fast hierarchical bayesian analysis of population structure (fastbaps) Search Results


fast hierarchical bayesian analysis of population structure (fastbaps)  (RStudio)
90
RStudio fast hierarchical bayesian analysis of population structure (fastbaps)
Phylogenetic analysis, transmission networks, and mobile genetic elements of carbapenem resistant A. baumannii ST2 isolates from Fiji (2020–2021). a) Core genome SNP phylogeny of carbapenem resistant A. baumannii ST2 isolates from Fiji (2020–2021). Phylogenetic tree inferred from core genome SNPs of 108 CR Ab ST2 isolates. The core genome was generated by aligning at least 92% of the available sequence data for all isolates. The core SNP density, representing the average number of SNPs per base pair in the core genome, was 163 SNPs across 4,062,284 base pairs in the reference genome. The reference genome used was from CR Ab ST2 (SAMN37733145) isolated from CWMH in 2019. The tree was rooted using the earliest isolate (reference) from CWMH. Isolation dates, patient admission locations, and AMR phenotypic and genotypic profiles are annotated on the tree. The scale bar on the tree represents the frequency of mutations per site, providing a measure of genetic distance between isolates. Clusters were determined by <t>fastbaps.</t> b) Putative transmission trees of CR Ab ST2 clones 1–3 among CWMH, LTKH, and LBSH, 2020–2021. Transmission trees showing inter-hospital transmission directions of CR Ab ST2 clones 1 (i), 2 (ii), and 3 (iii) based on sample SNP distance and collection timeline. Numbers in red signify the SNP distance. Transmission tree generated and visualised using GraphSNP. The black arrows represent the earliest positive isolate. c) Comparative distribution of mobile genetic elements and AMR genes in CR Ab ST2 isolates (clone 1–3) from Fiji, 2020–2021. The figure presents a circular depiction of the completed genomes of Fiji's CR Ab ST2 clone 1 (FJ567_LT), clone 2 (FJ437_LB), and clone 3 (FJ104_CW) isolates, alongside the dispersion of MGEs carrying AMR genes, visualised using BRIG. The innermost circle corresponds to CR Ab ST2 clone 1, the middle circle to CR Ab ST2 clone 2, and the outermost circle to CR Ab ST2 clone 3. Arrows indicate the existence of an MGE at that particular genome location. The detailed representation of MGEs can be found in the boxes (a–n). AMR abbreviation: aph , aminoglycoside phosphotransferase; arm , aminoglycoside resistance methylase; ant , aminoglycoside nucleotidyltransferase; aadA , aminoglycoside adenylyltransferase; abaQ , A. baumannii quinolone resistance transporter; ade , adenine deaminase; ampC , AmpC beta-lactamase; amvA, Acinetobacter baumannii AmvA efflux pump; ble-MBL , bleomycin resistance gene; bla NDM , New Delhi metallo-beta-lactamase; bla OXA , OXA-type beta-lactamase; bla PER , PER beta-lactamases; cat , chloramphenicol acetyltransferase; gyr , DNA gyrase; par , Type IV topoisomerase; qnrS1 , quinolone resistance gene; qacE , quaternary ammonium compounds; MFS, major facilitator superfamily; mph , macrolide phosphotransferase; msr(E) , macrolide resistance gene; RND, resistance nodulation-division; sul , sulfonamide resistance gene.
Fast Hierarchical Bayesian Analysis Of Population Structure (Fastbaps), supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/fast+hierarchical+bayesian+analysis+of+population+structure+%28fastbaps%29/pmc11166881-148-12-16?v=RStudio
Average 90 stars, based on 1 article reviews
fast hierarchical bayesian analysis of population structure (fastbaps) - by Bioz Stars, 2026-07
90/100 stars
  Buy from Supplier

