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Streptococcus

Streptococcus is a genus of Gram-positive, facultatively anaerobic, non-spore-forming cocci bacteria.
They are a common inhabitant of the human upper respiratory tract and can cause a variety of diseases, including streptococcal pharyngitis, scarlet fever, and pneumonia.
Streptococcus species are also involved in the formation of dental plaque and can contribute to tooth decay.
Accurate identification and characterization of Streptococcus species is crucial for effective diagnosis and treatment of associated infections.
Resaerchers can leverag the PubCompare.ai platform to optimie their Streptococcus reasearch, locating relevant protocols from literature, preprints, and patents, and using AI-powered comparisons to identify the best approaches for their experiments.
This enhances reproducibility and accuracy, empowering Streptococcus research.

Most cited protocols related to «Streptococcus»

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.
Publication 2017
Actinomycetes Bacillus Cyanobacteria Escherichia Firmicutes Genome Metagenome Mycobacterium Prokaryotic Cells Proteobacteria Proviruses Pseudomonas Staphylococcus Streptococcus Vibrio Viral Genome Virus
2
Predicting Plasmid Replicons using PlasmidFinder
To predict plasmid replicons using PlasmidFinder (25 (link)) we uploaded assembled sequences (filtered by length—as described above) to the PlasmidFinder webserver (https://cge.cbs.dtu.dk/services/PlasmidFinder/) and ran the computation selecting all available databases (Enterobacteriaceae and Enterecoccus, Streptococcus, Staphylococcus). The %ID threshold was set at 80% and ‘Assembled Genome/Contigs’ was chosen as the type of read. Results were downloaded as raw text files.
Krawczyk P.S., Lipinski L, & Dziembowski A. (2018). PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures. Nucleic Acids Research, 46(6), e35.
Publication 2018
Enterobacteriaceae Genome Plasmids Replicon Staphylococcus Streptococcus
3
Quantifying Cariogenic Biofilm Acid Production

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Publication 2012
Acids Agar Bacitracin Bacteria Biofilms Blood Culture Cardiac Arrest Cysteine Enzymes Genetic Heterogeneity Gram-Positive Bacteria Lactate Dehydrogenase Lactates Lactic Acid Lacticaseibacillus casei Peptones potassium tellurite Streptococcus Streptococcus mutans Sucrose Trypan Blue Trypsin Violet, Gentian
4
Multilocus Sequence Analysis of Viridans Streptococci
Suitable loci for the discrimination of species clusters must be present in all strains of the species under study, and should be sufficiently conserved that a fragment of each locus can readily be amplified from each species using a single set of primers, but sufficiently diverse that they are useful in resolving species clusters. Two of the loci used in the new MLSA scheme (rpoB and sodA) were included in the study of Hoshino et al [16 (link)]. To select additional house-keeping loci, we used the multi-genome homology comparison tool available through the Comprehensive Microbial Resource (CMR; ) to search for proteins present in all available streptococcal genomes that had at least 80% amino acid sequence identity. This retrieved 138 proteins and, from those that had house-keeping functions, the corresponding genes were selected at random and examined for their suitability as candidate MLSA loci. An alignment was produced of the sequences of each candidate locus from S. agalactiae NEM3 (GenBank:AL732656), S. mitis NCTC 12261 (available at J Craig Venter Institute website; ), S. mutans UA159 (GenBank:AE014133), S. pneumoniae TIGR4 (GenBank:AE005672), S. pyogenes MGAS10394 (GenBank:CP000003), S. thermophilus LMD-9 (GenBank:CP000421) and Lactococcus lactis II1403 (GenBank:AE005176). Degenerate primers were designed for each selected locus, based on stretches of six amino acids that were conserved in all these species, which would allow an internal gene fragment greater than about 350 bp to be fully sequenced on both strands, and in which no indels were found in any of these genomes.
The pairs of PCR primers were each checked for their ability to amplify the correct gene fragment from a diverse subset of the collection of viridans group streptococci. Those primers that failed to amplify the correct fragment from all of the subset of strains were replaced with primers for amplifying a fragment of another of the conserved house-keeping genes, until a set of eight genes and PCR primers were obtained that allowed amplification of an internal gene fragment of each gene from the subset of strains. On characterizing the full strain set it was found that the primers for guaA (and two alternative pairs of primers) failed to amplify the fragment from a small number of strains and this gene was dropped from the final MLSA scheme. The genes, gene products, primer sequences, length of the sequences used in the MLSA scheme, and the annealing temperatures for amplification are shown in Table 1.
The gene fragments were amplified by PCR (30 cycles) using, for each gene fragment, a single annealing temperature for all strains (Table 1), and were sequenced on both strands, using the primers for the initial amplification, with an ABI 3700 or ABI 3730xl DNA analyzer. The sequences were aligned and trimmed to defined start and end positions using MEGA version 4 [47 (link)]. The trimmed sequences of the seven gene fragments from strains of each species can be found at . The sequences of the seven gene fragments from each strain were joined in-frame, in the order map-pfl-ppaC-pyk-rpoB-sodA-tuf, to generate a single 3063 bp concatenated sequence. Unrooted individual gene trees, and trees obtained using the concatenated sequences, were generated by neighbour-joining or minimum evolution from the proportions of sequence differences between all strains using MEGA version 4 [47 (link)]. The robustness of the nodes was evaluated by bootstrapping (1000 replicates). All of the sequences (including the concatenated sequences and the sequences of each locus) from the 417 strains can be downloaded from .
Bishop C.J., Aanensen D.M., Jordan G.E., Kilian M., Hanage W.P, & Spratt B.G. (2009). Assigning strains to bacterial species via the internet. BMC Biology, 7, 3.
Publication 2009
Actin-Accumulation Myopathy Amino Acids Amino Acid Sequence Biological Evolution Discrimination, Psychology Gene Amplification Genes Genes, Housekeeping Genes, vif Genome INDEL Mutation Lactococcus lactis Oligonucleotide Primers Progressive pseudorheumatoid dysplasia Proteins Reading Frames Strains Streptococcus Streptococcus pneumoniae Streptococcus pyogenes Streptococcus viridans Trees
5
Molecular Characterization of Streptococcus suis Strains

