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Staphylococcus

Staphylococcus is a genus of Gram-positive bacteria that are spherical in shape and often arrange in grape-like clusters.
These ubiquitous microorganisms are commonly found on the skin and mucous membranes of humans and animals.
Staphylococcus species are known for their ability to cause a wide range of infections, from mild skin conditions to life-threatening sepsis.
The most well-known and clinically significant species is Staphylococcus aureus, which can produce toxins and develop resistance to numerous antibiotics, posing a significant public health challenge.
Reasearchers studying Staphylococcus must carefull select appropriate protocols and products to ensure reproducibile and accurate results in their studies.

Most cited protocols related to «Staphylococcus»

1
Virus Genome Fragmentation and Host Identification
We collected 1562 virus RefSeq genomes infecting prokaryotes and 31,986 prokaryotic host RefSeq genomes from NCBI in May 2015. The NCBI accession numbers of the RefSeq sequences are provided in the Additional file 2: Table S2. To mimic fragmented metagenomic sequences, for a given length L = 500, 1000, 3000, 5000, and 10000 bp, viruses were split into non-overlapping fragments of length L and the same number of non-overlapping fragments of length L were randomly subsampled from the prokaryotic genomes. Fragments were generated for virus genomes discovered before 1 January 2014 and after 1 January 2014 and were separately used as training and testing sets, respectively (Table 1). To generate evaluation datasets containing 10, 50, and 90% viral contigs, the number of viral contigs was set as in Table 1 and was combined with 9 times more, equal numbers, or 9-fold less randomly sampled host contigs, respectively.
Highly represented host phyla (Actinobacteria, Cyanobacteria, Firmicutes, Proteobacteria) and genera (Mycobacterium, Escherichia, Pseudomonas, Staphylococcus, Bacillus, Vibrio, and Streptococcus) were selected for the analyses where viruses infecting these taxa were excluded from the training of VirFinder. For evaluation of the different trained VirFinder models, equal numbers of contigs of the excluded viruses and all other viruses were selected and then combined with randomly selected host contigs such that total virus and host contigs were equal in number.
For the analysis of VirFinder trained with 14,722 prokaryotic genomes with or without proviruses removed, these genomes were downloaded from the database cited in [6 (link)]. Likewise, the positions of proviruses predicted by VirSorter in these 14,722 genomes were obtained from the published data of [6 (link)] and were used to remove theses sequence from their corresponding host genomes.
Ren J., Ahlgren N.A., Lu Y.Y., Fuhrman J.A, & Sun F. (2017). VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome, 5, 69.
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Publication 2017
Actinomycetes Bacillus Cyanobacteria Escherichia Firmicutes Genome Metagenome Mycobacterium Prokaryotic Cells Proteobacteria Proviruses Pseudomonas Staphylococcus Streptococcus Vibrio Viral Genome Virus
2
Staphylococcus pan-genome assembly and annotation
Sequence data (accession number SRP039360) was downloaded from NCBI Sequence Read Archive (SRA), subsampled to coverage 50 with khmer 2.0 [30 (link)], and assembled with mismatch correction in SPAdes 3.6.2 [31 (link)]. Contigs with length < 500 and coverage < 2.0 were removed by an in-house script. Assemblies were annotated with PROKKA 1.11 [32 (link)] using the Staphylococcus genus database. The pan-genome was constructed using Roary 3.4.2 [13 (link)]. Scoary 1.6.3 was run with the default options.
Brynildsrud O., Bohlin J., Scheffer L, & Eldholm V. (2016). Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biology, 17, 238.
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Publication 2016
Genome Staphylococcus
3
Temperature-sensitive vector for allelic replacement in Staphylococcus aureus
A new temperature-sensitive vector was constructed for allelic replacement mutagenesis in S. aureus. The vector is based on the replicon of the lactococcal plasmid pWV01ts (from pVE6007 [21 (link)]) rather than the commonly used staphylococcal pE194ts replicon (30 (link)). A hybrid vector (pIMC5) was created by spliced overlap extension (SOE) PCR. It comprises (i) the repBCAD(Ts) genes from pVE6007 and (ii) the E. coli backbone p15A rep and pBluescript KS multiple cloning site and the highly expressed chloramphenicol acyltransferase marker from pIMC (31 (link)). The counterselection marker encoding tetracycline-inducible antisense secY RNA was amplified from pKOR1 and introduced between the novel BglII and SphI sites to form pIMAY.
