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

Journal: Journal of Clinical Microbiology

Article Title: Performance assessment of the Bruker Biotyper MALDI-TOF MS for the identification of difficult-to-identify viridans group streptococci

doi: 10.1128/jcm.01143-23

Figure Lengend Snippet: Identification results of the three Bruker Biotyper systems for the reference strains

Article Snippet: TABLE 1 Group Strain 16S rDNA (%) a MALDI TOF MS Biotyper 3.1 (DB_5627) Biotyper 3.1 (DB_6903) Biotyper 4.1 (DB_10833) ID b Group ID b Group ID b Group Mitis S. mitis ATCC 49456 100 Spn Mitis Smi Mitis Smi Mitis Mitis S. oralis ATCC 35037 100 Spn Mitis Sor Mitis Sor Mitis Mitis S. pseudopneumoniae ATCC BAA-960 100 Spn Mitis Sps Mitis Sps Mitis Mitis S. pneumoniae ATCC 49619 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 6301 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 6305 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC BAA-255 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 33400 100 ND c ND c Spn Mitis Spn Mitis Bovis S. gallolyticus ATCC 43144 100 ND c ND c Sga Bovis Sga Bovis Bovis S. equinus ATCC 33317 100 ND c ND c Slu Bovis Slu Bovis Bovis S. infantarius ATCC BAA-102 100 ND c ND c Seq Bovis Sinf Bovis Bovis S. lutetiensis ATCC BAA-103 99.93 ND c ND c Slu Bovis Slu Bovis Anginosus S. anginosus ATCC 9895 100 San Anginosus San Anginosus San Anginosus Anginosus S. constellatus ATCC 27513 100 Sco Anginosus Sco Anginosus Sco Anginosus Anginosus S. intermedius ATCC 27335 100 Sint Anginosus Sint Anginosus Sint Anginosus Sanguinis S. sanguinis ATCC 10556 100 Ssan Sanguinis Ssan Sanguinis Ssan Sanguinis Sanguinis S. parasanguinis ATCC 15909 99.86 Spa Sanguinis Spa Sanguinis Spa Sanguinis Sanguinis S. gordonii ATCC 35105 100 Sgo Sanguinis Sgo Sanguinis Sgo Sanguinis Salivarius S. salivarius ATCC 7073 100 Ssal Salivarius Ssal Salivarius Ssal Salivarius Mutans S. mutans ATCC GS-5 100 Smu Mutans Smu Mutans Smu Mutans Open in a separate window a Percent homology to 16S rDNA sequences in the NCBI database. b The text in bold indicates discrepant results.

Techniques:

Journal: Journal of Clinical Microbiology

Article Title: Performance assessment of the Bruker Biotyper MALDI-TOF MS for the identification of difficult-to-identify viridans group streptococci

doi: 10.1128/jcm.01143-23

Figure Lengend Snippet: Comparison of MALDI-TOF MS scores between on-plate and tube-based extraction methods

Article Snippet: TABLE 1 Group Strain 16S rDNA (%) a MALDI TOF MS Biotyper 3.1 (DB_5627) Biotyper 3.1 (DB_6903) Biotyper 4.1 (DB_10833) ID b Group ID b Group ID b Group Mitis S. mitis ATCC 49456 100 Spn Mitis Smi Mitis Smi Mitis Mitis S. oralis ATCC 35037 100 Spn Mitis Sor Mitis Sor Mitis Mitis S. pseudopneumoniae ATCC BAA-960 100 Spn Mitis Sps Mitis Sps Mitis Mitis S. pneumoniae ATCC 49619 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 6301 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 6305 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC BAA-255 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 33400 100 ND c ND c Spn Mitis Spn Mitis Bovis S. gallolyticus ATCC 43144 100 ND c ND c Sga Bovis Sga Bovis Bovis S. equinus ATCC 33317 100 ND c ND c Slu Bovis Slu Bovis Bovis S. infantarius ATCC BAA-102 100 ND c ND c Seq Bovis Sinf Bovis Bovis S. lutetiensis ATCC BAA-103 99.93 ND c ND c Slu Bovis Slu Bovis Anginosus S. anginosus ATCC 9895 100 San Anginosus San Anginosus San Anginosus Anginosus S. constellatus ATCC 27513 100 Sco Anginosus Sco Anginosus Sco Anginosus Anginosus S. intermedius ATCC 27335 100 Sint Anginosus Sint Anginosus Sint Anginosus Sanguinis S. sanguinis ATCC 10556 100 Ssan Sanguinis Ssan Sanguinis Ssan Sanguinis Sanguinis S. parasanguinis ATCC 15909 99.86 Spa Sanguinis Spa Sanguinis Spa Sanguinis Sanguinis S. gordonii ATCC 35105 100 Sgo Sanguinis Sgo Sanguinis Sgo Sanguinis Salivarius S. salivarius ATCC 7073 100 Ssal Salivarius Ssal Salivarius Ssal Salivarius Mutans S. mutans ATCC GS-5 100 Smu Mutans Smu Mutans Smu Mutans Open in a separate window a Percent homology to 16S rDNA sequences in the NCBI database. b The text in bold indicates discrepant results.

