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. 2019 Apr 27;20(1):215.
doi: 10.1186/s12859-019-2806-5.

CSESA: an R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR

Lang Yang  1   2 , Xia Zhang  3 , Yuqi Liu  1   2 , Hao Li  1 , Shaofu Qiu  2 , Peng Li  4 , Hongbin Song  5
Affiliations

CSESA: an R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR

Lang Yang et al. BMC Bioinformatics. .

Abstract

Background: Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Immunological serotyping is the most commonly used typing method to characterize S. enterica isolates, but is time-consuming and requires expensive reagents. Here, we developed an R package CSESA (CRISPR-based Salmonella enterica Serotype Analyzer) to predict the serotype based on the CRISPR loci of S. enterica.

Results: CSESA has implemented the CRISPR typing method CLSPT and extended its coverage on diverse S. enterica serotypes. This package takes CRISPR sequences or the genome sequences as input and provides users with the predicted serotypes. CSESA has shown excellent performance with currently available sequences of S. enterica.

Conclusions: CSESA is a convenient and useful tool for the prediction of S. enterica serotypes. The application of CSESA package can improve the efficiency of serotyping for S. enterica and reduce the burden of manpower resources. CSESA is freely available from CRAN at https://cran.r-project.org/web/packages/CSESA/ .

Keywords: CSESA; S. enterica; Serotyping.

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The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
The flow diagram of CSESA package
Fig. 2
Fig. 2
The serotype composition among three types of CSESA output with current 5335 S. enterica genome sequences from NCBI. a The distribution of three types of output from CSESA. b, c and d The serotype composition of matched results, mismatched results and no prediction, respectively
Fig. 3
Fig. 3
The distribution of output among common S. enterica serotypes from (a) CSESA and (b) CCT. The blue, yellow and red columns represent results of matched serotypes, mismatched serotypes and no prediction, respectively. The left diagram in each subfigure shows the number of results among common S. enterica serotypes, while the right diagram shows their proportions
See this image and copyright information in PMC

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