Journal: Viruses

Article Title: Discovery of Three Toxic Proteins of Klebsiella Phage fHe-Kpn01

doi: 10.3390/v12050544

Figure Lengend Snippet: Growth curves of Klebsiella pneumoniae strains #5504 ( A ) and #6326 ( B ) infected with fHe-Kpn01. Bacteria were cultured with different initial multiplicities of infections (MOIs) in liquid LB-medium at 37 °C. Each data point represents the average optical density (OD) at 600 nm for four to five replicates and error bars represent the standard deviation (SD).

Article Snippet: The K. pneumoniae strains used in this work are described in and were mostly obtained from the hospital district of Helsinki and Uusimaa laboratories (HUSLAB), Finland.

Techniques: Infection, Bacteria, Cell Culture, Standard Deviation

Journal: Microbiology Spectrum

Article Title: The Origins of ST11 KL64 Klebsiella pneumoniae : a Genome-Based Study

doi: 10.1128/spectrum.04165-22

Figure Lengend Snippet: The phylogenomic tree of 730 ST11-KL64 K. pneumoniae strains. The tree was inferred using strain 090357 (accession number CP066523 ) as the reference. The phylogeny was inferred from core SNPs under a GTR model with site rate variation and a 100-bootstrap test. The outer circle is the geographic location, and the inner circle exhibits the two clades and the singleton (KP1517). The scale bar represents the number of nucleotide substitutions per site.

Article Snippet: To address this, we took advantage of a large number of K. pneumoniae sequences isolates available in the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov ) and performed a detailed genome-based analysis.

Techniques:

Journal: Microbiology Spectrum

Article Title: The Origins of ST11 KL64 Klebsiella pneumoniae : a Genome-Based Study

doi: 10.1128/spectrum.04165-22

Figure Lengend Snippet: The phylogenomic tree of 565 K. pneumoniae strains belonging to the branch containing ST11-KL64. The tree was inferred using strain 090357 (accession number CP066523 ) as the reference. The phylogeny was inferred from core SNPs under a GTR model with site rate variation and a 100-bootstrap test. The tree was midpoint-rooted with bootstrap support over 50% shown in gradients. The circles from the inner to the outer represent sequence types (ST), KL (capsular) types, and ST11-KL64 clades, respectively. The colored ranges represent ST11-KL47 and ST11-KL15 strains. The scale bar represents the number of nucleotide substitutions per site.

Article Snippet: To address this, we took advantage of a large number of K. pneumoniae sequences isolates available in the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov ) and performed a detailed genome-based analysis.

Techniques: Sequencing

Journal: Microbiology Spectrum

Article Title: The Origins of ST11 KL64 Klebsiella pneumoniae : a Genome-Based Study

doi: 10.1128/spectrum.04165-22

Figure Lengend Snippet: The phylogenetic tree of 857 K. pneumoniae strains based on the 483-kb recombination region. The tree was inferred using strain 090357 (accession number CP066523 ) as the reference. The phylogeny was inferred from core SNPs under a GTR model with site rate variation and a 100-bootstrap test. The tree was midpoint-rooted with bootstrap support of over 50% shown in gradients. The circles from the outer to the inner represent ST11-KL64 clades, KL64 or KL47 strains (regardless of STs), and ST11 or ST147 strains, respectively. The scale bar represents the number of nucleotide substitutions per site.

Article Snippet: To address this, we took advantage of a large number of K. pneumoniae sequences isolates available in the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov ) and performed a detailed genome-based analysis.

Techniques:

Journal: Microbiology Spectrum

Article Title: The Origins of ST11 KL64 Klebsiella pneumoniae : a Genome-Based Study

doi: 10.1128/spectrum.04165-22

Figure Lengend Snippet: The phylogenetic tree of 301 K. pneumoniae strains based on the 157-kb recombination region. The tree was inferred using strain 090357 (accession number CP066523 ) as the reference. The phylogeny was inferred from core SNPs under a GTR model with site rate variation and a 100-bootstrap test. The tree was midpoint-rooted with bootstrap support of over 50% shown in gradients. The circles from the outer to the inner represent ST11-KL64 clades, KL64 strains (regardless of STs), and ST11, ST30, or ST147, respectively. The scale bar represents the number of nucleotide substitutions per site.

