Biology subjects

Seck, A.

Publications and source records attributed to Seck, A..

4 recordsLinked to original sources

bioRxiv2025

Methods for Quantitative Analyses of Nerve Fiber Deformation in the Myenteric Plexus Under Loading of Mouse Distal Colon and Rectum

Visceral pain in the large bowel is a hallmark of irritable bowel syndrome (IBS) and the primary reason patients seek gastroenterological care. Notably, mechanical distension of the distal colon and rectum (colorectum) reliably evokes abdominal pain and thus understanding mechanotransduction of sensory nerve endings (nerve fibers) in the colorectum is crucial for understanding and treating IBS-related bowel pain. To facilitate such understanding we aimed to establish novel methods to mechanically test, image, and analyze large-strain deformations of networks of nerve fibers in the myenteric plexus of the colorectum, and thus enable quantitative analyses. We successfully delivered circumferential deformation (force or displacement driven) to intact segments of colorectum while maintaining the myenteric plexus in focus during fluorescent imaging to capture the deforming nerve fibers. We also established a semi-automated method to recapitulate the network morphology and a code to calculate the stretch ratios of individual nerve fibers deforming within the myenteric plexus of mouse colorectum. Our code allows plotting of stretch ratios for each fiber, stretch ratios vs. fiber angle, and stretch ratios vs. fiber length. Our methods not only facilitate analyses of deformations of networks of colorectal nerve fibers in the context of visceral nociception but are also applicable to analyzing the in-plane deformation of other two-dimensional fiber networks. We provide free, public access to our analysis code for MATLAB, including input files for a simple test case, at github.uconn.edu/imLab/Fiber-Network_Analyses.

bioengineering↗

bioRxiv2025

Colorectum and Embedded Networks of Nerve Fibers Present Auxetic Responses During Uniaxial Circumferential Extension

Understanding the multiscale mechanics of the colorectum is essential for uncovering the mechanotransductive pathways underlying visceral nociception. Intraluminal distension of the large intestine reliably evokes pain in disorders of gut-brain interaction (DGBIs), yet the tissue-level and nerve fiber-level responses to mechanical loading remain poorly defined. Here, we present results from a novel biomechanical testing framework that integrates uniaxial circumferential extension with high-resolution optical imaging to quantify deformation in both bulk colorectal tissue and embedded sensory nerve fibers. We tested intact, cylindrical colorectal segments from mice using a custom 3-D-printed chamber with intraluminal stainless-steel rods to apply circumferential stretch while maintaining a planar imaging field. We measured bulk-tissue deformation via Digital Image Correlation (DIC), while we assessed stretch in nerve fibers through fluorescence imaging of VGLUT2-labeled afferents analyzed using a custom fiber-network analyses. Across specimens, we observed a consistent auxetic response-characterized by positive axial strain during circumferential extension-at both the macroscale and microscale. Five out of six colorectal specimens exhibited positive axial Green-Lagrange strain (Exx), with an average median Exx of 0.0177, during circumferential extension generating an average median Eyy of 0.1273. Nerve fiber analysis across nine specimens revealed an average median stretch ratio of 1.0631, indicating 6.31% elongation, with substantial heterogeneity driven by fiber orientation. These findings demonstrate that the colorectum and its embedded network of nerve fibers exhibit auxetic behavior, a property that may amplify mechanical signaling and influence nociceptive signaling. Our methods and results provide foundational insight into structure-function relationships of colorectum and inform design of bioinspired auxetic materials.

bioengineering↗

bioRxiv2024

Genomic Diversity and Antimicrobial Resistance of Vibrio cholerae Isolates from Africa: A PulseNet Africa Initiative Using Nanopore Sequencing to Enhance Genomic Surveillance

