title: Genetic and resistance phenotypic subtyping of Salmonella Saintpaul isolates from various food sources and humans: Phylogenetic concordance in combinatory analyses.
abstract: Bacterial pathogen subtyping for public health traceback of foodborne outbreaks has increasingly produced a number of disparate molecular techniques of varying resolution. Here, we bridge the molecular divide across three methodologies, transform data types for cross-comparison, and test phylogenetic concordance. Single nucleotide polymorphism (SNP) discovery was combined with pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility profiles for identifying and differentiating 183 strains of closely related Salmonella enterica serovar Saintpaul isolates from retail meats, produce-associated outbreaks, and clinical sources. Fifty-six SNPs across 30 different genes were identified by comparative genomic analysis. These SNPs stratified general, monophyletic S. Saintpaul serovar specific signatures down to informative strain-specific markers. This SNP panel resulted in 17 distinct genotypes that, in concert with standard PFGE profiling, generated additional discriminatory power among clonal swarms of isolates when the data were transformed into a cross-comparable binary format. In a limited number of cases, antimicrobial susceptibility profiles (ASP) provided additional attributes for some strains when combined similarly. However, as expected from presumably acquired elements, resistant and susceptible populations produced some conflicting signals in most clonal complexes but they remained largely undisruptive to the general concordance. Taken in concert together, the three datasets (SNPs, PFGE,ASP) yielded a matrix of 156 independent phylogenetic characters that were statistically evaluated and found to be largely congruent, resulting in a consistently structured, non-homoplastic, phylogenetic signal and tree topology.
authors: Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA. Electronic address: alice.hayford@fda.hhs.gov.
authors: Alice E
authors: AE
authors: Hayford
authors: Division of Microbiology, Center for Food Safety and Applied Nutrition, U S Food and Drug Administration, College Park, MD 20740, USA.
authors: Eric W
authors: EW
authors: Brown
authors: Division of Animal and Food Microbiology, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
authors: Shaohua
authors: S
authors: Zhao
authors: Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
authors: Mark K
authors: MK
authors: Mammel
authors: Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
authors: Jayanthi
authors: J
authors: Gangiredla
authors: Division of Animal and Food Microbiology, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
authors: Jason W
authors: JW
authors: Abbott
authors: Division of Animal and Food Microbiology, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
authors: Sharon L
authors: SL
authors: Friedman
authors: Division of Animal and Food Microbiology, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
authors: Sherry L
authors: SL
authors: Ayers
authors: Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
authors: Jada L
authors: JL
authors: Lewis
authors: Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
authors: David W
authors: DW
authors: Lacher
authors: National Antimicrobial Resistance Monitoring System,Center for Veterinary Medicine, U. S. Food Drug Administration, Laurel, MD 20708, USA.
authors: Patrick
authors: P
authors: McDermott
authors: Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
authors: Christopher A
authors: CA
authors: Elkins
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D015373:Bacterial Typing Techniques; D024881:Drug Resistance, Bacterial; D016521:Electrophoresis, Gel, Pulsed-Field; D005516:Food Microbiology; D005798:Genes, Bacterial; D020043:Genes, Essential; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008826:Microbial Sensitivity Tests; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012478:Salmonella Food Poisoning / Q000382:microbiology*; D019779:Salmonella enterica / Q000145:classification / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D012641:Selection, Genetic
chemical_list: D000900:Anti-Bacterial Agents
keywords: Antibiotic resistance; PFGE; Phylogenetics; Salmonella Saintpaul; Single nucleotide polymorphism