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.克罗诺杆菌（Cronobacter）的鉴定，对于开展粉状婴儿配方奶粉（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种生化鉴定板条与3种分子生物学方法，对不同来源的276株克罗诺杆菌属（Cronobacter spp.）菌株及非克罗诺杆菌分离株进行确认鉴定。依托API 20 E与ID 32 E两款微型生化鉴定试剂盒的最新数据库，分别可鉴定出53%与78%的受试分离株。基于现有结果，克罗诺杆菌鉴定的总准确率在API 20 E检测体系中为97.3%，在ID 32 E检测体系中为99.1%。3种分子生物学方法分别为基于核糖体RNA（rRNA）的侧向流检测技术、搭载杂交探针的实时荧光定量聚合酶链式反应（Real Time PCR）以及搭载水解探针的实时荧光定量PCR，三者对克罗诺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）的概念性预试验，可在DNA混合样本中正确鉴定出67株分离株中的58株，准确率达86.5%。上述结果表明，商品化的ID 32 E检测体系、基于rRNA的侧向流检测技术以及实时荧光定量PCR，均适用于属水平的克罗诺杆菌确认鉴定。若能完善测序数据库，下一代测序（NGS）或可成为复杂混合样本中克罗诺杆菌菌种鉴定的备选方案。