Article Snippet: To address this, we took advantage of a large number of K. pneumoniae sequences isolates available in the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov ) and performed a detailed genome-based analysis.

Techniques:

Journal: Infection and Drug Resistance

Article Title: Synergistic Effect and Mechanism of Plumbagin with Gentamicin Against Carbapenem-Resistant Klebsiella pneumoniae

doi: 10.2147/IDR.S265753

Figure Lengend Snippet: Plumbagin potentiates antibacterial activity of gentamicin against CRKp. ( A ) Susceptibility test to imipenem of antibiotics-susceptible strain of Klebsiella pneumoniae CCTCC AB 2010163 (left) and CRKp strain ATCC BAA-1705 (right) on LB agar plates. ( B ) Susceptibility test to gentamicin of ATCC BAA-1705 (left) and its induced gentamicin-resistant strain (right) on LB agar plates. ( C ) Heatmap profile of synergistic effect of herbal compounds with gentamicin. Red, no synergistic effect; green, low synergistic effect; and purplish red, high synergistic effect. ( D ) The inhibition of combination treatments against the CRKp. ( E ) The inhibition of combination treatments against antibiotics-susceptible strain of Klebsiella pneumoniae . ( F ) Growth curves of CRKp with different treatments. * P <0.05, ** P <0.01, *** P <0.001, and **** P <0.0001 compared with gentamicin monotherapy.

Article Snippet: The antibiotics-susceptible strain of Klebsiella pneumoniae CCTCC AB 2010163 was obtained from China Center for Type Culture Collection (CCTCC), Wuhan, China.

Techniques: Activity Assay, Inhibition

Journal: Microbial Genomics

Article Title: Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction

doi: 10.1099/mgen.0.000910

Figure Lengend Snippet: Sequencing read statistics by sequencing modality and bacterial species. Note for R.9.4/Kit10 four isolates were plexed and the total data output is a composite of the individual outputs; for the R10.3/Kit12 and R10.4/Kit12 evaluations each isolate extract was initially run separately. The same flowcell was washed and then re-used for the R10.4 evaluation for the S. aureus and then P. aeruginosa isolates. Finally, the four DNA extracts were also multiplexed on a single R10.4/Kit12 run

Article Snippet: K. pneumoniae , Illumina , 3,202,356 , 483,555,756 , 151 , 97.45.

Techniques: Sequencing

Journal: Microbial Genomics

Article Title: Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction

doi: 10.1099/mgen.0.000910

Figure Lengend Snippet: Number of unique contigs by sequencing modality and bacterial species. Using the complete data available (i.e. no subsampling). The first number in each cell represents the number of contigs assembled and matching to the Illumina-corrected reference using dnadiff, the total number of contigs assembled is shown in curved brackets, and the proportion of the reference chromosomal contig covered in square brackets. For E. coli , P. aeruginosa , S. aureus the total number of expected contigs is one, for K. pneumoniae one chromosome +5 plasmids. Orange shading shows absent contigs, and/or incomplete assembly ( n >1 contig matching to reference), and/or extra contigs not matching to reference. Green shaded cells denote complete singular contigs which reflect the reference DNA content at 100+/-1 %. “-“ denotes no relevant contig assembled

Article Snippet: K. pneumoniae , Illumina , 3,202,356 , 483,555,756 , 151 , 97.45.

Techniques: Sequencing, Plasmid Preparation

Journal: Microbial Genomics

Article Title: Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction

doi: 10.1099/mgen.0.000910

Figure Lengend Snippet: Assembly reference coverage percentage (%) by sequencing modality, assembler and species. Panel A represents the data for chromosomes and panel B evaluations for the five plasmids known to occur in the K. pneumoniae reference strain (labelled by their lengths in bp). Data shown for complete data only (i.e. no sub-sampling performed). ( a) Chromosomes ( b) Plasmids.

Article Snippet: K. pneumoniae , Illumina , 3,202,356 , 483,555,756 , 151 , 97.45.