Monk I.R., Shah I.M., Xu M., Tan M.W, & Foster T.J. (2012). Transforming the Untransformable: Application of Direct Transformation To Manipulate Genetically Staphylococcus aureus and Staphylococcus epidermidis. mBio, 3(2), e00277-11.
Publication 2012
Alleles Antisense RNA Chloramphenicol O-Acetyltransferase Cloning Vectors Escherichia coli Genes Hybrids Lactococcus Mutagenesis Plasmids Replicon Staphylococcus Staphylococcus aureus Tetracycline Vertebral Column
4
Expanding the Reference Gene Catalog for Stress and Virulence Genes
We have expanded the Reference Gene Catalog8 (link) to include genetic elements related to stress response and virulence genes; these expansions can be visualized in the Reference Gene Catalog Browser (https://www.ncbi.nlm.nih.gov/pathogens/refgene/). One reason we expanded AMRFinderPlus is to understand the linkages between AMR genes and stress response and virulence genes in food-borne pathogens; thus, the stress response and virulence genes included in the Reference Gene Catalog are composed primarily of E. coli-related genes derived primarily from González-Escalona et al.23 (link) as well as BacMet24 (link), but also have been supplemented by manual curation efforts for other taxa. Stx gene nomenclature adopts the system of Scheutz et al.25 (link) and the intimin (eae) gene nomenclature uses existing designations in the literature26 (link),27 (link). Genes are incorporated only if there is literature supporting the function of that protein or closely related sequences that meet the identification criteria. As a major focus of our work is to improve NCBI’s Pathogen Detection system16 (link), we excluded genes that belonged to organisms not deemed clinically relevant. To remove ‘housekeeping’ proteins that were universally found in one or more taxa in the Pathogen Detection system, sequences were not included if they were found at a frequency of greater than 95% in a survey of 58,531 RefSeq bacterial assemblies belonging to any of the following species: Acinetobacter, Campylobacter, Citrobacter, Enterococcus, Enterobacter, Escherichia/Shigella, Klebsiella, Listeria, Salmonella, Staphylococcus, Pseudomonas, and Vibrio. If genes of particular interest in foodborne pathogens exceeded this threshold, they were excluded in the taxa where they appear to be nearly universal (see “Identifying genomic elements” below). In addition, genes with misidentified functions, such as copper-binding proteins that use copper as a co-factor yet do not confer resistance to copper, also were excluded. As we continue to expand the database, we use similar criteria when adding genes.
Feldgarden M., Brover V., Gonzalez-Escalona N., Frye J.G., Haendiges J., Haft D.H., Hoffmann M., Pettengill J.B., Prasad A.B., Tillman G.E., Tyson G.H, & Klimke W. (2021). AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Scientific Reports, 11, 12728.
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Publication 2021
Acinetobacter Bacteria Bears Campylobacter Citrobacter Copper copper-binding protein Enterobacter Enterococcus Escherichia Escherichia coli factor A Food Gene Components Genome Components Klebsiella Linkage, Genetic Listeria Operator, Genetic Pathogenicity Proteins Pseudomonas Salmonella Shigella Staphylococcus Vibrio Virulence
5
Staphylococcal DNA Isolation and Manipulation
The bacterial strains and plasmids used in this study are described in Table 2. Oligonucleotides were purchased from Integrated DNA Technologies and are listed in Table 3. Genomic DNA was isolated using the Qiagen 100/G genomic tip (Qiagen). Weakening of the staphylococcal cell wall required the addition of 100 µg of lysostaphin (Ambi) into the lysis buffer and incubation at 37°C for 30 min. Plasmids and PCR products were isolated using the Wizard plus kits (Promega), with T4 DNA ligase also purchased from Promega. Plasmids were isolated from staphylococci as described previously (3 (link)). Restriction enzymes, T4 DNA polymerase, and Phusion DNA polymerase were purchased from New England Biolabs. Phire Hotstart DNA polymerase was purchased from Thermofisher. Sanger sequencing was supplied by Eurofins. Routine manipulation of S. aureus and E. coli was performed as described by Monk et al. (3 (link)). X-Gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside; Melford) was used at 50 µg/ml in E. coli and 100 µg/ml in S. aureus. Antibiotics were purchased from Sigma Aldrich and used at the following concentrations: carbenicillin (Car), 100 µg/ml; chloramphenicol (Cm), 10 µg/ml; and kanamycin (Kan), 50 µg/ml (E. coli) and 100 µg/ml (S. aureus).
