Journal: Journal of Clinical Microbiology

Article Title: Development of Real-Time PCR Assays for Detection of the Streptococcus milleri Group from Cystic Fibrosis Clinical Specimens by Targeting the cpn60 and 16S rRNA Genes

doi: 10.1128/jcm.02082-09

Figure Lengend Snippet: FIG. 1. Dendrogram analysis of a variety of Streptococcus spp. using a 1,515-bp portion of the 16S rRNA gene sequence corresponding to positions 33 to 1547 of S. anginosus AF104678. The dendrogram was generated using Splitstree4 version 4.10 (26). The SMG spp. are highlighted with a black box. The accession numbers for the nucleotide sequences used in this analysis are as follows: S. agalactiae, AE009948; S. alactolyticus, AF201899; S. anginosus, AF104678; S. australis, AY485604; S. bovis, AB002482; S. canis, DQ303184; S. constellatus, AF104676; S. cristatus, AY584476; S. didelphis, DQ303185; S. downei, AY188350; S. dysgalactiae, AY584478; S. equinus, AB362710; S. equi subsp. equi, EF406032; S. gordonii, CP000725; S. hyointestinalis, AF201898; S. infantarius, AF429762; S. iniae, DQ303187; S. intermedius, AF104671; S. mitis, AF003929; S. mutans, DQ303189; S. oralis, AY485602; S. orisratti, AF124350; S. parasanguinis, DQ303191; S. phocae, AF235052; S. pneumoniae, AY485600; S. porcinus, AB002523; S. pyogenes, FJ662846; S. salivarius, AY188352; S. sanguinis, AY691542; S. sinensis, AF432856; S. thermophilus, AY687382; S. thoraltensis, Y09007; S. uberis, AM946015; and S. vestibularis, AY188353.

Article Snippet: For S. anginosus, the majority of strains (24/40) had Tms similar to those of the type strain S. anginosus ATCC 33397 (53.23°C 0.38°C).

Techniques: Sequencing, Generated

Journal: Journal of Clinical Microbiology

Article Title: Development of Real-Time PCR Assays for Detection of the Streptococcus milleri Group from Cystic Fibrosis Clinical Specimens by Targeting the cpn60 and 16S rRNA Genes

doi: 10.1128/jcm.02082-09

Figure Lengend Snippet: FIG. 3. Detection limits for the SMG-specific real-time PCR assays showing the relationship between CFU and CP for each assay. (A) SMG_cpn60; (B) 16s_SA; and (C) 16s_SCI. In each graph, S. anginosus (S. ang) is represented by a circle, S. constellatus (S. const) by a square, and S. intermedius (S. inter) by a triangle. The gray vertical line represents the current detection limit for SMG using McKay agar (104 CFU/ml) to isolate SMG from sputum samples.

Article Snippet: For S. anginosus, the majority of strains (24/40) had Tms similar to those of the type strain S. anginosus ATCC 33397 (53.23°C 0.38°C).

Techniques: Real-time Polymerase Chain Reaction

Journal: Journal of Clinical Microbiology

Article Title: Development of Real-Time PCR Assays for Detection of the Streptococcus milleri Group from Cystic Fibrosis Clinical Specimens by Targeting the cpn60 and 16S rRNA Genes

doi: 10.1128/jcm.02082-09

Figure Lengend Snippet: FIG. 4. Alignment of partial sequence of the cpn60 gene-binding region for the SMG_cpn60 real-time PCR assay. The primers and probes were designed to match S. constellatus ATCC 27823 (no. 1). All S. intermedius strains have an SNP in the forward primer, and S. intermedius ATCC 27335 (no. 2) has 3 SNPs in the LCRed640-labeled probe, while the S. intermedius Tm 61.5 strain (no. 3) has two SNPs in the LCRed640 probe and the S. intermedius Tm 60.3 strain (no. 4) has 2 SNPs in the LCRed640-labeled probe and one SNP in the fluorescein-labeled probe. S. anginosus ATCC 33397 (no. 5) has three SNPs in the fluorescein-labeled probe and four SNPs in the LCRed640-labeled probe, as well as four SNPs in the reverse primer. Streptococcus bovis (no. 6), S. gordonii (no. 7), and S. infantis (no. 8) are the only non-SMG spp. tested that produce a signal using this assay, with Tms of 54.67°C 0.17°C, 51.24°C 0.14°C, and 52.04°C 0.23°C, respectively.

Article Snippet: For S. anginosus, the majority of strains (24/40) had Tms similar to those of the type strain S. anginosus ATCC 33397 (53.23°C 0.38°C).

Techniques: Sequencing, Binding Assay, Real-time Polymerase Chain Reaction, Labeling