S. suis strain P1/7 was isolated from an ante-mortem blood culture from a pig dying with meningitis [9] , and is ST1 by MLST [10] (link). S. suis strain BM407 is also ST1, and was isolated from CSF from a human case of meningitis in Ho Chi Minh City, Vietnam in 2004 [3] (link). S. suis strain SC84 is ST7, which is closely related to ST1, and was isolated from a case of streptococcal toxic shock-like syndrome in Sichuan Province, China in 2005 [8] (link). Strain P1/7 is resistant to gentamycin, streptomycin, neomycin, nalidixic acid, and sulfamethoxazole, and sensitive to penicillin, ampicillin, cephalotin, erythromycin, tulathromycin, clarythromycin, lincomycin, clindamycin, pirlimicin, tetracycline, trimethoprim-sulfa, ciprofloxacin, and chloramphenicol. Strain BM407 is resistant to trimethoprim-sulfamethoxazole, tetracycline, erythromycin, azithromycin and chloramphenicol and susceptible to penicillin, ceftriaxone and vancomycin. Strain SC84 is resistant to tetracycline, and susceptible to penicillin, ampicillin, cefotaxime, ceftriaxone, cefepime, meropenem, levofloxacin, chloramphenicol, erythromycin, azithromycin, clindamycin, and vancomycin [11] (link).
Bacteria were cultured in Todd-Hewitt-broth at 37°C for 18 h and pelleted at 10,000×g. The cells were resuspended in 30 ml of lysis solution (10 mM NaCl, 20 mM Tris HCl pH 8, 1 mM EDTA, 0.5% SDS) and incubated at 50°C overnight. Three ml of 5 M sodium perchlorate was added and incubated for 1 h at ambient temperature. After phenol chloroform extraction the DNA was precipitated with ethanol, spooled into deionised water and stored at −20°C. DNA was also extracted using a genomic DNA extraction kit (G-500, Qiagen).
Holden M.T., Hauser H., Sanders M., Ngo T.H., Cherevach I., Cronin A., Goodhead I., Mungall K., Quail M.A., Price C., Rabbinowitsch E., Sharp S., Croucher N.J., Chieu T.B., Thi Hoang Mai N., Diep T.S., Chinh N.T., Kehoe M., Leigh J.A., Ward P.N., Dowson C.G., Whatmore A.M., Chanter N., Iversen P., Gottschalk M., Slater J.D., Smith H.E., Spratt B.G., Xu J., Ye C., Bentley S., Barrell B.G., Schultsz C., Maskell D.J, & Parkhill J. (2009). Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis. PLoS ONE, 4(7), e6072.
Publication 2009
Ampicillin Azithromycin Bacteria Blood Culture Cefepime Cefotaxime Ceftriaxone Cells Cephalothin Chloramphenicol Chloroform Ciprofloxacin Clarithromycin Clindamycin Edetic Acid Erythromycin Ethanol Genome Gentamicin Homo sapiens Levofloxacin Lincomycin Meningitis Meropenem Nalidixic Acid Neomycin Penicillins Phenol Sodium Chloride sodium perchlorate Strains Streptococcus Streptomycin Sulfamethoxazole Tetracycline Toxic Shock Syndrome Trimethoprim-Sulfamethoxazole Combination Trimethoprimsulfa Tromethamine tulathromycin Vancomycin

