Construction Of DANMEL:A Manually Curated Reference Database For Analyzing Mobile Genetic Elements Associated With Bacterial Drug Resistance

Antibiotics represent one of the greatest medical discoveries of the 20^th century with their revolutionary advantages in the treatment of clinical infections.However,abuse of antibiotics has led increasing drug resistance in bacteria globally,creating a new challenge threatening human health and national development.Bacterial resistance comes from the expression of resistance genes in bacteria.Mobile genetic elements（MGEs）such as integrons,transposons and plasmids,as carriers for the spread of bacterial resistance,play a vital role in its spread.Therefore,detailed annotation of the structure,function,and evolution of MGEs is key to finding a practical solution for bacterial resistance transmission.We collected the majority of representative reference or prototype MGEs associated with bacterial drug resistance discovered to date,covering nearly all major categories（integrons,transposons,plasmids,putative resistance units,and complex multidrug-resistance（MDR）regions）.Using sequence alignment,gene prediction,and phylogenetic analysis,bioinformatics and structural genomics analysis was carried out on MGEs,to generate a detailed and accurate analysis of MGE internal structure.From this,we designed and constructed a web-based reference database DANMEL（a manually curated reference database for analyzing MGEs associated with bacterial drug resistance,http://39.100.87.11/danmel＿V1.0）that provides users with reference annotation information of MGEs associated with bacterial drug resistance on a web-based platform.We also developed and constructed the software,VPA（a software for visualization of plasmid gene annotation）,to provide users with automated drawing support.MGE annotationBased on MGE classification,this study collected 377 representative reference or prototype MGEs associated with bacterial drug resistance,including integrons,transposons,plasmids,putative resistance units,complex MDR regions,and their corresponding subtypes.Each MGE in DANMEL was annotated in detail and analyzed through a series of methods,such as literature research,sequence alignment,and bioinformatics analysis.Representative integrons（n = 45）were divided into classes 1（n = 38）,2（n = 5）and 3（n = 2）,according to their integrase（int I）genes.Representative transposons（n = 228）,belonged to eight major categories: IS elements（also called simple transposons;n = 59）,IS-based transposition units（n = 16）,composite transposons（n = 43）,miniature inverted-repeat transposable element（MITE）-flanking transposition unit（n = 1）,MITE-like transposition unit（n = 1）,unit transposons（n = 68）,integrative and conjugative elements（ICEs,also called conjugative transposons;n = 15）,and integrative and mobilizable elements（IMEs,also called mobilizable transposons;n = 25）.Representative plasmids（n = 53）,belonged to 25 incompatibility（Inc）groups.In addition,we collected 44 putative resistance units and seven representative complex MDR regions.DANMEL databaseThe DANMEL web-based database platform has two main modules:REMED（reference mobile element database）and MEAP（mobile element annotation pipeline）.REMED provides browsing and file download functions of MGE annotation information according to MGE classification.MEAP guides users in completion of the annotation analysis of a newly sequenced MGE.In addition,DANMEL provides a SEARCH module that can be used to search MGEs in DANMEL using a basic search based on keywords or a complex search based on string combinations.DANMEL also provides a BLAST module that can be used to compare the new sequence with the existing MGEs in the database to quickly obtain the relevant reference MGE annotation information.Visualization softwareTo better display the internal structure of MGEs,we designed an automated software called VPA V1.0.The input files for VPA are.color files,.desc files,.frame files,and.fasta files,which are used to set the coloring information,structure and function information,shading information of backbone and accessory regions,and plasmid sequence information,respectively.Four processing modules are provided:file module,color module,graphics generation module,and help module.VPA provides researchers with efficient drawing support,allowing users to generate personalized plasmid gene structure organization without about the drawing process.ConclusionTo the best of our knowledge,DANMEL is the first specialized reference database for annotating and genetically dissecting MGEs associated with bacterial drug resistance.Its REMED module contains 377 representative MGEs belonging to five major categories with accurate and detailed re-annotated information.The MEAP module provides a step-by-step MGE annotation pipeline that will allow researchers to analyze their own sequenced MGEs.The manually curated reference database of DANMEL for MGEs associated with bacterial drug resistance,will facilitate understanding and analysis of MGEs by researchers.When encountering an unknown drug-resistant bacteria,users can browse the DANMEL database to obtain data on MGEs associated with bacterial drug resistance and complete the analysis and tracking of unknown sequence data through sequence comparison and other functions.DANMEL allows in-depth analysis of MGEs that may be carried into unknown bacteria,providing a theoretical basis for the timely formulation of defense strategies.