title: Clostridium difficile and Clostridium perfringens species detected in infant faecal microbiota using 16S rRNA targeted probes.
abstract: Clostridium perfringens and Clostridium difficile are pathogenic clostridia potentially associated with gastrointestinal infections and allergy in infants. To enable the molecular detection and quantification of these species in the infant gut, two 16S rRNA oligonucleotide probes were developed: Cdif198 for C. difficile and Cperf191 for C. perfringens. We defined the probes in silico using the RDP sequence database. The probes were then validated using FISH combined with flow cytometry and a collection of target and non-target strains, and faecal samples inoculated with dilutions of C. difficile and C. perfringens strains. These new probes were used to assess the composition of the intestinal microbiota of 33 infants of 1.5 to 18.5 months of age, associated with a panel of 8 probes targeting the predominant faecal bacterial groups of humans. The probes designed allowed detection and quantification of the relative proportions of C. difficile (0.5+/-1.0%) and C. perfringens (2.1+/-2.3%) in the microbiota of infants.
authors.affiliation: Institut National de la Recherche Agronomique, Unité d'Ecologie et de Physiologie du Système Digestif, Jouy en Josas, France.
authors.forename: Matteo
authors.initials: M
authors.lastname: Fallani
authors.forename: Lionel
authors.initials: L
authors.lastname: Rigottier-Gois
authors.forename: Marga
authors.initials: M
authors.lastname: Aguilera
authors.forename: Chantal
authors.initials: C
authors.lastname: Bridonneau
authors.forename: Anne
authors.initials: A
authors.lastname: Collignon
authors.forename: Christine A
authors.initials: CA
authors.lastname: Edwards
authors.forename: Gérard
authors.initials: G
authors.lastname: Corthier
authors.forename: Joël
authors.initials: J
authors.lastname: Doré
mesh_terms: D016360:Clostridioides difficile / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D003015:Clostridium Infections / Q000382:microbiology*; D003016:Clostridium perfringens / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D005243:Feces / Q000382:microbiology; D005434:Flow Cytometry / Q000379:methods; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D007223:Infant; D015345:Oligonucleotide Probes / Q000737:chemistry; D012336:RNA, Ribosomal, 16S / Q000032:analysis*
chemical_list: D015345:Oligonucleotide Probes; D012336:RNA, Ribosomal, 16S