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 – Resistance -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 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

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

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 ? – Web • Standalone – unix command line – Standalone based • Batch analysis (right now) can be done only by command line • 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” Future of AMR tool

• Machine learning • Deep learning

Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer” Thank you for your attention

Pimlapas Leekitcharoenphon (Shinny) Research group for Genomic Epidemiology WHO Collaborating Centre for Antimicrobial Resistance in Food borne Pathogens European Union Reference Laboratory for Antimicrobial Resistance

National Food Institute, Technical University of Denmark

[email protected]

Add Presentation Title DTU Food, Technical University of Denmark in Footer via ”Insert”; ”Header & Footer”