scholarly journals Population structure and minimum core genome typing of Legionella pneumophila

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Tian Qin ◽  
Wen Zhang ◽  
Wenbin Liu ◽  
Haijian Zhou ◽  
Hongyu Ren ◽  
...  
Keyword(s):  
Population Structure ◽  
Legionella Pneumophila ◽  
Core Genome ◽  
Genome Typing

scholarly journals Geography Shapes the Population Genomics of Salmonella enterica Dublin

2019 ◽  
Vol 11 (8) ◽  
pp. 2220-2231 ◽  
Author(s):  
Gavin J Fenske ◽  
Anil Thachil ◽  
Patrick L McDonough ◽  
Amy Glaser ◽  
Joy Scaria
Keyword(s):  
Population Structure ◽  
Salmonella Enterica ◽  
Core Genome ◽  
Population Genomics ◽  
Negative Impact ◽  
Antibiotic Resistance Genes ◽  
Virulence Plasmid ◽  
Ancestral State ◽  
Secretion Systems ◽  
Data Set

Abstract Salmonella enterica serotype Dublin (S. Dublin) is a bovine-adapted serotype that can cause serious systemic infections in humans. Despite the increasing prevalence of human infections and the negative impact on agricultural processes, little is known about the population structure of the serotype. To this end, we compiled a manually curated data set comprising of 880 S. Dublin genomes. Core genome phylogeny and ancestral state reconstruction revealed that region-specific clades dominate the global population structure of S. Dublin. Strains of S. Dublin in the UK are genomically distinct from US, Brazilian, and African strains. The geographical partitioning impacts the composition of the core genome as well as the ancillary genome. Antibiotic resistance genes are almost exclusively found in US genomes and are mediated by an IncA/C2 plasmid. Phage content and the S. Dublin virulence plasmid were strongly conserved in the serotype. Comparison of S. Dublin to a closely related serotype, S. enterica serotype Enteritidis, revealed that S. Dublin contains 82 serotype specific genes that are not found in S. Enteritidis. Said genes encode metabolic functions involved in the uptake and catabolism of carbohydrates and virulence genes associated with type VI secretion systems and fimbria assembly respectively.

scholarly journals Population Genetic Structure of Legionella pneumophila Inferred from RNA Polymerase Gene (rpoB) and DotA Gene (dotA) Sequences

2002 ◽  
Vol 184 (8) ◽  
pp. 2123-2130 ◽  
Author(s):  
Kwan Soo Ko ◽  
Hae Kyung Lee ◽  
Mi-Yeoun Park ◽  
Man-Suk Park ◽  
Keun-Hwa Lee ◽  
...  
Keyword(s):  
Population Structure ◽  
Rna Polymerase ◽  
Legionella Pneumophila ◽  
Population Genetic ◽  
Genetic Recombination ◽  
Gene Trees ◽  
Polymerase Gene ◽  
Local Sample ◽  
Type Strains ◽  
Rna Polymerase Gene

ABSTRACT The population structure of Legionella pneumophila was studied by using partial RNA polymerase gene (rpoB) and DotA gene (dotA) sequences. Trees inferred from rpoB sequences showed that two subspecies of L. pneumophila, Legionella pneumophila subsp. pneumophila and Legionella pneumophila subsp. fraseri, were clearly separated genetically. In both rpoB and dotA trees, 79 Korean isolates used in this study constituted six clonal populations, four of which (designated subgroups P-I to P-IV) were identified in L. pneumophila subsp. pneumophila and two of which (designated subgroups F-I and F-II) were identified in L. pneumophila subsp. fraseri. Although the relationships among subgroups were not identical, such subgrouping was congruent between the rpoB and dotA trees. Type strains of several serogroups did not belong to any subgroup, presumably because isolates similar to these strains were not present among our local sample of the population. There was evidence that horizontal gene transfer or recombination had occurred within L. pneumophila. Contrary to the phylogeny from rpoB and the taxonomic context, subgroups P-III and P-IV of L. pneumophila subsp. pneumophila proved to be closely related to those of L. pneumophila subsp. fraseri or showed a distinct clustering in the dotA tree. It can be inferred that dotA of subgroups P-III and P-IV has been transferred horizontally from other subspecies. The diverse distribution of serogroup 1 strains through the gene trees suggests that surface antigen-coding genes that determine serogroup can be exchanged. Thus, it can be inferred that genetic recombination has been important in the evolution of L. pneumophila.

scholarly journals PATO: Pangenome Analysis Toolkit

2021 ◽  
Author(s):  
Miguel D. Fernández-de-Bobadilla ◽  
Alba Talavera-Rodríguez ◽  
Lucía Chacón ◽  
Fernando Baquero ◽  
Teresa M. Coque ◽  
...  
Keyword(s):  
Population Structure ◽  
Statistical Analysis ◽  
Core Genome ◽  
State Of The Art ◽  
Source Code ◽  
Supplementary Information ◽  
Complete Analysis ◽  
Large Set ◽  
Supplementary Data ◽  
Desktop Computer

