. However, other species of this genus including Escherichia albertii and Escherichia fergusonii are repeatedly reported as diarrhoeagenic. We hypothesized that some bacteria fitting the definition of enteroaggregative E. coli (EAEC) belong to species other than E. coli. We used phylogeny to determine the species of 2,818 Escherichia genomes from diarrhoea epidemiology studies in Nigeria. Phylogeny speciation was confirmed using GTDB-tk and ClermonTyping. Virulence genes were detected using ARIBA/Virulencefinder database and multilocus sequence typing performed using the Achtman scheme. Fourteen non-coli Escherichia genomes were identified-- Escherichia clade I ST485 (11), Escherichia ruysiae ST5792 (2) and Escherichia fergusonii ST5636 (1). All the Escherichia clade I ST485 carry EAEC virulence genes aap, aar, astA and air, as well as hlyF, eatA, tsh, traT, and chuA virulence genes. Interestingly, 62% of enteroaggregative Escherichia clade I ST485 genomes listed on Enterobase are from Africa isolates, despite only 3% of genomes overall coming from the continent. Our results suggest that non-coli Escherichia species are infrequently isolated from human stool, but, when they are, they are misidentified as E. coli so that their significance is largely overlooked. Escherichia clade I ST485 is a globally disseminated enteroaggregative Escherichia clade I lineage that is common in Africa. Author SummaryEscherichia clade I are rarely associated with disease and because of the difficulty in differentiating them from Escherichia coli in routine laboratory, they are often misidentified as Escherichia coli leading to the underestimation of their impact on the burden of disease. Additionally, some clones of Escherichia clade I also carry genetic markers that have been used to define Enteroaggregative Escherichia coli (EAEC), a cause of persistent diarrhoea in developing countries and travellers diarrhoea in developed economies. EAEC has also been associated with malnutrition and poor growth among children in developing economies. We here describe clones of Escherichia clade I (ST485) that carries enteroaggregative genes and in some cases, recovered from diarrhoeal cases. We show from genomes deposited on Enterobase and our study, that this clone is globally disseminated, often associated with human infections and often misidentified as Escherichia coli. We also describe other non-coli Escherichia other than Escherichia clade I isolated from humans. We suggest that the Escherichia clade I clone carrying enteroaggregative genes may be described as Enteroaggregative Escherichia clade I.

microbiology↗

bioRxiv2026

Refining the Serine Protease Autotransporters of Enterobacteriaceae (SPATE) gene detection in Enteroaggregative Escherichia coli genomes uncovers differential SPATE distribution by phylogeny

BackgroundEnteroaggregative Escherichia coli (EAEC) are a heterogenous pathotype, implicated in acute and persistent diarrhoea especially in developing countries. Serine Protease Autotransporters of Enterobacteriaceae (SPATEs) are Type V Secretory System trypsin-like proteases repeatedly reported from EAEC. This study aimed to determine SPATE encoding-gene prevalence among EAEC and their association with diarrhoea. We screened 881 EAEC genomes from four recent epidemiological studies in Nigeria for 23 SPATE-encoding genes, initially using ARIBA and the Virulencefinder database. ResultsInitial screening inflated SPATE gene content, particularly in genomes with multiple SPATEs, due to cross detection of highly similar sequences and other artefacts. We developed and validated refined methodology, which detected 478 of 1,156 original SPATE calls and also identified SPATE miscalls from previous datasets in the literature. The most prevalent SPATE-encoding gene in our EAEC collection was sepA 297(33.71%), closely followed by sat 360 (29.74%). pic, encoding a SPATE with mucinase activity, was found in 65 (7.4%) genomes and associated with diarrhoea (p=0.00004). EAEC strains belonging to E. coli phylogroups A, B1 or C carried, on average, one SPATE gene per genome while >1 was typically detected in phylogroup B2 EAEC. Other EAEC carried few or no SPATE genes. ConclusionsOur study shows that multifunctional genome analysis tools may have to be refined for certain gene families to avoid overestimation. SPATEs are not as prevalent as previously thought but they remain common among EAEC, particularly among phylogroup A, B1, B2 and C, pointing to the possibility that they make lineage-specific contributions to disease.

