dndC基因在脉冲场凝胶电泳基因组降解中的作用及降解处理方法

濮吉 周娟 赫自强 熊衍文 金东

濮吉, 周娟, 赫自强, 熊衍文, 金东. dndC基因在脉冲场凝胶电泳基因组降解中的作用及降解处理方法[J]. 疾病监测, 2022, 37(6): 796-801. doi: 10.3784/jbjc.202110260558
引用本文: 濮吉, 周娟, 赫自强, 熊衍文, 金东. dndC基因在脉冲场凝胶电泳基因组降解中的作用及降解处理方法[J]. 疾病监测, 2022, 37(6): 796-801. doi: 10.3784/jbjc.202110260558
Pu Ji, Zhou Juan, He Ziqiang, Xiong Yanwen, Jin Dong. Role of dndC gene in DNA degeneration in pulsed-field gel electrophoresis and treatment method[J]. Disease Surveillance, 2022, 37(6): 796-801. doi: 10.3784/jbjc.202110260558
Citation: Pu Ji, Zhou Juan, He Ziqiang, Xiong Yanwen, Jin Dong. Role of dndC gene in DNA degeneration in pulsed-field gel electrophoresis and treatment method[J]. Disease Surveillance, 2022, 37(6): 796-801. doi: 10.3784/jbjc.202110260558

dndC基因在脉冲场凝胶电泳基因组降解中的作用及降解处理方法

doi: 10.3784/jbjc.202110260558
基金项目: 海关总署项目(No. 2019HK125)
详细信息
    作者简介:

    濮吉,男,北京市人,助理研究员,主要从事传染病预防控制工作,Email:puji@icdc.cn

    通讯作者:

    金东,Tel:010–58900749,Email:jindong@icdc.cn

  • 中图分类号: R211; R378

Role of dndC gene in DNA degeneration in pulsed-field gel electrophoresis and treatment method

Funds: This study was supported by the Project of General Administration of Customs, P.R. China (No. 2019HK125)
More Information
  • 摘要:   目的  了解大肠埃希菌和弗格森埃希菌dndC基因的携带情况,以及该基因与脉冲场凝胶电泳(PFGE)基因组降解表型之间的关系,探讨PFGE中菌株基因组降解的原因及处理方法。  方法  使用PFGE对450株大肠埃希菌和弗格森埃希菌进行分析,设计引物检测dndC基因的携带情况并进行序列测定。 通过dndC基因序列比对和进化树的构建,获得dndC基因型别以及其在不同型别大肠埃希菌中的分布。 通过添加硫脲和消毒电泳仪研究基因组降解的处理方法。  结果  450株大肠埃希菌和弗格森埃希菌中,降解的菌株为40株(8.89%)。 dndC基因阳性菌株33株(7.33%),均出现了降解。 大肠埃希菌携带的dndC基因可分为8个群。 不同型别大肠埃希菌中均存在dndC基因阳性菌株,且阳性率存在差异。 添加硫脲可以有效缓解PFGE分析中dndC基因导致的降解,电泳仪消毒可以缓解全胶降解的情况。  结论  dndC基因会导致大肠埃希菌和弗格森埃希菌PFGE分析中基因组降解,添加硫脲可以缓解此降解。
  • 图  1  基于dndC基因构建的Neighbor-Joining进化树

    Figure  1.  Neighbor-Joining phylogenetic tree based on dndC genes

    图  2  电泳液加入硫脲前后(A)及电泳仪消毒前后(B)降解菌株的脉冲场凝胶电泳情况

    注:M. 分子量标准;1~11. 具有降解表型的菌株

    Figure  2.  PFGE for strains with DNA degradation before and after addition of thiourea (A) and before and after disinfection of electrophoresis equipment (B)

    表  1  450株菌的dndC基因携带情况及降解表型

    Table  1.   Carriage of dndC gene and DNA degeneration phenotype of 450 E. coli and E. fergusonii strains

    菌株来源菌种类别菌株数(株)降解表型dndC基因阳性
    菌株
    阳性率
    (%)
    菌株
    阳性率
    (%)
    环境弗格森埃希菌1101412.731412.73
    野生动物大肠埃希菌 23622 9.3215 6.36
    患者和食品大肠埃希菌 104 4 3.85 4 3.85
     合计45040 8.8933 7.33
    下载: 导出CSV

    表  2  不同型别大肠埃希菌中dndC基因的携带情况

    Table  2.   Carriage of dndC gene in different types of E.coli

    型别/亚型菌株数(株)dndC基因阳性菌株数(株)阳性率(%)
    A2 191964.38
    B12 8202027.16
    B21 907241.26
    B2-154130.55
    B2-21 366211.54
    C540101.85
    D6169615.58
    D12735720.88
    D21733117.92
    D317084.71
    E1 020222.15
    E1270228.15
    E2750101.33
    F197126.09
    G9699.38
    合计9 3874815.12
    下载: 导出CSV
  • [1] 汪皓秋, 郑伟, 俞骅, 等. 2002-2013年杭州地区甲型副伤寒沙门菌分子分型研究[J]. 中华微生物学和免疫学杂志,2017,37(1):57–61. DOI:10.3760/cma.j.issn.0254−5101.2017.01.009.

