Whole genome sequencing (WGS) as a tool for monitoring purposes. Henrik Hasman DTU - Food

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1 Whole genome sequencing (WGS) as a tool for monitoring purposes Henrik Hasman DTU - Food

2 The Challenge Is to: Continue to increase the power of surveillance and diagnostic using molecular tools Develop sequenced-based diagnostics that can be used as close to the patient/sample as possible Google maps

3 Center for Genomic Epidemiology (CGE)

4 Purpose of CGE Provide a proof of concept of combining bioinformatics with both local diagnostics and global epidemiology in real-time

5 Server side Client side Raw DNA sequences Rough assembly and compression Fine assembly Identification Gene finding Comparison Summary of: What it is? Has it been seen before? How we can fight/treat? What is new/unusual? What is already known? Pathogenicity islands Virulence genes Resistance genes MLST type What is novel? Vaccine targets Virulence genes Resistance genes SNPs Google maps like view Reports Outbreaks

6 The Evolving Scale of Science: 1980s: One gene One technician One project 1990s: Whole-genome sequencing of single Reference strains 2000s: Whole-genome sequencing of multiple strains ATG 6

7 Bacterial identification and typing... Serotyping Phage typing Bacteriocin typing Plasmid profiles REA IS-typing RFLP PFGE MLEE RAPD VTNR MLST AFLP flj-typing Evolution of typing methods

8 Second generation sequencing

9 History 2004 Next Generation Sequencing <100 Euro/bacterial isolate

10 NGS output Huge numbers of small fragments ( bp)

11 Reference vs. de novo assembly Reference assembly Known genome De novo assembly Smaller fragments (Unknown order)

12 Reference vs. de novo assembly

13 1G bases NGS Illumina PacBio Assembly pipeline 3-5M bases Allele 1 Allele 2 Resistance Allele 3 MLST gene Outbreak profile strain SNP* Species based ID typing Allele 4 Allele 5 } AAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAA Epidemiological Resistance Virulence AAAATAAAAAAAAAAA genes AATAAATAATAATAAA markers ST List of genes (100% or >95%) Theoretical resistance phenotype *SNP Single Nucleotide Polymorphism (extreme MLST)

14 Examples MLST and Resfinder VTEC O104:H4 outbreak strain

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16 Examples MLST and Resfinder VTEC O104:H4 outbreak strain

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18 For publication in: Journal of Antimicrobial Chemotherapy Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing Ea Zankari 1,2, Henrik Hasman 1, Rolf Sommer Kaas 1,2, Anne Mette Seyfarth 1, Yvonne Agersø 1, Ole Lund 2, Mette Voldby Larsen 2, Frank M. Aarestrup 1,# 200 isolates reduced to 197 (Salmonella, E. coli, E. faecium, E. faecalis) 3,051 individual susceptibility tests