microbiology↗

bioRxiv2025

Genomic epidemiology of enteropathogenic Escherichia coli (EPEC) in southwestern Nigeria

BackgroundEnteropathogenic Escherichia coli (EPEC) are etiological agents of diarrhea. We studied the genetic diversity and virulence factors of EPEC in southwestern Nigeria, where this pathotype is rarely characterized. Methodology/ Principal findingsEPEC isolates (n=96) recovered from recent southwestern Nigeria diarrhea case-control studies were whole genome-sequenced using Illumina technology. Genomes were assembled using SPAdes and quality was evaluated using QUAST. Virulencefinder, SeroTypefinder, and Resfinder were used to identify virulence genes, serotypes, and resistance genes, while multilocus sequence typing was done by STtyping. Single nucleotide polymorphisms (SNPs) were called out of whole genome alignment using SNP-sites and a phylogenetic tree was constructed using IQtree. Thirty-nine of the 96 (40.6%) EPEC isolates were from cases of diarrhea. Nine isolates from diarrhea patients and four from healthy controls were typical EPEC, harboring bundle-forming pilus (bfp) genes whilst the rest were atypical EPEC. Fifteen isolates were EPEC-EAEC hybrids. Atypical serotypes O71:H19 (16, 16.6%), O108:H21 (6, 6.3%), O157:H39 (5, 5.2%), and O165:H9 (4, 4.2%) were most prevalent; only 8(8.3%) isolates belonged to classical EPEC serovars. The largest clade comprised ST517 isolates, of O71:H19 and O165:H9 serovars harboring multiple siderophore and serine protease autotransporter genes. An O71:H19 subclade comprised isolates <10 SNPs apart, representing a likely outbreak involving 15 children, four presenting with diarrhea. Conclusion/ SignificanceLikely outbreaks, of typical O119:H6(ST28) and atypical O127:H29(ST7798) were additionally identified. EPEC circulating in southwestern Nigeria are diverse and differ substantially from well-characterized lineages seen previously elsewhere. EPEC carriage and outbreaks could be commonplace but are largely undetected, hence, unreported, and require genomic surveillance for identification.

microbiology↗

bioRxiv2025

Transmissible antimicrobial resistance in Escherichia coli isolated from household drinking water in Ibadan, Nigeria

Contaminated household water in peri-urban urban communities is a reservoir for virulent Escherichia coli, but its role in the environmental transmission of antibiotic resistance genes (ARGs) remains poorly understood. This study characterized E. coli from household water and additionally aimed to investigate the transmissibility of ARGs from drug-resistant isolates. Twenty-five E. coli from thirteen household well water sources were tested for resistance to 14 antibiotics by disc diffusion and whole-genome sequenced using the Illumina platform. The ARGs and plasmid replicon types were respectively predicted using ResFinder and PlasmidFinder. Multidrug-resistant strains carrying plasmid replicons found in unrelated strains were conjugated with nalidixic acid-resistant (NALR) E. coli C600 using the solid plate method. Fifteen isolates displayed a multi-drug resistance (MDR) phenotype with 18 possessing ARGs that confer resistance to trimethoprim-sulfamethoxazole, macrolide, sulphonamide, aminoglycoside, chloramphenicol, {beta}-lactams, and tetracycline. Fifteen of the 25 isolates belonged to sequence type detected more than once, and fourteen of these were multidrug resistant. Through solid plate mating, beta-lactam-resistant qnrS1-tet-dfrA14-positive strains bearing IncFI-, IncHI2, and IncHI2A successfully transferred ampicillin resistance to a nalidixic acid-resistant derivative of E. coli-C600. This research highlights the urgent need to safeguard household water sources against fecal contamination to curb the dissemination of ARGs among bacterial populations in this environment.

microbiology↗