Monk I.R., Tree J.J., Howden B.P., Stinear T.P, & Foster T.J. (2015). Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages. mBio, 6(3), e00308-15.
Publication 2015
5-bromo-4-chloro-3-indolyl beta-galactoside Antibiotics Bacteria Buffers Carbenicillin Cell Wall Chloramphenicol DNA-Directed DNA Polymerase DNA Restriction Enzymes Escherichia coli Galactose Genome Kanamycin Lysostaphin Monks Oligonucleotides Plasmids Promega Staphylococcus Staphylococcus aureus Strains T4 DNA Ligase

Most recents protocols related to «Staphylococcus»

1
Deduplicating Blood Culture Contaminants
One pair of bottles (aerobic + anaerobic) with a result in the microbiology database formed a blood culture set. A positive blood culture was defined as a blood culture set with one or more positive findings. Potential contaminants were bacteria that are part of the normal skin microbiota (e.g. Coagulase-negative staphylococci, Corynebacterium, Cutibacterium), see Supplementary material S2, Classification of potential contaminants for details. These were considered contaminants if only one blood culture set was positive within 48 hours.
The deduplication period, the period during which only one BSI episode was registered, was set to 14 days. As the deduplication period varies between previous studies, sensitivity analyses were performed for 30, 90 and 365 days. A duplicate was defined as a culture for which there was another positive blood culture with the same finding, taken within the deduplication period. The positive blood cultures remaining after removal of contaminations and duplicates were considered relevant findings.
A polymicrobial finding was two or more different relevant findings from the same patient, obtained within the deduplication period. A BSI episode was defined as an episode with at least one relevant finding and where polymicrobial findings are deduplicated. Thus, if a blood culture set simultaneously grew Escherichia coli and Klebsiella spp., this would count as two relevant findings but only one BSI episode. An R classification in the original microbiology report defined antimicrobial resistance.
Ljungquist O., Blomstergren A., Merkel A., Sunnerhagen T., Holm K, & Torisson G. (2023). Incidence, aetiology and temporal trend of bloodstream infections in southern Sweden from 2006 to 2019: a population-based study. Eurosurveillance, 28(10), 2200519.
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Publication 2023
Bacteria Bacteria, Aerobic Blood Culture Coagulase Corynebacterium Escherichia coli Hypersensitivity Klebsiella Microbial Community Microbicides Patients Skin Staphylococcus
2
Antimicrobial Efficacy of Iron Nanoparticles
The anti-microbial efficient acts of iron nanoparticles were calculated using a well-gar dispersion strategy. They were cultured on Mueller-Hinton Agar at a concentration of 108/ml for bacterial growth and potato agar for fungal growth. Three fungi forms, Aspergillus niger, Alternaria sp., Rhizopus sp., and bacteria forms, the gram-positive Staphylococcus sp., Bacillus subtilis, and gram-negative community Klebsiella pneumonia, Shigella sp., Pseudomonas aeruginosa, and Escherichia coli, have been examined (Table 1). To measure antimicrobial efficiency, 100 μL of biosynthesized iron oxide nanoparticles and 100 μL of water were added as a negative agent. Bacterial strains were isolated in 0.2 mL (CFU 2.5*105 mL). On every agar plate, sterile swabs are placed at irregular intervals. Three of them were properly separated. The sterile cultivation agar surface was used to create wells (holes) with a diameter of 4 mm per plate. Use a metal cork to bore the hole. The aseptic use of 0.2 mL of extract at every hole was performed in the room. The excerpts can be dispersed and cultivated in the agar medium after 1 hour at room temperature. The negative control used in comparison was aseptic pure water. The plates were kept for 24–48 hours at 37°C and 25°C. Inhibition zones were identified as distinct regions surrounding the pools [30 (link)].
