APPLICATION OF WHOLE GENOME SEQUENCING IN THE

INFECTIOUS DISEASE’ IVD INDUSTRY

Alex van BelkumCorporate VP Microbiology R&D, bioMérieux, FranceHonorary Professor Molecular MicrobiologyRotterdam, The Netherlands

IMPORTANT STATEMENTS1. I accept monthly sums of bioMérieux money.2.This presentation will not define overall

bioMérieux strategies and policies.3.This review is biased because of personal (not

business) preferences.4.This certainly is incomplete!

API/ID32® STRIPS: A NEW DATA BASE BUILT ON 56277 MICROBIAL PROFILES.

L. Nougier2, F. Allard2, B. Celliere2, N. Desserrieres2, R. Martelin2, Y. Bentoumi1, A. Van Belkum2 , G. Durand2

1 Systems R & D,  2Microbiology R & D, bioMérieux, La Balme Les Grottes, France 

Results:  Performance went up to 90% of correct identification. The database optimization now allows to claim the identification of 901 different species, where 49 species have been renamed and 11 species have been added. Conclusion: The API/ID32® range is recognized as a gold standard bacterial identification tool and is still considered as very attractive despite the emergence of more innovative technologies. The range provides ease of use and reliable identification for developing countries and remains an alternative and backup method for the automated solutions.

WHAT IS A (BACTERIAL) SPECIESIN THE ERA OF BACTERIAL GENOME SEQUENCING?

● A phylogenomic species concept that relies on phylogenetic and genomic approaches for describing species is proposed.

● Although 16S rRNA sequences are still often used to ascertain the taxonomy of Bacteria and Archaea, less conserved genes must be added.

● Current applications of the phylogenomic species concept, including multiple-locus sequence analysis, are being introduced to identify clades that can be classified as species.

● Horizontal gene transfers pose a major challenge for any taxonomy, but genomic approaches will help resolve this issue.

TEST DEVELOPMENT PROCESS

BIG DATA IN CLINICAL MICROBIOLOGY PRACTICE?

7

BIG DATA IN CLINICAL MICROBIOLOGY PRACTICE

NEXT GENERATION SEQUENCING AND WHOLE GENOME SEQUENCES

DNA sequencing Proteins

Other polymers Small molecules

The

begi

nnin

g of

a n

ew A

ST e

ra??

Results :•Assembly•Resistance•Virulence•Phylogeny

reads

OUTBREAKSUSPICION

ORDER SEND

RECEIVE

DECIDE& ACT

1 2

3

4

NGS Added-Value made ACCESSIBLE

Service Lab using MiSeq

BACTERIAL EPIDEMIOLOGY USING EpiSeq

BIOLOGICALLY AND CLINICALLY INSTRUCTIVE?

SEQUENCE EXPLOITATION:“CLASSIC DNA MAP” WITH ANNOTATION

Pseudomonas aeruginosa ANTIBIOGRAM:PHENOTYPE TO GENOTYPE

AR GENES CATALOGUE

Provided by Stéphane Schicklin

β-lactams

Locus known to confer resistance to:

TrimethoprimAminoglycosidesQuninolonesGlycopeptidesFusidic acid

Pseudomonas aeruginosa RESISTANCE GENESIN THE MAJOR CLONES

Pseudomonas aeruginosa INTEGROMICS

THE Pseudomonas aeruginosa RESISTOME

P. aeruginosaRESISTOME-WIDE ASSOCIATION STUDIES

SOME GLOBAL STATEMENTS

1. Regulatory agencies need to be “educated” towards optimal processing of new genomic testing formats.

2. IVD companies need to work with regulatory agencies to develop optimal models for guaranteeing data quality.

3. Sharing data works well in emergency situations (SARS, MERS etc), the moment research is more independent and externally (publicly) funded the need to publish or patent may interfere with open data policies.

4. Genomic testing formats should be amenable to step-by-step development where new bacterial species or new markers can be introduced sequentially.

5. Database management and quality control should usually be quite centralized.

6. Garbage in, garbage out …