Abstract
Antimicrobial resistance (AMR) monitoring in animals is performed in commensal Escherichia coli, and other microorganisms relevant for human or veterinary health. Due to advances in the field and major reductions in cost, it is expected that whole-genome sequencing (WGS)-based antimicrobial susceptibility testing (AST) will (partly) replace culture-based AST. So far, no studies have been performed without using culture-based AST as the gold standard. Our aim was to use Bayesian latent class analysis to evaluate the accuracy of susceptibility testing of commensal E. coli by WGS-based AST versus culture-based AST as this test does not assume a gold standard. OpenBUGS was used to model two independent tests in three animal populations (N = 150, 50 bacterial isolates per population): veal calves, pigs, and broilers. This resulted in the first estimation of sensitivity and specificity of WGS-based AST versus culture-based AST to detect AMR without a gold standard. Both methods had high sensitivity (>0.92, lowest limit probability interval: 0.76) and specificity was generally high for both methods for all antimicrobial classes except for aminoglycosides and macrolides. We compared WGS results for different length and identity settings (%) of gene alignment and found few differences between the 60/90, 90/90 and 95/95 settings. We recommend to further investigate sensitivity and specificity of WGS-based AST by means of latent class analysis, especially for low-prevalent resistance.
Highlights
As part of global efforts to control antimicrobial resistance (AMR) (O’Neill, 2016), monitoring AMR in animals is performed in sentinel organisms such as commensal Escherichia coli (Frimodt-Moller, 2004; European Food Safety Authority (EFSA) et al, 2019)
whole-genome sequencing (WGS) has other advantages over culture-based antimicro bial susceptibility typing: the potential to store sequence data indefi nitely, data is easier to share with other laboratories and stakeholders, and it solves the lack of reproducibility across different laboratories described for broth microdilution (Bortolaia et al, 2020)
Culture-based antimicrobial susceptibility testing (AST) for AMR monitoring in E. coli was performed using the broth micro-dilution reference method according to ISO standards (ISO 20776− 1) with a fixed panel of antimicrobials relevant to human healthcare according to EU legislation and European Food Safety Authority (EFSA) guidelines (Sensititre, EUVSEC antimicrobial panel)
Summary
As part of global efforts to control antimicrobial resistance (AMR) (O’Neill, 2016), monitoring AMR in animals is performed in sentinel organisms such as commensal Escherichia coli (Frimodt-Moller, 2004; EFSA et al, 2019). This is mostly done with culture-based antimicrobial susceptibility testing (AST) method broth microdilution, determining minimum inhibitory concentrations (MIC) for pre-defined panels of antimicrobials. WGS elucidates the genetic relatedness of resistant strains, as well as information on viru lence factors, and potentially the genetic link between AMR genes and mobile genetic elements When these are linked, resistance genes can spread among bacteria, for example from commensal organism E. coli to veterinary pathogens. WGS has other advantages over culture-based antimicro bial susceptibility typing: the potential to store sequence data indefi nitely, data is easier to share with other laboratories and stakeholders, and it solves the lack of reproducibility across different laboratories described for broth microdilution (Bortolaia et al, 2020)
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