ST37型艰难梭菌分子流行病学研究

Investigation of molecular epidemiology in Clostridium difficile ST37

目的应用全基因组分析方法对艰难梭菌感染可能的暴发流行进行识别和调查,为艰难梭菌感染防控提供可靠的分子流行病学基础。方法对8株ST37型艰难梭菌进行第二代高通量测序,并完成序列的拼接和注释。通过对其核心基因组进行SNP分析,根据SNP数量以及相关临床资料分析有无院内暴发流行。同时将Genbank中公布了全基因组序列的艰难梭菌,进行MLST分析,对其分析结果为ST37的菌株与本研究中的8株菌株进行SNP分析比较,了解这8株菌的可能来源。结果以最早收集的菌株WCHCD770作为参照,其他7株菌株的SNP值,最大为59,最小为38,提示它们并不是近期发生的传播事件。而这8株菌两两相互进行SNP计算,其中WCHCD1577、WCHCD1641仅为10,提示它们可能来源于一个克隆,可能存在院内传播。通过分析比较这8株菌与Genbank中的其他ST37型艰难梭菌发现,它们的致病决定区(PaLoc)序列完全相同,证实了ST37型艰难梭菌的PaLoc在世界范围克隆传播,同时对它们的SNP比较分析,发现WCHCD1577、WCHCD1641、WCHCD1216、WCHCD109、WCHCD159与2006年在爱尔兰分离的菌株M68的SNP最小,WCHCD770、WCHCD1262、WCHCD1450与加拿大分离的菌株VL-0005的SNP最小。提示这些菌株的可能来源。结论8株ST37型艰难梭菌可能存在克隆传播,值得感染防控重视。

Objective To identify and investigate the outbreak of Clostridium difficile infection using whole genome sequence,and provide basic molecular epidemiology for preventing and controlling Clostridium difficile ST37.Methods High-throughput genome sequencing and annotation of eight clinical isolates of Clostridium difficile ST37 were completed.Single nucleotide polymorphism was analyzed by the core genome.Whether there is nosocomial infection outbreak was analyzed according to the number of SNPs.The whole genome sequence of Clostridium difficile was deposited in Genbank,and multiple locus sequence typing(MLST)was conducted and analyzed.SNP analysis of ST37 strains and our eight clinical isolates were performed in order to understand the possible source of our eight clinical isolates.Results Using the earliest strain WCHCD770 as the reference,we found the biggest SNPs was 59,the smallest one was 38.It suggested that they were not recent spread events.But the smallest SNP of the eight clinical Clostridium difficile strains was 10,which was between WCHCD1577 and WCHCD1641,indicating possible nosocomial transmission.Comparing to other ST37 strains in Genbank,we found Pathogenicity Locus(PaLoc)sequences of all Clostridium difficile ST37 were identical.It was confirmed that PaLoc of Clostridium difficile ST37 was spread around the world.We found the Clostridium difficile strain M68 which was collected from Ireland in 2006 had smaller SNP than WCHCD1216,WCHCD1577,WCHCD1641,WCHCD109,and WCHCD159.At the same time,the strain VL-0005 which was collected from Canada had smaller SNP than WCHCD770,WCHCD1262,and WCHCD1450.This suggested possible strains source.Conclusion This experiment confirmed the possible spread event and source in Clostridium difficile ST37,which was helpful to guide prevention and control of Clostridium difficile.