Techniques: Sequencing, Sampling

Journal: Microbial Genomics

Article Title: Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction

doi: 10.1099/mgen.0.000910

Figure Lengend Snippet: Impact of subsampling of long-read datasets on assembly accuracy. Presented here by species for Indels (top panels), and SNPs (lower panels). For ease of representation, only data for Flye assemblies polished with one round of Medaka are shown, as the effects of additional polishing was shown to be marginal for most modalities (Fig. S6, Table S7). Data for 10× long-read coverage is omitted for Canu assemblies as this coverage was considered too low for default settings and was unlikely to improve results. ( a) E. coli ( b) K. pneumoniae (chromosome only) ( c) P. aeruginosa ( d) S. aureus .

Article Snippet: K. pneumoniae , Illumina , 3,202,356 , 483,555,756 , 151 , 97.45.

Techniques:

Journal: Microbial Genomics

Article Title: Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction

doi: 10.1099/mgen.0.000910

Figure Lengend Snippet: Coding sequence (CDS) recovery on the basis of exact CDS (amino acid sequence) matches with respect to the Prokka-annotated Illumina-corrected reference (chromosome +all plasmids for K. pneumoniae ). Plot shows the percentage of reference coding sequences missed by each modality. For long-read data only Flye assemblies with one round of polishing with Medaka are shown; for R10.3 and R10.4 datasets these were from non-multiplexed evaluations (i.e. only single extracts per flowcell). For Unicycler, the assembly using R.9.4 hac +Illumina data is shown. The total number of coding sequences missed by each approach is shown as a number at the top of each bar.

Article Snippet: K. pneumoniae , Illumina , 3,202,356 , 483,555,756 , 151 , 97.45.

Techniques: Sequencing

Journal: Endoscopy International Open

Article Title: Duodenoscope-associated infection prevention: A call for evidence-based decision making

doi: 10.1055/a-1264-7173

Figure Lengend Snippet: Duodenoscope-associated infections reported in peer-reviewed journal articles.

Article Snippet: 8825520 , 3 , Olympus , 3 , MDR K. pneumoniae , Cultures were negative for K. pneumoniae.

Techniques:

Journal: Endoscopy International Open

Article Title: Duodenoscope-associated infection prevention: A call for evidence-based decision making

doi: 10.1055/a-1264-7173

Figure Lengend Snippet: Comparison of evidence from multiple sources describing four duodenoscope-associated outbreaks.

Article Snippet: 8825520 , 3 , Olympus , 3 , MDR K. pneumoniae , Cultures were negative for K. pneumoniae.

Techniques: Transmission Assay

Journal: Endoscopy International Open

Article Title: Duodenoscope-associated infection prevention: A call for evidence-based decision making

doi: 10.1055/a-1264-7173

Figure Lengend Snippet: Infections described in reports submitted to FDA MAUDE database (2017 – 2019).

Article Snippet: 8825520 , 3 , Olympus , 3 , MDR K. pneumoniae , Cultures were negative for K. pneumoniae.

Techniques:

Journal: Endoscopy International Open

Article Title: Duodenoscope-associated infection prevention: A call for evidence-based decision making

doi: 10.1055/a-1264-7173

Figure Lengend Snippet: Effectiveness of HLD, double HLD, and sterilization in real-world settings.

Article Snippet: 8825520 , 3 , Olympus , 3 , MDR K. pneumoniae , Cultures were negative for K. pneumoniae.

Techniques:

Journal: PLoS ONE

Article Title: Competition is the basis of the transport mechanism of the NhaB Na + /H + exchanger from Klebsiella pneumoniae

doi: 10.1371/journal.pone.0182293

Figure Lengend Snippet: A, Sequence alignment of NhaA exchangers from K . pneumoniae (KpNhaA1, KpNhaA2) and E . coli (EcNhaA). B, Sequence alignment of NhaB exchangers from K . pneumoniae (KpNhaB), E . coli (EcNhaB) and V . alginolyticus (VaNhaB). Horizontal lines denote transmembrane helices in EcNhaA (A) or VaNhaB (B), as determined in and , respectively. Red asterisks show conserved charged residues shown to be essential for transport function or stability of the exchangers. Alignments were performed using Clustal Omega and drawn using Jalview .

