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Klebsiella pneumoniae

Klebsiella pneumoniae is a Gram-negative bacterium that commonly causes pneumonia and other severe infections.
It is an opportunistic pathogen, often affecting individuals with weakened immune systems.
This bacterium can also lead to sepsis, urinary tract infections, and wound infections.
Klebsiella pneumoniae is known for its ability to develop antimicrobial resistance, making it a significant public health concern.
Researchers and clinicians must stay informed about the latest advancements in detecting, treating, and preventing Klebsiella pneumoniae infections to provide optimal patient care.
PubCompare.ai offers a valuable resource to optimize Klebsiella pneumoniae research by identifying the most accurate and reproducible protocols from the literature, preprints, and patents.
Its AI-driven platform enables researchers to leverage intelligent comparisons to find the best products and protocols for their work, enhancing the quality and efficiecny of Klebsiella pneumoniae studies.

Most cited protocols related to «Klebsiella pneumoniae»

1
Verification of Antimicrobial Resistance Genes
Verification of the databases was made by testing ResFinder with the 1862 GenBank files from which the genes were collected, to verify that the method would find all genes with ID = 100%.
Short sequence reads from 23 isolates of five different species, Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Staphylococcus aureus and Vibrio cholerae, were also submitted to ResFinder. All 23 isolates had been sequenced on the Illumina platform using paired-end reads. A ResFinder threshold of ID = 98.00% was selected, as previous tests of ResFinder had shown that a threshold lower than this gives too much noise (e.g. fragments of genes). Phenotypic antimicrobial susceptibility testing was determined as MIC determinations, as previously described.8 (link)With ‘(chromosome and plasmid)(multi-drug or antimicrobial or antibiotic)(resistant or resistance) pathogen’ as search criteria, one isolate from each species with completely sequenced and assembled, and chromosome and plasmid data were collected from the NCBI Genomes database (http://www.ncbi.nlm.nih.gov/genome). This resulted in 30 isolates, from 30 different species, containing 85 chromosome/plasmid sequences. All sequences were run through all databases in ResFinder with a selected threshold of ID = 98.00%.
Zankari E., Hasman H., Cosentino S., Vestergaard M., Rasmussen S., Lund O., Aarestrup F.M, & Larsen M.V. (2012). Identification of acquired antimicrobial resistance genes. Journal of Antimicrobial Chemotherapy, 67(11), 2640-2644.
Publication 2012
Antibiotics Chromosomes Escherichia coli Genes Genome Klebsiella pneumoniae Microbicides Pathogenicity Pharmaceutical Preparations Phenotype Plasmids Salmonella enterica Staphylococcus aureus Susceptibility, Disease Vibrio cholerae
2
Comprehensive Klebsiella Genomic Analysis
The analyses reported here result from applying Kleborate v2.0.0 (doi:10.5281/zenodo.4923015) to publicly available genome collections. A total of 13,156 Klebsiella WGS assemblies, encompassing non-duplicate isolates with unique BioSample accessions identified from published studies (some deposited as read sets only, which were assembled using Unicycler v0.4.778 (link), data sources summarized in Supplementary Data 13) plus any additional genomes designated as Klebsiella in NCBI’s RefSeq repository of genome assemblies (as of 17 July 2020). In order to minimize the impact of sampling bias favoring common MDR and/or virulent lineages and those causing outbreaks, we subsampled the collection into a ‘non-redundant’ dataset of 11,277 genomes (9705 K. pneumoniae) as follows. Pairwise Mash distances were calculated using Mash v2.1, and used to cluster genomes using single-linkage clustering with a threshold of 0.0003. These clusters were further divided into non-redundant groups with unique combinations of (i) Mash cluster, (ii) chromosomal ST, (iii) virulence gene profiles (i.e. presence of ybt/clb/iro/iuc loci and lineage assignment), (iv) AMR profiles, (v) year and country of isolation, and (vii) specimen type where available. For each resulting non-redundant group, one genome was selected at random as the representative for analyses. The full list of genomes, including database accessions, isolate information, cluster/group assignment, and Kleborate results are provided in Supplementary Data 2. The subset of 1624 K. pneumoniae assemblies deposited in RefSeq by the European EuSCAPE surveillance study33 (out of 1649 reported in original study; Supplementary Data 2) were used for the EuSCAPE analyses reported in Figs. 2 and 3. The Kleborate-Viz web application is pre-loaded with the non-redundant and EuSCAPE WGS datasets reported in this paper, and can be used to reproduce the plots shown in Figs. 1a–c, 2b, c, 3, 6a, b and to further explore the Kleborate results.
Lam M.M., Wick R.R., Watts S.C., Cerdeira L.T., Wyres K.L, & Holt K.E. (2021). A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature Communications, 12, 4188.
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Publication 2021
Chromosomes Disease Outbreaks Europeans Figs Genetic Profile Genome isolation Klebsiella Klebsiella pneumoniae Virulence
3
Comprehensive Klebsiella Genome Characterization
Sequence read data for 309 K. pneumoniae organisms were obtained as part of the global diversity study (54 (link)), and 13 O3 antigen-producing isolates (20 (link)) were assembled de novo using Unicycler v0.4.1 (55 (link)). Genome assemblies were uploaded to Kaptive Web in a single compressed data directory and analyzed with the Klebsiella primary K locus and the Klebsiella O locus databases. The total Kaptive Web analysis times for the global data set were 52 min (K locus) and 12 min (O locus). The results were inspected via the Kaptive Web graphical interface and downloaded in tabular format (see Data Set S1 in the supplemental material).