    Wang HQ, Zheng W, Yu H, et al. Molecular typing of Salmonella paratyphi A strains isolated in Hangzhou area from 2002 to 2013[J]. Chin J Microbiol Immunol, 2017, 37(1): 57–61. DOI: 10.3760/cma.j.issn.0254−5101.2017.01.009.
    [2] 吴伟元, 王辉, 陆坚, 等. 多位点串联重复序列分析和脉冲场凝胶电泳对伤寒沙门菌基因分型[J]. 中华微生物学和免疫学杂志,2014,34(4):264–268. DOI:10.3760/cma.j.issn.0254−5101.2014.04.003.

    Wu WY, Wang H, Lu J, et al. Comparative evaluation of multilocus variable-number tandem-repeat analysis and pulsed-field gel electrophoresis for genotyping Salmonella enterica serovar Typhi isolates[J]. Chin J Microbiol Immunol, 2014, 34(4): 264–268. DOI: 10.3760/cma.j.issn.0254−5101.2014.04.003.
    [3] Silbert S, Boyken L, Hollis RJ, et al. Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea[J]. Diagn Microbiol Infect Dis, 2003, 47(4): 619–621. DOI: 10.1016/S0732−8893(03)00164−0.
    [4] Wang LR, Chen S, Vergin KL, et al. DNA phosphorothioation is widespread and quantized in bacterial genomes[J]. Proc Natl Acad Sci USA, 2011, 108(7): 2963–2968. DOI:  10.1073/pnas.1017261108.
    [5] Wang LR, Chen S, Xu TG, et al. Phosphorothioation of DNA in bacteria by dnd genes[J]. Nat Chem Biol, 2007, 3(11): 709–710. DOI:  10.1038/nchembio.2007.39.
    [6] Liesegang A, Tschäpe H. Short communication-modified pulsed-field gel electrophoresis method for DNA degradation-sensitive Salmonella enterica and Escherichia coli strains[J]. Int J Med Microbiol, 2002, 291(8): 645–648. DOI: 10.1078/1438−4221−00180.
    [7] O'Reilly LC. A method for overcoming DNA degradation during PFGE for Serratia marcescens[J]. J Microbiol Methods, 2011, 85(2): 173–174. DOI:  10.1016/j.mimet.2011.02.014.
    [8] Corkill JE, Graham R, Hart CA, et al. Pulsed-field gel electrophoresis of degradation-sensitive DNAs from Clostridium difficile PCR ribotype 1 strains[J]. J Clin Microbiol, 2000, 38(7): 2791–2792. DOI: 10.1128/JCM.38.7.2791−2792.2000.
    [9] Römling U, Tümmler B. Achieving 100% typeability of Pseudomonas aeruginosa by pulsed-field gel electrophoresis[J]. J Clin Microbiol, 2000, 38(1): 464–465. DOI: 10.1128/JCM.38.1.464−465.2000.
    [10] Ho WS, Ou HY, Yeo CC, et al. The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands[J]. BMC Genomics, 2015, 16: 199. DOI: 10.1186/s12864−015−1421−8.
    [11] Ray T, Mills A, Dyson P. Tris-dependent oxidative DNA strand scission during electrophoresis[J]. Electrophoresis, 1995, 16(1): 888–894. DOI:  10.1002/elps.11501601149.
    [12] Ye J, Coulouris G, Zaretskaya I, et al. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction[J]. BMC Bioinformatics, 2012, 13(1): 134. DOI: 10.1186/1471−2105−13−134.
    [13] Abram K, Udaondo Z, Bleker C, et al. Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups[J]. Commun Biol, 2021, 4: 117. DOI: 10.1038/s42003−020−01626−5.
    [14] Xu TG, Yao F, Zhou XF, et al. A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella[J]. Nucleic Acids Res, 2010, 38(20): 7133–7141. DOI:  10.1093/nar/gkq610.
    [15] Clermont O, Christenson JK, Denamur E, et al. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups[J]. Environ Microbiol Rep, 2013, 5(1): 58–65. DOI: 10.1111/1758−2229.12019.
    [16] Fibke CD, Croxen MA, Geum HM, et al. Genomic epidemiology of major extraintestinal pathogenic Escherichia coli lineages causing urinary tract infections in young women across Canada[J]. Open Forum Infect Dis, 2019, 6(11): ofz431. DOI:  10.1093/ofid/ofz431.
  • 加载中
图(2) / 表(2)
计量
  • 文章访问数:  65
  • HTML全文浏览量:  51
  • PDF下载量:  8
  • 被引次数: 0
出版历程
  • 收稿日期:  2021-10-26
  • 网络出版日期:  2022-03-05
  • 刊出日期:  2022-07-14

目录

    /

    返回文章
    返回

    在线交流

    防诈骗公告

    近期有不法分子以本刊编辑身份添加作者微信,请务必提高警惕!本刊关于稿件的一切事项通知均采用编辑部唯一邮箱(jbjc@icdc.cn)和座机(010-58900732)联系作者,且在录用稿件后仅收取版面费,无其他任何名目费用(如审稿费和加急费等),非编辑部邮箱发送的本刊收费用通知等均为诈骗,不要随意汇入款项!如有可疑及时致电编辑部核实确认!