The AMR-ARRAY: A modular bead array detecting β-lactam, (fluoro) quinolone, colistin, aminoglycoside and macrolide resistance determinants in Gram-negative bacteria.
[en] The aim of this study was to develop a highly multiplexed bead array to detect genes and/or mutations frequently associated with resistance to antimicrobials of the β-lactam, (fluoro)quinolone, colistin, macrolide and aminoglycoside families in Enterobacteriaceae such as Escherichia coli, Shigella spp. and Salmonella spp. Ligase Chain Reaction and the Luminex® technology were combined in a 53-plex assay designed to target selected genetic markers with 3 internal controls. The AMR-ARRAY consistently detected resistance determinants as compared to phenotypically expressed resistance for 94.7% (856/904) of the assessed resistances. When compared to resistance profiles inferred from whole genome sequencing results, the AMR-ARRAY showed a selectivity and specificity of 99.3% and 100%, respectively. The strong features of the AMR-ARRAY are (i) its competitive cost, currently 18€/sample (ii) its wide analytical scope, currently 50 markers covering 5 antimicrobial families, (iii) its robust and user-friendly design consisting in a single-tube assay conducted in 4 successive steps (iv) its relatively short turnaround time, less than 8 h (v) its ability to detect allelic variability at critical SNPs (vi) its open access and easily upgradable design, with probes sequences, procedure and software source code freely available. The use of the AMR-ARRAY as a screening method in official antimicrobial resistance monitoring could improve the granularity of the collected data and pinpoint remarkable isolates harbouring unusual resistance determinants thereby enabling fit-for-purpose selection of isolates for Whole Genome analysis.
Disciplines :
Microbiology
Author, co-author :
Timmermans, Michaël; Veterinary Bacteriology, Sciensano, Ixelles, Belgium, Faculté de médecine, Université Libre de Bruxelles, Brussels, Belgium
Latour, Samuel ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA) > Génomique animale ; Veterinary Bacteriology, Sciensano, Ixelles, Belgium
Denis, Olivier; Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium, Laboratory of Clinical Microbiology, National Reference Center for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
The AMR-ARRAY: A modular bead array detecting β-lactam, (fluoro) quinolone, colistin, aminoglycoside and macrolide resistance determinants in Gram-negative bacteria.
This research was funded by the Belgian Federal Public Service of Health, Food Chain Safety and Environment through the contract RF16/6302 AMR-ARRAY. Preliminary research was financed in part by a grant from the Belgian Scientific Policy E1122-P1.We thank the FASFC for organising the sampling and isolation of the microorganisms used in this study. We also thank the EURL who provide isolates for controls and analysis. Technical support from A. Radu was highly appreciated. We thank also the service Transversal Activities in Applied Genomics from Sciensano for the paired-end sequencing reactions and for the development and maintenance of the in-house instance of the Galaxy workflow management system. Many thanks to Henrik Hasman from the Statens Serum Institut (SSI), Denmark, the Ruhr Universit?t Bochum, Germany, Manal AbuOun from the Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey KT153NB, UK and National Institute for Health Research Health Protection Research Unit, University of Oxford in partnership with PHE, Oxford, UK who provided us with strains to control some of our PLPs.This research was funded by the Belgian Federal Public Service of Health , Food Chain Safety and Environment through the contract RF16/6302 AMR-ARRAY. Preliminary research was financed in part by a grant from the Belgian Scientific Policy E1122-P1 .
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