Computational protocol: Complete Genome Sequences of Four Toxigenic Clostridium difficile Clinical Isolates from Patients of the Lower Hudson Valley, New York, USA

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[…] Clostridium (Clostridiodes) difficile is a Gram-positive, spore-forming, anaerobic bacterium that causes antibiotic-associated diarrhea and life-threatening pseudomembranous colitis. The incidence of C. difficile infections (CDIs) has dramatically increased in the last decade. It is estimated that approximately 453,000 incident infections with approximately 29,000 deaths occurred in the United States in 2011 (). The pathogenicity of C. difficile is closely linked to two major exotoxins (toxin A and toxin B) encoded by genes tcdA and tcdB, respectively, in a pathogenicity locus (PaLoc) (, ). The virulence of C. difficile can be enhanced by producing binary toxin (CDT) (, ). Genes encoding the binary toxin, cdtA and cdtB, together with a regulation gene cdtR, are located on the CDT locus (CdtLoc) ().Genomic sequence analysis provides insights into the genomic diversity, evolution, and transmission of C. difficile (). However, among 17 C. difficile complete genomes publicly available to date in the GenBank database (https://www.ncbi.nlm.nih.gov/genome/genomes/535, accessed on 11 December 2017), only 3 (BI1, DH, and FDAARGOS_267) were from humans in the United States. In this study, we sequenced four C. difficile clinical isolates (W0003a, W0022a, W0023a, and R0104a) from patients of the lower Hudson Valley, New York, USA. These isolates were recovered from patients with symptomatic CDIs and represented the most common strains in this region. Total genomic DNA of each isolate was extracted with a Qiagen QIAamp genomic DNA kit. Whole-genome sequencing was performed on both the Pacific Bioscience (PacBio) RS II and Illumina MiSeq platforms. A sequencing library for the MiSeq platform was prepared using the Illumina Nextera XT DNA sample prep kit, and paired-end (2 × 150-bp) sequencing was performed. A library for the PacBio single-molecule real-time (SMRT) sequencing system was processed with the PacBio SMRTbell template preparation kit. Genome sequences were de novo assembled by PacBio SMRT analysis and/or the SPAdes assembler (), polished by aligning and mapping the short reads generated from the MiSeq run, and visualized under the Integrative Genomics Viewer ().The genomes of W0003a, W0023a, and R0104a each contain a single circular chromosome of 4,075,361, 4,110,080, and 4,190,038 bp, respectively. W0022a consists of a circular chromosome of 4,188,456 bp and a circular phage of 31,888 bp. The sequence type (ST) of each C. difficile strain was determined by querying the whole-genome sequence to the public multilocus sequence typing (MLST) database (http://pubmlst.org/cdifficile): R0104a (ST1), W0022a (ST2), W0003a (ST8), and W0023a (ST42). The four isolates represent the most common strains recovered in this region. MLST-based phylogeny further designated these isolates into two distinct phylogenetic clades: R0104a as clade 2, and the others as clade 1.Compared to the reference genome C. difficile 630 (GenBank accession number NC_009089), the genomes of all four toxigenic C. difficile isolates contain intact tcdA and tcdB genes in the PaLoc, of 7,133 and 7,101 bp, respectively. In addition, a complete CdtLoc, including intact binary toxin genes cdtA and cdtB and their regulatory cdtR, was identified in R0104a, whereas an incomplete CdtLoc, containing only the cdtR gene, was observed in isolates W0003a, W0022a, and W0023a (, ). […]

Pipeline specifications

Software tools SMRT-Analysis, SPAdes, IGV
Databases TCDB PubMLST
Applications Phylogenetics, WGS analysis
Organisms Clostridioides difficile, Homo sapiens