, & Al-brahim J.S. (2023). Saussurea costus extract as bio mediator in synthesis iron oxide nanoparticles (IONPs) and their antimicrobial ability. PLOS ONE, 18(3), e0282443.
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Publication 2023
Agar Alternaria Asepsis Aspergillus niger Bacteria Bears Escherichia coli Fungi Gram-Positive Rods Iron Iron Oxide Nanoparticles Klebsiella Metals Microbicides Pneumonia Pseudomonas aeruginosa Psychological Inhibition Rhizopus SERPINA3 protein, human Shigella Solanum tuberosum Staphylococcus Sterility, Reproductive Strains
3
Microbial Strain Characterization Protocol
We utilized 6 bacterial and 3 fungal strains, including Staphylococcus sp., Bacillus subtilis gram-positive, Klebsiella pneumonia, Shigella sp., Pseudomonas aeruginosa, Escherichia coli gram-negative, and Aspergillus niger, Alternaria sp., and Rhizopus sp. Fungi, obtained from the biology department faculty of sciences, university of princess Nourha bint Abdulrahman (Table 1).
, & Al-brahim J.S. (2023). Saussurea costus extract as bio mediator in synthesis iron oxide nanoparticles (IONPs) and their antimicrobial ability. PLOS ONE, 18(3), e0282443.
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Publication 2023
Alternaria Aspergillus niger Bacillus subtilis Bacteria Escherichia coli Faculty Fungi Klebsiella Pneumonia Pseudomonas aeruginosa Rhizopus Shigella Staphylococcus Strains
4
Diagnosing Bacterial and Fungal Infections
Bacterial infections are classified as bacteremia or site-specific infections. Multiple positive blood cultures for different organisms on the same day are considered distinct events. If bacterial isolates were a possible skin contaminant (diphtheria, bacillus or coagulase-negative staphylococci) and were isolated in only one blood culture, they were excluded unless systemic antibiotics were given. Infections were recorded if there was a microbiologic or histopathologic diagnosis, and the date of onset of infection was defined as the date on which diagnostic testing was performed. A second event was considered if repeated positive cultures and intermediate cultures were negative >21 days after the initial diagnosis. Site-specific bacterial infection was defined as evidence of bacterial infection by the culture of a normally sterile site or culture of a nonsterile site and evidence of tissue invasion. Lower respiratory tract infection was defined as the detection of a respiratory virus in bronchoalveolar lavage fluid with new or changing pulmonary infiltrates and lower respiratory tract symptoms. Invasive mycosis may be present, and fungal infection is documented. Infections caused by respiratory viruses were classified as upper respiratory tract infections if the virus was detected in nasopharyngeal/throat washes or swabs, sinuses or sputum without symptoms or clinical evidence of lower respiratory tract infection.
Gao Z., Lian Y., Ti J., Ren R, & Ma L. (2023). Therapeutic efficacy and infectious complications of CD19-targeted chimeric antigen receptor-modified T cell immunotherapy. Anti-Cancer Drugs, 34(4), 551-557.
Publication 2023
Antibiotics Bacteremia Bacteria Bacterial Infections Blood Culture Bronchoalveolar Lavage Fluid Coagulase Diagnosis Diphtheria Infection Lacticaseibacillus casei Lung Mycoses Nasopharynx Pharynx Respiratory Rate Respiratory Tract Infections Signs and Symptoms, Respiratory Sinuses, Nasal Skin Sputum Staphylococcus Sterility, Reproductive Tissues Upper Respiratory Infections Virus
5
Isolation and Characterization of Vaginal Lactobacilli
Lactobacilli included in this study were previously isolated from vaginal swabs of healthy pre-menopause Caucasian women, according to the protocol approved by the Ethics Committee of the University of Bologna, Bologna, Italy (52/2014/U/Tess) [47 (link)]. According to a recent reclassification of Lactobacillus genus [48 (link)], they belong to the species Lactobacillus crispatus (BC1, BC3, BC4, and BC5), Lactobacillus gasseri (BC9, BC10, BC12, and BC14) and Limosilactobacillus vaginalis (BC16 and BC17). Lactobacilli were routinely grown in de Man, Rogosa, and Sharpe broth (MRS) (Difco, Detroit, MI, USA) with the addition of L-cysteine 0.05% (w/v) (Merck, Milan, Italy), at 37 °C; the anaerobic conditions were guaranteed by incubation in anaerobic jars containing Gas-Pak EZ (Beckton, Dickinson and Co., Milan, Italy).
