全基因组测序技术对沙门氏菌血清型和耐药性的预测能力分析

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

摘要:

[目的] 评价全基因组测序技术在沙门氏菌血清型和耐药性检测方面的应用能力。[方法] 对我国1950-2015年分离的290株鸡源沙门氏菌用常规检测方法进行了血清分型和药敏试验；提取全基因组进行测序，应用SeqSero和ResFinder数据库分析沙门氏菌的血清型和耐药性；对用常规检测方法和全基因组测序分析方法得到的血清型和耐药性结果进行比较，分析两种方法所得结果的符合性情况。[结果] 沙门氏菌的主要血清型为肠炎和鸡白痢（≥84.5%），常规检测方法和全基因组测序分析方法在沙门氏菌血清分型方面的总体符合率为97.6%。对11种抗菌药物的最小抑菌浓度（MIC）检测结果显示，沙门氏菌对磺胺异噁唑（39.3%）、氨苄西林（39.0%）和粘菌素（39.0%）的耐药率较高，对其他抗菌药物的耐药率较低。全基因组测序分析能够100%预测美罗培南、氟苯尼考、阿奇霉素和阿莫西林/克拉维酸的耐药性，而且对恩诺沙星、四环素、复方新诺明、氨苄西林、头孢噻呋、磺胺异噁唑的预测符合率均超过95.0%。[结论] 本研究结果表明，全基因组测序技术对沙门氏菌的血清分型和耐药性的预测具有较高的准确性和敏感性，是分析沙门氏菌血清型和耐药性的有效工具，具备良好的应用前景。

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.