Additional file 1 of Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection

Additional file 1: Fig. S1. Pan- and core-genome box plot of 60 C. difficile strains with standard deviations. The pan-genome represents the total set of genes of the 60 C. difficile strains, while the core-genome represents the common genes across all genomes. Fig. S2. In silico DNA-DNA hybridization (DDH) analyses showing the pair-wise relatedness of 60 C. difficile strains and two reference strains (C. mangenotii DSM 1289T and Clostridium hiranonis TO-931). Strains CBA7201–CBA7209 isolated from Korean patients with CDI are highlighted in bold. The hierarchical clusters represented by dendrograms were constructed by simple linkage of the in silico DDH values. The vertical bar on the right side of the figure indicates the MLST clade to which each C. difficile strain belongs. Fig. S3. Diagram of the structural components involved in C. difficile flagella assembly defined by the number of KEGG orthology genes identified from the genomes of 60 C. difficile strains. Flagella assembly genes belonging to the core genome of the 60 C. difficile strains are indicated in red; flagella assembly genes belonging to the accessory genome identified from 2–56 genomes are indicated in blue

MRSA infections detected during the ICU stay.

<p><b>NOTE</b>. MRSA, methicillin-resistant <i>Staphylococcus aureus</i>.</p

Risk factors for MRSA colonization in 282 patients.

<p><b>NOTE</b>. MRSA, methicillin-resistant <i>Staphylococcus aureus</i>.</p

Importance ranking of the characteristics of critical patients with COVID-19, according to the Gini index using random forest method.

Importance ranking of the characteristics of critical patients with COVID-19, according to the Gini index using random forest method.</p

List of population-based previous studies to investigate risk factors for COVID-19 severity.

List of population-based previous studies to investigate risk factors for COVID-19 severity.</p

Result of logistic regression analysis for severe or critical COVID-19 illness.

Result of logistic regression analysis for severe or critical COVID-19 illness.</p

Sociodemographic and clinical characteristics of COVID-19 confirmed cases during Delta and Omicron predominant periods.

Sociodemographic and clinical characteristics of COVID-19 confirmed cases during Delta and Omicron predominant periods.</p

Severity classification of patients with SARS-CoV-2 infection during Delta and Omicron predominant periods.

Severity classification of patients with SARS-CoV-2 infection during Delta and Omicron predominant periods.</p

Univariate and Multivariate analyses for risk factors associated with 30-day mortality in patients with MRSA bacteremia.

<p><b>NOTE</b>. HR, hazard ratio; CI, confidence interval; APACHE, acute physiology and chronic health evaluation; SCC<i>mec</i> IV/IVa MRSA, MRSA possessing SCC<i>mec</i> type IV or IVa; hetero-VISA, hetero-vancomycin-intermediate <i>S. aureus</i>; MIC, minimum inhibitory concentration.</p>a<p>Continuous variables are expressed as means (±SD).</p>b<p>Statistically significant (<i>P</i>≤0.05).</p

Additional file 2 of Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection

Additional file 2: Table S1. The number of the core-genes, accessory-genes (present in more than two strains), and unique-genes present in 60 C. difficile strains. Table S2. OrthoANI (average nucleotide identity) analyses showing the pair-wise relatedness of 51 C. difficile strains and two reference strains (C. mangenotii DSM 1289T and Clostridium hiranonis TO-931) for nine C. difficile strains isolated from Korea. Table S3. Lists of antibiotics resistance gene present in 60 C. difficile strains