title: Emergence of an outbreak-associated Clostridium difficile variant with increased virulence.
abstract: The prevalence of Clostridium difficile infections has increased due to the emergence of epidemic variants from diverse genetic lineages. Here we describe the emergence of a novel variant during an outbreak in a Costa Rican hospital that was associated with severe clinical presentations. This C. difficile variant elicited higher white blood cell counts and caused disease in younger patients than did other strains isolated during the outbreak. Furthermore, it had a recurrence rate, a 30-day attributable disease rate, and disease severity as great as those of the epidemic strain NAP1. Pulsed-field gel electrophoresis genotyping indicated that the outbreak strains belong to a previously undescribed variant, designated NAPCR1. Whole-genome sequencing and ribotyping indicated that the NAPCR1 variant belongs to C. difficile ribotype 012 and sequence type 54, as does the reference strain 630. NAPCR1 strains are resistant to fluoroquinolones due to a mutation in gyrA, and they possess an 18-bp deletion in tcdC that is characteristic of the epidemic, evolutionarily distinct, C. difficile NAP1 variant. NAPCR1 genomes contain 10% more predicted genes than strain 630, most of which are of hypothetical function and are present on phages and other mobile genetic elements. The increased virulence of NAPCR1 was confirmed by mortality rates in the hamster model and strong inflammatory responses induced by bacteria-free supernatants in the murine ligated loop model. However, NAPCR1 strains do not synthesize toxin A and toxin B at levels comparable to those in NAP1 strains. Our results suggest that the pathogenic potential of this emerging C. difficile variant is due to the acquisition of hypothetical functions associated with laterally acquired DNA.
authors: Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica.
authors: Carlos
authors: C
authors: Quesada-Gómez
authors: Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica.
authors: Diana
authors: D
authors: López-Ureña
authors: Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica.
authors: Luis
authors: L
authors: Acuña-Amador
authors: Hospital San Juan de Dios, CCSS, San José, Costa Rica.
authors: Manuel
authors: M
authors: Villalobos-Zúñiga
authors: National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
authors: Tim
authors: T
authors: Du
authors: Departamento de Morfologia, Universidade Federal do Ceará, Fortaleza, Brazil.
authors: Rosemayre
authors: R
authors: Freire
authors: Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica.
authors: Caterina
authors: C
authors: Guzmán-Verri
authors: Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica.
authors: María
authors: M
authors: del Mar Gamboa-Coronado
authors: Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors: Trevor D
authors: TD
authors: Lawley
authors: Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica.
authors: Edgardo
authors: E
authors: Moreno
authors: National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
authors: Michael R
authors: MR
authors: Mulvey
authors: Departamento de Morfologia, Universidade Federal do Ceará, Fortaleza, Brazil.
authors: Gerly Anne
authors: GA
authors: de Castro Brito
authors: Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica.
authors: Evelyn
authors: E
authors: Rodríguez-Cavallini
authors: Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica.
authors: César
authors: C
authors: Rodríguez
authors: Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica esteban.chaves@ucr.ac.cr.
authors: Esteban
authors: E
authors: Chaves-Olarte
mesh_terms: D000818:Animals; D016360:Clostridioides difficile / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000472:pathogenicity*; D003015:Clostridium Infections / Q000453:epidemiology* / Q000382:microbiology / Q000473:pathology; D003364:Costa Rica / Q000453:epidemiology; D003428:Cross Infection / Q000139:chemically induced / Q000453:epidemiology / Q000382:microbiology; D004269:DNA, Bacterial / Q000235:genetics; D003967:Diarrhea / Q000453:epidemiology* / Q000382:microbiology / Q000473:pathology; D004195:Disease Models, Animal; D004196:Disease Outbreaks; D016521:Electrophoresis, Gel, Pulsed-Field; D005260:Female; D022761:Gene Transfer, Horizontal; D005838:Genotype; D006761:Hospitals; D006801:Humans; D007422:Intestines / Q000473:pathology; D008297:Male; D008647:Mesocricetus; D051379:Mice; D008969:Molecular Sequence Data; D058889:Molecular Typing; D012189:Retrospective Studies; D021521:Ribotyping; D017422:Sequence Analysis, DNA; D016019:Survival Analysis; D014774:Virulence; D037521:Virulence Factors / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D037521:Virulence Factors
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