Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan

Abstract

Background Clostridium difficile is a Gram-positive anaerobe and the leading cause of antibiotic-associated diarrhea worldwide. The emergence of ribotype 027 (RT027) strains is associated with increased incidence of infection and mortality. To further understand the relationship between C. difficile NCKUH-21, a RT027 strain isolated from a patient in Taiwan, and other RT027 strains, we performed whole-genome shotgun sequencing on NCKUH-21 and comparative genomic analyses.ResultsThe genome size, G+C content, and gene number for the NCKUH-21 strain were determined to be similar to those for other C. difficile strains. The core genome phylogeny indicated that the five RT027 strains R20291, CD196, NCKUH-21, BI1, and 2007855 formed a clade. A pathogenicity locus, tcdR-tcdB-tcdE-orf-tcdA-tcdC, was conserved in the genome. A genomic region highly similar to the Clostridium phage CD38-2 was present in the NCKUH-21 strain but absent in the other RT027 strains and designated as the prophage NCKUH-21. The prophage NCKUH-21 genes were significantly higher in G+C content than the other genes in the NCKUH-21 genome, indicating that the prophage does not match the base composition of the host genome.ConclusionsThis is the first whole-genome analysis of a RT027 C. difficile strain isolated from Taiwan. Due to the high identity with CD38-2, the prophage identified in the NCKUH-21 genome has the potential to regulate toxin production. These results provide important information for understanding the pathogenicity of RT027 C. difficile in Taiwan.Electronic supplementary materialThe online version of this article (10.1186/s13099-017-0219-4) contains supplementary material, which is available to authorized users.

Phage transcriptional regulator X (PtrX)-mediated augmentation of toxin production and virulence inClostridioides difficilestrain R20291

“…Previously, we observed a 99% identity match between the genomic DNA sequences of φNCKUH-21 (Fig 1A , S3 Table) and φCD38-2 (43). The genetic organization between these two phages was 100% identical except for some nucleotide differences.…”

“…For example, a lysogenic phage markedly upregulates the expression of the Shiga toxin in E. coli and enhances the secretion of the cholera toxin from V. cholerae (42). Moreover, some lysogenic C. difficile strains exhibit high pathogenicity and increased toxin production (2,43).…”

“…We previously discovered a prophage-like sequence in the genome of C. difficile ribotype 027 (RT027) strain NCKUH-21; this prophage was named φNCKUH-21 (43). The genomic sequence of φNCKUH-21 is considerably similar to the φCD38-2 genome with some nucleotide differences (2).…”

“…Notably, prophage φCD38-2 exists as a circular plasmid in the lysogenic host. A ParA/Soj-like protein, involving plasmid maintenance, was encoded in the genome of φCD38-2 and φNCKUH-21 (2,43,44). Moreover, φCD38-2 can upregulate toxin expression in the host bacterium (2), and influence the phase variation of C. difficile surface protein gene (cwpV) and the expression of metabolic genes (45).…”

Clostridioides difficile from Fecally Contaminated Environmental Sources: Resistance and Genetic Relatedness from a Molecular Epidemiological Perspective

“…For beta-lactam resistance, blaCDD-1 or blaCDD-2 genes were detected in all isolates analyzed, which confer resistance against various beta-lactam antibiotics. These enzymes previously identified in C. difficile strains allowing to have intrinsic resistance to antimicrobials, such as penicillins and cephalosporins [74], which is highly conserved among those C. difficile genomes.…”