EpiSeq : A Next-Generation Sequencing Service for Infectious Disease Outbreak Management

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1 EpiSeq : A Next-Generation Sequencing Service for Infectious Disease Outbreak Management CPTR 2016 Workshop Washington, DC M.Rodrigue April 7th,

2 Healthcare Associated Infection A Global Burden KNOWING IS KEY 1 Annual epidemiological report on communicable diseases in Europe Report on the state of communicable diseases in the EU and EEA/EFTA countries. Stockholm, European Centre for Disease Prevention and Control, Klevens R.M., et al. Estimating health care associated infections and deaths in U.S. hospitals, Public Health Reports. 2007;122: Krzowska-Firych J., et al. Hospital-acquired infections caused by antibiotic resistant bacteria. Postepy Nauk Medycznych. 2014, t. XXVII, nr 11. 2

3 Healthcare Associated Infection Can it be prevented? biomerieux Episeq TM Service offer is today available for S. aureus The offer will be expanded to other bacterial species 5 European Center for Disease Control and Prevention. Healthcare Associated infections index.aspx Accessed 10/07/15. 6 Jain R., et al. Veterans Affairs initiative to prevent methicillin-resistant Staphylococcus aureus infections. N Engl J Med. 2011;364(15):

4 Two world leaders : One partnership 4

5 Accurate identification of HAI through superior resolution of strain typing Making Next Generation Sequencing service accessible to healthcare institutions and public health services. Better understanding of transmission events: high-resolution inference of phylogenic. relationships and of the sequence of transmission events Enables exploration of isolates virulome, resistome, concordantly with molecular epidemiology investigation Unique ability to define strain relationships for epidemiological investigation of bacterial outbreaks, significantly impacting infection control for better patient outcomes and cost control. biomérieux EpiSeq TM is NOT intended for Diagnostic Use 5

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7 biomérieux EpiSeq TM How does it work? 1 ORDER 2 SEND OUTBREAK SUSPICION NGS Added-Value made ACCESSIBLE 4 DECIDE & ACT 3 RECEIVE Results : Assembly Resistance Virulence Phylogeny reads 7

8 1 st Step 2 nd Step 3 rd Step 4 th Step 5 th Step biomérieux EpiSeq TM Service lab workflow Sample Reception and Control Subculture & DNA Isolation Library Preparation Sequencing Run Cloud Submission and Analysis Petri Dishes/Swabs/ Portagerm ID and Charact. UltraClean Microbial DNA Isolation Kit Nextera XT kit and Index kit MiSeq Reagent kit and Platform and BaseSpace BaseSpace > biomérieux EpiSeq Server Up to 7 Days 8

9 biomérieux EpiSeq TM Analysis pipeline EpiSeq BioMérieux reads 1 - Assembly 2 - Marker Detection & characterization 3 - Phylogeny 9

10 biomérieux EpiSeq Marker calling 16S rdna db Confirmation of identification 16S MLST db Typing wgmllst db Phylogeny Resistome db Virulome db Annotation Presence / absence of marker No link with phenotype 10

11 biomérieux EpiSeq Characterization report (example) 11

12 biomérieux EpiSeq Characterization report (example) 12

13 biomérieux EpiSeq TM Phylogenetic tree One view allowing to compare all the characteristics of the strains involved in an epidemic and showing how strains are related. Comparison to reference strains is also possible. 13

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16 Sample Prep 16

17 Metagenomics & Microbiota Relative abundances Taxonomic profiles I D Metagenomic based diagnosis Microbiome profiling 7: ECCMID 2015 presentation:pathogen Characterization within the Microbial Flora of Bronchoalveolar Lavages by Direct Sample Sequencing, Guigon G, and col. 17

18 Next to come TB sequencing directly from Smear positive samples Sputum Smear Pos. Sample Prep Sequencing Interpretation Patient Report: ID/AST 18

19 TB Drug Resistance Two new drugs: bedaquiline 2012 delamanid 2013 Treatment costs & Knowledge access justify Seq pricing 19

20 Medico Economic Study Full WGS diagnostics could be generated: in 9 days, 21 days faster than final reference laboratory reports at a cost of 481 per culture-positive specimen vs 518, WGS-based diagnosis cost is 7% cheaper annually than current diagnostic 20

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