The same protocol was used for characterization of 201 publicly available CG258 genome assemblies (see Data Set S3). These genomes were identified among the complete set of Klebsiella genomes (downloaded from GenBank on 12 October 2017) on the basis of ST information generated using Kleborate (https://github.com/katholt/Kleborate). STs 11, 258, 340, 395, 437, 512, 855, and 895 were included in the analyses.
Wick R.R., Heinz E., Holt K.E, & Wyres K.L. (2018). Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes. Journal of Clinical Microbiology, 56(6), e00197-18.
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Publication 2018
Antigens Genome Klebsiella Klebsiella pneumoniae
4
Invasive Klebsiella pneumoniae Strains
Clinical K. pneumoniae strains isolated from patients with septicemia were collected at National Taiwan University Hospital (NTUH) from 1996 to 2001. Identification of the isolates was according to standard clinical microbiologic methods (1 ). All strains were stored at −80°C before use.
Among the total of 1,352 isolates obtained from patients with septicemia, 101 strains were obtained from patients displaying primary liver abscess. The diagnosis of primary liver abscess was confirmed by sonography-guided aspiration or surgical drainage in 53 of these 101 patients. Of these 53 patients, 26 had diabetes mellitus, 25 were otherwise healthy before development of the abscess, one patient had nephrotic syndrome, and one patient displayed hepatic failure associated with advanced liver cirrhosis. The strains isolated from the 53 patients were designated as tissue-invasive (invasive) strains. In addition to displaying primary liver abscesses, four patients displayed metastatic endophthalmitis, whereas another displayed metastatic meningitis.
Of the remaining 1,251 patients who did not display clinical symptoms of liver abscess, meningitis, or endophthalmitis, 52 patients were confirmed to be free of abscess by either abdominal sonography or computed tomography. The K. pneumoniae strains from these patients were designated as nontissue invasive (noninvasive) strains.
For comparative purposes, we obtained 21 nonblood isolates from nonseptic patients at NTUH, and 101 strains from other facilities. These included 15 strains (6 of which were found capable of causing primary liver abscess) were obtained from the National Cheng Kung University Hospital (NCKUH; a gift from I.-J. Su, National Health Research Institute, Taipei, Taiwan). Another 13 strains (1 of which caused meningitis without liver abscess and 1 that caused abscess) were a gift from S.-S. Wang (ECK Hospital, Sansia, Taiwan). 34 strains, all of which caused nosocomial infections without liver abscess, meningitis, or endophthalmitis, were a gift from J.-T. Wang (Far Eastern Memorial Hospital, Banciao, Taiwan). 15 strains from Hong Kong were a gift from L.K. Siu (National Health Research Institute, Taipei, Taiwan). Finally, 24 strains, none of which caused liver abscess, were purchased from the American Type Culture Collection, including strain MGH-78578, which caused pneumonia and was selected for genome sequencing.
For general use, both K. pneumoniae and Escherichia coli were grown in Luria-Bertani (LB) broth or agar at 37°C. When necessary, 50 μg/ml of either kanamycin or chloramphenicol was added.
Fang C.T., Chuang Y.P., Shun C.T., Chang S.C, & Wang J.T. (2004). A Novel Virulence Gene in Klebsiella pneumoniae Strains Causing Primary Liver Abscess and Septic Metastatic Complications. The Journal of Experimental Medicine, 199(5), 697-705.
Publication 2004
Abdomen Abscess Agar Chloramphenicol Diabetes Mellitus Diagnosis Drainage Endophthalmitis Escherichia coli Genome Hepatic Insufficiency Infections, Hospital Kanamycin Klebsiella pneumoniae Liver Abscess Liver Cirrhosis Meningitis Microbiological Techniques Nephrotic Syndrome Operative Surgical Procedures Patients Pneumonia Septicemia Strains Tissues Ultrasonography X-Ray Computed Tomography
5
Polymyxin Antibiotic Pharmacokinetics and Toxicity
The recommendations in this guideline were developed following a review of studies published before December 31, 2018, in English. Studies were identified through Library of Congress, LISTA (Library, Information Science & Technology Abstracts [EBSCO]), and PubMed database searches with no date restrictions using Medical Subject Headings. Examples of keywords used to conduct literature searches were polymyxin, colistin, polymyxin B, nephrotoxicity, pharmacokinetics, pharmacodynamics, area under the curve, toxicodynamics, resistance, carbapenem, A. baumannii, P. aeruginosa, and Klebsiella pneumoniae.
Tsuji B.T., Pogue J.M., Zavascki A.P., Paul M., Daikos G.L., Forrest A., Giacobbe D.R., Viscoli C., Giamarellou H., Karaiskos I., Kaye D., Mouton J.W., Tam V.H., Thamlikitkul V., Wunderink R.G., Li J., Nation R.L, & Kaye K.S. (2019). International Consensus Guidelines for the Optimal Use of the Polymyxins: Endorsed by the American College of Clinical Pharmacy (ACCP), European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Infectious Diseases Society of America (IDSA), International Society for Anti-infective Pharmacology (ISAP), Society of Critical Care Medicine (SCCM), and Society of Infectious Diseases Pharmacists (SIDP). Pharmacotherapy, 39(1), 10-39.
Publication 2019
Carbapenems cDNA Library Colistin Drug Kinetics Klebsiella pneumoniae Polymyxin B Polymyxins Pseudomonas aeruginosa