AbstractMotivationComparative genomics is a growing field but one that will be eventually overtaken by sample size studies and the increase of available genomes in public databases. We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.ResultsPATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20–30x times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Lastly, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R.AvailabilityThe source code for PATO is freely available at https://github.com/irycisBioinfo/PATO under the GPLv3 [email protected] informationSupplementary data are available at Bioinformatics online

Genetic diversity and population structure of pear (Pyrus spp.) collections revealed by a set of core genome-wide SSR markers

2015 ◽  
Vol 11 (6) ◽  
Author(s):  
Qingwen Liu ◽  
Yue Song ◽  
Lun Liu ◽  
Mingyue Zhang ◽  
Jiangmei Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Core Genome ◽  
Genome Wide

scholarly journals Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing

2013 ◽  
Vol 13 (1) ◽  
pp. 302 ◽  
Author(s):  
Anthony P Underwood ◽  
Garan Jones ◽  
Massimo Mentasti ◽  
Norman K Fry ◽  
Timothy G Harrison
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Legionella Pneumophila ◽  
Whole Genome

scholarly journals Investigation of the population structure of Legionella pneumophila by analysis of tandem repeat copy number and internal sequence variation

Microbiology ◽  
2011 ◽  
Vol 157 (9) ◽  
pp. 2582-2594 ◽  
Author(s):  
Paolo Visca ◽  
Silvia D'Arezzo ◽  
Françoise Ramisse ◽  
Yevgeniy Gelfand ◽  
Gary Benson ◽  
...  
Keyword(s):  
Population Structure ◽  
Legionella Pneumophila ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Epidemiological Studies ◽  
Variable Number ◽  
Vntr Locus ◽  
Internal Repeat ◽  
High Level ◽  
Small Clusters

The population structure of the species Legionella pneumophila was investigated by multilocus variable number of tandem repeats (VNTR) analysis (MLVA) and sequencing of three VNTRs (Lpms01, Lpms04 and Lpms13) in selected strains. Of 150 isolates of diverse origins, 136 (86 %) were distributed into eight large MLVA clonal complexes (VACCs) and the rest were either unique or formed small clusters of up to two MLVA genotypes. In spite of the lower degree of genome-wide linkage disequilibrium of the MLVA loci compared with sequence-based typing, the clustering achieved by the two methods was highly congruent. The detailed analysis of VNTR Lpms04 alleles showed a very complex organization, with five different repeat unit lengths and a high level of internal variation. Within each MLVA-defined VACC, Lpms04 was endowed with a common recognizable pattern with some interesting exceptions. Evidence of recombination events was suggested by analysis of internal repeat variations at the two additional VNTR loci, Lpms01 and Lpms13. Sequence analysis of L. pneumophila VNTR locus Lpms04 alone provides a first-line assay for allocation of a new isolate within the L. pneumophila population structure and for epidemiological studies.

Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies

2018 ◽  
Vol 59 ◽  
pp. 172-185 ◽  
Author(s):  
Natalia A. Kozak-Muiznieks ◽  
Shatavia S. Morrison ◽  
Jeffrey W. Mercante ◽  
Maliha K. Ishaq ◽  
Taccara Johnson ◽  
...  
Keyword(s):  
Population Structure ◽  
Legionella Pneumophila ◽  
Genome Analysis ◽  
Comparative Genome Analysis ◽  
Comparative Genome ◽  
Complex Population

Phylogenomic grouping of Listeria monocytogenes

2015 ◽  
Vol 61 (9) ◽  
pp. 637-646 ◽  
Author(s):  
Swapnil Doijad ◽  
Markus Weigel ◽  
Sukhadeo Barbuddhe ◽  
Jochen Blom ◽  
Alexander Goesmann ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Epidemiological Studies ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Subsequent Evolution ◽  
Pathogenic Potential ◽  
Core Genes ◽  
Genome Typing

The precise delineation of lineages and clonal groups are a prerequisite to examine within-species genetic variations, particularly with respect to pathogenic potential. A whole-genome-based approach was used to subtype and subgroup isolates of Listeria monocytogenes. Core-genome typing was performed, employing 3 different approaches: total core genes (CG), high-scoring segment pairs (HSPs), and average nucleotide identity (ANI). Examination of 113 L. monocytogenes genomes available in-house and in public domains revealed 33 phylogenomic groups (PGs). Each PG could be differentiated into a number of genomic types (GTs), depending on the approach used: HSPs (n = 57 GTs), CG (n = 71 GTs), and ANI (n = 83 GTs). Demarcation of the PGs was concordant with the 4 known lineages and led to the identification of sublineages in the lineage groups I, II, and III. In addition, PG assignments had discriminatory power similar to multi-virulence-locus sequence typing types and clonal complexes of multilocus sequence typing. Clustering of genomically highly similar isolates from different countries, sources, and isolation dates using whole-genome-based PG suggested that dispersion of phylogenomic clones of L. monocytogenes preceded their subsequent evolution. Classification according to PG may act as a guideline for future epidemiological studies.

