scholarly journals The Continuing Evolution of Community-Associated MRSA ST93-IV in Australia

2020 ◽  
Author(s):  
Stanley Pang ◽  
Denise A Daley ◽  
Shafi Sahibzada ◽  
Shakeel Mowlaboccus ◽  
Marc Stegger ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genetic Traits ◽  
Genome Wide ◽  
A Genome ◽  
High Prevalence ◽  
Northern Regions ◽  
Australian Community ◽  
Gwas Approach

Abstract BackgroundThe global emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has seen the dominance of specific clones in different regions around the world with the PVL-positive ST93-IV as the predominant CA-MRSA clone in Australia. In this study we applied a genome-wide association study (GWAS) approach on a collection of Australian ST93-IV MRSA genomes to identify genetic traits that may have assisted the ongoing transmission of ST93-IV in Australia. We also compared the genomes of ST93-IV bacteraemia and non-bacteraemia isolates to identify potential virulence factors associated with bacteraemia.ResultsBased on single nucleotide polymorphism phylogenetics we identified two distinct ST93-IV clades circulating concurrently in Australia. One of the clades contained isolates primarily isolated in the northern regions of Australia whilst isolates in the second clade were distributed across the country. Analyses of the ST93-IV genome plasticity over a 15-year period (2002-2017) revealed an observed gain in accessory genes amongst the clone’s population. The GWAS analysis on the bacteraemia identified two genes that have also previously been associated to this kind of infection. ConclusionsThe emergence of a ST93-IV clade containing additional virulence genes may explain the high prevalence of ST93-IV infections amongst the indigenous population living in the northern regions of Australia. In summary, this study has shown ST93-IV is evolving with multiple additional genes possibly contributing to its dominance in the Australian community.

scholarly journals The continuing evolution of community-associated MRSA ST93-IV in Australia

2020 ◽  
Author(s):  
Stanley Pang ◽  
Denise A Daley ◽  
Shafi Sahibzada ◽  
Shakeel Mowlaboccus ◽  
Marc Stegger ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genetic Traits ◽  
Genome Wide ◽  
A Genome ◽  
High Prevalence ◽  
Northern Regions ◽  
Australian Community ◽  
Gwas Approach

Abstract Background The global emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has seen the dominance of specific clones in different regions around the world with the PVL-positive ST93-IV as the predominant CA-MRSA clone in Australia. In this study we applied a genome-wide association study (GWAS) approach on a collection of Australian ST93-IV MRSA genomes to identify genetic traits that may have assisted the ongoing transmission of ST93-IV in Australia. We also compared the genomes of ST93-IV bacteraemia and non-bacteraemia isolates to identify potential virulence factors associated with bacteraemia.Results Based on single nucleotide polymorphism phylogenetics we identified two distinct ST93-IV clades circulating concurrently in Australia. One of the clades contained isolates primarily isolated in the northern regions of Australia whilst isolates in the second clade were distributed across the country. Analyses of the ST93-IV genome plasticity over a 15-year period (2002-2017) revealed an observed gain in accessory genes amongst the clone’s population. The GWAS analysis on the bacteraemia isolates identified two genes that have also previously been associated to this kind of infection. Conclusions The emergence of a ST93-IV clade containing additional virulence genes may explain the high prevalence of ST93-IV infections amongst the indigenous population living in the northern regions of Australia. In summary, this study has shown ST93-IV is evolving with multiple additional genes possibly contributing to its dominance in the Australian community.

Common susceptibility alleles are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach

Blood ◽  
2009 ◽  
Vol 113 (21) ◽  
pp. 5298-5303 ◽  
Author(s):  
David-Alexandre Trégouët ◽  
Simon Heath ◽  
Noémie Saut ◽  
Christine Biron-Andreani ◽  
Jean-François Schved ◽  
...  
Keyword(s):  
Complex Disease ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Increased Risk ◽  
Fv Leiden ◽  
Gwas Approach

Abstract Venous thromboembolism (VTE) is a complex disease that has a major genetic component of risk. To identify genetic factors that may modify the risk of VTE, we conducted a genome-wide association study by analyzing approximately 317 000 single nucleotide polymorphisms (SNPs) in 453 VTE cases and 1327 controls. Only 3 SNPs located in the FV and ABO blood group genes were found associated with VTE at a genome-wide significant level of 1.7 × 10−7. Detailed analysis of these SNPs in additional cohorts of more than 1700 cases and 1400 controls revealed that the association observed at the FV locus was the result of the increased risk mediated by the FV Leiden mutation, whereas O and A2 blood groups were found to be at lower risk for VTE. Apart from the FV and ABO loci, no other locus was found strongly associated with VTE. However, using this large cohort of subjects, we were able to replicate the mild effects of 2 nonsynonymous SNPs, rs1613662 in GP6 and rs13146272 in CYP4V2, recently suspected to be associated with VTE.