Most recents protocols related to «Streptococcus»

1
Genomic Analysis of Outbreak Strains
The presence of AMR genes was scanned in the genomic assemblies of the outbreak strains clade using AMRFinderPlus v3.10.16 [49 (link)]. To assess penicillin susceptibility, the protein sequences of the penicillin binding proteins (PBPs) were extracted and screened for amino acid substitutions known to correlate with decreased penicillin susceptibility in streptococci [50 (link)]. In brief, the sequence of each PBP was aligned using muscle v3.8.1551 [51 (link)] and visualized in SEAVIEW v5.0.5 [52 (link)]. The prokka annotations of the Thai zoonotic clade were queried to identify acquired resistance genes in the outbreak strain using Panaroov1.2.9 [53 (link)]. In addition, the STC78 complete genome was scanned for integrative and conjugative elements (ICEs) and prophages using ICEFinder [54 (link)] and PHASTER [55 (link)], respectively. Acquired AMR genes and their genomic context were manually inspected using Artemis v18.1.0 [56 (link)]. PubMed was searched for primary research articles describing mobile genetic elements (MGEs) carrying the same AMR genes to identify putative homologous MGEs. The annotated MGEs were aligned using clinker and clustermap.js v.0.021 [57 (link)]. The plasmid acquired by the outbreak strain was visualized using ApE v3.0.8 [58 (link)] and a blastn [59 (link)] search was performed against bacterial reference genomes. To assess the presence of potential genes of interest, ABRicate (https://github.com/tseemann/abricate) was used with a custom database containing the sequences of 52 genes previously found to be putatively associated with zoonotic potential of S. suis strains [46 (link)].
Brizuela J., Kajeekul R., Roodsant T.J., Riwload A., Boueroy P., Pattanapongpaibool A., Thaipadungpanit J., Jenjaroenpun P., Wongsurawat T., Batty E.M., van der Putten B.C., Schultsz C, & Kerdsin A. (2023). Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand. Microbial Genomics, 9(2), mgen000952.
Publication 2023
Amino Acid Sequence Amino Acid Substitution Genes Genome Genome, Bacterial Mobile Genetic Elements Muscle Tissue Penicillin-Binding Proteins Penicillins Plasmids Prophages Strains Streptococcus Susceptibility, Disease Thai
2
Phylogenetic Analysis of Streptococcus ASVs
To examine relatedness between ASV sequences affiliated with the genus Streptococcus and others, including pathogenic, Streptococcus spp., a phylogenetic tree was calculated. This was done by alignment of all ASV sequences affiliated with the genus Streptococcus found in this study to the Arb-Silva small subunit ribosomal RNA database. The ACT engine of arb-silva web tools3 was used for alignment, and the 5 closest relatives from the databases for each ASV was curated along with ASV sequences. The alignment of ASV and relative sequences were used to calculate a phylogenetic tree (FastTree algorithm) in the ACT engine. The tree was visualized in FigTree.
Bregman G., Lalzar M., Livne L., Bigal E., Zemah-Shamir Z., Morick D., Tchernov D., Scheinin A, & Meron D. (2023). Preliminary study of shark microbiota at a unique mix-species shark aggregation site, in the Eastern Mediterranean Sea. Frontiers in Microbiology, 14, 1027804.
Publication 2023
Pathogenicity Protein Subunits Ribosomes Sequence Alignment Streptococcus Trees
3
Environmental 16S Amplicon Sequencing Protocol
Universal primers targeting the V4 hypervariable region of 16S ribosomal RNA (rRNA) genes were used to PCR amplify the gene fragments from DNA extracts from the environmental samples. We used a version of the 515F primer with a single-base change (in bold) to increase the coverage of certain taxonomic groups including the archaea (515F-Y, 5′-GTGYCAGCMGCCGCGGTAA; Parada et al., 2016 (link)). PCR reactions were carried out as described previously (Coskun et al., 2019 (link)). The 16S rRNA genes were subjected to dual-indexed barcoded sequencing of 16S rRNA gene amplicons on the Illumina MiniSeq as described previously (Pichler et al., 2018 (link)).
