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Haemophilus influenzae

Haemophilus influenzae: A gram-negative coccobacillus bacteria commonly found in the upper respiratory tract of humans.
It is a leading cause of respiratory infections, including pneumonia, bronchitis, and sinusitis.
Accurate and reproducible research protocols are crucial for studying this pathogen and developing effective treatments.
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Most cited protocols related to «Haemophilus influenzae»

The genome sequencing revolution has radically altered the field of microbiology. Whole-genome sequencing for prokaryotes became a standard method of study ever since the first complete genome of free-living organism, Haemophilus influenza, was sequenced in 1995 (14 (link)). Due to the widespread use of the next generation sequencing (NGS) techniques, thousands of genomes of prokaryotic species are now available, including genomes of multiple isolates of the same species, typically human pathogens. Thus, the mere density of comparative genomic information for high interest organisms provides an opportunity to introduce a pan-genome based approach to prediction of the protein complement of a species.
The collection of prokaryotic genomes available at NCBI is growing exponentially and shows no signs of abating: as of January 2016 NCBI's assembly resource contains 57 890 genome assemblies representing 8047 species (see genome browser https://www.ncbi.nlm.nih.gov/genome/browse/, for the up-to-date information). Notably, genomes of different strains of the same species can vary considerably in size, gene content and nucleotide composition. In 2005, Tettelin et al. (15 (link)) introduced the concept of pan-genome, aiming to provide a compact description of the full complement of genes of all the strains of a species. Genes common to all pan-genome members (or to the vast majority of them) are called core genes; those present in just a few clade members are termed accessory or dispensable genes; genes specific to a particular genome (strain) are termed unique genes (16 (link)).
In PGAP we define the pan-genome of a clade at a species or higher level (17 ). To be included as a core gene for a species-level pan-genome, we require the gene to be present in the vast majority—at least 80%—of all genomes in the clade. A set of core genes gives rise to a set of core proteins. We show in Figure 1 how the number of protein clusters, for each of four well studied large clades, depends on the fraction of the clade members that contribute proteins to the cluster. There are three critical regions in this analysis: (i) unique genes, present in less than 1% of all clade members; (ii) dispensable genes, present in 1–20% of genomes; and (iii) core genes, found in at least 80% of the represented genomes. Based on our analysis, there are very few clusters appearing in at least 20% of the members of a clade but no more than 80% of the members. The use of a cutoff of 80% was chosen to capture a wide set of genes conserved within the whole clade while eliminating genes having less abundant representation. We further subject the core proteins to clustering using USearch to reduce the total number of proteins required to represent the full protein complement of the pan-genome (18 (link)). We use the representative core proteins to infer genes for homologous core proteins in a newly sequenced genome (19 ).
The notion of the pan-genome can be generalized beyond a species level and applies, in fact, to any taxonomy level (from genus to phylum to kingdom). Notably, in the pan-genomes of Archaea and Bacteria, the universally conserved ribosomal genes make a group of core genes. The main practical value of the pan-genome approach is in formulating an efficient framework for comparative analysis of large groups of closely related organisms separated by small evolutionary distances as defined by ribosomal protein markers (20 (link),21 (link)).
Publication 2016
Bacteria Biological Evolution Complement System Proteins Gene Products, Protein Genes Genes, vif Genome Genome, Archaeal Haemophilus influenzae Homo sapiens Nucleotides Pathogenicity Prokaryotic Cells Proteins Ribosomal Proteins Ribosomes SET protein, human Strains
Gram stain and bacterial culture were performed on blood, PF, ET aspirates, and BAL specimens at each site using standard techniques; only high-quality ET aspirates and quantified BAL specimens were included (Supplementary Appendix).15 ,16 (link) Real-time polymerase chain reaction (PCR) targeting Streptococcus pneumoniae (lyt-A) and Streptococcus pyogenes (spy) genes was performed on whole blood and PF at CDC.17 (link) PF was also tested at the University of Utah for H. influenzae and other Gram-negative bacteria, Staphylococcus aureus, Streptococcus anginosus/mitis, S. pneumoniae, and S. pyogenes using PCR (Supplementary Appendix).18 (link),19 (link) PCR was performed at the study sites on NP/OP swabs from children with pneumonia and controls using CDC-developed methods for detection of adenovirus (AdV); Chlamydophila pneumoniae; coronaviruses 229E, HKU1, NL63, and OC43 (CoV); human metapneumovirus (HMPV); human rhinovirus (HRV); influenza A/B viruses; Mycoplasma pneumoniae; parainfluenza viruses 1, 2, 3 (PIV); and respiratory syncytial virus (RSV).20 (link)-24 Quality assurance and monitoring protocols maintained standardization among sites.25 (link),26 (link) Serology for AdV, HMPV, influenza A/B, PIV, and RSV was performed at CDC on available paired acute and convalescent sera (Supplementary Appendix).27 (link)-32
Publication 2015
Adenoviruses Bacteria Blood Child Chlamydophila pneumoniae Coronavirus 229E, Human Genes Gram's stain Gram Negative Bacteria Haemophilus influenzae Homo sapiens Human Metapneumovirus Human respiratory syncytial virus Influenza A virus Influenza B virus Mycoplasma pneumoniae Para-Influenza Virus Type 1 Pneumonia Polymerase Chain Reaction Real-Time Polymerase Chain Reaction Rhinovirus Serum Staphylococcus aureus Infection Streptococcus mitis Streptococcus pneumoniae Streptococcus pyogenes Virus Vaccine, Influenza

