Resistance to antibiotics is a major problem for health. To monitor the level and development of antibiotic resistance in bacteria more effectively, it is essential to determine which genes or mutations are the cause of the resistance. In this project, we are developing a test that makes it possible to detect the principal genetic determinants of critical antibiotic resistance in the fight against enterobacteria (E. coli, Salmonella, etc.).
This project is aimed at developing a system that can:
- substantially broaden the scope of the official antimicrobial resistance (AMR) surveillance campaigns
- improve the routine analyses of veterinary and human clinical samples and of the food chain in an affordable and controlled manner that poses no intellectual property issues, is not dependent on a particular software package and only requires standard laboratory reagents.
It will supply the genetic data that are complementary to the phenotypic data obtained by antibiogram.
Description of the test
The AMR-ARRAY is a homemade multiplexed test based on the specific ligation of a cocktail of probes and linked to an instrument using microbeads, that requires limited manual work. Given that there is no free-access AMR test that uses microbeads in liquid suspension, this project fills a methodological gap in the set of tests currently available for the identification of AMR genes. Using this experimental approach, the improvements/updates are easily achievable (simple addition of probes) according to the constantly evolving epidemiological situation and the available sequence data, without requiring revalidation of the entire technique.
Genetic determinants targeted
The microarray will target the principal genetic determinants of antibiotic resistance that are of critical importance for human medicine in the fight against Gram-negative bacteria. That includes the genes or mutations conferring resistance to β-lactams (AmpC, ESBLs, and carbapenemases), fluoroquinolones, colistin, macrolides and aminoglycosides. This microarray will make it possible to determine the main genotypes observed in Belgium in the isolated bacteria of production animals, in the food chain or in humans. This test will make it possible to establish an AMR genotype for each strain tested. The concordance between this genotype and the phenotype determined by micro-dilution will then be evaluated. Should the genotypes obtained not correspond to the phenotypes observed, this test will then be able to highlight the rarest genetic determinants of resistance, or those as yet unknown, using genome sequencing analysis of this selection of atypical bacteria.