s capitis subsp ureolyticus  (ATCC)

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Genomic Analysis of Multiresistant Staphylococcus capitis Associated with Neonatal Sepsis

doi: 10.1128/AAC.00898-18

Figure Lengend Snippet: Maximum likelihood (ML) trees demonstrating the population structure of Staphylococcus capitis . ML trees were inferred from core-genome single nucleotide polymorphisms (SNPs) and rooted using the minimal ancestor deviation method . (A) ML tree of all 135 included S. capitis isolates, with metadata indicating source, highest level BAPS grouping, and presence/absence of antimicrobial resistance (AMR) genes ( mecA and plasmid-carried fusB , aadD , and qacA ) and embp . (B) ML tree of isolates classified as part of BAPS group 3, with metadata indicating source and BAPS grouping of isolates within BAPS group 3 (indicated in panel A).

Article Snippet: Initial identification of S. capitis isolates was performed using matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (Bruker Daltonics, USA), and urease and maltose fermentation tests were used to differentiate between S. capitis subsp. urealyticus and S. capitis subsp. capitis .

Techniques: Plasmid Preparation

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Genomic Analysis of Multiresistant Staphylococcus capitis Associated with Neonatal Sepsis

doi: 10.1128/AAC.00898-18

Figure Lengend Snippet: (A) Comparison of representative S. capitis chromosome sequences relative to S. capitis NZ-SC16875, illustrating a high level of conservation among the international NICU-associated S. capitis BP3 isolates (inner six rings). Variable regions are annotated in the outer ring. These regions include two putative bacteriophages (phage 1 and phage 2), the SCC cad -SCC ars -SCC cop region, and the embp gene (B) Schematic diagram illustrating the genetic organization of the composite SCC cad -SCC ars -SCC cop element in BP3 lineage S. capitis isolates NZ-SC16875 and CR01. Also included are the SCC mec V elements of S. schleiferi TSCC54, S. pseudintermedius 06-3228, S. aureus JCSC6944, and MRSA P126, and S. haemolyticus NW19A, as well as the SCC cad -SCC ars -SCC cop regions of S. haemolyticus S167 and SH621 and S. simulans FDAARGOS_124 for comparison. Green and yellow arrows indicate sequences present within SCC mec V regions; orange arrows are CRISPR-associated genes; and blue, purple, and red arrows indicate genes within SCC cad -SCC ars -SCC cop regions. The direction of the arrows indicates the direction of transcription for open reading frames. Only coding sequences of >200 bp are shown. Shaded areas represent regions that share >99% nucleotide sequence identity (pink denotes the same orientation, and blue denotes the reverse orientation). Note that the S. capitis NZ-SC16875 region is shown at the top and bottom of the figure for ease of comparison.

Article Snippet: Initial identification of S. capitis isolates was performed using matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (Bruker Daltonics, USA), and urease and maltose fermentation tests were used to differentiate between S. capitis subsp. urealyticus and S. capitis subsp. capitis .

Techniques: CRISPR, Sequencing

Journal: Gut Pathogens

Article Title: Whole genome sequence and comparative genomic analysis of multidrug-resistant Staphylococcus capitis subsp. urealyticus strain LNZR-1

doi: 10.1186/s13099-014-0045-x

Figure Lengend Snippet: Phylogenetic tree highlighting the position of S. capitis subsp. urealyticus strain LNZR-1 relative to other type strains within the genus Staphylococcus. The strains and their corresponding GenBank accession numbers for 16S rRNA genes are shown following the organism names. Numbers at the branching nodes are percentages of bootstrap values based on 1,000 replications. Bootstrap values greater than 50% are shown at the branch points. Macrococcus caseolyticus ATCC 13548 T was used as an out group. The scale bar represents 0.005 substitutions per nucleotide position.

Article Snippet: The genome of S. capitis subsp. urealyticus strain LNZR-1 was sequenced using a standard run of Illumina HiSeq 2000 sequencing technology which generated paired-end libraries (500-bp insert size) according to the manufacturer’s instructions.

Techniques:

Journal: Gut Pathogens

Article Title: Whole genome sequence and comparative genomic analysis of multidrug-resistant Staphylococcus capitis subsp. urealyticus strain LNZR-1

doi: 10.1186/s13099-014-0045-x

Figure Lengend Snippet: Subsystems distribution statistic of S. capitis subsp. urealyticus strain LNZR-1 based on genome annotations performed according to RAST server. The pie chart presents the abundance of each subsystem category and the count of each subsystem feature is listed in parentheses at the chart legend.

Article Snippet: The genome of S. capitis subsp. urealyticus strain LNZR-1 was sequenced using a standard run of Illumina HiSeq 2000 sequencing technology which generated paired-end libraries (500-bp insert size) according to the manufacturer’s instructions.

Techniques:

Journal: Gut Pathogens

Article Title: Whole genome sequence and comparative genomic analysis of multidrug-resistant Staphylococcus capitis subsp. urealyticus strain LNZR-1

doi: 10.1186/s13099-014-0045-x

Figure Lengend Snippet: COGs distribution of S. capitis subsp. urealyticus strain LNZR-1. Statistics of annotated genes for LNZR-1 were based on COG database.

