First Complete Genome Sequences of Staphylococcus aureus subsp.
            <i>aureus</i>
            Rosenbach 1884 (DSM 20231
            <sup>T</sup>
            ), Determined by PacBio Single-Molecule Real-Time Technology

Shiroma, Akino; Terabayashi, Yasunobu; Nakano, Kazuma; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

doi:10.1128/genomea.00800-15

Cited by 12 publications

(13 citation statements)

References 15 publications

(15 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…One possible reason could be the difference in GC contents of the bacteria’s genome. While Gram-negative had a GC content between 50–53% [ 29 , 30 ], Gram-positive were reported to be within 33–36% [ 31 , 32 , 33 ]. This makes the genome of E. coli and Klebsiella sp.…”

Section: Resultsmentioning

confidence: 99%

Multiple Bacteria Identification in the Point-of-Care: an Old Method Serving a New Approach

Viveiros

Rodrigues

Albuquerque

et al. 2020

Sensors

View full text Add to dashboard Cite

The accurate diagnosis of bacterial infections is of critical importance for effective treatment decisions. Due to the multietiologic nature of most infectious diseases, multiplex assays are essential for diagnostics. However, multiplexability in nucleic acid amplification-based methods commonly resorts to multiple primers and/or multiple reaction chambers, which increases analysis cost and complexity. Herein, a polymerase chain reaction (PCR) offer method based on a universal pair of primers and an array of specific oligonucleotide probes was developed through the analysis of the bacterial 16S ribosomal RNA gene. The detection system consisted of DNA hybridization over an array of magnetoresistive sensors in a microfabricated biochip coupled to an electronic reader. Immobilized probes interrogated single-stranded biotinylated amplicons and were obtained using asymmetric PCR. Moreover, they were magnetically labelled with streptavidin-coated superparamagnetic nanoparticles. The benchmarking of the system was demonstrated to detect five major bovine mastitis-causing pathogens: Escherichia coli, Klebsiella sp., Staphylococcus aureus, Streptococcus uberis, and Streptococcus agalactiae. All selected probes proved to specifically detect their respective amplicon without significant cross reactivity. A calibration curve was performed for S. agalactiae, which demonstrates demonstrating a limit of detection below 30 fg/µL. Thus, a sensitive and specific multiplex detection assay was established, demonstrating its potential as a bioanalytical device for point-of-care applications.

show abstract

Section: Resultsmentioning

confidence: 99%

Multiple Bacteria Identification in the Point-of-Care: an Old Method Serving a New Approach

Viveiros

Rodrigues

Albuquerque

et al. 2020

Sensors

View full text Add to dashboard Cite

show abstract

“…Identification of the core genome and pan-genome was performed using the EDGAR software platform [ 59 ]. Several tools have been made available recently as stand-alone, open source, or web-based tools [ 60 ]. EDAGR 2.2 is a powerful tool that uses several publicly available genomes but also accommodates customized projects and genomes.…”

Section: Methodsmentioning

confidence: 99%

Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer

Matelska¹,

Ginalski²,

Riegel³

et al. 2018

BMC Genomics

View full text Add to dashboard Cite

BackgroundCoagulase negative staphylococci (CoNS) are commensal bacteria on human skin. Staphylococcus lugdunensis is a unique CoNS which produces various virulence factors and may, like S. aureus, cause severe infections, particularly in hospital settings. Unlike other staphylococci, it remains highly susceptible to antimicrobials, and genome-based phylogenetic studies have evidenced a highly conserved genome that distinguishes it from all other staphylococci.ResultsWe demonstrate that S. lugdunensis possesses a closed pan-genome with a very limited number of new genes, in contrast to other staphylococci that have an open pan-genome. Whole-genome nucleotide and amino acid identity levels are also higher than in other staphylococci. We identified numerous genetic barriers to horizontal gene transfer that might explain this result. The S. lugdunensis genome has multiple operons encoding for restriction-modification, CRISPR/Cas and toxin/antitoxin systems. We also identified a new PIN-like domain-associated protein that might belong to a larger operon, comprising a metalloprotease, that could function as a new toxin/antitoxin or detoxification system.ConclusionWe show that S. lugdunensis has a unique genome profile within staphylococci, with a closed pan-genome and several systems to prevent horizontal gene transfer. Its virulence in clinical settings does not rely on its ability to acquire and exchange antibiotic resistance genes or other virulence factors as shown for other staphylococci.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4978-1) contains supplementary material, which is available to authorized users.