scholarly journals Neisseria gonorrhoeae Population Genomics: Use of the Gonococcal Core Genome to Improve Surveillance of Antimicrobial Resistance

2020 ◽  
Vol 222 (11) ◽  
pp. 1816-1825 ◽  
Author(s):  
Odile B Harrison ◽  
Ana Cehovin ◽  
Jessica Skett ◽  
Keith A Jolley ◽  
Paola Massari ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Population Biology ◽  
Clustering Algorithm ◽  
Core Genome ◽  
Population Genomics ◽  
Transmitted Infection ◽  
Sexually Transmitted ◽  
Allelic Differences

Abstract Background Gonorrhea, caused by the bacterium Neisseria gonorrhoeae, is a globally prevalent sexually transmitted infection. The dynamics of gonococcal population biology have been poorly defined due to a lack of resolution in strain typing methods. Methods In this study, we assess how the core genome can be used to improve our understanding of gonococcal population structure compared with current typing schemes. Results A total of 1668 loci were identified as core to the gonococcal genome. These were organized into a core genome multilocus sequence typing scheme (N gonorrhoeae cgMLST v1.0). A clustering algorithm using a threshold of 400 allelic differences between isolates resolved gonococci into discrete and stable core genome groups, some of which persisted for multiple decades. These groups were associated with antimicrobial genotypes and non-overlapping NG-STAR and NG-MAST sequence types. The MLST-STs were more widely distributed among core genome groups. Conclusions Clustering with cgMLST identified globally distributed, persistent, gonococcal lineages improving understanding of the population biology of gonococci and revealing its population structure. These findings have implications for the emergence of antimicrobial resistance in gonococci and how this is associated with lineages, some of which are more predisposed to developing antimicrobial resistance than others.

scholarly journals Geography Shapes the Population Genomics ofSalmonella entericaDublin

2019 ◽  
Author(s):  
Gavin J. Fenske ◽  
Anil Thachil ◽  
Patrick L. McDonough ◽  
Amy Glaser ◽  
Joy Scaria
Keyword(s):  
Population Structure ◽  
Salmonella Enterica ◽  
Core Genome ◽  
Population Genomics ◽  
Negative Impact ◽  
Virulence Plasmid ◽  
Ancestral State ◽  
Secretion Systems ◽  
The Us ◽  
Human Infections

ABSTRACTSalmonella enterica serotypeDublin (S.Dublin) is a bovine-adapted serotype that can cause serious systemic infections in humans. Despite the increasing prevalence of human infections and the negative impact on agricultural processes, little is known about the population structure of the serotype. To this end, we compiled a manually curated dataset comprising of 880S.Dublin genomes. Core genome phylogeny and ancestral state reconstruction revealed that region-specific clades dominate the global population structure ofS.Dublin. Strains ofS.Dublin in the UK are genomically distinct from US, Brazilian and African strains. The geographical partitioning impacts the composition of the core genome as well as the ancillary genome. Antibiotic resistance genes are almost exclusively found in US genomes and is mediated by an IncA/C2 plasmid. Phage content and theS.Dublin virulence plasmid were strongly conserved in the serotype. Comparison ofS.Dublin to a closely related serotype,Salmonella enterica serotypeEnteritidis, revealed thatS.Dublin contains 82 serotype specific genes that are not found inS. Enteritidis. Said genes encode metabolic functions involved in the uptake and catabolism of carbohydrates and virulence genes associated with type VI secretion systems and fimbria assembly respectively.IMPORTANCES.Dublin is a bovine-adapted strain that can also cause human infections. TypicalS.Dublin human infections are characterized by invasion of tissue that ultimately traverses to the bloodstream causing life-threatening systemic cases. The preferred course of treatment for such infection is the administration of antibiotics. Thus, it is important to study the population structure of the serotype to monitor and identify which strains present the greatest threats to public health. Consequently, in this work, it was found thatS.Dublin genomic features are greatly influenced by the region in which they populate. Our analysis found that mostS.Dublin isolates from the US are distinct and have gained multidrug resistance through a new hybrid plasmid. Thus, it would be expected that infections in the US would respond less favorably to the first line of therapy and the region acts as the major source of a multidrug-resistantS.Dublin.

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