Full
Outline
To analyze and compare the Salmonella serotyping methods based on multiplex quantitative polymerase chain reaction (multiplex qPCR) and whole-genome sequencing (WGS), and to evaluate the serotyping capability and application scenarios of each method.
A total of 242 Salmonella strains isolated in our province, covering 96 serotypes, were subjected to whole-genome sequencing. The serotypes of these strains were predicted using SeqSero2 and SISTR, followed by a concordance analysis of the results. Meanwhile, multiplex qPCR was employed for the identification of each serotype, so as to assess the accuracy and applicability of this method.
Three methods were used to detect 96 Salmonella serovars. The overall concordance rates of SeqSero2 and SISTR were both 87.50% (84/96), which were significantly higher than that of multiplex qPCR (52.08%, 50/96). For the 242 Salmonella strains, the discordance rates of SeqSero2 and SISTR were 2.48% (6/242) and 7.85% (19/242), respectively. The multiplex qPCR method could only accurately distinguish common serotypes. The main reasons for the discordance of the SeqSero2 method included the deletion or error of O antigen genes. The main reasons for partial concordance were the interference from the similarity of H antigen alleles and the inability to distinguish some serovars in the C2 serogroup that differ only in the O6 antigen. The main reasons for the discordance of the SISTR method were cgMLST cluster misclassification, O antigen gene deletion, and the inability to distinguish monophasic variant strains.
The WGS-based serotyping method exhibits high accuracy and can replace the traditional serum agglutination test for Salmonella serotyping in numerous application scenarios. Although the multiplex qPCR method has limitations with a lower concordance rate than WGS-based methods, it features a short detection time and can accurately identify common serotypes, thus being suitable for emergency rapid detection.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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