志贺菌中成簇的规律间隔短回文重复序列与毒力基因和耐药基因的关系
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摘要
目的探索志贺菌中成簇的规律间隔短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)与毒力基因和耐药基因的关系。方法从GenBank数据库中获得志贺菌的基因组、毒力基因和耐药基因的序列,通过多序列比对等方法获得志贺菌中CRISPR1、CRISPR2和CRISPR-Q1的分布情况、重复序列和间隔序列信息,通过BLAST方法获得毒力基因和耐药基因在志贺菌中的分布情况,SPSS 21.0软件分析CRISPR与毒力基因和耐药基因的关系。结果志贺菌中的CRISPR1和CRISPR2在不同菌株中的间隔序列差别较大,CRISPRQ1分布更为广泛(超过99%)。毒力基因在志贺菌中分布比较广泛(均超过56%),耐药基因中的blaOXA-1、camr、Sul2、tetB分布也比较广(超过50%)。CRISPR1/CRISPR2与是否携带9种毒力基因、4种耐药基因有关(P<0.05),CRISPR-Q1与是否携带3种毒力基因、4种耐药基因有关(P<0.05)。CRISPR1/CRISPR2和CRISPR-Q1均与志贺菌中存在的毒力基因和耐药基因的个数间有统计学关联(P<0.05)。CRISPR1/CRISPR2与CRISPR-Q1的间隔序列数目之间存在统计学关联(χ2=61.6,P<0.001)。结论志贺菌中不同CRISPR的分布差异比较大,存在的间隔序列数目不等;志贺菌CRISPR与部分毒力基因和耐药基因之间存在负相关;CRISPR1/CRISPR2与CRISPR-Q1的间隔序列数目存在正相关。
Objective To investigate the relationship of the clustered regularly interspaced short palindromic repeats(CRISPR)with resistance genes and virulence genes.Methods The Shigella genome sequences,resistance genes and virulence genes sequences were obtained from GenBank Database.Then we obtained the distribution of CRISPR1,CRISPR2 and CRISPR-Q1 and the information of repeat and spacers in Shigella by multiple sequences alignment.Meanwhile,the distribution of resistance genes and virulence genes in Shigella were obtained by BLAST and the relationship of the CRISPR with resistance genes and virulence genes was computed by SPSS 17.0.Results The spacers of CRISPR1 and CRISPR2showed obvious differences in different Shigella strains,and the CRISPR-Q1 was more widely distributed(over 99%).The virulence genes were widely distributed in Shigella(more than 56%);the distribution of resistance genes(blaOXA-1,camr,Sul2,and tetB)was also wide(over 50%).There were significant differences between the CRISPR1/CRISPR2 and 9kinds of virulence genes and 4kinds of resistance genes(P<0.05).There were significant differences between the CRISPR-Q1 and 3kinds of virulence genes and 4kinds of resistance genes(P<0.05).There were significant differences between the CRISPR1/CRISPR2,CRISPR-Q1 and the number of virulence genes and resistance genes(P<0.05).There were significant differences between the CRISPR1/CRISPR2 and the number of spacers of CRISPR-Q1(χ2=61.6,P<0.001).Conclusion The distribution of CRISPR was quite different in Shigella,and the number of spacers was also different.There were negative correlation of CRISPR of Shigella with some resistance genes and virulence genes.The CRISPR1/CRISPR2 had a positive relationship with the number of the spacers.
Objective To investigate the relationship of the clustered regularly interspaced short palindromic repeats(CRISPR)with resistance genes and virulence genes.Methods The Shigella genome sequences,resistance genes and virulence genes sequences were obtained from GenBank Database.Then we obtained the distribution of CRISPR1,CRISPR2 and CRISPR-Q1 and the information of repeat and spacers in Shigella by multiple sequences alignment.Meanwhile,the distribution of resistance genes and virulence genes in Shigella were obtained by BLAST and the relationship of the CRISPR with resistance genes and virulence genes was computed by SPSS 17.0.Results The spacers of CRISPR1 and CRISPR2showed obvious differences in different Shigella strains,and the CRISPR-Q1 was more widely distributed(over 99%).The virulence genes were widely distributed in Shigella(more than 56%);the distribution of resistance genes(blaOXA-1,camr,Sul2,and tetB)was also wide(over 50%).There were significant differences between the CRISPR1/CRISPR2 and 9kinds of virulence genes and 4kinds of resistance genes(P<0.05).There were significant differences between the CRISPR-Q1 and 3kinds of virulence genes and 4kinds of resistance genes(P<0.05).There were significant differences between the CRISPR1/CRISPR2,CRISPR-Q1 and the number of virulence genes and resistance genes(P<0.05).There were significant differences between the CRISPR1/CRISPR2 and the number of spacers of CRISPR-Q1(χ2=61.6,P<0.001).Conclusion The distribution of CRISPR was quite different in Shigella,and the number of spacers was also different.There were negative correlation of CRISPR of Shigella with some resistance genes and virulence genes.The CRISPR1/CRISPR2 had a positive relationship with the number of the spacers.
引文
[1]WANG P,ZHANG B,DUAN G,et al.Bioinformatics analyses of Shigella CRISPR structure and spacer classification[J].World J Microbiol Biotechnol,2016,32(3):1-9.
