Identification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

由于该复合物的异质性，因此对青枯雷尔氏菌物种复合物（RSSC）成员的鉴定和分类具有挑战性。根据平均核苷酸同一性（ANI）和多基因座序列分析（MLSA），使用225个菌株的全基因组序列数据对菌株进行分类。基于该ANI分数（> 95％），191出来的192（99.5％）RSSC菌株可分为三个种类青枯菌，R. pseudosolanacearum，和R. syzygii，并进入RSSC内的四个种系型（ I，II，III和IV）。青枯菌系统型II可以分为两组（IIA和IIB），IIB可以分为三个亚组（IIBa，IIBb和IIBc）。ANI的这一划分符合MLSA的规定。ANI和MLSA发现的IIB亚组在各种测定的引物和探针位点中的SNP数量也有所不同。一种在计算机芯片使用整个基因组序列对八种TaqMan和11种常规PCR分析进行了分析。基于此分析，在将这些测定用于其预期的目标生物时，可能会出现几种假阳性或假阴性的情况。两种针对16S rDNA序列的TaqMan检测和两种PCR检测应能够检测RSSC的所有系统型。我们得出的结论是，增加全基因组序列的可用性不仅可用于菌株分类，而且还显示了RSSC内基于进化枝特定核酸的扩增方法的选择和评估潜力。