Molecular characterization of extended-spectrum beta-lactamase-producing extra-intestinal pathogenic Escherichia coli isolated in a university teaching hospital Dakar-Senegal

DOSSOUVI, K. M.; Sambe Ba, B.; Lo, G.; Cisse, A.; Ba-Diallo, A.; Ndiaye, I.; Dieng, A.; Ndiaye, S. M. L.; Fall, C.; Tine, A.; Karam, F.; Diagne-Samb, H.; Ngom-Cisse, S.; Diop-Ndiaye, H.; Toure-Kane, C.; Gaye-Diallo, A.; Mboup, S.; Boye, C. S. B.; Dieye, Y.; Seck, A.; Camara, M.

doi:10.1101/2022.07.20.500880

Home/Archive/bioRxiv

bioRxiv · 10.1101/2022.07.20.500880

Molecular characterization of extended-spectrum beta-lactamase-producing extra-intestinal pathogenic Escherichia coli isolated in a university teaching hospital Dakar-Senegal

View original source ↗Export metadata ↓

Abstract

Extra-intestinal pathogenic Escherichia coli (ExPEC), a predominant Gram-negative bacterial pathogen, express a wide range of virulence factors and is responsible of several diseases including urinary tract infections (UTI), nosocomial pneumonia, bacteremia, and neonatal meningitis. ExPEC isolates are often multidrug resistant (MDR) and clones producing extended-spectrum beta-lactamases (ESBL) are increasingly reported all over the world. Seventy-eight clinical ExPEC strains were selected for this study. The majority was from UTIs (n=51), while the rest (n=27) was from pus, sputum, bronchial fluid and vaginal samples (non-uropathogenic ExPEC). Interestingly, 49 out of the 78 ExPEC isolates where considered as community-acquired (CA) and 29 hospital-acquired (HA) bacteria. Antibiotic susceptibility testing was performed using the Kirby-Bauer disc diffusion method. Standard polymerase chain reaction (PCR) was used to screen major ESBL genes (blaCTX-M, blaOXA-1, blaTEM, blaSHV) and blaCTX-M variants (blaCTX-M-1, blaCTX-M-9, blaCTX-M-15, blaCTX-M-25). All the ExPEC strains were resistant to ampicillin, ticarcillin, amoxicillin/clavulanic acid combination, cefalotin, cefotaxime, ceftazidime, cefepime and aztreonam, but showed a high susceptibity to fosfomycin (98.7%, n = 77), ertapenem (96.2%, n = 75), and imipenem (100%). Moreover, isolates harbored at least one ESBL gene, including blaCTX-M (98.7%), blaOXA-1 (78.2%), blaTEM (44.9%) and blaSHV (3.8%). The CTX-M variants were also found with the predominance of blaCTX-M-1 (90.9%) and blaCTX-M-15 (90.9%) followed by blaCTX-M-9 (11.7%), while blaCTX-M-25 was not detected. Despite the resistance to most of the tested antibiotics, ExPEC isolates showed fortunately a good susceptibility to fosfomycin and carbapenems. blaCTX-M (blaCTX-M1, blaCTX-M15) and blaOXA-1 seem to be E. coli major ESBL genes circulating in Senegal. No significant difference was noted when comparing prevalence of ESBL genes detected from CA and HA strains, and from UPEC and non-uropathogenic ExPEC. The high level of resistance to antimicrobials observed stresses the need of establishing an epidemiological surveillance of antimicrobial resistance in both community and hospital settings.

Explore related subjects

microbiology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

DOSSOUVI, K. M., Sambe Ba, B., Lo, G., Cisse, A., Ba-Diallo, A., Ndiaye, I., Dieng, A., Ndiaye, S. M. L., Fall, C., Tine, A., Karam, F., Diagne-Samb, H., Ngom-Cisse, S., Diop-Ndiaye, H., Toure-Kane, C., Gaye-Diallo, A., Mboup, S., Boye, C. S. B., Dieye, Y., Seck, A., Camara, M.. 2022-07-21. Molecular characterization of extended-spectrum beta-lactamase-producing extra-intestinal pathogenic Escherichia coli isolated in a university teaching hospital Dakar-Senegal. https://doi.org/10.1101/2022.07.20.500880

