Table_2_Salmonella Serotyping; Comparison of the Traditional Method to a Microarray-Based Method and an in silico Platform Using Whole Genome Sequencing Data.docx

Salmonella is one of the most common causes of food-borne diseases worldwide. While Salmonella molecular subtyping by Whole Genome Sequencing (WGS) is increasingly used for outbreak and source tracking investigations, serotyping remains as a first-line characterization of Salmonella isolates. The traditional phenotypic method for serotyping is logistically challenging, as it requires the use of more than 150 specific antisera and well trained personnel to interpret the results. Consequently, it is not a routine method for the majority of laboratories. Several rapid molecular methods targeting O and H loci or surrogate genomic markers have been developed as alternative solutions. With the expansion of WGS, in silico Salmonella serotype prediction using WGS data is available. Here, we compared a microarray method using molecular markers, the Check and Trace Salmonella assay (CTS) and a WGS-based serotype prediction tool that targets molecular determinants of serotype (SeqSero) to the traditional phenotypic method using 100 strains representing 45 common and uncommon serotypes. Compared to the traditional method, the CTS assay correctly serotyped 97% of the strains, four strains gave a double serotype prediction. Among the inconclusive data, one strain was not predicted and two strains were incorrectly identified. SeqSero was evaluated with two versions (SeqSero 1 and the alpha test version of SeqSero 2). The correct antigenic formula was predicted by SeqSero 1 for 96 and 95% of strains using raw reads and assembly, respectively. However, 34 and 33% of these predictions included multiple serotypes by raw reads and assembly. With raw reads, one strain was not identified and three strains were discordant with phenotypic serotyping result. With assembly, three strains were not predicted and two strains were incorrectly predicted. While still under development, SeqSero 2 maintained the accuracy of antigenic formula prediction at 98% and reduced multiple serotype prediction rate to 13%. One strain had no prediction and one strain was incorrectly predicted. Our study indicates that the CTS assay is a good alternative for routine laboratories as it is an easy to use method with a short turn-around-time. SeqSero is a reliable replacement for phenotypic serotyping if WGS is routinely implemented.

沙门氏菌（Salmonella）是全球范围内最常见的食源性致病菌之一。尽管基于全基因组测序（Whole Genome Sequencing, WGS）的沙门氏菌分子分型技术正日益广泛应用于暴发调查与溯源追踪工作，血清分型仍是沙门氏菌分离株的一线鉴定手段。传统血清分型表型方法操作流程复杂，需使用超过150种特异性抗血清，且需要经过专业培训的人员解读实验结果，因此多数实验室无法将其作为常规检测方法。为此，学界已开发出多种针对O抗原、H抗原位点或替代基因组标记的快速分子检测方法作为替代方案。随着WGS技术的普及，基于WGS数据的计算机辅助沙门氏菌血清型预测技术应运而生。本研究针对100株涵盖45种常见与罕见血清型的沙门氏菌，对比了基于分子标记的微阵列检测方法——Check and Trace Salmonella检测（CTS）、靶向血清型分子决定簇的WGS血清型预测工具SeqSero，与传统表型分型方法的检测效果。相较于传统方法，CTS检测可对97%的菌株实现正确血清分型，仅4株菌株出现双重血清型预测结果；在不确定结果的样本中，1株未获得预测结果，2株被错误鉴定。SeqSero包含两个版本（SeqSero 1与SeqSero 2的α测试版）。SeqSero 1分别基于原始测序读段与组装序列，可对96%与95%的菌株实现正确的抗原式预测，但其中分别有34%与33%的预测结果包含多种血清型。使用原始测序读段时，1株菌株未被鉴定，3株菌株的分型结果与表型血清分型不符；使用组装序列时，3株菌株未获得预测结果，2株被错误预测。尽管仍处于开发阶段，SeqSero 2的抗原式预测准确率仍达到98%，并将多重血清型预测率降至13%，仅1株未获得预测结果，1株被错误鉴定。本研究表明，CTS检测操作简便、周转时间短，可作为常规实验室的理想替代方案；若实验室常规开展WGS检测，SeqSero则是表型血清分型的可靠替代手段。