title: Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing.
abstract: Clostridium sporogenes PA 3679 is a nonpathogenic, nontoxic model organism for proteolytic Clostridium botulinum used in the validation of conventional thermal food processes due to its ability to produce highly heat-resistant endospores. Because of its public safety importance, the uncertain taxonomic classification and genetic diversity of PA 3679 are concerns. Therefore, isolates of C. sporogenes PA 3679 were obtained from various sources and characterized using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. The phylogenetic relatedness and genetic variability were assessed based on 16S rRNA gene sequencing and whole-genome single nucleotide polymorphism (SNP) analysis. All C. sporogenes PA 3679 isolates were categorized into two clades (clade I containing ATCC 7955 NCA3679 isolates 1961-2, 1990, and 2007 and clade II containing PA 3679 isolates NFL, UW, FDA, and Campbell and ATCC 7955 NCA3679 isolate 1961-4). The 16S maximum likelihood (ML) tree clustered both clades within proteolytic C. botulinum strains, with clade I forming a distinct cluster with other C. sporogenes non-PA 3679 strains. SNP analysis revealed that clade I isolates were more similar to the genomic reference PA 3679 (NCTC8594) genome (GenBank accession number AGAH00000000.1) than clade II isolates were. The genomic reference C. sporogenes PA 3679 (NCTC8594) genome and clade I C. sporogenes isolates were genetically distinct from those obtained from other sources (University of Wisconsin, National Food Laboratory, U.S. Food and Drug Administration, and Campbell's Soup Company). Thermal destruction studies revealed that clade I isolates were more sensitive to high temperature than clade II isolates were. Considering the widespread use of C. sporogenes PA 3679 and its genetic information in numerous studies, the accurate identification and genetic characterization of C. sporogenes PA 3679 are of critical importance.
authors.affiliation: Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Bedford Park, Illinois, USA Kristin.Schill@fda.hhs.gov jpombert@iit.edu.
authors.forename: Kristin M
authors.initials: KM
authors.lastname: Schill
authors.affiliation: Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Bedford Park, Illinois, USA.
authors.forename: Yun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Illinois Institute of Technology, Department of Biology, Chicago, Illinois, USA.
authors.forename: Robert R
authors.initials: RR
authors.lastname: Butler
authors.affiliation: Illinois Institute of Technology, Department of Biology, Chicago, Illinois, USA Kristin.Schill@fda.hhs.gov jpombert@iit.edu.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Pombert
authors.affiliation: Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Bedford Park, Illinois, USA.
authors.forename: N Rukma
authors.initials: NR
authors.lastname: Reddy
authors.affiliation: Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Bedford Park, Illinois, USA.
authors.forename: Guy E
authors.initials: GE
authors.lastname: Skinner
authors.affiliation: Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Bedford Park, Illinois, USA.
authors.forename: John W
authors.initials: JW
authors.lastname: Larkin
mesh_terms: D003013:Clostridium / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D003014:Clostridium botulinum / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics*; D016521:Electrophoresis, Gel, Pulsed-Field; D005516:Food Microbiology; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012336:RNA, Ribosomal, 16S; D013171:Spores, Bacterial; D014481:United States
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S