Most recents protocols related to «Klebsiella pneumoniae»

1
Bacterial Uptake of Radiotracer F-PABA
Not available on PMC !

Example 3

The ability of different bacterial species to take up [18F]F-PABA was studied. The radiotracer accumulated in both methicillin sensitive S. aureus (MSSA, Newman) and methicillin-resistant S. aureus (MRSA), as well as the Gram negative bacteria E. coli and Klebsiela pneumoniae.

In the case of MSSA we also demonstrated that heat-killed cells were unable to take up [18F]F-PABA (FIG. 1). In contrast, [18F]F-PABA was not taken up by Enterococcus faecalis. E. faecalis has a folate salvage pathway and can take up folate from the environment. Thus, folic acid biosynthesis is dispensable in this organism, which also explains why sulfonamides are not used to treat infection by E. faecalis. These studies suggest that F-PABA uptake depends on on the de novo biosynthesis of folate.

US11857352B2. Positron imaging tomography imaging agent composition and method for bacterial infection (2024-01-02). The Research Foundation for the State University of New York [US]. Inventors: Peter Tonge [US], Zhuo Zhang [US], Peter Smith-Jones [US], Li Liu [US], Hui Wang [US].
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Patent 2024
4-Aminobenzoic Acid Anabolism Bacteria Cells Enterococcus faecalis Escherichia coli Folate Folic Acid Gram Negative Bacteria Infection Klebsiella pneumoniae Methicillin Methicillin-Resistant Pneumonia Staphylococcus aureus Sulfonamides
2
Epitope-based Vaccine Design for K. pneumoniae and P. aeruginosa
The reference proteomes of K. pneumoniae (strain ATCC 700721/MGH 78578) and P. aeruginosa (strain ATCC 15692/DSM 22644/CIP 104116/JCM 14847/LMG 12228/1C/PRS 101/PAO1) were downloaded from the UniProt webserver (https://www.uniprot.org/) under the proteome ID of UP000000265 and UP000002438, respectively. As mentioned in the introduction section, the current study aims to design an epitope-based vaccine through the filtration of protein candidates belonging to the outer membrane and iron uptake proteins. Therefore, we selected nine K. pneumoniae protein candidates namely FepA, FepB, FepC, FhuA, FhuF, FuR (iron uptake proteins), OmpA, OmpC, and OmpF (outer membrane proteins), and filtered them through their antigenicity score estimated by VaxiJen v2.0 (Doytchinova and Flower, 2007 (link)) with the cutoff score of 0.4 (the threshold value of bacterial antigenic proteins). The assessment of the antigenicity score revealed that there were 8 antigenic proteins, out of the selected 9 ones therefore we selected the top 2 proteins (one protein from each category) based on their antigenicity score where the final 2 protein candidates of K. pneumoniae were FepA and OmpF with antigenicity scores of 0.76 and 0.81 respectively. Moving to P. aeruginosa, we followed the same approach where six protein candidates namely FoxA, FpvA, HasR, HitA (iron uptake proteins), OprF, and OprH (outer membrane proteins) were filtered and 2 proteins (also one from each category) namely HasR and OprF with the antigenicity scores of 0.59 and 0.8 respectively were selected as our final candidates for P. aeruginosa.
Gouda A.M., Soltan M.A., Abd-Elghany K., Sileem A.E., Elnahas H.M., Ateya M.A., Elbatreek M.H., Darwish K.M., Bogari H.A., Lashkar M.O., Aldurdunji M.M., Elhady S.S., Ahmad T.A, & Said A.M. (2023). Integration of immunoinformatics and cheminformatics to design and evaluate a multitope vaccine against Klebsiella pneumoniae and Pseudomonas aeruginosa coinfection. Frontiers in Molecular Biosciences, 10, 1123411.
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Publication 2023
Antigens Antigens, Bacterial Bacterial Proteins Epitopes Filtration Iron Klebsiella pneumoniae Membrane Proteins OmpC protein Proteins Proteome Pseudomonas aeruginosa Tissue, Membrane vaccin
3
Multitope Vaccine Design for K. pneumoniae and P. aeruginosa
An overview of the applied strategy for a potential multitope vaccine design against K. pneumoniae and P. aeruginosa coinfection is shown in Figure 1.
