Zaiss N Henning, Rupnik Maja, Kuijper Ed J, Harmanus Celine, Michielsen Dolf, Janssens Koen, Nübel Ulrich
Robert Koch Institute, Wernigerode, Germany.
BMC Microbiol. 2009 Jan 8;9:6. doi: 10.1186/1471-2180-9-6.
Genotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread. Portability of genotyping data is desirable to facilitate inter-laboratory comparisons and epidemiological studies.
This report presents results from a systematic screen for variation in repetitive DNA in the genome of C. difficile. We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. Based on an investigation of 154 C. difficile isolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history.
We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. difficile. Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains.
对艰难梭菌流行菌株进行基因分型对于追踪其出现和传播情况很有必要。基因分型数据的可移植性有助于实验室间的比较和流行病学研究。
本报告展示了对艰难梭菌基因组中重复DNA变异进行系统筛选的结果。我们描述了两个串联重复位点，命名为“TR6”和“TR10”，它们表现出广泛的序列变异，可能有助于基于序列的菌株分型。通过对包含75个核糖体分型的154株艰难梭菌分离株进行调查，串联重复序列测序显示与广泛使用的PCR核糖体分型具有高度一致性和同等的鉴别能力。此外，串联重复序列能够重建分离株的主要克隆群体结构和进化历史。
我们得出结论，此处引入的两个重复位点的序列分析对于艰难梭菌的常规分型可能非常有用。串联重复序列分型将系统发育多样性解析到与PCR核糖体分型相当的水平。DNA序列可以存储在可通过互联网访问的数据库中，无需交换参考菌株。