Article Snippet: The genes encoding the K . pneumoniae exchangers KpNhaA1 (Strain MGH 78578, Uniprot accession number: A6T4F6), KpNhaA2 (Strain MGH 78578, Uniprot accession number: A6TJ58) and KpNhaB (Strain 342, Uniprot accession number: B5XQ77) were synthesized by Genscript (Piscataway, NJ, USA) in the pET-21d(+) vector (Merck Millipore, Billerica, MA, USA).

Techniques: Sequencing

Journal: PLoS ONE

Article Title: Competition is the basis of the transport mechanism of the NhaB Na + /H + exchanger from Klebsiella pneumoniae

doi: 10.1371/journal.pone.0182293

Figure Lengend Snippet: A, E . coli membrane vesicles (100 μg total protein) were subjected to SDS-PAGE, followed by Western blot using an anti-His primary antibody. B, Purified KpNhaB, KpNhaA1 and KpNhaA2 (5 μg protein) were subjected to SDS-PAGE, followed by Coomassie Blue staining.

Article Snippet: The genes encoding the K . pneumoniae exchangers KpNhaA1 (Strain MGH 78578, Uniprot accession number: A6T4F6), KpNhaA2 (Strain MGH 78578, Uniprot accession number: A6TJ58) and KpNhaB (Strain 342, Uniprot accession number: B5XQ77) were synthesized by Genscript (Piscataway, NJ, USA) in the pET-21d(+) vector (Merck Millipore, Billerica, MA, USA).

Techniques: Membrane, SDS Page, Western Blot, Purification, Staining

Journal: PLoS ONE

Article Title: Competition is the basis of the transport mechanism of the NhaB Na + /H + exchanger from Klebsiella pneumoniae

doi: 10.1371/journal.pone.0182293

Figure Lengend Snippet: Survival of the Na + /H + exchanger-deficient E . coli strain KNabc overexpressing K . pneumoniae Na + /H + exchangers.

Article Snippet: The genes encoding the K . pneumoniae exchangers KpNhaA1 (Strain MGH 78578, Uniprot accession number: A6T4F6), KpNhaA2 (Strain MGH 78578, Uniprot accession number: A6TJ58) and KpNhaB (Strain 342, Uniprot accession number: B5XQ77) were synthesized by Genscript (Piscataway, NJ, USA) in the pET-21d(+) vector (Merck Millipore, Billerica, MA, USA).

Techniques: Plasmid Preparation

Journal: PLoS ONE

Article Title: Competition is the basis of the transport mechanism of the NhaB Na + /H + exchanger from Klebsiella pneumoniae

doi: 10.1371/journal.pone.0182293

Figure Lengend Snippet: E . coli KNabc membranes overexpressing KpNhaB (A), KpNhaA1 (B) and KpNhaA2 (C) were subjected to acridine orange dequenching assays at pH 8.5. The traces show the change of acridine orange fluorescence, F, over time. Addition of 2.5 mM Tris-D-lactate is marked by asterisks, while addition of 50 mM NaCl is marked by downward pointing arrows. D, pH dependence of the transport activity of KpNhaB recorded by acridine orange dequenching. Dequenching in D was induced by addition of 10 mM NaCl.

Article Snippet: The genes encoding the K . pneumoniae exchangers KpNhaA1 (Strain MGH 78578, Uniprot accession number: A6T4F6), KpNhaA2 (Strain MGH 78578, Uniprot accession number: A6TJ58) and KpNhaB (Strain 342, Uniprot accession number: B5XQ77) were synthesized by Genscript (Piscataway, NJ, USA) in the pET-21d(+) vector (Merck Millipore, Billerica, MA, USA).

Techniques: Fluorescence, Activity Assay

Journal: PLoS ONE

Article Title: Competition is the basis of the transport mechanism of the NhaB Na + /H + exchanger from Klebsiella pneumoniae

doi: 10.1371/journal.pone.0182293

Figure Lengend Snippet: A-C, Transient currents obtained following concentration jumps of 100 mM Na + on KpNhaB (A), KpNhaA1 (B) and KpNhaA2 (C). D-F, Peak currents recorded following 100 mM or 10 mM Na + concentration jumps on KpNhaB (D), KpNhaA1 (E) and KpNhaA2 (F). Data in D-F are presented as average of measurements performed on 3 different sensors ± s.d. and normalized to the maximum peak current. For (F), values for pH 9 and pH 9.5 were obtained following reconstruction of the transporter currents. Lines in D-F are guides to the eye.