show abstract

“…The dDDH values were calculated using the web-based genome-to-genome distance calculator (GGDC) version 2.1 (71), and the recommended formula 2 was taken into account to interpret the results. Whole-genome sequences of related staphylococcal species were obtained from the NCBI database (72)(73)(74)(75).…”

Section: Methodsmentioning

confidence: 99%

Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments

Pantůček

Sedláček

Indráková

et al. 2018

Appl Environ Microbiol

View full text Add to dashboard Cite

Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources, stone fragments and sandy soil in James Ross Island, Antarctica. Here we describe properties of novel species of the genus that has near identical 16S rRNA gene sequence to However, compared to and the next closest relatives, the new species demonstrates considerable phylogenetic distance at whole genome level, average nucleotide identity<85 %, and inferred DNA-DNA hybridization <30%. It forms a separate branch in phylogenetic clade confirmed by multilocus sequence analysis of six housekeeping genes, ,, ,, and MALDI-TOF MS and key biochemical characteristics allowed these bacteria to be distinguished from their nearest phylogenetic neighbours. In contrast to subsp. , strains were pyrrolidonyl arylamidase- and β-glucuronidase-positive, β -galactosidase-negative, nitrate was reduced and acid produced aerobically from d-mannose. Whole genome sequencing of 2.75 Mb large chromosome revealed the presence of a number of mobile genetic elements including the 27-kb-long pseudo staphylococcus cassette chromosome (ψSCC) harboring gene, two composite phage-inducible chromosomal islands probably essential to adaptation to extreme environment, and one complete and one defective prophage. Both strains are resistant to penicillin G, ampicillin, ceftazidin, methicillin, cefoxitin, and fosfomycin. We hypothesize that antibiotic resistance might represent an evolutionary advantage against beta-lactams producers, which are common in a polar environment. Based on these results, a novel species of the genus is described and named sp. nov. The type strain is P5085 (=CCM 8730 = DSM 104441). The description of sp. nov. enables the comparison of multidrug-resistant staphylococci from human and veterinary sources evolved in the globalized world to their geographically distant relative from the extreme Antarctic environment. Although this new species was not exposed to the pressure of antibiotic treatment in human or veterinary practice, mobile genetic elements carrying antimicrobial resistance genes were found in the genome. The presented genomic characteristics elucidate the evolutionary relationships in the genus with a special focus on antimicrobial resistance, pathogenicity and survival traits. Genes encoded on mobile genetic elements were arranged in unique combinations but retained conserved locations for the integration of mobile genetic elements. These findings point to enormous plasticity of the staphylococcal pangenome shaped by horizontal gene transfer. Thus can act not only as a reservoir of antibiotic resistance in a natural environment, but also as a mediator for the spread and evolution of resistance genes.

show abstract

First Complete Genome Sequences of Staphylococcus aureus subsp. aureus Rosenbach 1884 (DSM 20231 ^T ), Determined by PacBio Single-Molecule Real-Time Technology

Cited by 12 publications

References 15 publications

Multiple Bacteria Identification in the Point-of-Care: an Old Method Serving a New Approach

Multiple Bacteria Identification in the Point-of-Care: an Old Method Serving a New Approach

Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer

Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments

Contact Info

Product

Resources

About

First Complete Genome Sequences of Staphylococcus aureus subsp. aureus Rosenbach 1884 (DSM 20231 T ), Determined by PacBio Single-Molecule Real-Time Technology

Cited by 12 publications

References 15 publications

Multiple Bacteria Identification in the Point-of-Care: an Old Method Serving a New Approach

Multiple Bacteria Identification in the Point-of-Care: an Old Method Serving a New Approach

Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer

Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments

Contact Info

Product

Resources

About

First Complete Genome Sequences of Staphylococcus aureus subsp. aureus Rosenbach 1884 (DSM 20231 ^T ), Determined by PacBio Single-Molecule Real-Time Technology