Techniques: Comparison, Extraction

Journal: Journal of Clinical Microbiology

Article Title: Performance assessment of the Bruker Biotyper MALDI-TOF MS for the identification of difficult-to-identify viridans group streptococci

doi: 10.1128/jcm.01143-23

Figure Lengend Snippet: Resolution of discrepancies between the gene sequencing method and the three Bruker Biotyper systems

Article Snippet: TABLE 1 Group Strain 16S rDNA (%) a MALDI TOF MS Biotyper 3.1 (DB_5627) Biotyper 3.1 (DB_6903) Biotyper 4.1 (DB_10833) ID b Group ID b Group ID b Group Mitis S. mitis ATCC 49456 100 Spn Mitis Smi Mitis Smi Mitis Mitis S. oralis ATCC 35037 100 Spn Mitis Sor Mitis Sor Mitis Mitis S. pseudopneumoniae ATCC BAA-960 100 Spn Mitis Sps Mitis Sps Mitis Mitis S. pneumoniae ATCC 49619 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 6301 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 6305 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC BAA-255 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 33400 100 ND c ND c Spn Mitis Spn Mitis Bovis S. gallolyticus ATCC 43144 100 ND c ND c Sga Bovis Sga Bovis Bovis S. equinus ATCC 33317 100 ND c ND c Slu Bovis Slu Bovis Bovis S. infantarius ATCC BAA-102 100 ND c ND c Seq Bovis Sinf Bovis Bovis S. lutetiensis ATCC BAA-103 99.93 ND c ND c Slu Bovis Slu Bovis Anginosus S. anginosus ATCC 9895 100 San Anginosus San Anginosus San Anginosus Anginosus S. constellatus ATCC 27513 100 Sco Anginosus Sco Anginosus Sco Anginosus Anginosus S. intermedius ATCC 27335 100 Sint Anginosus Sint Anginosus Sint Anginosus Sanguinis S. sanguinis ATCC 10556 100 Ssan Sanguinis Ssan Sanguinis Ssan Sanguinis Sanguinis S. parasanguinis ATCC 15909 99.86 Spa Sanguinis Spa Sanguinis Spa Sanguinis Sanguinis S. gordonii ATCC 35105 100 Sgo Sanguinis Sgo Sanguinis Sgo Sanguinis Salivarius S. salivarius ATCC 7073 100 Ssal Salivarius Ssal Salivarius Ssal Salivarius Mutans S. mutans ATCC GS-5 100 Smu Mutans Smu Mutans Smu Mutans Open in a separate window a Percent homology to 16S rDNA sequences in the NCBI database. b The text in bold indicates discrepant results.

Techniques: Sequencing

Journal: Journal of Clinical Microbiology

Article Title: Performance assessment of the Bruker Biotyper MALDI-TOF MS for the identification of difficult-to-identify viridans group streptococci

doi: 10.1128/jcm.01143-23

Figure Lengend Snippet: Accuracy ratios of VGS species identification among clinical isolates using three Bruker Biotyper systems

Article Snippet: TABLE 1 Group Strain 16S rDNA (%) a MALDI TOF MS Biotyper 3.1 (DB_5627) Biotyper 3.1 (DB_6903) Biotyper 4.1 (DB_10833) ID b Group ID b Group ID b Group Mitis S. mitis ATCC 49456 100 Spn Mitis Smi Mitis Smi Mitis Mitis S. oralis ATCC 35037 100 Spn Mitis Sor Mitis Sor Mitis Mitis S. pseudopneumoniae ATCC BAA-960 100 Spn Mitis Sps Mitis Sps Mitis Mitis S. pneumoniae ATCC 49619 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 6301 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 6305 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC BAA-255 100 ND c ND c Spn Mitis Spn Mitis Mitis S. pneumoniae ATCC 33400 100 ND c ND c Spn Mitis Spn Mitis Bovis S. gallolyticus ATCC 43144 100 ND c ND c Sga Bovis Sga Bovis Bovis S. equinus ATCC 33317 100 ND c ND c Slu Bovis Slu Bovis Bovis S. infantarius ATCC BAA-102 100 ND c ND c Seq Bovis Sinf Bovis Bovis S. lutetiensis ATCC BAA-103 99.93 ND c ND c Slu Bovis Slu Bovis Anginosus S. anginosus ATCC 9895 100 San Anginosus San Anginosus San Anginosus Anginosus S. constellatus ATCC 27513 100 Sco Anginosus Sco Anginosus Sco Anginosus Anginosus S. intermedius ATCC 27335 100 Sint Anginosus Sint Anginosus Sint Anginosus Sanguinis S. sanguinis ATCC 10556 100 Ssan Sanguinis Ssan Sanguinis Ssan Sanguinis Sanguinis S. parasanguinis ATCC 15909 99.86 Spa Sanguinis Spa Sanguinis Spa Sanguinis Sanguinis S. gordonii ATCC 35105 100 Sgo Sanguinis Sgo Sanguinis Sgo Sanguinis Salivarius S. salivarius ATCC 7073 100 Ssal Salivarius Ssal Salivarius Ssal Salivarius Mutans S. mutans ATCC GS-5 100 Smu Mutans Smu Mutans Smu Mutans Open in a separate window a Percent homology to 16S rDNA sequences in the NCBI database. b The text in bold indicates discrepant results.

Techniques: