dejenie21/ecoli-sepsis-genomics-ethiopia

Genomic characterization (clonal diversity, resistome, and virulome) of Escherichia coli causing sepsis in Ethiopian tertiary hospitals. # High Clonal Diversity, Resistome, and Virulome of Escherichia coli Causing Sepsis in Ethiopian Tertiary Hospitals: A Multicenter Genomic Study This repository contains the data analysis documentation, custom scripts, and supplementary tracking files for the manuscript: > **High Clonal Diversity, Resistome, and Virulome of Escherichia coli Causing Sepsis in Ethiopian Tertiary Hospitals: A Multicenter Genomic Study** > > *Melese Hailu Legese, Daniel Asrat, Dejenie Shiferaw Teklu, Badrul Hasan, Adane Mihret, Abraham Aseffa, Göte Swedberg* --- ## Project Overview This study presents a multicenter genomic epidemiology surveillance of *Escherichia coli* strains isolated from blood cultures of sepsis patients across tertiary hospitals in Ethiopia. Using Whole Genome Sequencing (WGS), we characterized sequence types (STs), antimicrobial resistance (AMR) genes, virulence factor profiles, and phylogenomic relationships to map out pathogen diversity and transmission dynamics. ## Repository Structure * `data/`: Contains clinical/epidemiological metadata templates and NCBI accession mappings. * `scripts/`: Custom bash, R, and python scripts used for high-performance computing genomic analysis. * `results/`: Standardized outputs from bioinformatic profiling (e.g., MLST, AMRFinderPlus, VFDB, phylogenomics). * `figures_and_tables/`: Code used to generate the plots and figures present in the manuscript. ## Data Availability * **Raw Sequencing Reads:** Deposited in the NCBI Sequence Read Archive (SRA) under BioProject accession number **PRJNA787062**. * **Isolate Metadata:** Fully annotated metadata mapping phenotypic profiles to genomic features can be found in `data/metadata.csv`. ## Contact Updated upstream For queries regarding the bioinformatics pipelines or data anaysis, please open an issue or contact: ======= For queries regarding the bioinformatics pipelines or data analysis, please open an issue or contact: * **Dejenie Shiferaw Teklu** - dejenie21@gmail.com (Ethio …