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PRAP: Pan Resistome analysis pipeline
- Source :
- BMC Bioinformatics, BMC Bioinformatics, Vol 21, Iss 1, Pp 1-8 (2020)
- Publication Year :
- 2020
- Publisher :
- BioMed Central, 2020.
-
Abstract
- Background Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species. Therefore, a pan-genome approach to analyzing resistomes is necessary for thoroughly characterizing patterns of ARGs distribution within particular pathogen populations. Software tools are readily available for either ARGs identification or pan-genome analysis, but few exist to combine the two functions. Results We developed Pan Resistome Analysis Pipeline (PRAP) for the rapid identification of antibiotic resistance genes from various formats of whole genome sequences based on the CARD or ResFinder databases. Detailed annotations were used to analyze pan-resistome features and characterize distributions of ARGs. The contribution of different alleles to antibiotic resistance was predicted by a random forest classifier. Results of analysis were presented in browsable files along with a variety of visualization options. We demonstrated the performance of PRAP by analyzing the genomes of 26 Salmonella enterica isolates from Shanghai, China. Conclusions PRAP was effective for identifying ARGs and visualizing pan-resistome features, therefore facilitating pan-genomic investigation of ARGs. This tool has the ability to further excavate potential relationships between antibiotic resistance genes and their phenotypic traits.
- Subjects :
- Identification
China
Pan-resistome
Computational biology
Biology
lcsh:Computer applications to medicine. Medical informatics
Biochemistry
Genome
03 medical and health sciences
Antibiotic resistance
Structural Biology
Machine learning
Molecular Biology
lcsh:QH301-705.5
Alleles
030304 developmental biology
Visualization
0303 health sciences
Whole Genome Sequencing
030306 microbiology
Applied Mathematics
Salmonella enterica
Drug Resistance, Microbial
Phenotypic trait
Pipeline (software)
Computer Science Applications
Resistome
lcsh:Biology (General)
Horizontal gene transfer
lcsh:R858-859.7
Identification (biology)
DNA microarray
Software
Subjects
Details
- Language :
- English
- ISSN :
- 14712105
- Volume :
- 21
- Database :
- OpenAIRE
- Journal :
- BMC Bioinformatics
- Accession number :
- edsair.doi.dedup.....925bb3d56f094caafaef4b32d59222ed