Hybrid Genome Assemblies of 245 Avian and Broiler Barn Environment-Associated Escherichia coli Strains Isolated from Saskatchewan Broiler Farms

Sanderson, Haley; Nnajide, Chinenye R; McCarthy, Madeline C.; Singh, Reema; Rubin, Joseph E.; Dillon, Jo-Anne R.; White, Aaron P.

doi:10.1128/mra.00110-23

Cited by 4 publications

(2 citation statements)

References 24 publications

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“…The isolates in this analysis belong to a collection of E. coli strains collected from Saskatchewan broiler farms by Sanderson et al [28]. The hybrid assemblies, combining short and long reads, were obtained using Unicycler (v0.5.0) [31] in hybrid mode, and were used to define the ground truth for each sample.…”

Section: Resultsmentioning

confidence: 99%

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PlasEval: a framework for comparing and evaluating plasmid detection tools

Mane,

Sanderson,

White

et al. 2024

Preprint

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Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them. We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools - PlasBin-flow, HyAsP, gplas, and MOB-recon - on a data set of 54 E. coli bacterial genomes. PlasEval is freely available at https://github.com/acme92/PlasEval

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Section: Resultsmentioning

confidence: 99%

“…In this section, we use PlasEval to evaluate four plasmid binning tools on a set of 54 samples from a collection of Escherichia coli genomes sequenced using both short and long reads by Sanderson et al [28].…”

Section: Resultsmentioning

confidence: 99%

PlasEval: a framework for comparing and evaluating plasmid detection tools

Mane,

Sanderson,

White

et al. 2024

Preprint

Self Cite

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Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella

Sanderson,

White

2024

Methods in Molecular Biology

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Plaseval: a framework for comparing and evaluating plasmid detection tools

Mane,

Sanderson,

White

et al. 2024

BMC Bioinformatics

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Background Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them. Results We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools—PlasBin-flow, HyAsP, gplas, and MOB-recon—on a data set of 53 E. coli bacterial genomes. Conclusion Analysis of the results of plasmid binning methods using PlasEval shows that their behaviour varies significantly. PlasEval can be used to decide which specific plasmid binning method should be used for a specific dataset. The disagreement between different methods also suggests that the problem of plasmid binning on short-read contigs requires further research. We believe that PlasEval can prove to be an effective tool in this regard. PlasEval is publicly available at https://github.com/acme92/PlasEval

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Hybrid Genome Assemblies of 245 Avian and Broiler Barn Environment-Associated Escherichia coli Strains Isolated from Saskatchewan Broiler Farms

Cited by 4 publications

References 24 publications

PlasEval: a framework for comparing and evaluating plasmid detection tools

PlasEval: a framework for comparing and evaluating plasmid detection tools

Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella

Plaseval: a framework for comparing and evaluating plasmid detection tools

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