ObjectivesVibrio cholerae remains a significant public health threat in Africa, with antimicrobial resistance (AMR) complicating treatment. This study leverages whole-genome sequencing (WGS) of V. cholerae isolates from Cote dIvoire, Ghana, Zambia and South Africa to assess genomic diversity, AMR profiles, and virulence, demonstrating the utility of WGS for enhanced surveillance within the PulseNet Africa network. MethodsWe analysed Vibrio isolates from clinical and environmental sources (2010-2024) using Oxford Nanopore sequencing and hybracter assembly. Phylogenetic analysis, multilocus sequence typing (MLST), virulence and AMR gene detection were performed using Terra, Pathogenwatch, and Cloud Infrastructure for Microbial Bioinformatics (CLMB) platforms, with comparisons against 88 global reference genomes for broader genomic context. ResultsOf 79 high-quality assemblies, 67 were confirmed as V. cholerae, with serogroup O1 accounting for the majority (43/67, 67%). ST69 accounted for 60% (40/67) of isolates, with eight sequence types identified overall. Thirty-seven isolates formed novel sub-clades within AFR12 and AFR15 O1 lineages, suggesting local clonal expansions. AMR gene analysis revealed high resistance to trimethoprim (96%) and quinolones (83%), while resistance to azithromycin, rifampicin, and tetracycline remained low ([≤]7%). A significant proportion of the serogroup O1 isolates (41/43, 95%) harboured resistance genes in at least three antibiotic classes. ConclusionsThis study highlights significant genetic diversity and AMR prevalence in African V. cholerae isolates, with expanding AFR12 and AFR15 clades in the region. The widespread resistance to trimethoprim and quinolones raises concerns for treatment efficacy, although azithromycin and tetracycline remain viable options. WGS enables precise identification of species and genotyping, reinforcing PulseNet Africas pivotal role in advancing genomic surveillance and enabling timely public health responses to cholera outbreaks. Data summaryAll supporting data and protocols have been provided within the article or as supplementary data files. The ONT reads have been deposited under BioProject accession PRJNA1192988, while the high-quality Vibrio spp. assemblies have been shared via figshare (Foster-Nyarko, Ebenezer (2024). Genomic Diversity and Antimicrobial Resistance of Vibrio spp. Isolates from Africa: A PulseNet Africa Initiative Using Nanopore Sequencing to Enhance Genomic Surveillance. figshare. Dataset. https://doi.org/10.6084/m9.figshare.27941376.v1). Individual accession numbers for these reads and Biosample IDs are provided in File S2, available with the online version of this article. The accession numbers for the 88 reference genome assemblies included in our analysis are also provided in File S3. Impact statementCholera remains a significant public health challenge in Africa, disproportionately affecting the region due to the ongoing transmission of Vibrio cholerae O1 and the emergence of antimicrobial resistance (AMR). This study demonstrates the utility of Oxford Nanopore Technology (ONT) sequencing in providing high-resolution insights into the genomic diversity, transmission dynamics, and AMR profiles of V. cholerae isolates across Africa. By generating and analysing whole-genome sequences, we identified novel sublineages, high prevalence rates of AMR genes, and virulence traits critical to cholera pathogenesis. These findings contribute to a deeper understanding of the epidemiology and evolution of V. cholerae in Africa, informing targeted intervention strategies. Furthermore, the study highlights the growing threat posed by AMR among V. cholerae isolates, including resistance to key therapeutic antibiotics, such as quinolones and trimethoprim, which could undermine current treatment protocols. Despite this, the absence of resistance to azithromycin and rifampicin among the O1 isolates suggests these drugs may remain viable treatment options, offering a critical avenue for preserving treatment efficacy. This research also underscores the importance of sustained genomic surveillance, capacity building, and regional collaboration to mitigate the public health impact of cholera and other foodborne pathogens. By leveraging WGS technologies and training initiatives, such as the PulseNet Africa genomics workshop, this study provides a framework for strengthening regional capacities to detect, monitor, and respond to cholera outbreaks and the spread of AMR. These efforts align with the African Union and Africa CDCs strategic priorities on health security and AMR, contributing to improved public health systems and cholera control across the continent.

genomics↗

bioRxiv2022

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

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.

microbiology↗