Gouda A.M., Soltan M.A., Abd-Elghany K., Sileem A.E., Elnahas H.M., Ateya M.A., Elbatreek M.H., Darwish K.M., Bogari H.A., Lashkar M.O., Aldurdunji M.M., Elhady S.S., Ahmad T.A, & Said A.M. (2023). Integration of immunoinformatics and cheminformatics to design and evaluate a multitope vaccine against Klebsiella pneumoniae and Pseudomonas aeruginosa coinfection. Frontiers in Molecular Biosciences, 10, 1123411.
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Publication 2023
Coinfection Klebsiella pneumoniae Pseudomonas aeruginosa Vaccines
4
Microbial Cultures for Susceptibility Testing
Standard microbial cultures of E. coli ATCC 25922, K. pneumoniae ATCC 700603, S. aureus ATCC 25923, B. cereus ATCC 11778, and S. typhi ATCC 6539 were obtained from the Research Unit of the Bacteriology Lab at the Faculty of Veterinary Medicine, University of Nairobi. All the bacteria were subcultured in Mueller Hinton Agar (MHA) for susceptibility testing after 24 hours.
Okumu M.O., Eyaan K.L., Bett L.K, & Gitahi N. (2023). Antibacterial Activity of Venom from the Puff Adder (Bitis arietans), Egyptian Cobra (Naja haje), and Red Spitting Cobra (Naja pallida). International Journal of Microbiology, 2023, 7924853.
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Publication 2023
Agar Bacteria Escherichia coli Faculty Klebsiella pneumoniae Salmonella typhi Staphylococcus aureus Susceptibility, Disease
5
Comparative Analysis of Aerobactin-Harboring Plasmids
The 16 aerobactin-harbouring plasmids, in addition to the three reference plasmids mentioned above, were compared to two plasmids from previous studies that investigated K. pneumoniae harbouring aerobactin in pigs [12, 15 (link)]. However, only short reads were available from these studies. Therefore, these were compared to the rest of the above sequences on a gene level. Reads from one sample from each study (accession numbers SAMN07319199 and ERR3932286 for Germany and Italy, respectively) were downloaded and quality-checked before being assembled as described above. The draft genomes were subjected to VirulenceFinder, using the extended database, to identify the contig harbouring aerobactin. This contig was subsequently annotated using Bakta. The genetic neighbourhood of the aerobactin operon was manually scanned using the gff3 file from the annotation for all the 21 sequences. Potential composite transposons and other mobile elements were detected by using MobileElementFinder [43 (link)] version 1.0.3, database version 1.0.2, and the results were compared to the manual investigation. The detected composite transposon harbouring the aerobactin operon was extracted from the plasmid fasta sequence using Seqkit, and annotated with Bakta as described above, excluding the --circular option. ISFinder [44 (link)] blast was used to characterize the potential insertion sequence (IS) elements flanking the putative composite transposon. The IS elements that were closest to the genetic coordinates of the putative composite transposons were selected. If ties occurred, the highest scoring result was selected based on the blast results.
To confirm the presence of the composite transposon in the aerobactin-harbouring samples that were not long-read sequenced, the raw reads were mapped to a representative sequence of the composite transposon. This was performed in the Ellipsis pipeline by mapping with bwa [45 (link)] version 0.7.17 and SAMtools [46 (link)] version 1.9.
To determine the phylogenetic relationship between the composite transposons, ParSNP [47 (link)] version 1.6.1 was used to generate an alignment, using one of the input sequences as a reference at random, followed by a phylogenetic inference with iq-tree with the same settings as described above. Snp-dists was used to generate SNP distances from the ParSNP alignment.
Kaspersen H., Franklin-Alming F.V., Hetland M.A., Bernhoff E., Löhr I.H., Jiwakanon J., Urdahl A.M., Leangapichart T, & Sunde M. (2023). Highly conserved composite transposon harbouring aerobactin iuc3 in Klebsiella pneumoniae from pigs. Microbial Genomics, 9(2), mgen000960.
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Publication 2023
aerobactin Genes Genome Insertion Sequence Elements Jumping Genes Klebsiella pneumoniae Operon Pigs Plasmids Trees