Article Snippet: The genome of S. capitis subsp. urealyticus strain LNZR-1 was sequenced using a standard run of Illumina HiSeq 2000 sequencing technology which generated paired-end libraries (500-bp insert size) according to the manufacturer’s instructions.

Techniques:

Journal: Gut Pathogens

Article Title: Whole genome sequence and comparative genomic analysis of multidrug-resistant Staphylococcus capitis subsp. urealyticus strain LNZR-1

doi: 10.1186/s13099-014-0045-x

Figure Lengend Snippet: MAUVE alignment of the genomes of S. capitis subsp. urealyticus LNZR-1, S. capitis C87, S. capitis SK14, S. capitis CR01, S. capitis VCU116 and S. capitis QN1. MAUVE identifies and aligns regions of local collinearity called locally collinear blocks (LCBs), a region without rearrangement of homologous backbone sequence. LCBs below a genome’s center line are in the reverse complement orientation relative to the reference genome. Lines between genomes trace each orthologous LCB through every genome.

Article Snippet: The genome of S. capitis subsp. urealyticus strain LNZR-1 was sequenced using a standard run of Illumina HiSeq 2000 sequencing technology which generated paired-end libraries (500-bp insert size) according to the manufacturer’s instructions.

Techniques: Sequencing

Journal: Gut Pathogens

Article Title: Whole genome sequence and comparative genomic analysis of multidrug-resistant Staphylococcus capitis subsp. urealyticus strain LNZR-1

doi: 10.1186/s13099-014-0045-x

Figure Lengend Snippet: Venn diagram representing the pan-genome of S. capitis subsp. urealyticus LNZR-1, S. capitis C87, S. capitis CR01, S. capitis VCU116 and S. capitis QN1. Numbers inside the Venn diagram indicate the number of genes found to be shared among the indicated genomes.

Article Snippet: The genome of S. capitis subsp. urealyticus strain LNZR-1 was sequenced using a standard run of Illumina HiSeq 2000 sequencing technology which generated paired-end libraries (500-bp insert size) according to the manufacturer’s instructions.

Techniques:

Journal:

Article Title: SdrX, a Serine-Aspartate Repeat Protein Expressed by Staphylococcus capitis with Collagen VI Binding Activity

doi: 10.1128/IAI.72.11.6237-6244.2004

Figure Lengend Snippet: Identification and cloning of S. capitis ATCC 49326 genomic sequences with homology to the repeat region of sdrG. (A) Schematic representation of the SdrG protein and the corresponding region of the gene sequence that was used as a hybridization probe (arrows). (B) Southern hybridization. Genomic DNA was digested with HindIII, separated on a 1% agarose gel, and transferred onto a Zeta-probe membrane. The blot was hybridized with a digoxigenin-labeled probe from the B and R regions of sdrG. Lane 1: 1-kb DNA molecular weight marker; lane2: genomic DNA from S. epidermidis K28; lane 3: genomic DNA from S. capitis ATCC 49326. (C) Deduced amino acid sequence of SdrX from S. capitis ATCC 49326. The vertical arrow indicates the signal peptide cleavage site (amino acid 39). The A region (amino acids 40 to 254) is shown in boldface type. The B repeat region (BX) (amino acids 255 to 420) is underlined. The R region (amino acids 421 to 630) containing the SD repetitive sequence is in italics. The cell wall-anchoring motif LPDTG (amino acids 674 to 678) is in italic boldface type.

Article Snippet: Lane 1: 1-kb DNA molecular weight marker; lane2: genomic DNA from S. epidermidis K28; lane 3: genomic DNA from S. capitis ATCC 49326. (C) Deduced amino acid sequence of SdrX from S. capitis ATCC 49326.

Techniques: Clone Assay, Genomic Sequencing, Sequencing, Hybridization, Agarose Gel Electrophoresis, Labeling, Molecular Weight, Marker

Journal:

Article Title: SdrX, a Serine-Aspartate Repeat Protein Expressed by Staphylococcus capitis with Collagen VI Binding Activity

doi: 10.1128/IAI.72.11.6237-6244.2004

Figure Lengend Snippet: Detection of sdrX mRNA by RT-PCR. Total RNA was isolated from S. capitis ATCC 49326 culture at early log, mid-log, and stationary phases. 16S rRNA and sdrX RNA were converted into cDNA by using sequence-specific primers and amplified by RT-PCR. RT+ and RT− indicate with and without reverse transcriptase, respectively. The positions of the sdrX and 16S rRNA products are indicated.

Article Snippet: Lane 1: 1-kb DNA molecular weight marker; lane2: genomic DNA from S. epidermidis K28; lane 3: genomic DNA from S. capitis ATCC 49326. (C) Deduced amino acid sequence of SdrX from S. capitis ATCC 49326.

Techniques: Reverse Transcription Polymerase Chain Reaction, Isolation, Sequencing, Amplification