Article Snippet: The genes encoding the K . pneumoniae exchangers KpNhaA1 (Strain MGH 78578, Uniprot accession number: A6T4F6), KpNhaA2 (Strain MGH 78578, Uniprot accession number: A6TJ58) and KpNhaB (Strain 342, Uniprot accession number: B5XQ77) were synthesized by Genscript (Piscataway, NJ, USA) in the pET-21d(+) vector (Merck Millipore, Billerica, MA, USA).

Techniques: Concentration Assay

Journal: PLoS ONE

Article Title: Competition is the basis of the transport mechanism of the NhaB Na + /H + exchanger from Klebsiella pneumoniae

doi: 10.1371/journal.pone.0182293

Figure Lengend Snippet: A-C, Na + dependence of transient currents following Na + concentration jumps at pH 8.5 for KpNhaB (A), KpNhaA1 (B) and KpNhaA2 (C). D-F, Peak currents recorded following Na + concentration jumps at various pH values for KpNhaB (D), KpNhaA1 (E) and KpNhaA2 (F). G-I, Li + dependence of transport in KpNhaB (G), KpNhaA1 (H), KpNhaA2 (I) at pH 8.5. Curves represent hyperbolic fits to the data with the exception of the Na + dependence of KpNhaB at pH 7 (D), where a Hill function was used. Data in D-I are normalized to the determined v max values and presented as average of measurements performed on 3 independent sensors ± s.d.

Article Snippet: The genes encoding the K . pneumoniae exchangers KpNhaA1 (Strain MGH 78578, Uniprot accession number: A6T4F6), KpNhaA2 (Strain MGH 78578, Uniprot accession number: A6TJ58) and KpNhaB (Strain 342, Uniprot accession number: B5XQ77) were synthesized by Genscript (Piscataway, NJ, USA) in the pET-21d(+) vector (Merck Millipore, Billerica, MA, USA).

Techniques: Concentration Assay

Journal: PLoS ONE

Article Title: Competition is the basis of the transport mechanism of the NhaB Na + /H + exchanger from Klebsiella pneumoniae

doi: 10.1371/journal.pone.0182293

Figure Lengend Snippet: Kinetic parameters of K . pneumoniae Na + /H + exchangers.

Article Snippet: The genes encoding the K . pneumoniae exchangers KpNhaA1 (Strain MGH 78578, Uniprot accession number: A6T4F6), KpNhaA2 (Strain MGH 78578, Uniprot accession number: A6TJ58) and KpNhaB (Strain 342, Uniprot accession number: B5XQ77) were synthesized by Genscript (Piscataway, NJ, USA) in the pET-21d(+) vector (Merck Millipore, Billerica, MA, USA).

Techniques:

Journal: PLoS ONE

Article Title: Competition is the basis of the transport mechanism of the NhaB Na + /H + exchanger from Klebsiella pneumoniae

doi: 10.1371/journal.pone.0182293

Figure Lengend Snippet: The steady-state solution of the kinetic model was fitted simultaneously to the experimental data determined for the pH (top panel) and Na + (bottom panel) dependences of KpNhaB (A), KpNhaA1 (B) and KpNhaA2 (C). Determined kinetic parameters are presented in . Exp. = experimentally determined data points, fit = modeled curve following the fit of the kinetic model to the experimental data.

Article Snippet: The genes encoding the K . pneumoniae exchangers KpNhaA1 (Strain MGH 78578, Uniprot accession number: A6T4F6), KpNhaA2 (Strain MGH 78578, Uniprot accession number: A6TJ58) and KpNhaB (Strain 342, Uniprot accession number: B5XQ77) were synthesized by Genscript (Piscataway, NJ, USA) in the pET-21d(+) vector (Merck Millipore, Billerica, MA, USA).

Techniques: