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.

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 Structure of Salmonella enterica Serovar 4,[5],12:b:− Strains and Likely Sources of Human Infection

2013 ◽  
Vol 79 (17) ◽  
pp. 5121-5129 ◽  
Author(s):  
Anne Toboldt ◽  
Erhard Tietze ◽  
Reiner Helmuth ◽  
Ernst Junker ◽  
Angelika Fruth ◽  
...  
Keyword(s):  
Population Structure ◽  
Salmonella Enterica ◽  
Human Infection ◽  
Second Phase ◽  
Gene Repertoire ◽  
Fish Food ◽  
Content Type ◽  
Potential Sources ◽  
Human Infections ◽  
Sequence Types

ABSTRACTSalmonella entericaserovar 4,[5],12:b:− is a monophasic serovar not able to express the second-phase flagellar antigen (H2 antigen). In Germany, the serovar is occasionally isolated from poultry, reptiles, fish, food, and humans. In this study, a selection of 67 epidemiologically unrelatedSalmonella entericaserovar 4,[5],12:b:− strains isolated in Germany between 2000 and 2011 from the environment, animal, food, and humans was investigated by phenotypic and genotypic methods to better understand the population structure and to identify potential sources of human infections. Strains of this monophasic serovar were highly diverse. Within the 67 strains analyzed, we identified 52 different pulsed-field gel electrophoresis XbaI profiles, 12 different multilocus sequence types (STs), and 18 different pathogenicity array types. The relatedness of strains based on the pathogenicity gene repertoire (102 markers tested) was in good agreement with grouping by MLST.S. entericaserovar 4,[5],12:b:− is distributed across multiple unrelated eBurst groups and consequently is highly polyphyletic. Two sequence types (ST88 and ST127) were linked toS. entericaserovar Paratyphi B (d-tartrate positive), two single-locus variants of ST1583 were linked toS. entericaserovar Abony, and one sequence type (ST1484) was associated withS. entericaserovar Mygdal, a recently defined, new serovar. From the characterization of clinical isolates and those of nonhuman origin, it can be concluded that the potential sources of sporadic human infections withS. entericaserovar 4,[5],12:b:− most likely are mushrooms, shellfish/fish, and poultry.

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.

Transcriptional regulation of Salmonella enterica virulence plasmid genes in cultured macrophages

1993 ◽  
Vol 10 (1) ◽  
pp. 45-56 ◽  
Author(s):  
Mikael Rhen ◽  
Petri Riikonen ◽  
Suvi Taira
Keyword(s):  
Transcriptional Regulation ◽  
Salmonella Enterica ◽  
Virulence Plasmid ◽  
Plasmid Genes

Key Insights and Research Prospects at the Dawn of the Population Genomics Era for Verticillium dahliae

2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Jie-Yin Chen ◽  
Steven J. Klosterman ◽  
Xiao-Ping Hu ◽  
Xiao-Feng Dai ◽  
Krishna V. Subbarao
Keyword(s):  
Population Structure ◽  
Verticillium Dahliae ◽  
Plant Pathogens ◽  
Population Genomics ◽  
Population Divergence ◽  
Annual Review ◽  
Publication Date ◽  
Disease Symptoms ◽  
Historical Perspectives ◽  
Characteristic Features

The genomics era has ushered in exciting possibilities to examine the genetic bases that undergird the characteristic features of Verticillium dahliae and other plant pathogens. In this review, we provide historical perspectives on some of the salient biological characteristics of V. dahliae, including its morphology, microsclerotia formation, host range, disease symptoms, vascular niche, reproduction, and population structure. The kaleidoscopic population structure of this pathogen is summarized, including different races of the pathogen, defoliating and nondefoliating phenotypes, vegetative compatibility groupings, and clonal populations. Where possible, we place the characteristic differences in the context of comparative and functional genomics analyses that have offered insights into population divergence within V. dahliae and the related species. Current challenges are highlighted along with some suggested future population genomics studies that will contribute to advancing our understanding of the population divergence in V. dahliae. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Optimization of the Hybrid Ship Transport Factor through Retrofitted Wave Cancelling Side-Hull Expansions and Bow Bulb

