摘要
目的 了解近年来杭州地区甲型副伤寒沙门菌的基因组流行病学特征.方法 采用二代测序技术（NGS）对2002—2013年杭州地区分离的60株甲型副伤寒沙门菌代表株进行测序并下载公共数据库中的391株甲型副伤寒沙门菌基因组数据.以ATCC9150基因组为参考序列,鉴定所有基因组的单核苷酸多态性（SNP）位点并去除重组,构建基于SNP位点的系统发育树.用SRST2和多位点序列分型（MLST）工具扫描获得MLST型别,用SISTR扫描获得核心基因组多位点序列分型（cgMLST）型别,用SRST2和BLASTN扫描获得耐药基因.选择7种抗生素对60株杭州菌株进行药物敏感试验.结果 451株甲型副伤寒沙门菌基因组序列去重组后共鉴定得到19258个SNP位点,菌株平均距离为0.0070,距离小于0.05的占96.73%,提示451株甲型副伤寒沙门菌基因组差异较小.58株杭州ST85型分离株基因组序列高度相似,提示2002—2013年杭州地区甲型副伤寒疫情主要由ST85型菌株克隆传播引起.杭州菌株与5株国内5省菌株遗传距离较远（平均距离为0.057）,与15株云南菌株距离较近（平均距离为0.0032）,与柬埔寨菌株的距离最近（平均距离为0.0018）,提示ST85型菌株存在跨国传播的可能性.2株杭州ST129型分离株中,HZ333与分离自江苏的两株菌近源（平均距离为0.0097）,提示ST129型部分菌株存在国内传播的可能性.60株杭州菌株除2株未分型外,其余58株菌被分为9个cgMLST型别;公共数据库中391株菌除57株未分型外,其余334株菌被分为165个cgMLST型别.60株杭州菌株均携带耐药基因,其中56株菌携带aac6-Iy耐药基因,4株菌携带aac6-Iaa耐药基因;公共数据库中的391株甲型副伤寒沙门菌除了13株菌未携带耐药基因,其他378株菌均携带aac6-Iy耐药基因.60株杭州菌株中56株菌对7种抗生素均敏感;3株菌对复方新诺明耐药;1株菌对氨苄西林、四环素耐药.结论 2002—2013年杭州地区甲型副�
Objective To understand the genomic epidemiology of Salmonella paratyphi A strains circulating in Hangzhou area in recent years. Methods Next generation sequencing（NGS） technology was used to obtain genomes of 60 Salmonella paratyphi A strains isolated in Hangzhou area from 2002 to 2013. Genomes of 391 Salmonella paratyphi A strains were downloaded from the Sequence Read Archive （SRA） and Assembly database. After removing recombinations, the phylogenetic tree of all 451 genomes based on single nucleotide polymorphisms（SNP） was constructed using ATCC9150 as the reference. SRST2 and mul-tilocus sequence typing （MLST） were used to analyze sequence types（ST）. The Salmonella In Silico Typ-ing Resource （SISTR） was used for core genome multilocus sequence typing （cgMLST）. Resistant genes were screened out with SRST2 and BLASTN. Seven kinds of antibiotics were selected to conduct drug sus-ceptibility test in the 60 strains isolated in Hangzhou. Results A total of 19 258 SNP loci were found in 451 genomes. The average distance in the phylogenetic tree between strains was 0.007 0 and the distance less than 0.05 accounted for 96.73%, indicating a little difference in the 451 Salmonella paratyphi A ge-nomes. Fifty-eight Hangzhou strains of ST85 were highly similar in genomic sequences,which suggested that the clonal spread of ST85 strains caused the epidemic of paratyphoid A in Hangzhou area during 2002-2013. Salmonella paratyphi A strains isolated in Hangzhou were distantly related to five domestic strains （average distance：0.057）,but close to 15 Yunnan strains（average distance：0.003 2） and closest to strains isola-ted in Cambodia （average distance： 0.001 8）, suggesting the possibility of transnational spread of ST85 strains. Among two Hangzhou strains of ST129,HZ333 was closely related to two strains isolated in Jiangsu Province（average distance：0.009 7）,suggesting the possibility of domestic transmission of ST129 strains. Except for two untyped strains,the other 58 strai
作者
汪皓秋
俞骅
郑伟
郑之北
潘劲草
Wang Haoqiu;Yu Hua;Zheng Wei;Zheng Zhibei;Pan Jincao(Hangzhou Center for Disease Control and Prevention, Hangzhou 310021, China)
出处
《中华微生物学和免疫学杂志》
CAS
CSCD
北大核心
2018年第2期116-123,共8页
Chinese Journal of Microbiology and Immunology
基金
杭州市科技发展计划重点专病专科项目（20150733Q46）
关键词
甲型副伤寒沙门菌
二代测序
单核苷酸多态性
多位点序列分型
核心基因组多位点序列分型
耐药基因
Salmonella paratyphi A
Next generation sequencing
Single nucleotide polymor-phisms
Multilocus sequence typing
Core genome multilocus sequence typing
Drug resistant gene
