ResFinder 4.0: towards in silico antibiograms
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1 ResFinder 4.0: towards in silico antibiograms Valeria Bortolaia, DVM, PhD Research group for Genomic Epidemiology National Food Institute Technical University of Denmark
2 The path to WGS-based AMR prediction Why should we use WGS to infer AMR phenotypes? What is ResFinder? What s new in ResFinder 4.0? Are in silico antibiograms the future? 2 DTU Food, Technical University of Denmark
3 AMR surveillance data serve epidemiological purposes Comparability and accessibility: across animal species across time across countries 3 DTU Food, Technical University of Denmark
4 WGS-based surveillance data to define AMR epidemiology across species Species AMR phenotype 317 ESBL/AmpCproducing E. coli from human bloodstream infections 48 and 52 ESBL/AmpC-producing E. coli from broilers and broiler meat, respectively WGS data 1. The same combinations of ESBL/pAmpC genes and STs were detected in E. coli of human and animal origin on 5 occasions (21 isolates); 2. The number of SNPs supported possible link on 1 occasion (6 isolates) DANMAP DTU Food, Technical University of Denmark
5 WGS-based surveillance data for rapid AMR epidemiology AMR phenotype DANMAP 2008: 10 COL R E. coli DANMAP 2009: 8 COL R E. coli WGS data Specific subsets of DANMAP isolates are WGS since Nov. 15: mcr-1 published Time DANMAP 2010: 11 COL R E. coli DANMAP 2011: 6 COL R E. coli DANMAP 2012: 5 COL R E. coli DANMAP 2013: 1 COL R E. coli DANMAP 2014: 1 COL R E. coli 24 Nov. 15: mcr-1 added to ResFinder 10 Dec. 15, DK: mcr-1 in 1 E. coli from human bloodstream infection (2015) and 5 E. coli from imported broiler meat (2012, 2013, 2014)(Eurosurveillance, 2015) (all from imported broiler meat) Unpublished data 18: all DANMAP COL R E. coli harbour mcr-1 5 DTU Food, Technical University of Denmark
6 ResFinder in a nutshell ResFinder is a database of AMR genes: de facto AMR genes (e.g. blactx-m, mcr, etc.) chromosomal mutations leading to resistance (e.g. ampc promoter mutations, gyra mutations, etc.) 6 DTU Food, Technical University of Denmark
7 ResFinder in a nutshell 7 DTU Food, Technical University of Denmark
8 ResFinder 1.0 to 3.0 answers one question Does the input sequence contain any of the genes from the database? 8 DTU Food, Technical University of Denmark
9 ResFinder detects genes from its database in the input WGS data 9 DTU Food, Technical University of Denmark
10 ResFinder 4.0 answers two questions Does the input sequence contain any of the genes from the database? What is the AMR phenotype of the bacterial cell represented by the input genome sequence? 10 DTU Food, Technical University of Denmark
11 ResFinder 4.0: the additional database Gene_accession no. Class Phenotype PMID fosb1_1_cp Fosfomycin Fosfomycin fosx_1_ap Fosfomycin Fosfomycin fos_1_accv Fosfomycin Fosfomycin unpublished fosb3_1_hq Fosfomycin Fosfomycin teta(46)_1_hq tetb(46)_1_hq tet(57)_1_ KP Tetracycline Tetracycline Tetracycline Doxycycline, Tetracycline, Tigecycline,see Notes Doxycycline, Tetracycline, Tigecycline,see Notes Doxycycline, Tetracycline, Increased efflux Increased efflux unpublished Mechanism of Notes resistance Enzymatic inactivation Enzymatic inactivation Enzymatic inactivation Enzymatic inactivation Increased efflux both teta(46) and tetb(46) must be present to confer resistance both teta(46) and tetb(46) must be present to confer resistance 11 DTU Food, Technical University of Denmark