Escherichia coli DSM1900, E. coli DSM18039 and Staphylococcus aureus DSM2569 were purchased from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ, Braunschweig, Germany). Staphylococcus lugdunensis BC102, Enterococcus faecalis BC101 and Enterococcus faecium BC105 belong to the Department of Pharmacy and Biotechnology of the University of Bologna (Italy). Staphylococcus aureus SO88, Streptococcus agalactiae SO104, Candida albicans SO1 and Candida glabrata SO17 were isolated at Sant’Orsola-Malpighi University Hospital of Bologna during routine diagnostic procedures. The microbial identification was obtained by means of a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), using a Bruker Microflex MALDI-TOF MS instrument (Bruker Daltonics) [49 (link)]. Staphylococcus spp., E. coli, Enterococcus spp. and S. agalactiae were aerobically grown at 37 °C in Brain Heart Infusion medium (BHI) (Difco, Detroit, MI, USA), while Candida spp. were aerobically cultured at 35 °C in Sabouraud dextrose medium (SD) (Difco, Detroit, MI, USA).
Giordani B., Naldi M., Croatti V., Parolin C., Erdoğan Ü., Bartolini M, & Vitali B. (2023). Exopolysaccharides from vaginal lactobacilli modulate microbial biofilms. Microbial Cell Factories, 22, 45.
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Publication 2023
BC-105 Brain Candida Candida albicans Candida glabrata Caucasoid Races Cell Culture Techniques Culture Media Cysteine Diagnostic Tests, Routine Enterococcus Enterococcus faecalis Enterococcus faecium Escherichia coli Ethics Committees Glucose Heart Lactobacillus Lactobacillus crispatus Lactobacillus gasseri Lactobacillus vaginalis N-tris(hydroxymethyl)methyl-2-aminomethane sulfonate Premenopause Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Staphylococcus Staphylococcus aureus Staphylococcus lugdunensis Streptococcus agalactiae Vagina Woman

Top products related to «Staphylococcus»

1
Mannitol salt agar by Thermo Fisher Scientific
Sourced in United Kingdom, United States, Italy, France, Poland, Germany
Mannitol salt agar is a microbiological growth medium used for the selective isolation and identification of Staphylococcus species. It contains mannitol as the carbohydrate source and high concentrations of sodium chloride, which inhibit the growth of many non-Staphylococcus bacterial species.
2
Vitek 2 by bioMérieux
Sourced in France, United States, Germany, Italy, United Kingdom, Canada, Poland, Macao
The Vitek 2 is a compact automated microbiology system designed for the identification and antimicrobial susceptibility testing of clinically significant bacteria and yeasts. The system utilizes advanced colorimetric technology to enable rapid and accurate results for clinical decision-making.
3
Vitek 2 system by bioMérieux
Sourced in France, United States, Germany, Italy, Macao, United Kingdom, Sweden, Belgium, India, Japan, Brazil
The Vitek 2 system is an automated microbiology platform designed for the rapid identification and antimicrobial susceptibility testing of microorganisms. The system utilizes miniaturized biochemical testing to provide accurate results for a wide range of bacterial and yeast species.
4
Lysostaphin by Merck Group
Sourced in United States, Germany, United Kingdom, China, Canada, Portugal, France, Sao Tome and Principe
Lysostaphin is a bacteriolytic enzyme that is effective against Staphylococcus aureus, including methicillin-resistant strains. It is produced by the bacterium Staphylococcus simulans. Lysostaphin functions by cleaving the pentaglycine cross-links in the peptidoglycan layer of the Staphylococcus cell wall, leading to cell lysis.
