Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes

Collins, Caitlin; Didelot, Xavier

doi:10.1007/978-1-4939-6673-8_8

Cited by 5 publications

(4 citation statements)

References 133 publications

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“…STEC O157:H7 has an extensive prophage repertoire comprising up to 15 % of the genome [ 27 ] with such loci known to be subject to intra- and inter-strain recombination events [ 28 ]. As such, every effort must be taken to detect and mask these regions of relatedness during the analysis, as the incorporation of exogenous DNA may distort interpretations of genetic similarity [ 29 ].…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic structure of Shiga toxin-producing Escherichia coli O157:H7 from sub-lineage to SNPs

et al. 2021

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Sequence similarity of pathogen genomes can infer the relatedness between isolates as the fewer genetic differences identified between pairs of isolates, the less time since divergence from a common ancestor. Clustering based on hierarchical single linkage clustering of pairwise SNP distances has been employed to detect and investigate outbreaks. Here, we evaluated the evidence-base for the interpretation of phylogenetic clusters of Shiga toxin-producing Escherichia coli (STEC) O157:H7. Whole genome sequences of 1193 isolates of STEC O157:H7 submitted to Public Health England between July 2015 and December 2016 were mapped to the Sakai reference strain. Hierarchical single linkage clustering was performed on the pairwise SNP difference between all isolates at descending distance thresholds. Cases with known epidemiological links fell within 5-SNP single linkage clusters. Five-SNP single linkage community clusters where an epidemiological link was not identified were more likely to be temporally and/or geographically related than sporadic cases. Ten-SNP single linkage clusters occurred infrequently and were challenging to investigate as cases were few, and temporally and/or geographically dispersed. A single linkage cluster threshold of 5-SNPs has utility for the detection of outbreaks linked to both persistent and point sources. Deeper phylogenetic analysis revealed that the distinction between domestic UK and imported isolates could be inferred at the sub-lineage level. Cases associated with domestically acquired infection that fall within clusters that are predominantly travel associated are likely to be caused by contaminated imported food.

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Section: Discussionmentioning

confidence: 99%

Phylogenetic structure of Shiga toxin-producing Escherichia coli O157:H7 from sub-lineage to SNPs

et al. 2021

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“…To infer the evolutionary relationship of the isolates within a data set, therefore, a phylogeny must be constructed. For more detailed and technical information on reconstructing bacterial phylogenies from WGS data, the reader is referred to two in-depth reviews on this subject (Collins and Xavier, 2017; Patané et al, 2018).…”

Section: Banding Pattern-based and Sequencing-based Characterization mentioning

confidence: 99%

Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella

et al. 2019

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The food industry is facing a major transition regarding methods for confirmation, characterization, and subtyping of Salmonella . Whole-genome sequencing (WGS) is rapidly becoming both the method of choice and the gold standard for Salmonella subtyping; however, routine use of WGS by the food industry is often not feasible due to cost constraints or the need for rapid results. To facilitate selection of subtyping methods by the food industry, we present: (i) a comparison between classical serotyping and selected widely used molecular-based subtyping methods including pulsed-field gel electrophoresis, multilocus sequence typing, and WGS (including WGS-based serovar prediction) and (ii) a scoring system to evaluate and compare Salmonella subtyping assays. This literature-based assessment supports the superior discriminatory power of WGS for source tracking and root cause elimination in food safety incident; however, circumstances in which use of other subtyping methods may be warranted were also identified. This review provides practical guidance for the food industry and presents a starting point for further comparative evaluation of Salmonella characterization and subtyping methods.

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“…N. meningitidis has a high recombination rate, though recombination in N. meningitidis is not so rampant as to entirely obscure the clonal genealogy, as would be the case for example in Helicobacter pylori [ 56 ]. Because treeWAS accounts explicitly for the confounding effects of recombination, our approach was appropriate for this context, provided recombination-aware phylogenetic methods were used [ 57 ]. treeWAS completed the analysis of the accessory genome in 23 seconds and analysed the SNPs matrix in 24 minutes.…”

Section: Resultsmentioning

confidence: 99%

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

2018

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Genome-Wide Association Studies (GWAS) in microbial organisms have the potential to vastly improve the way we understand, manage, and treat infectious diseases. Yet, microbial GWAS methods established thus far remain insufficiently able to capitalise on the growing wealth of bacterial and viral genetic sequence data. Facing clonal population structure and homologous recombination, existing GWAS methods struggle to achieve both the precision necessary to reject spurious findings and the power required to detect associations in microbes. In this paper, we introduce a novel phylogenetic approach that has been tailor-made for microbial GWAS, which is applicable to organisms ranging from purely clonal to frequently recombining, and to both binary and continuous phenotypes. Our approach is robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Thorough testing via application to simulated data provides strong support for the power and specificity of our approach and demonstrates the advantages offered over alternative cluster-based and dimension-reduction methods. Two applications to Neisseria meningitidis illustrate the versatility and potential of our method, confirming previously-identified penicillin resistance loci and resulting in the identification of both well-characterised and novel drivers of invasive disease. Our method is implemented as an open-source R package called treeWAS which is freely available at https://github.com/caitiecollins/treeWAS.

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Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes

Cited by 5 publications

References 133 publications

Phylogenetic structure of Shiga toxin-producing Escherichia coli O157:H7 from sub-lineage to SNPs

Phylogenetic structure of Shiga toxin-producing Escherichia coli O157:H7 from sub-lineage to SNPs

Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

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