Whole-genome analysis reveals the evolution and transmission of an MDR DH/NAP11/106 Clostridium difficile clone in a paediatric hospital Journal Article

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Authors: Kociolek, L. K.; Ozer, E. A.; Gerding, D. N.; Hecht, D. W.; Patel, S. J.; Hauser, A. R.
Article Title: Whole-genome analysis reveals the evolution and transmission of an MDR DH/NAP11/106 Clostridium difficile clone in a paediatric hospital
Abstract: Background: Clostridium difficile strain DH/NAP11/106, a relatively antibiotic-susceptible strain, is now the most common cause of C. difficile infection (CDI) among adults in the USA. Objectives: To identify mechanisms underlying the evolution and transmission of an MDR DH/NAP11/106 clone. Methods: WGS (Illumina MiSeq), restriction endonuclease analysis (REA) and antibiotic susceptibility testing were performed on 134 C. difficile isolates collected from paediatric patients with CDI over a 2 year period. Results: Thirty-one of 134 (23%) isolates were REA group DH. Pairwise single-nucleotide variant (SNV) analyses identified a DH clone causing seven instances of CDI in two patients. During the 337 days between the first and second CDI, Patient 1 (P1) received 313 days of antibiotic therapy. Clindamycin and rifaximin resistance, and reduced vancomycin susceptibility (MIC 0.5-2 mg/L), were newly identified in the relapsed isolate. This MDR clone was transmitted to Patient 2 (P2) while P1 and P2 received care in adjacent private rooms. P1 and P2 each developed two additional CDI relapses. Comparative genomics analyses demonstrated SNVs in multiple antibiotic resistance genes, including rpoB (rifaximin resistance), gyrB and a gene encoding PBP; gyrB and PBP mutations did not consistently confer a resistance phenotype. The clone also acquired a 46000 bp genomic element, likely a conjugative plasmid, which contained ermB (clindamycin resistance). The element shared 99% identity with the genomic sequence of Faecalibacterium prausnitzii, an enteric commensal. Conclusions: These data highlight the emergence of MDR in C. difficile strain DH/NAP11/106 through multiple independent mechanisms probably as a consequence of profound antibiotic pressure.
Journal Title: The Journal of antimicrobial chemotherapy
ISSN: 1460-2091; 0305-7453
Publisher: . Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy  
Journal Place: England
Date Published: 2018
Language: eng
DOI/URL:

10.1093/jac/dkx523
Notes: LR: 20180308; CI: (c) The Author(s) 2018; JID: 7513617; 2017/08/25 00:00 [received]; 2017/12/13 00:00 [accepted]; 2018/01/18 06:00 [entrez]; 2018/01/18 06:00 [pubmed]; 2018/01/18 06:00 [medline]; aheadofprint