Predictive analysis of whole genome sequencing for Salmonella serotype and antimicrobial resistance phenotypes

Abstract:

[Objectives] To evaluate the application of whole genome sequencing technology on the detection of Salmonella serotype and antimicrobial resistance phenotype. [Methods] Two hundred and ninty strains isolated from chicken from 1950 to 2015 in China were serotyped and tested for antimicrobial sensitivity. The whole genomes were extracted and sequenced, and the serotype and antimicrobial resistance of each Salmonella strain were analyzed by submitting the genomic sequences to SeqSero and ResFinder databases, respectively. Results of serotypes and antimicrobial resistances obtained by conventional detection methods and whole genome sequencing analysis were compared, and the compliance status of two detection methods were analyzed. [Results] The results showed that the major serotypes were S. enteritidis and S. gallinarum (≥ 84.5%). The coincidence rate of Salmonella serotype between the results of conventional detection method and whole genome sequencing analysis was 97.6%. The results of minial inhibitory concentration to 11 drugs indicated that the Salmonella isolates had the higher resistance rate to sulfisoxazole (39.3%), tetracycline (39.0%) and colistin (39.0%), but showed lower resistance rates to other antimicrobial agents. The predicted resistance of meropenem, florfenicol, azithromycin and amoxicillin/clavulanic acid was 100% by whole genome sequencing, and the coincidence rate of enrofloxacin, tetracycline, trimethoprim-sulfamethoxazole, ampicillin, ceftiofur, and sulfisoxazole exceeded 95.0%. [Conclusions] High accuracy and sensitivity of whole genome sequencing technology in Salmonella serotype and antimicrobial resistance was seen in this study. As an effective tool, whole genome sequencing technology has a good application prospects on serotyping and antimicrobial resistance analysis of Salmonella.