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Publication 2005
Adenoviruses Bacteria Bordetella bronchiseptica Bordetella parapertussis Bordetella pertussis Burkholderia cepacia Chlamydophila pneumoniae Coronavirus 229E, Human Coxsackie Viruses Echovirus Haemophilus influenzae Human parechovirus 1 Klebsiella pneumoniae Legionella pneumophila Measles virus Multiplex Polymerase Chain Reaction Mumps virus Mycoplasma pneumoniae Nucleic Acids Pseudomonas aeruginosa Respiratory Rate Respiratory System Staphylococcus aureus Infection Streptococcus pneumoniae Virus Virus Vaccine, Influenza

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Publication 2017
Cholera Haemophilus influenzae Immunization Programs Rotavirus Tissue Donors Vaccination Vaccine, Pneumococcal Polysaccharide Vaccines Virus Vaccine, Influenza
The genomes chosen for this study correspond to 13 γ-Proteobacterial taxa that show different degrees of relatedness based on divergence of SSU rRNA and that include two symbionts having undergone large-scale genomic reduction (Shigenobu et al. 2000 (link); Akman et al. 2002 (link)). The protein sequences of the 13 complete genomes were retrieved from the GenBank database (Benson et al. 2002 (link)). The species used were Escherichia coli K12 (accession number NC_000913; Blattner et al. 1997 (link)), Buchnera aphidicola APS (NC_002528; Shigenobu et al. 2000 (link)), Haemophilus influenzae Rd (NC_000907; Fleischmann et al. 1995 (link)), Pasteurella multocida Pm70 (NC_002663; May et al. 2001 (link)), Salmonella typhimurium LT2 (NC_003197; McClelland et al. 2001 (link)), Yersinia pestis CO_92 (NC_003143; Parkhill et al. 2000 (link)), Yersinia pestis KIM5 P12 (NC_004088; Deng et al. 2002 (link)), Vibrio cholerae (NC_002505 for chromosome 1 and NC_002506 for chromosome 2; Heidelberg et al. 2000 (link)), Xanthomonas axonopodis pv. citri 306 (NC_003919; da Silva et al. 2002 (link)), Xanthomonas campestris (NC_003902; da Silva et al. 2002 (link)), Xylella fastidiosa 9a5c (NC_002488; Simpson et al. 2000 (link)), Pseudomonas aeruginosa PA01 (NC_002516; Stover et al. 2000 (link)), and Wigglesworthia glossinidia brevipalpis (NC_004344; Akman et al. 2002 (link)).
To identify genes likely to have been transmitted vertically through the history of the γ-Proteobacteria, we first eliminated proteins annotated as elements of insertion sequences or as bacteriophage sequences, since they are likely to be subject to lateral transfer. Such sequences were present in most genomes but lacking in a few (B. aphidicola, W. brevipalpis, and P. multocida). Table 1 shows the number of proteins that remain in each genome after such elimination.
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Publication 2003
Amino Acid Sequence Bacteriophages Buchnera aphidicola Chromosomes, Human, Pair 1 Chromosomes, Human, Pair 2 Escherichia coli K12 Genes Genome Haemophilus influenzae Insertion Sequence Elements Pasteurella multocida Proteins Proteobacteria Pseudomonas aeruginosa Ribosomal RNA Salmonella typhimurium LT2 Vibrio cholerae Wigglesworthia glossinidia Xanthomonas campestris Xanthomonas citri Xylella fastidiosa Yersinia pestis

