Single-molecule long-read sequencing to enable high-resolution analysis and comparative genomics of the clinical Clostridioides difficile ECDC/Leeds-Leiden reference collection

Clostridioides difficile constitutes the main source of healthcare-associated infectious diarrhea across the globe, causing a disease known as C. difficile infection (CDI) associated with prolonged hospital stay and increased mortality. Whole-genome sequencing (WGS) approaches applied to the study of C. difficile have revealed a highly variable 4.1-4.3 Mb genome that is not only rich in mobile genetic elements but is also highly complex to assemble due to the presence of numerous repeat regions. Thus, conventional short-read sequencing technologies have had limited success in resolving C. difficile genomes and have led to incomplete, and incorrectly assembled genomes. In this study, we intend to employ single-molecule real-time (SMRT) long-read sequencing to obtain complete, gapless C. difficile genomes and enable a high-resolution genome-wide analysis and comparison of clinical reference strains isolated from patients across Europe contained in the ECDC/Leeds-Leiden reference collection. This sequenced collection will be made publicly available in the European Nucleotide Archive (ENA)/NCBI to stimulate further research on different aspects, both fundamental and clinical, of CDI with the aim of developing better preventive, therapeutic/diagnostic, and typing strategies.

Keywords:BIOINFORMATICS, SEQUENCE ANALYSIS, BACTERIOLOGY

Disciplines:Analysis of next-generation sequence data, Bioinformatics data integration and network biology, Bacteriology, Infectious diseases