我国食品来源金黄色葡萄球菌种群结构分析

Population structure of food-borne Staphylococcus aureus in China

目的了解我国食源性金黄色葡萄球菌(金葡菌)的种群结构。方法通过全基因组测序方法对2006-2020年我国16个省份收集的763株食源性金葡菌进行多位点序列分型、葡萄球菌蛋白A编码基因(spa)和葡萄球菌染色体mec基因盒(SCCmec)分型,使用BioNumerics 7.5软件创建基于ST类型的最小生成树。国外进口食品分离到的金葡菌31株被纳入基因组系统发育树的构建。结果763株金葡菌共鉴定出90个ST型和160个spa型别,其中20种为新ST型别。72个(72/90,80.0%)ST型属于22个克隆群,其中主要型别为CC7、CC1、CC5、CC398、CC188、CC59、CC6、CC88、CC15和CC25,占82.44%(629/763)。其中优势克隆群中ST型和spa型别随着时间的变化呈多态性变化。耐甲氧西林金葡菌(MRSA)的阳性率为7.60%,共鉴定出7种SCCmec型别,以ST59-t437-Ⅳa(17.24%,10/58)、ST239-t030-Ⅲ(12.07%,7/58)、ST59-t437-Ⅴb(8.62%,5/58)、ST338-t437-Ⅴb(6.90%,4/58)和ST338-t441-Ⅴb(6.90%,4/58)为主。本研究分离株在系统发育树上被分为2个种群分支,命名为Clade1和Clade2,相同克隆群、ST型和spa型别的菌株呈聚集分布。Clade1全部为CC7甲氧西林敏感菌株,Clade2中包括21种克隆群和所有MRSA菌株,MRSA菌株按照SCCmec和ST型呈聚集分布。CC398、CC7、CC30、CC12和CC188中的国外分离株与我国分离株进化关系较远。结论本研究中食源性菌株主要优势克隆群型别为CC7、CC1、CC5、CC398、CC188、CC59、CC6、CC88、CC15和CC25,与既往报道的我国医院、社区感染和食物中毒的克隆群存在重叠现象,这提示食品作为病原体社区传播和食物中毒的载体,需高度关注。

Objective To understand the population structure of food-borne Staphylococcus(S.)aureus in China.Methods Whole genome sequencing was used to analyze 763 food-borne S.aureus strains from 16 provinces in China from 2006 to 2020.Multilocus sequence typing(MLST),staphylococcal protein A gene(spa)typing,and staphylococcal chromosome cassettemec(SCCmec)typing were conducted,and minimum spanning tree based on ST types(STs)was constructed by BioNumerics 7.5 software.Thirty-one S.aureus strains isolated from imported food products were also included in constructing the genome phylogenetic tree.Results A total of 90 STs(20 novel types)and 160 spa types were detected in the 763 S.aureus isolates.The 72 STs(72/90,80.0%)were related to 22 clone complexes.The predominant clone complexes were CC7,CC1,CC5,CC398,CC188,CC59,CC6,CC88,CC15,and CC25,accounting for 82.44%(629/763)of the total.The STs and spa types in the predominant clone complexes changed over the years.The methicillin-resistant S.aureus(MRSA)detection rate was 7.60%,and 7 SCCmec types were identified.The ST59-t437-Ⅳa(17.24%,10/58),ST239-t030-Ⅲ(12.07%,7/58),ST59-t437-Ⅴb(8.62%,5/58),ST338-t437-Ⅴb(6.90%,4/58)and ST338-t441-Ⅴb(6.90%,4/58)were the main types in MRSA strains.The genome phylogenetic tree had two clades,and the strains with the same CC,ST,and spa types clustered together.All CC7 methicillin sensitive S.aureus strains were included in Clade1,while 21 clone complexes and all MRSA strains were in Clade2.The MRSA strains clustered according to the SCCmec and STs.The strains from imported food products in CC398,CC7,CC30,CC12,and CC188 had far distances from Chinese strains in the tree.Conclusions In this study,the predominant clone complexes of food-borne strains were CC7,CC1,CC5,CC398,CC188,CC59,CC6,CC88,CC15,and CC25,which overlapped with the previously reported clone complexes of hospital and community-associated strains in China,suggesting that close attention needs to be paid to food,a vehicle of pathogen transmission in community and food poisoning.