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Tools for AMR Detection

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Tools for AMR Detection Tools for AMR detection Pimlapas Leekitcharoenphon (Shinny) Researcher Research Group of Genomic Epidemiology EURL AMR / WHO CC AMR & Genomics National Food Institute, Technical University of Denmark [email protected] ShinnyPimlapas 13th EURL-AR Workshop 2019 26th April 2019 AMR tools • Accessibility – Web – Standalone • Approach – Assembly based – Read based • Type – Tool – Database • Status (Active and update) Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” Source Accessibility Approach Type Year Status Assembly-based and read Tool and Resfinder Web and standalone based tool database 2012 Active update regularly Tool and Archived last update in ARG-ANNOT Standalone Assembly-based tools database 2014 May 2018 Tool and Active last update in ResfinderFG Web Assembly-based tool database 2016 November 2016 RGI Web and/or standalone Assembly-based tools Tool 2015 Active ARGs-OAP (v2) Web and/or standalone Assembly-based tools Tool 2016 Active ARIBA Standalone Assembly-based tools Tool 2017 Active NCBI-AMRFinder Standalone Assembly-based tools Tool 2018 Active SRST2 Standalone Read-based tools Tool 2014 Active Web and/or standalone SEAR (archived) Read-based tools Tool 2015 Archived ShortBRED Standalone Read-based tools Tool 2015 Active PATRIC Web Read-based tools Tool 2016 Active SSTAR Standalone Read-based tools Tool 2016 Active KmerResistance Web Read-based tools Tool 2016 Active GROOT Standalone Read-based tools Tool 2018 Active DeepArgs Web Read-based tools Tool 2018 Active Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; Boolchandani M, D'Souza AW, Dantas G. Nat Rev Genet. 2019 ”Header & Footer” Source Accessibility Type Year Status CARD Web Database 2013 Active updated monthly Resfams Web Database 2015 Active last update in January 2015 ARDB Web Database 2009 Archived last updated in 2009 MEGARes Web Database 2016 Active; last update in December 2016 NDARO Web Database 2016 Active; started in 2016 Mustard Web Database 2018 Active; last update in November 2018 FARME database Web Database 2017 Active; last update in 2017 SARG (v2) Web Database Active Lahey list of β- lactamases Web Database 2015 Archived; last update in 2015 BLDB Web Database 2018 Active; last update in November 2018 TEMLacED active: last update in 2017; LacED Web Database SHVED archived: last update in April 2010 CBMAR Web Database Last update in September 2014 MUBII-TB-DB Web Database Last update in December 2013 u-CARE Web Database Last update in 2016 Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; Boolchandani M, D'Souza AW, Dantas G. Nat Rev Genet. 2019 ”Header & Footer” ARG-ANNOT – Antibiotic Resistance Gene-ANNOTation https://omictools.com/arg-annot-tool Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARG-ANNOT – Antibiotic Resistance Gene-ANNOTation • Bio-Edit software (Standalone) that allows the user to analyze sequences without web interface • Single file covering nucleotide sequences in FASTA format • Additional database/BLAST for point mutations from NCBI and ARDB databases Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARG-ANNOT – Antibiotic Resistance Gene-ANNOTation Copy results to Excel and remove redundancy Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARG-ANNOT – Antibiotic Resistance Gene-ANNOTation Manually remove genes detected from the same query region Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARG-ANNOT – Antibiotic Resistance Gene-ANNOTation Final list Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARG-ANNOT – Antibiotic Resistance Gene-ANNOTation Example from Mutation database Difficult to interpret based on output Is the mismatch the mutation or error Manual check of the sequence position Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARG-ANNOT – Antibiotic Resistance Gene-ANNOTation Pros Cons • Uses the same BLAST • Need to download the program program as NCBI to run it • It is possible to run without • Need to download database file internet/web interface – keep an eye for updates • Manuel removal of duplicates in results • Actually, ”just” a database file which utilize other programs to analyze data • Separat point-mutation database • Only one isolate per run Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARDB – Antibiotic Resistance Gene Database https://ardb.cbcb.umd.edu/ Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARDB – Antibiotic Resistance Gene Database Resistance Gene Search Database Resistance Gene BLAST Database Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARDB – Antibiotic Resistance Gene Database Resistance Gene Search Database - Example with Vancomycin Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARDB – Antibiotic Resistance Gene Database Resistance Gene BLAST Database – Example Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ARDB – Antibiotic Resistance Gene Database Pros Cons • Great database for • ARDB is not being maintained searching resistance genes at the moment due to funding • Only a search engine for resistance genes • ARDB BLAST searches does not run optimal for assembled genomes Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” CARD – The Comprehensive Antibiotic Resistance Database https://card.mcmaster.ca/ Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” CARD – Browse Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” CARD – Analyze option Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” CARD – Analyze option Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” CARD – Resistance Gene Identifier Tab delimited text format Report all hits – not only the best Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” CARD – Resistance Gene Identifier Pros Cons • Userfriendly interfase • Output all hits per ORF • Easy to save reports • No phonotypes included • Maintains the ARDB • Downloaded output is not real database user friendly • Only one isolate per run and the input file need to be a single FASTA file Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” Resfams http://www.dantaslab.org/resfams/ Only run command-line Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” Resfams Pros Cons ?? • Based on the ResFinder and • Only run standalone command ARG-ANNOT databases line • Only database/ no web-user interface with an oppotunity for sequence alignment Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” https://github.com/katholt/srst2 SSTAR – Sequence Search Tool for Antimicrobial Resistance Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” SSTAR – Sequence Search Tool for Antimicrobial Resistance Pros Cons • Identification of truncated • In order to run SSTAR you need genes because it only Java Runtime Environment analyses reads not (JRE) 6 or newer and assembled genomes standalone BLAST 2.2.29+, BLAST 2.2.30+ or BLAST 2.2.31+ installed on your system Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” Center for Genomic Epidemiology – ResFinder https://cge.cbs.dtu.dk/services/ResFinder/ !X Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ResFinder - Standalone https://bitbucket.org/genomicepidemiology/resfinder Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ResFinder - Standalone https://bitbucket.org/genomicepidemiology/resfinder Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ResFinder - Standalone https://bitbucket.org/genomicepidemiology/resfinder Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” https://bitbucket.org/genomicepidemiology/resfinder_db/src Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” https://bitbucket.org/genomicepidemiology/pointfinder_db/src Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” ResFinder • Accessibility Cons ?
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