Whole genome dataset of bacterial strains isolated from urine analysed by Oxford Nanopore sequencing technologies in Ouagadougou, Burkina Faso

Abstract

A collection of 21 bacterial isolates recovered from urine specimens collected between September 2018 and February 2019 at Saint-Camille and SCHIPHRA hospitals in Ouagadougou, Burkina Faso, is presented. Isolates were identified using the API 20E system and tested for antibiotic susceptibility according to CASFM 2018 guidelines. Genomic DNA was extracted, barcoded with the SQK-RBK114.96 Rapid Barcoding Kit, and sequenced on an Oxford Nanopore MinION Mk1C using an R10.4.1 flowcell. Basecalling was performed with Dorado, and reads were quality filtered prior to de novo assembly with Flye, followed by polishing with Racon and Medaka. Assemblies were evaluated with QUAST, taxonomically assigned with Kraken2, and annotated with Bakta. The dataset comprises 21 barcode-specific raw read sets (1.5 million reads; 4.9 Gb), polished genome assemblies, per-isolate metadata including collection site, collection date, and antibiotic susceptibility measurements, and quality assessment outputs including read statistics, assembly metrics, and functional annotation completeness estimates. All data are available under NCBI BioProject PRJNA1307828. These data provide a useful resource for long-read bacterial genome assembly benchmarking, comparative genomics, and analyses integrating phenotypic and genomic antimicrobial resistance information.