5
Maldi tof ms by Bruker
Sourced in Germany, United States, France, United Kingdom, Japan, Italy, Switzerland, Canada, Poland
MALDI-TOF MS is a type of mass spectrometry instrument that uses Matrix-Assisted Laser Desorption/Ionization (MALDI) as the ionization technique and Time-of-Flight (TOF) as the mass analyzer. It is designed to analyze and identify a wide range of compounds, including proteins, peptides, lipids, and small molecules.
6
Macconkey agar by Thermo Fisher Scientific
Sourced in United Kingdom, United States, Germany, Italy, India, Canada, Poland, France, Australia, Spain, Belgium
MacConkey agar is a selective and differential culture medium used for the isolation and identification of Gram-negative enteric bacteria, particularly members of the Enterobacteriaceae family. It inhibits the growth of Gram-positive bacteria while allowing the growth of Gram-negative bacteria.
7
Microflex lt by Bruker
Sourced in Germany, United States, United Kingdom, France, Finland
The Microflex LT is a compact, lightweight MALDI-TOF mass spectrometer designed for routine protein and peptide analysis. It provides reliable performance and ease of use for a wide range of applications in life science research and clinical diagnostics.
8
Mueller hinton agar (mha) by Thermo Fisher Scientific
Sourced in United Kingdom, United States, Italy, Germany, France, India, Spain, China
Mueller-Hinton agar is a microbiological growth medium used for the antimicrobial susceptibility testing of bacteria. It is a standardized agar formulation that supports the growth of a wide range of bacteria and allows for the consistent evaluation of their susceptibility to various antimicrobial agents.
9
Qiaamp dna mini kit by Qiagen
Sourced in Germany, United States, France, United Kingdom, Netherlands, Spain, Japan, China, Italy, Canada, Switzerland, Australia, Sweden, India, Belgium, Brazil, Denmark
The QIAamp DNA Mini Kit is a laboratory equipment product designed for the purification of genomic DNA from a variety of sample types. It utilizes a silica-membrane-based technology to efficiently capture and purify DNA, which can then be used for various downstream applications.
10
Api staph by bioMérieux
Sourced in France, United States
The API Staph is a miniaturized identification system for the differentiation and identification of Staphylococcus species. It consists of a standardized set of biochemical tests that allow rapid and accurate identification of Staphylococcus isolates.

More about "Staphylococcus"

Staphylococcus is a ubiquitous genus of Gram-positive, spherical bacteria that often form grape-like clusters.
These microorganisms are commonly found on the skin and mucous membranes of humans and animals.
The most clinically significant Staphylococcus species is Staphylococcus aureus, which can produce toxins and develop resistance to numerous antibiotics, posing a significant public health challenge.
Researchers studying Staphylococcus must carefully select appropriate protocols and products to ensure reproducible and accurate results.
Mannitol salt agar is a selective medium used to isolate and identify Staphylococcus species, while the Vitek 2 system is an automated microbiology platform that can rapidly identify and perform antimicrobial susceptibility testing on Staphylococcus isolates.
Lysostaphin is an enzyme that can be used to lyse Staphylococcus cells, and MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry) is a powerful technique for the rapid identification of Staphylococcus species.
MacConkey agar is another selective medium that can be used to differentiate Gram-negative from Gram-positive bacteria, including Staphylococcus.
The Microflex LT is a MALDI-TOF MS instrument that can be used for the identification of Staphylococcus and other bacteria, while the Mueller-Hinton agar is a standard medium used for antimicrobial susceptibility testing.
The QIAamp DNA Mini Kit is a commonly used DNA extraction kit that can be used to isolate genomic DNA from Staphylococcus samples.
Finally, the API Staph system is a biochemical identification method that can be used to identify Staphylococcus species based on their metabolic characteristics.
By leveraging these tools and techniques, researchers can optimize their Staphylococcus studies and contribute to advancing our understanding of this important genus of bacteria.