The MiniSeq reads (Pichler et al., 2018 (link)) were quality trimmed and assembled using USEARCH version 11.0.667 with the default parameters (Edgar, 2010 (link)). Reads were then de novo clustered at 97% identity using UPARSE; operational taxonomic units (OTUs) represented by a single sequence were discarded (Edgar, 2013 (link)). Taxonomic assignments were generated by QIIME 1.9.1 (Caporaso et al., 2010 (link)) using the implemented BLAST method against the SILVA rRNA gene database release 132 (Quast et al., 2013 (link)). The genera Pseudomonas, Ralstonia, Variovorax, or Streptococcus were also removed as these are common contaminants of molecular reagent kits (Salter et al., 2014 (link)) and we typically find these genera in DNA extraction blanks from our lab (Coskun et al., 2018 (link); Pichler et al., 2018 (link)). Statistical analyses and plots were performed using R. Studio version 3.3.0 (RStudio Team, 2015 ). The 16S rRNA gene sequence data is stored in the NCBI Short Read Archive under BioProject ID PRJNA888248.
Coskun Ö.K., Gomez-Saez G.V., Beren M., Ozcan D., Hosgormez H., Einsiedl F, & Orsi W.D. (2023). Carbon metabolism and biogeography of candidate phylum “Candidatus Bipolaricaulota” in geothermal environments of Biga Peninsula, Turkey. Frontiers in Microbiology, 14, 1063139.
Publication 2023
Archaea Genes Oligonucleotide Primers Pseudomonas Ralstonia Ribosomal RNA Genes RNA, Ribosomal, 16S Streptococcus
4
Construction of cba Deletion Mutants
The construction of non-polar knockout mutants and complementation strains was performed as previously reported (Hu et al., 2018 (link)). Briefly, SS9-P10 genomic DNA was used as a template to amplify the upstream and downstream homologous arms of the cba gene using primers Cba-LF/Cba-LR (enzyme cut site: HindIII, SalI) and Cba-RF/Cba-RR (enzyme cut site: BamHI, EcoRI) to obtain cbaL and cbaR fragments, respectively. The pSET4S plasmid was used as a template to amplify the spc gene fragment using primers Spc-F/Spc-R (enzyme cut site: SalI, BamHI). The spc, cbaR, and cbaL fragments obtained by PCR were sequentially cloned into the pSET6s vector and verified using Sanger sequencing at BIOSUNE Biotechnology Co., Ltd (China) to obtain a pSET6s-Δcba knockout plasmid. Competent streptococcal cells were prepared under electroporation conditions according to a previous report (Takamatsu et al., 2001 (link)). After introducing pSET6s-Δcba into SS9-P10, double-crossover cba deletion mutants (SS9-P10:Δcba) were screened. The complementary DNA fragments of the cba by PCR using primers CbaF and CbaR. The resultant product was then inserted into pSET1 at BamHI/PstI sites to generate pSET1-cba. This plasmid was used to introduce a functional cba gene into SS9-P10:Δcba to generate complementing strains SS9-P10:CΔcba. Empty pSET1 was introduced into SS9-P10 as a control to exclude the effect of the vector. Primer sequences are listed in Table 2.
Yang P., Yang L., Cao K., Hu Q., Hu Y., Shi J., Zhao D, & Yu X. (2023). Novel virulence factor Cba induces antibody-dependent enhancement (ADE) of Streptococcus suis Serotype 9 infection in a mouse model. Frontiers in Cellular and Infection Microbiology, 13, 1027419.
Publication 2023
Arm, Upper Cells Cloning Vectors Deletion Mutation Deoxyribonuclease EcoRI DNA, Complementary Electroporation Enzymes Genes Genes, vif Genome Oligonucleotide Primers Plasmids Strains Streptococcus
5
CSF Bacterial Pathogen Identification
Patients were divided into 5 groups based on CSF bacteriological results: Streptococcus Pneumoniae, Haemophilus influenzae, Neisseria meningitidis, other pathogen (Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, non- and β-hemolytic streptococci), and unidentified pathogen. Clinical, biochemical, and microbiological data were recorded on admission.
Jensen E.S., Cayé-Thomasen P., Bodilsen J., Nielsen H., Friis-Hansen L., Christensen T., Christiansen M., Kirchmann M, & Brandt C.T. (2023). Hearing Loss in Bacterial Meningitis Revisited—Evolution and Recovery. Open Forum Infectious Diseases, 10(3), ofad056.
Publication 2023
Escherichia coli Haemophilus influenzae Hemolysis Listeria monocytogenes Neisseria meningitidis pathogenesis Patients Staphylococcus aureus Streptococcus Streptococcus pneumoniae

