Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr

Abstract

Whole genome sequencing (WGS) of Salmonella supports both molecular typing and detection of antimicrobial resistance (AMR). Here, we evaluated the correlation between phenotypic antimicrobial susceptibility testing (AST) and in silico prediction of AMR from WGS in Salmonella enterica (n = 1321) isolated from human infections in Canada. Phenotypic AMR results from broth microdilution testing were used as the gold standard. To facilitate high-throughput prediction of AMR from genome assemblies, we created a tool called Staramr, which incorporates the ResFinder and PointFinder databases and a custom gene-drug key for antibiogram prediction. Overall, there was 99% concordance between phenotypic and genotypic detection of categorical resistance for 14 antimicrobials in 1321 isolates (18,305 of 18,494 results in agreement). We observed an average sensitivity of 91.2% (range 80.5–100%), a specificity of 99.7% (98.6–100%), a positive predictive value of 95.4% (68.2–100%), and a negative predictive value of 99.1% (95.6–100%). The positive predictive value of gentamicin was 68%, due to seven isolates that carried aac(3)-IVa, which conferred MICs just below the breakpoint of resistance. Genetic mechanisms of resistance in these 1321 isolates included 64 unique acquired alleles and mutations in three chromosomal genes. In general, in silico prediction of AMR in Salmonella was reliable compared to the gold standard of broth microdilution. WGS can provide higher-resolution data on the epidemiology of resistance mechanisms and the emergence of new resistance alleles.

Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium

“…Regarding the five point mutations that occur in the quinolone resistance-determining regions (QRDR) of DNA gyrase ( gyrA ) and topoisomerase IV ( parC ) [ 60 ] found in the genomes of ST213 strains, the double mutant S83Y in gyrA and S80I in parC is interesting, since S. Typhimurium mutations in gyrA , in addition to playing a dominant role in resistance to fluoroquinolones, have a synergistic effect with other resistance mechanisms, while the S80I mutation in parC appears to have no effect on quinolone resistance without gyrA mutations [ 69 ]. Whereas QRDR mutations are frequent in bovine S. enterica isolated strains of different serotypes in Mexico [ 62 ] and Canada [ 70 ], it appears to be absent or to occur with low frequency in the USA [ 36 , 71 ].…”

One Health Genomic Analysis of Extended-Spectrum β-Lactamase‒Producing Salmonella enterica, Canada, 2012‒2016

“…We conducted plasmid assembly by using Unicycler version 0.4.7, which combines the accuracy of short reads with the scaffolding of long reads ( 19 ). Determinants of antimicrobial drug resistance and plasmids were detected by using the Public Health Agency of Canada StarAMR Tool ( 20 ), which incorporates the ResFinder, PointFinder, and PlasmidFinder databases ( 21 , 22 ). We created plasmid alignments by using the web-based GView server ( https://www.server.gview.ca ) parameters: minimum length 150 and minimum nucleotide identity 98%.…”

Outbreak of Salmonella Newport linked to imported frozen cooked crayfish in dill brine, Sweden, July to November 2019

“…Sequence type (ST) was determined using the Achtman seven-gene MLST scheme from Enterobase [ 20 , 21 ], and serotype prediction was performed in silico using SeqSero [ 22 ] and an in-house database of serotypes and STs. To predict antimicrobial resistance genes and point mutations, assembled genomes were analysed using StarAMR (with a genome size cut-off of 4.6–5.4 Mbp and PointFinder set to detect Salmonella mutations) to acquire ResFinder and PointFinder results for the genomes [ 23 ]. Clustering and comparison of human and food isolates were performed by SNP analyses, with the pipeline used as part of the routine clustering analysis at PHAS.…”