title: GyrB polymorphisms accurately assign invasive viridans group streptococcal species.
abstract: Viridans group streptococci (VGS) are a heterogeneous group of medically important bacteria that cannot be accurately assigned to a particular species using conventional phenotypic methods. Although multilocus sequence analysis (MLSA) is considered the gold standard for VGS species-level identification, MLSA is not yet feasible in the clinical setting. Conversely, molecular methods, such as sodA and 16S rRNA gene sequencing, are clinically practical but not sufficiently accurate for VGS species-level identification. Here, we present data regarding the use of an ∼ 400-nucleotide internal fragment of the gene encoding DNA gyrase subunit B (GyrB) for VGS species-level identification. MLSA, internal gyrB, sodA, full-length, and 5' 16S gene sequences were used to characterize 102 unique VGS blood isolates collected from 2011 to 2012. When using the MLSA species assignment as a reference, full-length and 5' partial 16S gene and sodA sequence analyses failed to correctly assign all strains to a species. Precise species determination was particularly problematic for Streptococcus mitis and Streptococcus oralis isolates. However, the internal gyrB fragment allowed for accurate species designations for all 102 strains. We validated these findings using 54 VGS strains for which MLSA, 16S gene, sodA, and gyrB data are available at the NCBI, showing that gyrB is superior to 16S gene and sodA sequence analyses for VGS species identification. We also observed that specific polymorphisms in the 133-amino acid sequence of the internal GyrB fragment can be used to identify invasive VGS species. Thus, the GyrB amino acid sequence may offer a more practical and accurate method for classifying invasive VGS strains to the species level.
authors.affiliation: Department of Infectious Diseases, Infection Control and Employee Health, MD Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Galloway-Peña
authors.affiliation: Department of Infectious Diseases, Infection Control and Employee Health, MD Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Pranoti
authors.initials: P
authors.lastname: Sahasrabhojane
authors.affiliation: Department of Laboratory Medicine, MD Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Tarrand
authors.affiliation: Department of Laboratory Medicine, MD Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Xiang Y
authors.initials: XY
authors.lastname: Han
authors.affiliation: Department of Infectious Diseases, Infection Control and Employee Health, MD Anderson Cancer Center, Houston, Texas, USA Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas, USA sshelburne@mdanderson.org.
authors.forename: Samuel A
authors.initials: SA
authors.lastname: Shelburne
mesh_terms: D016470:Bacteremia / Q000175:diagnosis / Q000382:microbiology; D027081:DNA Gyrase / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D018509:DNA, Helminth / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D011110:Polymorphism, Genetic; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013290:Streptococcal Infections / Q000175:diagnosis / Q000382:microbiology; D034363:Viridans Streptococci / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D004269:DNA, Bacterial; D018509:DNA, Helminth; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D027081:DNA Gyrase