ArticleBMC genomics2012
Genomic variation in Salmonella enterica core genes for epidemiological typing.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 82 citations in OpenAlex.
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- Antimicrobial Activity and Identification of the Biosynthetic Gene Cluster of X-14952B FromFrontiers in microbiology · 2021Article
- Complete Genome Sequence ofMicroorganisms · 2020Article
- Concordance of SNP- and allele-based typing workflows in the context of a large-scale internationalMicrobial genomics · 2020Article
- Network Approach to Source Attribution ofFrontiers in microbiology · 2020Article
- Genomic characterisation of Salmonella enterica serovar Wangata isolates obtained from different sources reveals low genomic diversity.PloS one · 2020Article
- Pathogenic potential of non-typhoidal Salmonella serovars isolated from aquatic environments in Mexico.Genes & genomics · 2019Article
- Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica.BMC evolutionary biology · 2019Article
- Association of Salmonella virulence factor alleles with intestinal and invasive serovars.BMC genomics · 2019Article
- Proteotyping as alternate typing method to differentiate Campylobacter coli clades.Scientific reports · 2019Article
- A One Health investigation of Salmonella enterica serovar Wangata in north-eastern New South Wales, Australia, 2016-2017.Epidemiology and infection · 2019Article
- Cross-Border Transmission ofFrontiers in microbiology · 2019Article
- Microbial sequence typing in the genomic era.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTechnological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over time. The core genes--the genes that are conserved in all (or most) members of a genus or species--are potentially good candidates for investigating genomic variation in phylogeny and epidemiology.
resultsWe identify a set of 2,882 core genes clusters based on 73 publicly available Salmonella enterica genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. A consensus tree based on variation of core genes gives much better resolution than 16S and MLST; the pan-genome family tree is similar to the consensus tree, but with higher confidence. The core genes can be divided into two categories: a few highly variable genes and a larger set of conserved core genes, with low variance. For the most variable core genes, the variance in amino acid sequences is higher than for the corresponding nucleotide sequences, suggesting that there is a positive selection towards mutations leading to amino acid changes.
conclusionsGenomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. Identification of genes with different degrees of variation is important especially in trend analysis.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.