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Klebsiella pneumoniae is a Gram-negative, non-spore-forming, encapsulated, lactose-fermenting, facultatively anaerobic, rod-shaped bacterium. It is a common inhabitant of the human gastrointestinal tract and can cause various types of infections, including pneumonia, urinary tract infections, and septicemia.
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Klebsiella pneumoniae is a Gram-negative, non-motile, encapsulated, lactose-fermenting, and rod-shaped bacterium. It is a common inhabitant of the human gastrointestinal tract and can cause various opportunistic infections in immunocompromised individuals.

More about "Klebsiella pneumoniae"

Klebsiella pneumoniae is a Gram-negative, rod-shaped bacterium that is a common cause of pneumonia and other severe infections.
As an opportunistic pathogen, it often affects individuals with weakened immune systems, such as those with chronic illnesses or compromised immunity.
In addition to pneumonia, K. pneumoniae can lead to a range of serious conditions, including sepsis, urinary tract infections, and wound infections.
One of the key challenges posed by K. pneumoniae is its ability to develop antimicrobial resistance, making it a significant public health concern.
Researchers and clinicians must stay informed about the latest advancements in detecting, treating, and preventing K. pneumoniae infections to provide optimal patient care.
Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa are other important bacterial pathogens that can cause similar types of infections, often with overlapping symptoms and treatment considerations.
The Vitek 2 system, including the Vitek 2 Compact, is a widely used automated platform for the identification and antimicrobial susceptibility testing of these and other clinically relevant bacteria.
In addition to traditional culture-based methods, advanced techniques like MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry) have gained prominence in the rapid and accurate identification of K. pneumoniae and other bacterial species.
Enterococcus faecalis is another bacterium that can be commonly encountered in clinical settings and may require specialized diagnostic and treatment approaches.
To optimize K. pneumoniae research, PubCompare.ai offers a valuable resource by identifying the most accurate and reproducible protocols from the literature, preprints, and patents.
Its AI-driven platform enables researchers to leverage intelligent comparisons to find the best products and protocols for their work, enhancing the quality and efficicncy of K. pneumoniae studies.