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Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5], 12:i:-

(2018) PLOS ONE. 13(2).
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Abstract
Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. Besides the technological advances which have pushed the approach forward, the last years have been marked by considerable evolution of the whole genome sequencing data analysis methods. Prior to application of the technology as a routine epidemiological typing tool, however, reliable and efficient data analysis strategies need to be identified among the wide variety of the emerged methodologies. In this work, we have compared three existing SNP-based subtyping workflows using a benchmark dataset of 32 Salmonella enterica subsp. enterica serovar Typhimurium and serovar 1,4,[5], 12:i:- isolates including five isolates from a confirmed outbreak and three isolates obtained from the same patient at different time points. The analysis was carried out using the original (high-coverage) and a down-sampled (low-coverage) datasets and two different reference genomes. All three tested workflows, namely CSI Phylogeny-based workflow, CFSAN-based workflow and PHEnix-based workflow, were able to correctly group the confirmed outbreak isolates and isolates from the same patient with all combinations of reference genomes and datasets. However, the workflows differed strongly with respect to the SNP distances between isolates and sensitivity towards sequencing coverage, which could be linked to the specific data analysis strategies used therein. To demonstrate the effect of particular data analysis steps, several modifications of the existing workflows were also tested. This allowed us to propose data analysis schemes most suitable for routine SNP-based subtyping applied to S. Typhimurium and S. 1,4,[5], 12: i:-. Results presented in this study illustrate the importance of using correct data analysis strategies and to define benchmark and fine-tune parameters applied within routine data analysis pipelines to obtain optimal results.
Keywords
SEQUENCING DATA, LEGIONELLA-PNEUMOPHILA, SEROVAR ENTERITIDIS, ESCHERICHIA-COLI, GENOME SEQUENCE, TYPING METHODS, SURVEILLANCE, OUTBREAKS, SCHEME, RESISTANCE

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Citation

Please use this url to cite or link to this publication:

Chicago
Saltykova, Assia, Véronique Wuyts, Wesley Mattheus, Sophie Bertrand, Nancy HC Roosens, Kathleen Marchal, and Sigrid De Keersmaecker. 2018. “Comparison of SNP-based Subtyping Workflows for Bacterial Isolates Using WGS Data, Applied to Salmonella Enterica Serotype Typhimurium and Serotype 1,4,[5], 12:i:-.” Plos One 13 (2).
APA
Saltykova, A., Wuyts, V., Mattheus, W., Bertrand, S., Roosens, N. H., Marchal, K., & De Keersmaecker, S. (2018). Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5], 12:i:-. PLOS ONE, 13(2).
Vancouver
1.
Saltykova A, Wuyts V, Mattheus W, Bertrand S, Roosens NH, Marchal K, et al. Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5], 12:i:-. PLOS ONE. 2018;13(2).
MLA
Saltykova, Assia, Véronique Wuyts, Wesley Mattheus, et al. “Comparison of SNP-based Subtyping Workflows for Bacterial Isolates Using WGS Data, Applied to Salmonella Enterica Serotype Typhimurium and Serotype 1,4,[5], 12:i:-.” PLOS ONE 13.2 (2018): n. pag. Print.
@article{8551491,
  abstract     = {Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. Besides the technological advances which have pushed the approach forward, the last years have been marked by considerable evolution of the whole genome sequencing data analysis methods. Prior to application of the technology as a routine epidemiological typing tool, however, reliable and efficient data analysis strategies need to be identified among the wide variety of the emerged methodologies. In this work, we have compared three existing SNP-based subtyping workflows using a benchmark dataset of 32 Salmonella enterica subsp. enterica serovar Typhimurium and serovar 1,4,[5], 12:i:- isolates including five isolates from a confirmed outbreak and three isolates obtained from the same patient at different time points. The analysis was carried out using the original (high-coverage) and a down-sampled (low-coverage) datasets and two different reference genomes. All three tested workflows, namely CSI Phylogeny-based workflow, CFSAN-based workflow and PHEnix-based workflow, were able to correctly group the confirmed outbreak isolates and isolates from the same patient with all combinations of reference genomes and datasets. However, the workflows differed strongly with respect to the SNP distances between isolates and sensitivity towards sequencing coverage, which could be linked to the specific data analysis strategies used therein. To demonstrate the effect of particular data analysis steps, several modifications of the existing workflows were also tested. This allowed us to propose data analysis schemes most suitable for routine SNP-based subtyping applied to S. Typhimurium and S. 1,4,[5], 12: i:-. Results presented in this study illustrate the importance of using correct data analysis strategies and to define benchmark and fine-tune parameters applied within routine data analysis pipelines to obtain optimal results.},
  articleno    = {e0192504},
  author       = {Saltykova, Assia and Wuyts, Véronique and Mattheus, Wesley and Bertrand, Sophie and Roosens, Nancy HC and Marchal, Kathleen and De Keersmaecker, Sigrid},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  keywords     = {SEQUENCING DATA,LEGIONELLA-PNEUMOPHILA,SEROVAR ENTERITIDIS,ESCHERICHIA-COLI,GENOME SEQUENCE,TYPING METHODS,SURVEILLANCE,OUTBREAKS,SCHEME,RESISTANCE},
  language     = {eng},
  number       = {2},
  pages        = {23},
  title        = {Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5], 12:i:-},
  url          = {http://dx.doi.org/10.1371/journal.pone.0192504},
  volume       = {13},
  year         = {2018},
}

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