Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection

Abstract

Background Clostridioides difficile infection (CDI) is an infectious nosocomial disease caused by Clostridioides difficile, an opportunistic pathogen that occurs in the intestine after extensive antibiotic regimens. Results Nine C. difficile strains (CBA7201–CBA7209) were isolated from nine patients diagnosed with CDI at the national university hospital in Korea, and the whole genomes of these strains were sequenced to identify their genomic characteristics. Comparative genomic analysis was performed using 51 reference strains and the nine isolated herein. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that all 60 C. difficile strains belong to the genus Clostridioides, while core-genome tree indicated that they were divided into five groups, which was consistent with the results of MLST clade analysis. All strains were confirmed to have a clindamycin antibiotic resistance gene, but the other antibiotic resistance genes differ depending on the MLST clade. Interestingly, the six strains belonging to the sequence type 17 among the nine C. difficile strains isolated here exhibited unique genomic characteristics for PaLoc and CdtLoc, the two toxin gene loci identified in this study, and harbored similar antibiotic resistance genes. Conclusion In this study, we identified the specific genomic characteristics of Korean C. difficile strains, which could serve as basic information for CDI prevention and treatment in Korea.

Detection and Genomic Characterisation of Clostridioides difficile from Spinach Fields

“…Hypervirulent RT126 was observed in clinical isolates in Taiwan by Hung et al [101], in Kuwait by Jamal and Rotimi [102] and in Australia by Knight et al [82]. The ribotype 126 detected in spinach leaves in our study was similar to C. difficile strain DSM 29020, which has been reported in hospital patients in Korea and China [103,104].…”

“…Indeed, the close proximity of the field where it was isolated to a stud farm might highlight the potential for its zoonotic transfer. Regarding its link to humans, in Germany, RT003 accounted for 11.1% of CDI cases in 2012-2013 [89], and strain W0023a, which is similar to our isolate by WGS, has been detected in clinical isolates from Korea and the USA [103,108].…”

“…However, due to the ribotype's lack of toxin genes, it may be carried asymptomatically [118] or be associated with hospital-acquired diarrhoea [119]. WGS analysis suggested that RT511 was most closely related to strain C. difficile W0003a, previously observed in clinical isolates in Korea [103].…”

Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile

“…4 ); ST17(018) strain CBA7209, accession no. QLOB00000000 ; ( 97 ) ( Fig. 5A ); ST3(001) strain BI9, accession no.…”

About Functional Foods: The Probiotics and Prebiotics State of Art

“…An infection of a strain of Clostridioides difficile, which is an opportunistic bacterium, can be life threatening. These infections are most often seen in hospitalized patients, elderly patients and in people who have experienced prolonged exposure to antibiotics [ 64 ]. Another group of bacteria found in abundance in the gastrointestinal tract from the Actinomycetota phyla is the Bifidobacterium genus, which play an important role in the host’s health.…”