Data for: Use of biochemical miniaturized galleries, rRNA based lateral flow assay and Real Time PCR for Cronobacter spp. confirmation

Identification of Cronobacter represent a major challenge for laboratories testing powdered infant formula (PIF). In the present study, two biochemical galleries and three molecular methods have been applied to confirm 276 Cronobacter spp. and non-Cronobacter isolates from different sources. Using the latest database of API 20 E and ID 32 E biochemical miniaturized kits, 53% and 78% of the isolates were identified respectively. From the available results, total accuracy for Cronobacter detection was in 97.3% (API 20 E) and 99.1% (ID 32 E). All three molecular methods based on rRNA based lateral flow, Real Time PCR with hybridization probe and with hydrolysis probe produced an accuracy for Cronobacter spp. confirmation of more than 99%. A pilot concept trial using Next Generation Sequencing (NGS) correctly identified 58 out of 67 isolates (86.5%) in DNA mixtures. These results indicate that the commercially available approaches ID 32 E, rRNA based lateral flow and Real Time PCR are all suitable for Cronobacter confirmation at genus level. NGS may provide an alternative in identification of Cronobacter species in complex mixtures, provided that the in sequence database will be improved.

阪崎肠杆菌（Cronobacter）的鉴定，对于开展婴幼儿配方粉（powdered infant formula, PIF）检测的实验室而言是一项重大挑战。本研究采用2种生化鉴定试剂盒与3种分子生物学方法，对不同来源的276株阪崎肠杆菌属菌株及非阪崎肠杆菌分离株进行了确认鉴定。使用API 20 E与ID 32 E微型生化鉴定试剂盒的最新数据库进行分析时，分别有53%和78%的分离株得到成功鉴定。综合现有结果来看，阪崎肠杆菌检测的总准确率在API 20 E试剂盒中为97.3%，在ID 32 E试剂盒中为99.1%。所有3种分子生物学方法——基于核糖体RNA（rRNA）的侧向流检测技术、带有杂交探针的实时荧光定量PCR（Real Time PCR）以及带有水解探针的实时荧光定量PCR——对阪崎肠杆菌属菌株的确认鉴定准确率均超过99%。一项采用下一代测序（Next Generation Sequencing, NGS）技术的概念性预试验，在DNA混合物样本中成功鉴定了67株分离株中的58株，鉴定准确率为86.5%。上述结果表明，市售的ID 32 E试剂盒、基于rRNA的侧向流检测技术以及实时荧光定量PCR方法，均适用于属水平的阪崎肠杆菌鉴定。若能对测序数据库进行优化完善，下一代测序（NGS）技术可为复杂混合物中的阪崎肠杆菌菌种鉴定提供一种可行的替代方案。