全基因组测序技术在猪源沙门氏菌血清分型和耐药性分析中的应用

Application of Whole Genome Sequencing Technology in Serotyping and antimicrobial resistance of Salmonella from swine

关键词:  沙门氏菌  全基因组测序  血清型  耐药表型  耐药基因

Key words:  Salmonella  whole genome sequencing  serotype  antimicrobial resistance phenotype  resistance genotypes

摘要:

【目的】为研究全基因组测序技术在猪源沙门氏菌血清型和耐药性检测方面的应用能力。【方法】以60株猪源沙门氏菌为研究对象，应用传统玻片凝集法和微量肉汤稀释法对其进行血清分型和耐药性检测，并提取所有菌株核酸进行全基因组测序组装，利用SeqSero2和ResFinder4在线预测每株菌的血清型和耐药基因，然后与传统方法进行比较分析。【结果】血清凝集试验共鉴定出8种沙门氏菌血清型，而全基因组测序鉴定出9种血清型，二者分型结果的符合率为90.0%；对11种抗菌药物的药敏试验显示：沙门氏菌对四环素（73.3%）的耐药率最高，其次为氨苄西林（66.7%）、磺胺异噁唑（66.7%）和复方新诺明（53.3%），基于全基因组预测的恩诺沙星、美罗培南、头孢噻呋和阿奇霉素的耐药性与药敏试验结果完全一致，对氨苄西林、磺胺异噁唑、四环素预测的结果符合率也均大于90.0%。【结论】全基因组测序分析的沙门氏菌血清型和耐药性与常规检测方法的符合率较高，且具有操作简便的优势，可以作为分析沙门氏菌血清型和耐药性的有效方法。

Abstract:

[Objectives]To study the application ability of whole genome sequencing technology in Salmonella serotype and antimicrobial resistance detection, [Methods] We used 60 strains of Salmonella as research objects, Salmonella serotyping and antimicrobial resistance were analyzed by traditional slide agglutination method and Broth microdilution method. The nucleic acids of 60 Salmonella strains were extracted for whole-genome sequenced and assembled, and predicted the serotype and antimicrobial resistance genes of the strains by online prediction using SeqSero2 and ResFinder4 to each strain online, then Compared and analyzed with traditional methods.[Results] A total of 8 Salmonella serotypes were identified by conventional serum agglutination test, while 9 serotypes were identified by whole genome sequencing. The coincidence rate of the results of the two methods was 90.0%. The results of antimicrobial susceptibility test to 11 drugs indicated that the Salmonella isolates had the highest resistance rate to tetracycline (73.3%), followed by ampicillin (66.7%), sulfisoxazole (66.7%) and trimethoprim-sulfamethoxazole (53.3%), The antimicrobial resistance of enrofloxacin, meropenem, ceftiofur and azithromycin predicted by the whole genome were completely consistent with the antimicrobial susceptibility test results, and the coincidence rate of the predicted results of ampicillin, sulfisoxazole and tetracycline were all more than 90.0%. [Conclusions]The Salmonella serotypes and antimicrobial resistance analyzed by genome sequencing have a high coincidence rate with conventional detection methods, and have the advantages of simple operation. It can be used as an efficient method for analyzing Salmonella serotypes and antimicrobial resistance