Most recents protocols related to «Haemophilus influenzae»

Example 6

TbpB and NMB0313 genes were amplified from the genome of Neisseria meningitidis serotype B strain B16B6. The LbpB gene was amplified from Neisseria meningitidis serotype B strain MC58. Full length TbpB was inserted into Multiple Cloning Site 2 of pETDuet using restriction free cloning ((F van den Ent, J. Löwe, Journal of Biochemical and Biophysical Methods (Jan. 1, 2006)).). NMB0313 was inserted into pET26, where the native signal peptide was replaced by that of pelB. Mutations and truncations were performed on these vectors using site directed mutagenesis and restriction free cloning, respectively. Pairs of vectors were transformed into E. coli C43 and were grown overnight in LB agar plates supplemented with kanamycin (50 μg/mL) and ampicillin (100 μg/mL).

tbpB genes were amplified from the genomes of M. catarrhalis strain 035E and H. influenzae strain 86-028NP and cloned into the pET52b plasmid by restriction free cloning as above. The corresponding SLAMs (M. catarrhalis SLAM 1, H. influenzae SLAM1) were inserted into pET26b also using restriction free cloning. A 6His-tag was inserted between the pelB and the mature SLAM sequences as above. Vectors were transformed into E. coli C43 as above.

Cells were harvested by centrifugation at 4000 g and were twice washed with 1 mL PBS to remove any remaining growth media. Cells were then incubated with either 0.05-0.1 mg/mL biotinylated human transferrin (Sigma-aldrich T3915-5 MG), α-TbpB (1:200 dilution from rabbit serum for M. catarrhalis and H. influenzae; 1:10000 dilution from rabbit serum for N. meningitidis), or α-LbpB (1:10000 dilution from rabbit serum-obtained a gift from J. Lemieux) or α-fHbp (1:5000 dilution from mouse, a gift from D. Granoff) for 1.5 hours at 4° C., followed by two washes with 1 mL of PBS. The cells were then incubated with R-Phycoerythrin-conjugated Streptavidin (0.5 mg/ml Cedarlane) or R-phycoerythrin conjugated Anti-rabbit IgG (Stock 0.5 mg/ml Rockland) at 25 ug/mL for 1.5 hours at 4° C. The cells were then washed with 1 mL PBS and resuspended in 200 uL fixing solution (PBS+2% formaldehyde) and left for 20 minutes. Finally, cells were washed with 2×1 mL PBS and transferred to 5 mL polystyrene FACS tubes. The PE fluorescence of each sample was measured for PE fluorescence using a Becton Dickinson FACSCalibur. The results were analyzed using FLOWJO software and were presented as mean fluorescence intensity (MFI) for each sample. For N. meningtidis experiments, all samples were compared to wildtype strains by normalizing wildtype fluorescent signals to 100%. Errors bars represent the standard error of the mean (SEM) across three experiments. Results were plotted statistically analysed using GraphPad Prism 5 software. The results shown in FIG. 6 for the SLPs, TbpB (FIG. 6A), LbpB. (FIG. 6B) and fHbp (FIG. 6C) demonstrate that SLAM effects translocation of all three SLP polypeptides in E. coli. The results shown in FIG. 10 demonstrate that translocation of TbpB from M. catarrhalis (FIG. 10C) and in H. influenzae (FIG. 10D) in E. coli require the co-expression of the required SLAM protein (Slam is an outer membrane protein that is required for the surface display of lipidated virulence factors in Neisseria. Hooda Y, Lai C C, Judd A, Buckwalter C M, Shin H E, Gray-Owen S D, Moraes T F. Nat Microbiol. 2016 Feb. 29; 1:16009).

