Evidence map›Paper›PMID 31941435›Full record

ArticleBMC bioinformatics2020

PRAP: Pan Resistome analysis pipeline.

Yichen He, Xiujuan Zhou, Ziyan Chen, Xiangyu Deng, Andrew Gehring, Hongyu Ou, Lida Zhang, Xianming Shi

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
0.9field-weighted citation impact, top 33% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed, 21 citations in OpenAlex.

  1. Review
  2. Pangenomics insights of enterococcus faecium human isolates and identification of novel therapeutic targets by in silico subtractive genomics.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026
    Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Review
  8. Insights into theAntibiotics (Basel, Switzerland) · 2022
    Article
  9. The Bacterial Urban Resistome: Recent Advances.Antibiotics (Basel, Switzerland) · 2022
    Review
  10. Avian strains of emerging pathogenFrontiers in microbiology · 2022
    Article
  11. Pan-Resistome Insights into the Multidrug Resistance ofAntibiotics (Basel, Switzerland) · 2021
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 3 institutions in 2 countries.

Yichen HeDepartment of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
Xiujuan ZhouDepartment of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
Ziyan ChenDepartment of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
Xiangyu DengCenter for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA, 30223, USA.
Andrew GehringUnited States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
Hongyu OuDepartment of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
Lida ZhangDepartment of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
Xianming ShiDepartment of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China. xmshi@sjtu.edu.cn.ORCID http://orcid.org/0000-0002-8929-4054
Shanghai Jiao Tong University · CNAgricultural Research Service · USUniversity of Georgia · US

Funding

Key Technologies Research and Development Program 2017YFC1601200National Natural Science Foundation of China 31601562
6 · The paper itself

Abstract

backgroundAntibiotic 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.

resultsWe 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.

conclusionsPRAP 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.

Indexed as

SoftwareAllelesChinaDrug Resistance, MicrobialSalmonella entericaWhole Genome SequencingIdentificationMachine learningPan-resistomeVisualization

Identifiers

PMID31941435
PMCPMC6964052
OpenAlexW3004081071

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.