PRAP: Pan Resistome analysis pipeline

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.

Pan-Resistome Insights into the Multidrug Resistance of Acinetobacter baumannii

“…A pan-resistome analysis contains analogous divisions applied to a pan-genomic analysis, but focused on microbial resistance factors [ 30 ]. Considering a similarity criterion greater than 70% and an E-value < 5 × 10 −6 , all the studied strains present a pan-resistome of 171 genes, and within that, a core resistome constituted of 9 genes is shown in Table 1 [ 11 ].…”

Reads2Resistome: An adaptable and high-throughput whole-genome sequencing pipeline for bacterial resistome characterization

“…Pipelines such as bacass from nf-core [25] provide genome assembly under short, long and hybrid approaches but do not offer resistome annotation. PRAP [26] and sraX [27] offer robust resistome analysis but do not provide genome assembly within the pipeline. Therefore, Reads2Resistome is the unique in providing a robust pipeline for genome assembly, genome annotation and resistome identification.…”

Combined Use of Niraparib Enhanced the Inhibitory Effect of Anti-GD2 Antibody on Osteosarcoma Cells

“…The preclinical studies indicate that OS cells are sensitive to PARP inhibitors in vitro [33][34][35] , but the e cacy of PARP inhibitors as monotherapy in OS is limited, highlighting the need for combination therapy. PARP inhibitors enhance DNA damage-mediated cytotoxicity caused by topoisomerase I poisons, DNA methylators, or radiation, which is relevant to the role of PARP in repairing DNA damage caused by these cytotoxic therapies [36][37][38][39] .…”