Ngeer/-PHYLOGENETIC-AND-GENOMIC-ANALYSIS-OF-MULTI-RESISTANCE-IN-SALMONELLA-ENTERICA-
Domain:
healthcareRecord type:
software
Creator:
Nge
Host:
The study investigates how phylogenetic relationships shape the distribution and evolution of multidrug resistance genes in Salmonella enterica from diverse African sources. It combines genomic characterization with evolutionary analysis to identify resistance determinants and their evolutionary relationships.
PHYLOGENETIC AND GENOMIC ANALYSIS OF MULTI RESISTANCE IN SALMONELLA ENTERICA
The study investigates how phylogenetic relationships shape the distribution and evolution of multidrug resistance genes in Salmonella enterica from diverse African sources. It combines genomic characterization with evolutionary analysis to identify resistance determinants and their evolutionary relationships.
Methodology Overview
-This repository contains a comprehensive bioinformatics pipeline for analyzing antimicrobial resistance (AMR) in Salmonella enterica isolates from African sources. The analysis integrates whole-genome sequencing, resistance gene profiling, phylogenetic reconstruction, and comparative genomics to elucidate the distribution and evolution of multidrug resistance mechanisms.
-Pipeline Architecture
The entire workflow is implemented using Nextflow, a workflow management system designed for scalable and reproducible bioinformatics analysis. All scripts and configuration files are located in the ./scripts directory.
-1. Data Retrieval
Source
Database: NCBI Pathogen Detection database
Isolates: 20 Salmonella enterica strains from diverse African countries (Tanzania, Nigeria, South Africa, Tunisia, Malawi, Ethiopia, Uganda, Kenya, Mauritius, Democratic Republic of the Congo, Burkina Faso)
Sequencing Platform: Illumina (short-read data)
Metadata Collected:
BioProject accession numbers
BioSample identifiers
SRA (Sequence Read Archive) accessions
Strain identifiers
Assembly accessions
Isolation source (clinical specimens, food animals, food products)
Geographic origin and year of isolation
Data Preparation
Genome sequences and associated metadata are downloaded and organized prior to analysis. A manifest file (Table 1 in manuscript) contains all strain information including size, region, source, and sequencing platform details.
Nextflow Script: scripts/01_data_retrieval.nf
2. Genome Annotation and Resistance Gene Identification
2.1 Genome Annotation
Tool: Rapid Annot …
Similar
Antimicrobial resistance in Salmonella enterica serovar Enteritidis in MoroccoGenomic Analysis of Antimicrobial Resistance and Resistance Plasmids in Salmonella Serovars from Poultry in NigeriaGenomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East AfricaEnteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar TyphiAntimicrobial resistance pattern in Salmonella enterica from clinical and poultry sources in Calabar, NigeriaGenomic surveillance of Salmonella enterica serotype Minnesota strains from poultry products imported into South Africa