2015 ◽  
Author(s):  
Manivannan Kandasamy ◽  
Ping C. Wu ◽  
Scott Bartlett ◽  
Loc Nguyen ◽  
Frederick Stern
Keyword(s):  
High Performance ◽  
Negative Impact ◽  
Fiscal Year ◽  
Hull Form ◽  
Transport Factor ◽  
Resistance Reduction ◽  
The Us ◽  
Us Navy ◽  
Speed Range ◽  
Design Speed

The US Navy is currently considering the introduction of a Flight III variant beginning with DDG-123 in Fiscal Year 2016. The new design incorporates a new combat system and associated power and cooling upgrades. The overall system improvements increase the payload of the ship and the resulting increased displacement has a negative impact on the service life allowance for range, fuel consumption and sea-keeping characteristics. The present objective is to increase the hull displacement without resistance and sea-keeping penalty and with minimal modifications to the baseline DTMB-5415 design (open literature surrogate of the existing DDG-51 hull form) by using retrofitted blisters in the form of side hull expansions and a bow-bulb. The investigation makes use of high-performance CFD computing for analysis of wave cancellation mechanisms. A candidate modified 5415 design with both blisters and bow bulb shows a resistance reduction of ~11% w.r.t.the baseline 5415 in the design speed range of 15-19 knots, even though the displacement is increased by 8%, such that the transport factor is increased by 19%.

scholarly journals Diversified sources for human infections by Salmonella enterica serovar newport

2019 ◽  
Vol 66 (2) ◽  
pp. 1044-1048 ◽  
Author(s):  
Hang Pan ◽  
Xin Zhou ◽  
Wenqin Chai ◽  
Narayan Paudyal ◽  
Shuning Li ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Human Infections

scholarly journals Shigella flexneri Phagosomal Escape Is Independent of Invasion

2007 ◽  
Vol 75 (10) ◽  
pp. 4826-4830 ◽  
Author(s):  
Susanne Paetzold ◽  
Sebastian Lourido ◽  
Bärbel Raupach ◽  
Arturo Zychlinsky
Keyword(s):  
Cell Invasion ◽  
Type Iii Secretion ◽  
Shigella Flexneri ◽  
Mucosal Inflammation ◽  
Virulence Plasmid ◽  
Secretion Systems ◽  
Type Iii Secretion Systems ◽  
Macrophage Cytotoxicity ◽  
Serovar Typhimurium ◽  
Epithelial Cell Invasion

ABSTRACT Infections with Salmonella enterica serovar Typhimurium and Shigella flexneri result in mucosal inflammation in response to epithelial cell invasion and macrophage cytotoxicity. These processes are mediated by type III secretion systems encoded in homologous virulence loci in the two species, namely, Salmonella pathogenicity island 1 (SPI-1), carried in the genome, and the Shigella entry region (SER), carried in a large virulence plasmid. Here we show that SPI-1 can functionally complement a deletion of SER in S. flexneri, restoring invasion of epithelial cells, macrophage cytotoxicity, and phagosomal escape. Furthermore, S. flexneri phagosomal escape requires the SER and another gene(s) carried on the large virulence plasmid. We demonstrate that the processes of invasion and phagosomal escape can be uncoupled in S. flexneri.

scholarly journals Evaluation of the live vaccine efficacy of virulence plasmid-cured, and phoP- or aroA-deficient Salmonella enterica serovar Typhimurium in mice

2015 ◽  
Vol 77 (2) ◽  
pp. 181-186 ◽  
Author(s):  
Hidenori MATSUI ◽  
Yasunori ISSHIKI ◽  
Masahiro EGUCHI ◽  
Yohsuke OGAWA ◽  
Yoshihiro SHIMOJI
Keyword(s):  
Vaccine Efficacy ◽  
Salmonella Enterica ◽  
Live Vaccine ◽  
Virulence Plasmid ◽  
Serovar Typhimurium
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