k. pneumoniae sequences  (Biotechnology Information)

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: One Health

Article Title: Human pandemic K27-ST392 CTX-M-15 extended-spectrum β-lactamase-positive Klebsiella pneumoniae : A one health clone threatening companion animals

doi: 10.1016/j.onehlt.2022.100414

Figure Lengend Snippet: In A, Single nucleotide polymorphism (SNP)-based phylogenomic relationship of 67 K. pneumoniae ST392 strains isolated globally from human and animal sources. The LcKp01 strain clustered (60–80 SNPs differences) with four Klebsiella pneumoniae ST392 strains isolated from human and animal samples, in Australia, France, Vietnam and China. Heatmap includes all 67 Klebsiella pneumoniae ST392 capsular serotyping, capsule-associated virulence genes, ESBL/carbapenemase genes, plasmid replicons, and epidemiological information (country and year). The companion animal strain analyzed in this study (accession number: JAEDYP000000000) is represented by red color. NI, Not informed. Countries are labeled according to ISO 3166-1 Alpha-3 code, as follows: AUS, Australia; BRA, Brazil; FRA, France; VNM, Vietnam; CHN, China; DEU, Germany; LUX, Luxembourg; TZA, Tanzania; CHE, Switzerland; ESP, Spain; COL, Colombia; TUR, Turkey; BEL, Belgium; ISR, Israel; AUT, Austria; TUN, Tunisia; ITA, Italy; POL, Poland; PHL, Philippines; MYS, Malaysia; USA, United States of America; GBR, United Kingdom; UKR, Ukraine; LBN, Lebanon; NGA, Nigeria; MEX, Mexico. Tree topology and scale bar were automatically generated in scale by default parameters of iTol v.6 and refers to branch lengths, which are measured in number of substitutions per site. In B, Heatmap displaying the acquired antibiotic resistance genes identified in all 67 K. pneumoniae ST392 genomes analyzed in this study. Light blue and white filled squares indicate gene presence and absence, respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: We performed whole-genome sequencing (WGS) of the K. pneumoniae LCKp01 using an Illumina MiSeq platform with 300-bp read lengths.

Techniques: Isolation, Plasmid Preparation, Labeling, Generated