Image Search Results


Phylogenetic analysis, transmission networks, and mobile genetic elements of carbapenem resistant A. baumannii ST2 isolates from Fiji (2020–2021). a) Core genome SNP phylogeny of carbapenem resistant A. baumannii ST2 isolates from Fiji (2020–2021). Phylogenetic tree inferred from core genome SNPs of 108 CR Ab ST2 isolates. The core genome was generated by aligning at least 92% of the available sequence data for all isolates. The core SNP density, representing the average number of SNPs per base pair in the core genome, was 163 SNPs across 4,062,284 base pairs in the reference genome. The reference genome used was from CR Ab ST2 (SAMN37733145) isolated from CWMH in 2019. The tree was rooted using the earliest isolate (reference) from CWMH. Isolation dates, patient admission locations, and AMR phenotypic and genotypic profiles are annotated on the tree. The scale bar on the tree represents the frequency of mutations per site, providing a measure of genetic distance between isolates. Clusters were determined by fastbaps. b) Putative transmission trees of CR Ab ST2 clones 1–3 among CWMH, LTKH, and LBSH, 2020–2021. Transmission trees showing inter-hospital transmission directions of CR Ab ST2 clones 1 (i), 2 (ii), and 3 (iii) based on sample SNP distance and collection timeline. Numbers in red signify the SNP distance. Transmission tree generated and visualised using GraphSNP. The black arrows represent the earliest positive isolate. c) Comparative distribution of mobile genetic elements and AMR genes in CR Ab ST2 isolates (clone 1–3) from Fiji, 2020–2021. The figure presents a circular depiction of the completed genomes of Fiji's CR Ab ST2 clone 1 (FJ567_LT), clone 2 (FJ437_LB), and clone 3 (FJ104_CW) isolates, alongside the dispersion of MGEs carrying AMR genes, visualised using BRIG. The innermost circle corresponds to CR Ab ST2 clone 1, the middle circle to CR Ab ST2 clone 2, and the outermost circle to CR Ab ST2 clone 3. Arrows indicate the existence of an MGE at that particular genome location. The detailed representation of MGEs can be found in the boxes (a–n). AMR abbreviation: aph , aminoglycoside phosphotransferase; arm , aminoglycoside resistance methylase; ant , aminoglycoside nucleotidyltransferase; aadA , aminoglycoside adenylyltransferase; abaQ , A. baumannii quinolone resistance transporter; ade , adenine deaminase; ampC , AmpC beta-lactamase; amvA, Acinetobacter baumannii AmvA efflux pump; ble-MBL , bleomycin resistance gene; bla NDM , New Delhi metallo-beta-lactamase; bla OXA , OXA-type beta-lactamase; bla PER , PER beta-lactamases; cat , chloramphenicol acetyltransferase; gyr , DNA gyrase; par , Type IV topoisomerase; qnrS1 , quinolone resistance gene; qacE , quaternary ammonium compounds; MFS, major facilitator superfamily; mph , macrolide phosphotransferase; msr(E) , macrolide resistance gene; RND, resistance nodulation-division; sul , sulfonamide resistance gene.

Journal: The Lancet Regional Health: Western Pacific

Article Title: Molecular and clinical epidemiology of carbapenem resistant Acinetobacter baumannii , Pseudomonas aeruginosa and Enterobacterales in Fiji: a multicentre prospective observational study

doi: 10.1016/j.lanwpc.2024.101095

Figure Lengend Snippet: Phylogenetic analysis, transmission networks, and mobile genetic elements of carbapenem resistant A. baumannii ST2 isolates from Fiji (2020–2021). a) Core genome SNP phylogeny of carbapenem resistant A. baumannii ST2 isolates from Fiji (2020–2021). Phylogenetic tree inferred from core genome SNPs of 108 CR Ab ST2 isolates. The core genome was generated by aligning at least 92% of the available sequence data for all isolates. The core SNP density, representing the average number of SNPs per base pair in the core genome, was 163 SNPs across 4,062,284 base pairs in the reference genome. The reference genome used was from CR Ab ST2 (SAMN37733145) isolated from CWMH in 2019. The tree was rooted using the earliest isolate (reference) from CWMH. Isolation dates, patient admission locations, and AMR phenotypic and genotypic profiles are annotated on the tree. The scale bar on the tree represents the frequency of mutations per site, providing a measure of genetic distance between isolates. Clusters were determined by fastbaps. b) Putative transmission trees of CR Ab ST2 clones 1–3 among CWMH, LTKH, and LBSH, 2020–2021. Transmission trees showing inter-hospital transmission directions of CR Ab ST2 clones 1 (i), 2 (ii), and 3 (iii) based on sample SNP distance and collection timeline. Numbers in red signify the SNP distance. Transmission tree generated and visualised using GraphSNP. The black arrows represent the earliest positive isolate. c) Comparative distribution of mobile genetic elements and AMR genes in CR Ab ST2 isolates (clone 1–3) from Fiji, 2020–2021. The figure presents a circular depiction of the completed genomes of Fiji's CR Ab ST2 clone 1 (FJ567_LT), clone 2 (FJ437_LB), and clone 3 (FJ104_CW) isolates, alongside the dispersion of MGEs carrying AMR genes, visualised using BRIG. The innermost circle corresponds to CR Ab ST2 clone 1, the middle circle to CR Ab ST2 clone 2, and the outermost circle to CR Ab ST2 clone 3. Arrows indicate the existence of an MGE at that particular genome location. The detailed representation of MGEs can be found in the boxes (a–n). AMR abbreviation: aph , aminoglycoside phosphotransferase; arm , aminoglycoside resistance methylase; ant , aminoglycoside nucleotidyltransferase; aadA , aminoglycoside adenylyltransferase; abaQ , A. baumannii quinolone resistance transporter; ade , adenine deaminase; ampC , AmpC beta-lactamase; amvA, Acinetobacter baumannii AmvA efflux pump; ble-MBL , bleomycin resistance gene; bla NDM , New Delhi metallo-beta-lactamase; bla OXA , OXA-type beta-lactamase; bla PER , PER beta-lactamases; cat , chloramphenicol acetyltransferase; gyr , DNA gyrase; par , Type IV topoisomerase; qnrS1 , quinolone resistance gene; qacE , quaternary ammonium compounds; MFS, major facilitator superfamily; mph , macrolide phosphotransferase; msr(E) , macrolide resistance gene; RND, resistance nodulation-division; sul , sulfonamide resistance gene.

Article Snippet: Genetic clustering of isolates was determined using Fast hierarchical Bayesian analysis of population structure (fastBAPS) in RStudio (v.4.1.2).

Techniques: Transmission Assay, Generated, Sequencing, Isolation, Clone Assay, Dispersion