19 Table 2. Overview of resistance genes detected in the isolates by ResFinder with an ID 98.0% Resistance gene No. of isolates (%)* S. Typhimurium (n = 49) E. coli (n = 48) E. faecalis (n = 50) E. faecium (n = 50) Aminoglycoside str 0 (0) 0 (0) 5 (10.0) 1 (2.0) ant(6)-ia 0 (0) 0 (0) 18 (36.0) 18 (36.0) ant(6')-ii 0 (0) 0 (0) 0 (0) 49 (98.0) aph(3')-ia 2 (4.1) 2 (4.2) 0 (0) 0 (0) aph(3')-ic 2 (4.1) 0 (0) 0 (0) 0 (0) aph(3')-iii 0 (0) 0 (0) 17 (34.0) 10 (20.0) aac(6')-aph(2'') 0 (0) 0 (0) 10 (20.0) 0 (0) stra/strb 19 (38.8) 10 (20.8) 0 (0) 0 (0) aada1 5 (10.2) 19 (39.6) 0 (0) 0 (0) aada2 2 (4.1) 4 (8.3) 0 (0) 0 (0) Gene blatem-1 blactx-m-14 blacarb-2 Salmonella 21 (42.9%) 0 (0%) 1 (2.1%) E. Coli 12 (25.0%) 1 (2.1%) 2 (4.1%) aada4 0 (0) 1 (2.1) 0 (0) 0 (0) aada13 1 (2.0) 0 (0) 0 (0) 0 (0) Beta-lactam pbp5 0 (0) 0 (0) 0 (0) 49 (98.0) blatem-1 21 (42.9) 12 (25.0) 0 (0) 0 (0) blatem (0) 1 (2.1) 0 (0) 0 (0) blactx-m-14 0 (0) 1 (2.1) 0 (0) 0 (0) blacarb-2 2 (4.1) 0 (0) 0 (0) 0 (0) MLS erm(b) 0 (0) 1 (2.1) 25 (50.0) 15 (30.0) Isa(A) 0 (0) 0 (0) 50 (100.0) 0 (0) Inu(B) 0 (0) 0 (0) 11 (22.0) 15 (30.0) msr(c) 0 (0) 0 (0) 0 (0) 44 (88.0) mph(a) 0 (0) 1 (2.1) 0 (0) 0 (0) Phenicol cata1 0 (0) 2 (4.2) 0 (0) 0 (0) flor 2 (4.1) 0 (0) 0 (0) 0 (0) cmla1 0 (0) 3 (6.3) 0 (0) 0 (0) cat(pc194) 0 (0) 0 (0) 0 (0) 1 (2.0) Sulphonamide sul1 9 (18.4) 8 (16.7) 0 (0) 0 (0) sul2 20 (40.8) 7 (14.6) 0 (0) 0 (0) sul3 0 (0) 3 (6.3) 0 (0) 0 (0) Tetracycline tet(a) 1 (2.0) 11 (22.9) 0 (0) 0 (0) tet(b) 19 (38.8) 4 (8.3) 0 (0) 0 (0) tet(g) 2 (4.1) 0 (0) 0 (0) 0 (0) tet(m) 0 (0) 0 (0) 34 (68.0) 27 (54.0) tet(l) 0 (0) 0 (0) 24 (48.0) 5 (10.0) tet(s) 0 (0) 0 (0) 0 (0) 1 (2.0) tet(o) 0 (0) 0 (0) 0 (0) 1 (2.0) Trimethoprim dfra1 1 (2.0) 9 (18.8) 0 (0) 0 (0) dfra12 0 (0) 2 (4.2) 0 (0) 0 (0) dfra14 1 (2.0) 0 (0) 0 (0) 0 (0) dfra21 0 (0) 1 (2.1) 0 (0) 0 (0) dfrd 0 (0) 0 (0) 0 (0) 1 (2.0) dfrg 0 (0) 0 (0) 17 (34.0) 0 (0) Glycopeptide Van-A 0 (0) 0 (0) 0 (0) 1 (2.0) MLS, Macrolide-Lincosamide-StreptograminB, *, Per cent resistance genes was determined by dividing the number of isolates harbouring the gene by the total number of isolates (per species).

20 Phenotypic Resistant Susceptible Predicted resistant Predicted susceptible % concordance retest Phenotypic Resistant Susceptible Resistant Susceptible % concordance Spectinomycin in E. coli

21 Genotypic resistance vs phenotypic susceptibility The 7 spectinomycin susceptible E. coli Of 48 E. coli isolates, 19 had the aada1 gene. Of these, 11 were associated with Class 1 and 8 with Class 2 integrons. All aada1 genes associated with Class 2 integrons were phenotypic resistant. Of the 11 aada1 genes associated with Class 1 integrons, 4 had additional genes conferring resistance to spectinomycin (aada2, stra/b, aada4). The remaining 7 aada1 genes were the only examples of genes associated with Class 1 integrons with no other resistance genes to spectinomycin present. The lack of phenotype it therefore most likely to be caused by weak promoter activity of the Class 1 integron.

22 Conclusions Next generation sequencing (NGS) has a potential to be used for typing. NGS is especially useful for surveillance as it gives data on clones and genes. Phenytypes can be differentiated into subgroups according to gene variants. We need to determine the best bioinformatic tool for outbreak detection. We also need to design databases for detection of relevant gene targets. We need more people to be sequencing their isolates..

23 Thank you for your attention!