Whole genome sequencing used in an industrial context reveals a Salmonella laboratory cross-contamination
Whole genome sequencing used in an industrial context reveals a Salmonella laboratory cross-contamination
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DOI：
10.1016/j.ijfoodmicro.2019.03.007
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发表时间：
2019-06-02
影响因子：
5.4
通讯作者：
Baert, Leen
中科院分区：
文献类型：
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作者：
Rouzeau-Szynalski, Katia;Barretto, Caroline;Baert, Leen
2013年，在对食品样本进行的常规实验室分析中，一家欧洲工厂的成品被检测出哈达尔沙门氏菌阳性。在同一时期，同一实验室的一个环境分离株被血清分型为哈达尔沙门氏菌。在此事件之前，实验室对加标NCTC 9877哈达尔沙门氏菌的样本进行了能力验证。哈达尔沙门氏菌检测的同时发生导致怀疑实验室能力验证中使用的哈达尔沙门氏菌分离株与同一实验室在成品上发现的哈达尔沙门氏菌分离株之间存在实验室交叉污染。由于经典的表型血清分型方法能够将血清型归因于具有共同抗原公式的沙门氏菌分离株，但不能区分亚种内相同血清型的菌株，因此使用全基因组测序来检验实验室交叉污染假设。此外，公共数据库中的12个哈达尔沙门氏菌（在事件发生前可用）被纳入全基因组测序分析，以更好地了解该血清型在欧洲的基因组多样性。分析结果显示，来自实验室的分离株和成品之间最多有10个单核苷酸多态性（SNP），因此证实了实验室交叉污染。这些结果与在工厂进行的所有额外调查相结合，允许放行生产的成品批次，从而避免了工厂不必要的食物浪费和经济损失。
In 2013, during a routine laboratory analysis performed on food samples, one finished product from a European factory was tested positive for Salmonella Hadar. At the same period, one environmental isolate in the same laboratory was serotyped Salmonella Hadar. Prior to this event, the laboratory performed a proficiency testing involving a sample spiked with NCTC 9877 Salmonella Hadar. The concomitance of Salmonella Hadar detection led to the suspicion of a laboratory cross-contamination between the Salmonella Hadar isolate used in the laboratory proficiency testing and the Salmonella Hadar isolate found on the finished product by the same laboratory. Since the classical phenotypic serotyping method is able to attribute a serotype to Salmonella isolates with a common antigenic formula, but cannot differentiate strains of the same serotype within the subspecies, whole genome sequencing was used to test the laboratory cross-contamination hypothesis. Additionally, 12 Salmonella Hadar from public databases, available until the time of the event, were included in the whole genome sequencing analysis to better understand the genomic diversity of this serotype in Europe. The outcome of the analysis showed a maximum of ten single nucleotide polymorphisms (SNPs) between the isolates coming from the laboratory and the finished product, and thus confirmed the laboratory cross-contamination. These results combined with all additional investigations done at the factory, allowed to release finished product batches produced and thus circumvented unnecessary food waste and economic losses for the factory.