基于PubMLST数据库的克罗诺杆菌全球分离株多位点序列分型分析

Mutilocus sequence typing of global Cronobacter strains based on the PubMLST database

目的了解PubMLST数据库中克罗诺杆菌(Cronobacter spp.)全球分离株的分子流行病学特征,为克罗诺杆菌病的预防和控制提供理论依据。方法利用PubMLST数据库收录的数据,筛选其中具有完整序列分型(sequence type,ST)的来自全球的克罗诺杆菌株数据,分别进行国别、来源、菌种构成、序列型及克隆复合体(Clonal complex,CC)的构成分析,并基于7个管家基因序列构建与人类致病密切相关的CC4和CC7型克罗诺杆菌分离株的系统发育树,进行遗传进化分析。结果从PubMLST数据库中筛选出1 603条菌株数据,共含有541个ST型和50个CC型,其中ST4型和CC4型居多,分别含有256和295条菌株数据。来自中国的克罗诺杆菌分离株数据有610条数据,包括315个ST型和40个CC型,其中ST4型和CC4型分别含有62条和75条菌株数据。1 603株克罗诺杆菌分离株中,来自中国的分离株数居多(610),其次为捷克(188)和美国(176);来源于食品的分离株数量居多(58.39%),其次为环境标本(21.83%)和临床标本(14.78%);菌种构成以阪崎克罗诺杆菌(C.sakazakii)数量居多(70.24%),其次为丙二酸盐阳性克罗诺杆菌(C.malonaticus,12.41%),都柏林克罗诺杆菌(C.dublinensis,8.98%),苏黎世克罗诺杆菌(C.turicensis,4.68%),穆汀斯克罗诺杆菌(C.muytjensii,2.5%),尤尼沃斯克罗诺杆菌(C.universalis,1.00%)和康迪蒙提克罗诺杆菌(C.condimenti,0.19%)。致病变种阪崎克罗诺杆菌、丙二酸盐阳性克罗诺杆菌和苏黎世克罗诺杆菌分别含有256、92,49个ST型以及27、10、5个CC型。与人类致病密切相关的CC4和CC7型分离株分别包括32和12个ST型,其中ST4型分离株在CC4型较多,ST7型分离株在CC7型较多。CC4和CC7型分离株分别分布在全球21和10个国家中,其中CC4和CC7型中国分离株分别占其总数的25.42%和36.00%。系统发育分析CC4和CC7型克罗诺杆菌分离株分布在两个不同的簇群,亲缘关系较远。结论克罗诺杆菌全球分离株具有高度遗传多样性,目前已分离出5种克罗诺杆菌临床分离株,且与致病相关的CC4和CC7型菌株占比较高,提示应加强对不同来源的克罗诺杆菌病的流行病学监测,以降低克罗诺杆菌爆发的风险。

Objective To ascertain the molecular epidemiological characteristics of global Cronobacter strains in the PubMLST database in order to provide evidence for the prevention and control of human infections caused by Cronobacter spp. Methods Global Cronobacterstrains in the PubMLST database with complete STs were screened and characterized by country,source,species,STs,and CCs.Based on multilocus sequence analysis of seven housekeeping genes of Cronobacterstrains（CC4 and CC7）closely related to Cronobacterinfections,a maximum likelihood phylogenetic tree was generated and analyzed. Results A total of 1 603 strains belonging to 541 STs and 50 CCs were screened from the PubMLST database,with ST4（256 isolates）being the most dominant ST and CC4（295 isolates）being the most dominant CC,respectively.Six hundred and ten of the strains were isolated from China belonging to 315 STs and 40 CCs,with ST4（62 isolates）being the most dominant ST and CC4（75 isolates）being the most dominant CC,respectively.Of the 1 603 strains screened,the first three countries that submitted isolates to the PubMLST database were China（610 isolates）,followed by the Czech Republic（188 isolates）,and the United States（176 isolates）.The most common strains were isolated from foods（58.35%）,followed by the environment（21.83%）,and clinical specimens（14.78%）.Themost common strains were isolated from foods（58.35%）,followed by environmental（21.83%）and clinical specimens（14.78%）.The most common species were C.sakazakii（70.24%）,followed by C.malonaticus（12.41%）,C.dublinensis（8.98%）,C.turicensis（4.68%）,C.muytjensii（2.5%）,C.universalis（1.00%）,and C.condiment（0.19%）.C.sakazakii,C.malonaticus,and C.turicensis are three pathovars of Cronobacter species;C.sakazakii had256 STs and 27 CCs,C.malonaticus had 92 STs and 10 CCs,and C.turicensis had 49 STs and 5 CCs.CC4 and CC7 are closely related to Cronobacterinfections.CC4 had 32 STs and CC7 had 12 STs.The most prevalent strains of CC4 and CC7 were isolates belonging to ST4 and ST7,respectively.Isolates belonging to CC4 were found in 21 counties（accounting for 25.42% of isolates in China）and isolates belonging to CC7 were found in 10 countries（accounting for 36.00% of isolates in China）.Phylogenetic analysis indicated that Cronobacter isolates belonging to CC4 and CC7 were clustered in two separate branches,which indicated that these strains were distantly related phylogenetically. Conclusion Considerable genetic diversity of global Cronobacter isolates was observed,with5 species of Cronobacter coming from clinical sources.A high proportion of Cronobacter strains belonging to CC4 and CC7（which are associated with human infections）was observed,suggesting the need to enhance the epidemiological surveillance of Cronobacter spp.from various sources in order to reduce the risk of human infections caused by Cronobacter spp.