title: Determining the cause of recurrent Clostridium difficile infection using whole genome sequencing.
abstract: Understanding the contribution of relapse and reinfection to recurrent Clostridium difficile infection (CDI) has implications for therapy and infection prevention, respectively. We used whole genome sequencing to determine the relation of C. difficile strains isolated from patients with recurrent CDI at an academic medical center in the United States. Thirty-five toxigenic C. difficile isolates from 16 patients with 19 recurrent CDI episodes with median time of 53.5days (range, 13-362) between episodes were whole genome sequenced on the Illumina MiSeq platform. In 84% (16) of recurrences, the cause of recurrence was relapse with prior strain of C. difficile. In 16% (3) of recurrent episodes, reinfection with a new strain of C. difficile was the cause. In conclusion, the majority of CDI recurrences at our institution were due to infection with the same strain rather than infection with a new strain.
authors: Department of Pathology, Stanford University, Stanford, CA, 94305.
authors: James Heng Chiak
authors: JH
authors: Sim
authors: Department of Pathology, Stanford University, Stanford, CA, 94305.
authors: Cynthia
authors: C
authors: Truong
authors: One Codex, San Francisco, CA, 94110.
authors: Samuel S
authors: SS
authors: Minot
authors: One Codex, San Francisco, CA, 94110.
authors: Nick
authors: N
authors: Greenfield
authors: Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, 94304.
authors: Indre
authors: I
authors: Budvytiene
authors: Department of Biomolecular Engineering, University of California Santa Cruz, CA, 95064.
authors: Akshar
authors: A
authors: Lohith
authors: Department of Pathology, Stanford University, Stanford, CA, 94305.
authors: Victoria
authors: V
authors: Anikst
authors: Department of Biomolecular Engineering, University of California Santa Cruz, CA, 95064.
authors: Nader
authors: N
authors: Pourmand
authors: Department of Pathology, Stanford University, Stanford, CA, 94305; Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, 94304; Department of Medicine, Stanford University, Stanford, CA, 94305. Electronic address: nbanaei@stanford.edu.
authors: Niaz
authors: N
authors: Banaei
mesh_terms: D000046:Academic Medical Centers; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D016360:Clostridioides difficile / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D003015:Clostridium Infections / Q000453:epidemiology* / Q000382:microbiology*; D005260:Female; D016680:Genome, Bacterial; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D012008:Recurrence; D017422:Sequence Analysis, DNA; D014481:United States / Q000453:epidemiology
keywords: Clostridium difficile; Reinfection; Relapse