scholarly journals SNP Alleles Associated With Low Bolting Tendency in Sugar Beet

2021 ◽  
Vol 12 ◽  
Author(s):  
Samathmika Ravi ◽  
Giovanni Campagna ◽  
Maria Cristina Della Lucia ◽  
Chiara Broccanello ◽  
Giovanni Bertoldo ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Allelic Status ◽  
The One ◽  
Detection Technologies

The identification of efficient molecular markers related to low bolting tendency is a priority in sugar beet (Beta vulgaris L.) breeding. This study aimed to identify SNP markers associated with low bolting tendency by establishing a genome-wide association study. An elaborate 3-year field trial comprising 13 sugar beet lines identified L14 as the one exhibiting the lowest bolting tendency along with an increased survival rate after autumnal sowing. For SNP discovery following phenotyping, contrasting phenotypes of 24 non-bolting and 15 bolting plants of the L14 line were sequenced by restriction site-associated DNA sequencing (RAD-seq). An association model was established with a set of 10,924 RAD-based single nucleotide polymorphism (SNP) markers. The allelic status of the most significantly associated SNPs ranked based on their differential allelic status between contrasting phenotypes (p < 0.01) was confirmed on three different validation datasets comprising diverse sugar beet lines and varieties adopting a range of SNP detection technologies. This study has led to the identification of SNP_36780842 and SNP_48607347 linked to low bolting tendency and can be used for marker-assisted breeding and selection in sugar beet.

scholarly journals GMStool: GWAS-based marker selection tool for genomic prediction from genomic data

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Seongmun Jeong ◽  
Jae-Yoon Kim ◽  
Namshin Kim
Keyword(s):  
Genomic Prediction ◽  
Genome Wide Association Study ◽  
Genomic Data ◽  
High Accuracy ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Machine Learning Methods ◽  
Marker Selection ◽  
Genome Wide ◽  
A Genome

AbstractThe increased accessibility to genomic data in recent years has laid the foundation for studies to predict various phenotypes of organisms based on the genome. Genomic prediction collectively refers to these studies, and it estimates an individual’s phenotypes mainly using single nucleotide polymorphism markers. Typically, the accuracy of these genomic prediction studies is highly dependent on the markers used; however, in practice, choosing optimal markers with high accuracy for the phenotype to be used is a challenging task. Therefore, we present a new tool called GMStool for selecting optimal marker sets and predicting quantitative phenotypes. The GMStool is based on a genome-wide association study (GWAS) and heuristically searches for optimal markers using statistical and machine-learning methods. The GMStool performs the genomic prediction using statistical and machine/deep-learning models and presents the best prediction model with the optimal marker-set. For the evaluation, the GMStool was tested on real datasets with four phenotypes. The prediction results showed higher performance than using the entire markers or the GWAS-top markers, which have been used frequently in prediction studies. Although the GMStool has several limitations, it is expected to contribute to various studies for predicting quantitative phenotypes. The GMStool written in R is available at www.github.com/JaeYoonKim72/GMStool.

scholarly journals Genome-wide association studies reveal candidate genes associated to bacteraemia caused by ST93-IV CA-MRSA

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Stanley Pang ◽  
Denise A Daley ◽  
Shafi Sahibzada ◽  
Shakeel Mowlaboccus ◽  
Marc Stegger ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Virulence Genes ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genetic Traits ◽  
Genome Wide ◽  
A Genome ◽  
Northern Regions

Abstract Background The global emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has seen the dominance of specific clones in different regions around the world with the PVL-positive ST93-IV as the predominant CA-MRSA clone in Australia. In this study we applied a genome-wide association study (GWAS) approach on a collection of Australian ST93-IV MRSA genomes to screen for genetic traits that might have assisted the ongoing transmission of ST93-IV in Australia. We also compared the genomes of ST93-IV bacteraemia and non-bacteraemia isolates to search for potential virulence genes associated with bacteraemia. Results Based on single nucleotide polymorphism phylogenetics we revealed two distinct ST93-IV clades circulating concurrently in Australia. One of the clades contained isolates primarily isolated in the northern regions of Australia whilst isolates in the second clade were distributed across the country. Analyses of the ST93-IV genome plasticity over a 15-year period (2002–2017) revealed an observed gain in accessory genes amongst the clone’s population. GWAS analysis on the bacteraemia isolates identified two gene candidates that have previously been associated to this kind of infection. Conclusions Although this hypothesis was not tested here, it is possible that the emergence of a ST93-IV clade containing additional virulence genes might be related to the high prevalence of ST93-IV infections amongst the indigenous population living in the northern regions of Australia. More importantly, our data also demonstrated that GWAS can reveal candidate genes for further investigations on the pathogenesis and evolution of MRSA strains within a same lineage.

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