This document discusses the application of whole genome sequencing in infectious disease diagnostics. It provides examples of how genome sequencing has been used to identify bacterial species, detect antibiotic resistance genes, and study outbreaks. The document also discusses challenges around regulatory approval of genomic tests, data sharing policies, and database management. Overall, it argues that whole genome sequencing is a valuable tool but that standards must be developed to ensure high quality data.

1. APPLICATION OF WHOLE
GENOME SEQUENCING IN THE
INFECTIOUS DISEASE’
IVD INDUSTRY
Alex van Belkum
Corporate VP Microbiology R&D, bioMérieux, France
Honorary Professor Molecular Microbiology
Rotterdam, The Netherlands

2. IMPORTANT STATEMENTS
1.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!

3. 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, 2
Microbiology 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.

4. WHAT IS A (BACTERIAL) SPECIES
IN 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.

5. TEST DEVELOPMENT
PROCESS

6. BIG DATA IN CLINICAL MICROBIOLOGY PRACTICE?

7. 7
BIG DATA IN CLINICAL MICROBIOLOGY PRACTICE

8. NEXT GENERATION SEQUENCING AND
WHOLE GENOME SEQUENCES
DNA sequencing Proteins
Other polymers Small molecules
ThebeginningofanewASTera??

9. Results :
•Assembly
•Resistance
•Virulence
•Phylogeny
reads
OUTBREAK
SUSPICION
ORDER
SEND
RECEIVE
DECIDE
& ACT
11
22
33
44
NGS Added-Value made
ACCESSIBLE
Service Lab using MiSeq
BACTERIAL EPIDEMIOLOGY USING EpiSeq

10. BIOLOGICALLY AND CLINICALLY INSTRUCTIVE?

11. SEQUENCE EXPLOITATION:
“CLASSIC DNA MAP” WITH ANNOTATION

12. Pseudomonas aeruginosa ANTIBIOGRAM:
PHENOTYPE TO GENOTYPE

13. AR GENES CATALOGUE
Provided by Stéphane Schicklin
β-lactams
Locus known to confer
resistance to:
Trimethoprim
Aminoglycosides
Quninolones
Glycopeptides
Fusidic acid

14. Pseudomonas aeruginosa RESISTANCE GENES
IN THE MAJOR CLONES

15. Pseudomonas aeruginosa INTEGROMICS

16. THE Pseudomonas aeruginosa RESISTOME

17. P. aeruginosa
RESISTOME-WIDE ASSOCIATION STUDIES

18. 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 …