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Patent 2024
ADRB2 protein, human Agar Ampicillin anti-IgG Cells Centrifugation Cloning Vectors Culture Media Escherichia coli Fluorescence Formaldehyde Genes Genome Haemophilus influenzae Homo sapiens Kanamycin Lipoproteins Membrane Proteins Moraxella catarrhalis Mus Mutagenesis, Site-Directed Mutation Neisseria Neisseria meningitidis Phycoerythrin Plasmids Polypeptides Polystyrenes prisma Rabbits Serum Signaling Lymphocytic Activation Molecule Family Member 1 Signal Peptides Strains Streptavidin Technique, Dilution Transferrin Translocation, Chromosomal Virulence Factors
Strains of Escherichia coli (ATCC 1100101)Pseudomonas aeruginosa (ATCC 109246)Streptococcus mitis (ATCC NCTC 12261)Haemophilus influenzae (ATCC NCTC 8143)Streptococcus pneumoniae (ATCC NCTC 7465)Staphylococcus aureus (ATCC B-71-1) were used for this experiment.
Bacterial suspensions were prepared to match the turbidity of a 0.5 McFarland Turbidity Standard (108 colony-forming units [cfu]/mL) according to the Kirby-Bauer method [23 (link)]. Columbia agar with 5% of sheep blood (COS, BioMerieux, Marcy-l'Étoile, Lyon, France) were used for E. coliP. aeruginosaS. mitisS. pneumoniaeS. aureus strains’ isolation. Chocolate agar plates (HAE, BioMerieux, Marcy-l'Étoile, Lyon, France) were used for the isolation of H. influenzae strains.
For each bacterial species, plates were prepared for the evaluation of the antibacterial activity of each drug tested. Each PRF membrane was placed, immediately after preparation, on the respective plate using sterile instruments.
The plates were incubated at 37 °C to observe the growth of any colony after 24 h [24 ]. At the end of the incubation, any growth or inhibition was observed. The plates were photographed to proceed with the measurement of any inhibition area.
The determination of the inhibition area was performed through the software Adobe Photoshop (Adobe Incorporated, San Jose, California, USA): the inhibition area was first outlined using the "magnetic lasso" function, trying to follow as much as possible the color differences within the bacterial growth area; then, a specific unit of measure for each photo was set, selecting the pixels contained in the plate diameter. In this way, each number of pixels corresponding to the known distance set would have had a value of 90 mm. The size of the inhibition area was obtained using Adobe Photoshop calculation function (Fig. 1).