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[3]WANG Y,SONG C,DUAN G,et al.Transposition of ISEcp1modulates blaCTX-M-55-mediated Shigella flexneri resistance to cefalothin[J].Int J Antimicrob Agents,2013,42(6):507-512.
[4]YANG H,SUN W,DUAN G,et al.Serotype distribution and characteristics of antimicrobial resistance in Shigella isolated from Henan province,China,2001-2008[J].Epidemiol Infect,2013,141(9):1946-1952.
[5]洪丽娟,张冰,段广才,等.CRISPR/Cas系统与志贺菌毒力和耐药的关系及插入序列IS600对cse2表达水平的影响[J].微生物学报,2016,56(12):1912-1923.
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[7]王鹏飞,王颖芳,段广才,等.志贺菌成簇的规律间隔的短回文重复序列系统结构特征的生物信息学分析[J].生物医学工程学杂志,2015,32(2):343-349.
[8]GUO X,WANG Y,DUAN G,et al.Detection and Analysis of CRISPRs of Shigella[J].Curr Microbiol,2014,70(1):85-90.
[9]王鹏飞,王颖芳,段广才,等.志贺菌成簇的规律间隔短回文重复序列的检测及同源性分析[J].吉林大学学报(医学版),2015,41(2):261-268.
[10]郭向娇,王颖芳,段广才,等.临床分离志贺菌中CRISPR/Cas系统的分布及其与毒力基因的关系[J].微生物学通报,2015,42(3):543-549.
[11]PALMER KL,GILMORE MS.Multidrug-resistant enterococci lack CRISPR-cas[J].M Bio,2010,1(4):e0022710.
[12]LI Q,XIE X,YIN K,et al.Characterization of CRISPR-Cas system in clinical Staphylococcus epidermidis strains revealed its potential association with bacterial infection sites[J].Microbiol Res,2016,193:103-110.
[13]TORO M,CAO G,JU W,et al.Association of clustered regularly interspaced short palindromic repeat(CRISPR)elements with specific serotypes and virulence potential of shiga toxin-producing Escherichia coli[J].Appl Environ Microbiol,2014,80(4):1411-1420.
[14]龙金照,徐亚珂,段广才,等.O26:H11及NM大肠埃希菌CRISPR的分子分布特征及其与stx噬菌体的关系[J].中华流行病学杂志,2017,38(7):944-949.
[15]YIN S,JENSEN MA,BAI J,et al.The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat(CRISPR)spacer composition[J].Appl Environ Microbiol,2013,79(18):5710-5720.
[2]YANG H,DUAN G,ZHU J,et al.Prevalence and characterisation of plasmid-mediated quinolone resistance and mutations in the gyrase and topoisomerase IV genes among Shigella isolates from Henan,China,between 2001and 2008[J].Int J Antimicrob Agents,2013,42(2):173-177.
[3]WANG Y,SONG C,DUAN G,et al.Transposition of ISEcp1modulates blaCTX-M-55-mediated Shigella flexneri resistance to cefalothin[J].Int J Antimicrob Agents,2013,42(6):507-512.
[4]YANG H,SUN W,DUAN G,et al.Serotype distribution and characteristics of antimicrobial resistance in Shigella isolated from Henan province,China,2001-2008[J].Epidemiol Infect,2013,141(9):1946-1952.
[5]洪丽娟,张冰,段广才,等.CRISPR/Cas系统与志贺菌毒力和耐药的关系及插入序列IS600对cse2表达水平的影响[J].微生物学报,2016,56(12):1912-1923.
[6]王琳琳,王颖芳,段广才,等.志贺菌CRISPR的检测及其与耐药的关系[J].微生物学报,2015,55(4):476-483.
[7]王鹏飞,王颖芳,段广才,等.志贺菌成簇的规律间隔的短回文重复序列系统结构特征的生物信息学分析[J].生物医学工程学杂志,2015,32(2):343-349.
[8]GUO X,WANG Y,DUAN G,et al.Detection and Analysis of CRISPRs of Shigella[J].Curr Microbiol,2014,70(1):85-90.
[9]王鹏飞,王颖芳,段广才,等.志贺菌成簇的规律间隔短回文重复序列的检测及同源性分析[J].吉林大学学报(医学版),2015,41(2):261-268.
[10]郭向娇,王颖芳,段广才,等.临床分离志贺菌中CRISPR/Cas系统的分布及其与毒力基因的关系[J].微生物学通报,2015,42(3):543-549.
[11]PALMER KL,GILMORE MS.Multidrug-resistant enterococci lack CRISPR-cas[J].M Bio,2010,1(4):e0022710.
[12]LI Q,XIE X,YIN K,et al.Characterization of CRISPR-Cas system in clinical Staphylococcus epidermidis strains revealed its potential association with bacterial infection sites[J].Microbiol Res,2016,193:103-110.
[13]TORO M,CAO G,JU W,et al.Association of clustered regularly interspaced short palindromic repeat(CRISPR)elements with specific serotypes and virulence potential of shiga toxin-producing Escherichia coli[J].Appl Environ Microbiol,2014,80(4):1411-1420.
[14]龙金照,徐亚珂,段广才,等.O26:H11及NM大肠埃希菌CRISPR的分子分布特征及其与stx噬菌体的关系[J].中华流行病学杂志,2017,38(7):944-949.
[15]YIN S,JENSEN MA,BAI J,et al.The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat(CRISPR)spacer composition[J].Appl Environ Microbiol,2013,79(18):5710-5720.