title: Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants.
abstract: Clostridium bolteae and Clostridium clostridioforme, previously included in the complex C. clostridioforme in the group Clostridium XIVa, remain difficult to distinguish by phenotypic methods. These bacteria, prevailing in the human intestinal microbiota, are opportunistic pathogens with various drug susceptibility patterns. In order to better characterize the two species and to obtain information on their antibiotic resistance genes, we analyzed the genomes of six strains of C. bolteae and six strains of C. clostridioforme, isolated from human infection.
  
  
  
  The genome length of C. bolteae varied from 6159 to 6398 kb, and 5719 to 6059 CDSs were detected. The genomes of C. clostridioforme were smaller, between 5467 and 5927 kb, and contained 5231 to 5916 CDSs. The two species display different metabolic pathways. The genomes of C. bolteae contained lactose operons involving PTS system and complex regulation, which contribute to phenotypic differentiation from C. clostridioforme. The Acetyl-CoA pathway, similar to that of Faecalibacterium prausnitzii, a major butyrate producer in the human gut, was only found in C. clostridioforme. The two species have also developed diverse flagella mobility systems contributing to gut colonization. Their genomes harboured many CDSs involved in resistance to beta-lactams, glycopeptides, macrolides, chloramphenicol, lincosamides, rifampin, linezolid, bacitracin, aminoglycosides and tetracyclines. Overall antimicrobial resistance genes were similar within a species, but strain-specific resistance genes were found. We discovered a new group of genes coding for rifampin resistance in C. bolteae. C. bolteae 90B3 was resistant to phenicols and linezolide in producing a 23S rRNA methyltransferase. C. clostridioforme 90A8 contained the VanB-type Tn1549 operon conferring vancomycin resistance. We also detected numerous genes encoding proteins related to efflux pump systems.
  
  
  
  Genomic comparison of C. bolteae and C. clostridiofrome revealed functional differences in butyrate pathways and in flagellar systems, which play a critical role within human microbiota. Most of the resistance genes detected in both species were previously characterized in other bacterial species. A few of them were related to antibiotics inactive against Clostridium spp. Some were part of mobile genetic elements suggesting that these commensals of the human microbiota act as reservoir of antimicrobial resistances.
authors: Department of Genomes and Genetics, Institut Pasteur, Paris, France.
authors: Pierre
authors: P
authors: Dehoux
authors: Faculté de Pharmacie, EA4043 "Unité Bactéries Pathogènes et Santé" (UBaPS), Université Paris Sud, Châtenay-Malabry Cedex, 92296, France.
authors: Jean Christophe
authors: JC
authors: Marvaud
authors: Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors: Amr
authors: A
authors: Abouelleil
authors: Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors: Ashlee M
authors: AM
authors: Earl
authors: Faculté de Pharmacie, EA4043 "Unité Bactéries Pathogènes et Santé" (UBaPS), Université Paris Sud, Châtenay-Malabry Cedex, 92296, France.|Antibacterial Agents Unit, Department of Microbiology, Institut Pasteur, Paris, France.
authors: Thierry
authors: T
authors: Lambert
authors: Department of Genomes and Genetics, Institut Pasteur, Paris, France. catherine.dauga@pasteur.fr.|International Group of Data Analysis, Centre for Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France. catherine.dauga@pasteur.fr.
authors: Catherine
authors: 0000-0002-1794-4871
authors: C
authors: Dauga
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D053898:Biosynthetic Pathways; D002087:Butyrates / Q000378:metabolism; D003013:Clostridium / Q000145:classification / Q000187:drug effects* / Q000235:genetics* / Q000378:metabolism; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D006801:Humans; D010802:Phylogeny
chemical_list: D000900:Anti-Bacterial Agents; D002087:Butyrates
keywords: Antimicrobial resistance; Butyrate pathway; Clostridium bolteae; Clostridium clostridioforme; Comparative genomics