Inhibition area calculation with Adobe Photoshop

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Publication 2023
Agar Anti-Bacterial Agents Bacteria Blood Cacao Domestic Sheep Escherichia coli Haemophilus influenzae isolation Pseudomonas aeruginosa Psychological Inhibition Staphylococcus aureus Sterility, Reproductive Strains Streptococcus mitis Streptococcus pneumoniae Tissue, Membrane
For S. maltophilia and P. aeruginosa studies, strain S. maltophilia K279a, a widely used model strain with a fully annotated genome, was provided by M. Herman (Kansas State University) [15 (link)]. Strain P. aeruginosa mPA08-31, a sputum-derived CF clinical isolate, was obtained from S. Birket (University of Alabama at Birmingham). All strains were routinely cultured on Luria–Bertani (LB) agar (Difco) or in LB broth. S. maltophilia was streaked for colony isolation before inoculation into LB broth and shaking overnight at 30 °C and 200 r.p.m. P. aeruginosa was streaked for colony isolation before inoculation into LB broth and shaking overnight at 37 °C and 200 r.p.m.
For nontypeable H. influenzae and P. aeruginosa studies, strain NTHi HI-1, a CF clinical isolate, was provided by Timothy Starner, University of Iowa Children’s Hospital. NTHi was routinely cultured on supplemented brain-heart infusion (sBHI) agar (RPI, ThermoFisher Scientific), containing 10 µg ml−1 of hemin (Sigma Aldrich, St. Louis, MO, USA) and 1 µg ml−1 of NAD (Sigma Aldrich). NTHi was cultured on supplemented BHI agar, incubated overnight at 37 °C+5 % CO2. Strain P. aeruginosa mPA 08–31 was cultured in LB broth and shaking overnight at 37 °C and 200 r.p.m.
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Publication 2023
Agar Brain Child Genome Haemophilus influenzae Heart Hemin isolation M-200 Pseudomonas aeruginosa Sputum Strains Vaccination
Each specimen was first screened for RSV by means of the Resp-4-Plex kit (Abbott Molecular Inc., Des Plaines, IL, USA) used with the fully automated Alinity m System (Abbott Molecular Inc., Des Plaines, IL, USA) and according to the manufacturer’s instructions. This kit is a multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) for the qualitative detection and differentiation of RNA from SARS-CoV-2, RSV, influenza A and B viruses. According to the manufacturer, the limit of detection is 0.300 and 0.100 median tissue culture infectious dose (TCID50)/ml for RSV-A and RSV-B, respectively [30 ].
To discern RSV subgroup and detect the presence of other respiratory pathogens, samples positive for RSV were further tested by means of the Allplex Respiratory Panel (RP) assays (Seegene Inc.; Seoul, Republic of Korea) according to the manufacturer’s instructions. Briefly, nucleic acids were first extracted using the STARMag Universal Cartridge Kit (Seegene Inc.; Seoul, Republic of Korea) on the automated Nimbus IVD (Seegene Inc.; Seoul, Republic of Korea) platform. For this purpose, 200 µl of each specimen was extracted and eluted with 100 µl of elution buffer and set up for RT-PCR. RT-PCR was then performed on a CFX96 instrument (Bio-Rad Laboratories, Inc; Hercules, CA, USA) with the Allplex RPs 1–4 kits. These four panels are able to detect the most common respiratory pathogens - both viruses [RP 1: RSV-A, RSV-B, influenza viruses A, A(H1N1), A(H1N1)pdm09, A(H3N2) and B; RP 2: adenovirus (AdV), enterovirus (EV), metapneumovirus (MPV), parainfluenza (PIV) viruses 1–4; RP 3: bocaviruses (BoV) 1–4, coronaviruses (CoV) 229E, NL63, OC43, rhinovirus (RV)] and bacteria [RP 4: Streptococcus pneumoniae (SP), Bordetella parapertussis (BPP), Bordetella pertussis (BP), Chlamydophila pneumoniae (CP), Haemophilus influenzae (HI), Legionella pneumophila (LP), Mycoplasma pneumoniae (MP)]. For each RT-PCR, 8 µl of the extracted nucleic acid in a final volume of 25 µl was used. The diagnostic accuracy of this assay in detecting RSV-A and RSV-B is 100% [31 (link)].
Samples showing cycle threshold (Ct) values < 40 in at least one assay were deemed positive. Ct values were used as a proxy measure of viral load: lower Ct values indicate higher viral load.
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Publication 2023