12 ResFinder 4.0: the additional database Gene_accession no. Class Phenotype PMID Mechanism of Notes resistance Enzymatic fosx_1_ap Fosfomycin Fosfomycin inactivation fos_1_accv Fosfomycin Fosfomycin unpublished Enzymatic inactivation teta(46)_1_hq Tetracycline Doxycycline, Tetracycline, Tigecycline,see Notes Increased efflux both teta(46) and tetb(46) must be present to confer resistance tetb(46)_1_hq Tetracycline Doxycycline, Tetracycline, Tigecycline,see Notes tet(57)_1_ KP Tetracycline Doxycycline, Tetracycline Increased efflux unpublished Increased efflux both teta(46) and tetb(46) must be present to confer resistance Based on ECOFFs Experts opinion & literature searches 12 DTU Food, Technical University of Denmark
13 ResFinder 4.0 differs from previous version for: Number of genes (from to ~3.400) Possibility to select bacterial species and associated panels of antimicrobials (E. coli, Salmonella spp., Campylobacter jejuni, C. coli, Enterococcus faecium, E. faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Neisseria gonorrhoeae, Mycobacterium tubercolosis) Algorithm 13 DTU Food, Technical University of Denmark
14 ResFinder 4.0: in silico antibiogram 14 DTU Food, Technical University of Denmark
15 No gene = No resistance: true? E. coli isolate: no colistin resistance gene found (chromosomal mutation, mcr variants known to date) MIC = 4 mg/l ECOFF = 2 mg/l Limitation of the MIC method? New colistin resistance gene? 15
16 Gene = Resistance: true? E. faecium isolate: vana The entire vancomycin resistance (vana) operon is present: vanr, vans, vany, vanz: 100% id vana: 99.9% id vanx: 99.8% id 16
17 MIC method does not measure AMR with 100% sensitivity and specificity ENT-11.5/AMP ST-11.6/CIP No. of laboratories MIC (mg/l) No. of laboratories (or >1) MIC (mg/l) 4 8 EC-11.7/FEP Legend: ECOFF Expected value No. of laboratories DTU Food, Technical University of Denmark MIC (mg/l)
![6% sensitivity [J Antimicrob Chemother 2015] 589 isolates (C. jejuni and C. coli) Concordance R pheno-geno ranged from 67.](/docs-images/92/110001111/images/18-2.jpg "9% to 100%; whereas concordance S pheno-geno ranged from 98.0% to 99.")
18 Performance of in silico antibiograms 640 isolates (43 serotypes) Resistance genotypes and phenotypes correlated in 99% of the cases [Antimicrob Agents Chemother 2016] 76 isolates Genotypes correlated with phenotypes with 97.8% specificity and 99.6% sensitivity [J Antimicrob Chemother 2015] 589 isolates (C. jejuni and C. coli) Concordance R pheno-geno ranged from 67.9% to 100%; whereas concordance S pheno-geno ranged from 98.0% to 99.6% 18 DTU Food, Technical University of Denmark [Food Microbiol 2018]
19 Take-home messages Neither phenotypic nor genotypic methods are perfect for AMR prediction Genotypic methods can perform in a comparable manner to phenotypic methods for AST of several bacterial species the main limitation is our incomplete knowledge of genetic bases of resistance For just 4 times the price (50 Euro WGS vs 12.5 Euro MIC), we obtain information that can really be useful to describe AMR epidemiology ResFinder 4.0 will be an online AST method 19 DTU Food, Technical University of Denmark
20 Acknowledgements Frank Aarestrup Rolf S. Kaas Kathrine Valentini Jensen EURL network for Campylobacter data Additional data providers (other volunteers?) Reviewers of databases 20 DTU Food, Technical University of Denmark
21 ResFinder 4.0: towards in silico antibiograms Valeria Bortolaia, DVM, PhD 21 DTU Food, Technical University of Denmark
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AMR prediction based on WGS data Valeria Bortolaia, DVM, PhD Research Group for Genomic Epidemiology National Food Institute Technical University of Denmark This lecture How to use WGS for AMR surveillance?
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