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Polyphyletic origins and lineage-specific expansion of chemosensory systems in phylum Actinomycetota

Phylum Actinomycetota (syn. Actinobacteriota or Actinobacteria), one of the largest well-studied bacterial phyla, is renowned for complex morphology, non-motility, ecological versatility, and secondary metabolite production. Chemosensory systems (CSS) are among the most sophisticated prokaryotic signal transduction architectures, yet their evolutionary distribution in this phylum remains poorly understood. Here, a comparative genomic analysis of 693 high-quality genomes spanning the phylum resolves the diversity, distribution, and evolutionary trajectories of CSS. Despite extensive genomic complexity and ecological versatility, only 6.9% of genomes encode complete CSS clusters, confined to a subset of lineages within a few classes, indicating lineage-specific retention or loss. In contrast, two-component systems (TCS) are ubiquitously abundant, with hybrid kinases enriched in CSS-deficient classes, suggesting functional compensation for the absence of dedicated chemosensory pathways. Basal lineages retain simplified CSS (F1 or F5), whereas Actinomycetes show lineage-specific expansion into multiple classes (F5, F8, F9, and ACF), often co-occurring, indicative of enhanced sensory complexity. The phylogeny of CheA homologs shows a polyphyletic distribution, supporting a mosaic evolutionary history shaped by multiple independent acquisitions, diversification, and gene loss. Collectively, our findings show that, unlike motile bacteria, members of Actinomycetota rely predominantly on TCS-driven regulatory networks, with CSS retained only in select lineages where ecological demands require enhanced environmental sensing. This work provides a phylum-wide evolutionary framework for the emergence, diversification, and functional specialization of CSS in non-motile bacteria.

microbiology↗

bioRxiv2026

Integrating Microbial Ecology and Sustainability: Linking Agricultural Waste Gas Streams to Microbial Community Shifts in a Photobioreactor

Photobioreactors (PBRs) coupled to animal housing offer potential for mitigating gaseous emissions such as CO2 and NH3 while simultaneously producing biomass. Here, we present a time-resolved characterization of microbial community dynamics, with a focus on the genetic potential for carbon and nitrogen metabolism. Using a cone-shaped, helical PBR cultivating Arthrospira platensis (Spirulina) and supplied with exhaust air from a chicken house, we characterized microbial communities over continuous exhaust-air exposure and periodic biomass harvesting. Microbiome and gene-centric profiling revealed temporal variation in community composition and in the representation of genes associated with carbon and nitrogen metabolism. Cycle-based dissolved inorganic nitrogen balances showed that the decrease in dissolved inorganic nitrogen was only partially recovered in harvested biomass, while ammonia-oxidizing microorganisms were associated with structured, low-light niches. These observations indicate ammonia-oxidizing potential but do not establish a quantitatively relevant nitrification flux. Structured carrier matrices provided attached-growth niches harboring microbial populations underrepresented in the circulating suspension, while pre-colonized carriers facilitated biomass development during re-inoculation. Overall, our results show that coupling PBRs to agricultural exhaust streams can support biomass production while sustaining spatially structured microbial communities with taxonomic and functional potential. These findings may inform their further development for emission mitigation and circular biomass production.

microbiology↗

bioRxiv2026

Engineered DNA materials shape microbial physiology and ecological selection

Extracellular DNA (eDNA) is both a structural component of microbial biofilms and a potential reservoir of genetic information, yet its role as an ecological material remains largely unexplored. Here we establish engineered extracellular materials as determinants of microbial physiology and community assembly across increasing biological complexity. A three-dimensional DNA hydrogel altered bacterial stress-associated responses, elicited species-dependent phenotypes and transcriptional changes in a defined consortium, and shaped community succession in wastewater-derived microbiomes. Distinct responses to surface-bound oligonucleotides reveal that DNA presentation matters beyond its mere presence. Strikingly, metagenomic sequencing identified rare, hydrogel-specific candidate junctions linking material-derived DNA to microbial genomic sequences, suggesting a previously unexplored interface between extracellular DNA materials and microbial genetic information. These findings reveal a dual role for engineered DNA: its material organization shapes microbial physiology and ecological selection, while its encoded sequences may engage with microbial genomic processes.

microbiology↗