Search

Francisella tularensis contains several highly pathogenic subspecies, including Francisella tularensis subsp. holarctica, whose distribution is circumpolar in the northern hemisphere. The phylogeography of these subspecies and their subclades was examined using whole-genome single nucleotide polymorphism (SNP) analysis, high-density microarray SNP genotyping, and real-time-PCR-based canonical SNP (canSNP) assays. Almost 30,000 SNPs were identified among 13 whole genomes for phylogenetic analysis. We selected 1,655 SNPs to genotype 95 isolates on a high-density microarray platform. Finally, 23 clade- and subclade-specific canSNPs were identified and used to genotype 496 isolates to establish global geographic genetic patterns. We confirm previous findings concerning the four subspecies and two Francisella tularensis subsp. tularensis subpopulations and identify additional structure within these groups. We identify 11 subclades within F. tularensis subsp. holarctica, including a new, genetically distinct subclade that appears intermediate between Japanese F. tularensis subsp. holarctica isolates and the common F. tularensis subsp. holarctica isolates associated with the radiation event (the B radiation) wherein this subspecies spread throughout the northern hemisphere. Phylogenetic analyses suggest a North American origin for this B-radiation clade and multiple dispersal events between North America and Eurasia. These findings indicate a complex transmission history for F. tularensis subsp. holarctica.

Abstract Background Francisella tularensis is the etiologic agent of tularemia and is classified as a select agent by the Centers for Disease Control and Prevention. Currently four known subspecies of F. tularensis that differ in virulence and geographical distribution are recognized:tularensis (type A), holarctica (type B), mediasiatica, and novicida. Because of the Select Agent status and differences in virulence and geographical location, the molecular analysis of any clinical case of tularemia is of particular interest. We analyzed an unusual Francisella clinical isolate from a human infection in Arizona using multiple DNA-based approaches. Findings We report that the isolate is F. tularensis subsp. novicida, a subspecies that is rarely isolated. Conclusion The rarity of this novicida subspecies in clinical settings makes each case study important for our understanding of its role in disease and its genetic relationship with other F. tularensis subspecies.

Objective: To characterize bacterial microbiota in middle ear, adenoid, and tonsil specimens using 16SrRNA genebased pyrosequencing analysis. Design: Cross-sectional study of bacterial microbiota in middle ear, adenoid, and tonsil specimens from a pediatric patient with chronic serous otitis media. Middle ear, adenoid, and tonsil specimens from a pediatric patient were collected and underwent cell lysis and DNA isolation. Pyrosequencing was performed on the 454 Life Sciences GS FLX platform (Roche Diagnostics Corp, Branford, Connecticut). Pyrosequencing data were processed, qualitychecked, and taxonomically classified to generate an abundance- based matrix. Ecological analyses were performed. Setting: Academic, tertiary referral center. Main Outcome Measures: Comparative microbiome analysis. Results: We detected a total of 17 unique bacterial families, with 9, 9, and 12 bacterial families from the middle ear, tonsil, and adenoid specimens, respectively. Pseudomonadaceae dominated the middle ear microbiota at 82.7% relative abundance, whereas Streptococcaceae dominated the tonsil microbiota at 69.2%. Multiple bacteria, including Pseudomonadaceae, Streptococcaceae, Fusobacteriaceae, and Pasteurellaceae, dominated the adenoid microbiota. Overlap between the middle ear and the tonsil microbiota was minimal. In contrast, the adenoid microbiota encompassed bacteria detected from middle ear and tonsil. Conclusions: Bacterial community analysis using pyrosequencing analysis revealed diverse, previously unknown bacterial communities in a set of pediatric middle ear, tonsil, and adenoid specimens. Our findings suggest that the adenoid may be a source site for both the middle ear and tonsil microbiota. An ecological framework is appropriate in comparative analysis of microbiota from nonsterile body sites. [ABSTRACT FROM AUTHOR]

Objective: To characterize bacterial microbiota in middle ear, adenoid, and tonsil specimens using 16SrRNA gene-based pyrosequencing analysis., Design: Cross-sectional study of bacterial microbiota in middle ear, adenoid, and tonsil specimens from a pediatric patient with chronic serous otitis media. Middle ear, adenoid, and tonsil specimens from a pediatric patient were collected and underwent cell lysis and DNA isolation. Pyrosequencing was performed on the 454 Life Sciences GS FLX platform (Roche Diagnostics Corp, Branford, Connecticut). Pyrosequencing data were processed, quality-checked, and taxonomically classified to generate an abundance-based matrix. Ecological analyses were performed., Setting: Academic, tertiary referral center., Main Outcome Measures: Comparative microbiome analysis., Results: We detected a total of 17 unique bacterial families, with 9, 9, and 12 bacterial families from the middle ear, tonsil, and adenoid specimens, respectively. Pseudomonadaceae dominated the middle ear microbiota at 82.7% relative abundance, whereas Streptococcaceae dominated the tonsil microbiota at 69.2%. Multiple bacteria, including Pseudomonadaceae, Streptococcaceae, Fusobacteriaceae, and Pasteurellaceae, dominated the adenoid microbiota. Overlap between the middle ear and the tonsil microbiota was minimal. In contrast, the adenoid microbiota encompassed bacteria detected from middle ear and tonsil., Conclusions: Bacterial community analysis using pyrosequencing analysis revealed diverse, previously unknown bacterial communities in a set of pediatric middle ear, tonsil, and adenoid specimens. Our findings suggest that the adenoid may be a source site for both the middle ear and tonsil microbiota. An ecological framework is appropriate in comparative analysis of microbiota from nonsterile body sites.