Adenoviruses Bacteria Biological Assay Bocavirus Bordetella parapertussis Bordetella pertussis Buffers Chlamydophila pneumoniae Coronavirus 229E, Human Diagnosis Enterovirus Haemophilus influenzae Herpesvirus 1, Cercopithecine Infection Influenza Legionella pneumophila Metapneumovirus Mycoplasma pneumoniae Nucleic Acids Orthomyxoviridae Parainfluenza Pathogenicity Real-Time Polymerase Chain Reaction Respiratory Rate Reverse Transcriptase Polymerase Chain Reaction Reverse Transcription Rhinovirus SARS-CoV-2 Streptococcus pneumoniae Tissues Virus
To determine the analytical sensitivity of the One-Step LAMP assay, tenfold serial dilutions from 1× 106 to 1 × 10− 3 copies of the RNA standard strain of SARS-CoV-2 were prepared in 1X HBSS (Gibco, 14,025–092) using the qPCR. The copy numbers of the RNA standard in each dilution were calculated using the qPCR according to Ji and colleagues’ method [38 (link)]. The accuracy of the analytical sensitivity results was confirmed by repeating the tests three times. Also, to ensure the results obtained for the analytical sensitivity test and to avoid possible visual error in the reaction tubes’ color examination, the reaction product was electrophoresed on a 1.5% agarose gel and evaluated under UV in the gel documentation. A set of 15 positive and 10 negative clinical samples previously tested by RT-qPCR were also selected to determine the clinical sensitivity of the One-Step LAMP assay using the optimized One-Step LAMP protocol.
The analytical specificity of the One-Step LAMP assay was examined by detecting the various templates, including Influenza A virus, Influenza B virus, Respiratory syncytial virus, Adenovirus, Parainfluenza virus, Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenza, Pseudomonas aeruginosa, Legionella pneumophila, Bordetella Pertussis, Staphylococcus aureus, Mycoplasma pneumoniae, and Chlamydia pneumoniae as well as human positive samples of HIV ، HBV ، HCV ، EBV ، CMV ، HPV, and HSV1, and 2., and synthetic nucleic acid sequences prepared as a gift from Infectious Disease Control Center, Ministry of Health and Medical Education, Tehran, Iran.
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Publication 2023
Adenovirus Infections Base Sequence Bordetella pertussis Chlamydophila pneumoniae Communicable Disease Control Education, Medical Haemophilus influenzae Hemoglobin, Sickle HIV Seropositivity Homo sapiens Human Herpesvirus 1 Hypersensitivity Influenza A virus Influenza B virus Klebsiella pneumoniae LAMP assay Legionella pneumophila Mycoplasma pneumoniae Parainfluenza Pseudomonas aeruginosa Respiratory Syncytial Virus SARS-CoV-2 Sepharose Staphylococcus aureus Infection Strains Streptococcus pneumoniae Technique, Dilution Virus

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More about "Haemophilus influenzae"

Haemophilus influenzae, also known as H. influenzae or Hi, is a small, gram-negative coccobacillus bacterium commonly found in the upper respiratory tract of humans.
This pathogenic microorganism is a leading cause of various respiratory infections, including pneumonia, bronchitis, and sinusitis.
Accurate and reproducible research protocols are crucial for studying H. influenzae and developing effective treatments.
Researchers often compare protocols from literature, preprints, and patents to ensure their work is efficient and effective.
Other similar bacteria, such as Staphylococcus aureus (S. aureus), Streptococcus pneumoniae (S. pneumoniae), and Escherichia coli (E. coli), also require careful protocol optimization.
In addition to H. influenzae, other respiratory pathogens like Moraxella catarrhalis and Pseudomonas aeruginosa (P. aeruginosa) can also cause significant health issues.
Proper sample collection, DNA extraction methods (e.g., QIAamp DNA Mini Kit), and bacterial identification techniques (e.g., hemin requirement, Enterococcus faecalis) are essential for accurate diagnosis and effective treatment of these infections.
PubCompare.ai's AI-driven comparisons help researchers locate the best protocols from a variety of sources, ensuring their work on Haemophilus influenzae and related bacteria is both efficient and effective.
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