Top products related to «Streptococcus»

1
Bhi broth by BD
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Vitek 2 system by bioMérieux
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5
Todd hewitt broth by Thermo Fisher Scientific
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Todd-Hewitt broth is a microbiological culture medium used for the growth and isolation of streptococcal and other bacterial species. It provides the necessary nutrients and growth factors required for the cultivation of these microorganisms.
6
M17 agar by Merck Group
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Erythromycin is a macrolide antibiotic produced by the bacterium Saccharopolyspora erythraea. It functions as a protein synthesis inhibitor by binding to the 50S subunit of the bacterial ribosome, preventing the translocation of the peptidyl-tRNA from the A-site to the P-site during translation.
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Ampicillin is a broad-spectrum antibiotic used in laboratory settings. It is a penicillin-based compound effective against a variety of gram-positive and gram-negative bacteria. Ampicillin functions by inhibiting cell wall synthesis, leading to bacterial cell lysis and death.
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Mrs agar by Merck Group
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MRS agar is a laboratory culture medium used for the selective isolation and enumeration of lactic acid bacteria. It is designed to support the growth of organisms such as Lactobacillus, Pediococcus, and Leuconostoc species. MRS agar provides the necessary nutrients and growth factors required by these microorganisms.

More about "Streptococcus"

Streptococcus is a genus of Gram-positive, facultatively anaerobic, non-spore-forming coccus bacteria.
They are a common inhabitant of the human upper respiratory tract and can cause a variety of diseases, including streptococcal pharyngitis, scarlet fever, and pneumonia.
Streptococcus species are also involved in the formation of dental plaque and can contribute to tooth decay.
Accurate identification and characterization of Streptococcus species is crucial for effective diagnosis and treatment of associated infections.
Researchers can leverage the PubCompare.ai platform to optimize their Streptococcus research, locating relevant protocols from literature, preprints, and patents, and using AI-powered comparisons to identify the best approaches for their experiments.
This enhances reproducibility and accuracy, empowering Streptococcus research.
Streptococcus can be cultured in various media, such as BHI (Brain Heart Infusion) broth, Todd-Hewitt broth, and M17 agar.
The Vitek 2 system is a commonly used automated platform for the identification and antimicrobial susceptibility testing of Streptococcus species.
Erythromycin and ampicillin are common antibiotics used to treat Streptococcus infections, and the Etest is a method for determining the minimum inhibitory concentration (MIC) of these antibiotics.
Yeast extract is an important component in many growth media for Streptococcus, providing essential nutrients.
MRS (Man, Rogosa, and Sharpe) agar is a selective medium used for the isolation and enumeration of lactic acid bacteria, including some Streptococcus species.
By leveraging the insights and tools provided by PubCompare.ai, researchers can streamline their Streptococcus research, optimizing protocols and enhancing the reproducibility and accuracy of their experiments.
This empowers advancements in the understanding and treatment of Streptococcus-related infections and diseases.