title: Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study.
abstract: Clostridium difficile infections (CDI) are a growing concern in North America, because of their increasing incidence and severity. Using integrated approaches, we correlated pathogen genotypes and host clinical characteristics for 46 C. difficile infections in a tertiary care medical center during a 6-month interval from January to June 2010. Multilocus sequence typing (MLST) demonstrated 21 known and 2 novel sequence types (STs), suggesting that the institution's C. difficile strains are genetically diverse. ST-1 (which corresponds to pulsed-field gel electrophoresis strain type NAP1/ribotype 027) was the most prevalent (32.6%); 43.5% of the isolates were binary toxin gene positive, of which 75% were ST-1. All strains were ciprofloxacin resistant and metronidazole susceptible, and 8.3% and 13.0% of the isolates were resistant to clindamycin and tetracycline, respectively. The corresponding resistance loci, including potential novel mutations, were identified from the whole-genome sequencing (WGS) of the resistant strains. Core genome single nucleotide polymorphisms (SNPs) determining the phylogenetic relatedness of the 46 strains recapitulated MLST types and provided greater interstrain differentiation. The disease severity was greatest in patients infected with ST-1 and/or binary gene-positive strains, but genome-wide SNP analysis failed to provide additional associations with CDI severity within the same STs. We conclude that MLST and core genome SNP typing result in the same phylogenetic grouping of the 46 C. difficile strains collected in a single hospital. WGS also has the capacity to differentiate those strains within STs and allows the comparison of strains at the individual gene level and at the whole-genome level.
authors.affiliation: Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.
authors.forename: Yanjiao
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Pathology and Immunology and Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.
authors.forename: Carey-Ann D
authors.identifier: http://orcid.org/0000-0002-1137-840X
authors.initials: CA
authors.lastname: Burnham
authors.affiliation: Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
authors.forename: Tiffany
authors.initials: T
authors.lastname: Hink
authors.affiliation: The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.affiliation: Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.
authors.forename: Nurmohammad
authors.initials: N
authors.lastname: Shaikh
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.
authors.forename: Aye
authors.initials: A
authors.lastname: Wollam
authors.affiliation: The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
authors.forename: Erica
authors.initials: E
authors.lastname: Sodergren
authors.affiliation: The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.affiliation: Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.
authors.forename: Phillip I
authors.initials: PI
authors.lastname: Tarr
authors.affiliation: Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA edubberk@dom.wustl.edu.
authors.forename: Erik R
authors.initials: ER
authors.lastname: Dubberke
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001427:Bacterial Toxins / Q000235:genetics; D016360:Clostridioides difficile / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology*; D003015:Clostridium Infections / Q000382:microbiology* / Q000473:pathology*; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D024881:Drug Resistance, Bacterial; D005838:Genotype; D006801:Humans; D008826:Microbial Sensitivity Tests; D058885:Multilocus Sequence Typing; D009656:North America; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D062606:Tertiary Care Centers
chemical_list: D000900:Anti-Bacterial Agents; D001427:Bacterial Toxins; D004269:DNA, Bacterial