一株含有5个原噬菌体的单增李斯特菌比较基因组分析
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摘要
单增李斯特菌是一种重要的人畜共患病原菌,对食品安全和人类健康造成了严重威胁,但现阶段对其进化规律的研究仍相对较少。本研究运用Illumina测序技术对一株中国单增李斯特菌WaX12的基因组进行了测定,并通过比较基因组学分析了该菌的微进化规律。结果表明:WaX12的基因组与Finland 1998相似度最高,但两者基因组间存在135个基因的差异,主要集中在WaX12的原噬菌体上。进一步分析可知,WaX12的基因组携带5个原噬菌体,除原噬菌体1外,其余4个原噬菌体均未存在于Finland 1998中。原噬菌体3和原噬菌体5来源于其他单增李斯特菌的基因组,而原噬菌体2和原噬菌体4则分别来自于大肠杆菌和粪球菌。由此可见,原噬菌体是该单增李斯特菌微进化的主要原因,而这种微进化的发生不仅限于同一种属的细菌之间,还可能源于不同种属细菌间的基因转移。
Listeria monocytogenes, an important zoonotic pathogen, poses a serious threat to food safety and human health, but the research on its evolution is still relatively limited at present. In this study, we sequenced the genome of L. monocytogenes WaX12 isolated from China by using Illumina technology, and analyzed its microevolution by comparative genome. The results showed that WaX12 strain had the highest similarity in genomic sequences with the Finland 1998 strain, but there were 135 different genes between two genomes, which mainly located on the prophages in WaX12. Further analysis indicated that L. monocytogenes strain WaX12 contained five prophages, of which four prophages didn't exist in Finland 1998 except for prophage 1. In addition,prophage 3 and prophage 5 came from other strains of L. monocytogenes, while prophage 2 and prophage 4 came from Escherichia coli and Enterococcus respectively. Thus, prophages were the major reason of the microevolution of WaX12, and this occurrence not only limited in the same species of L. monocytogenes, but may also result from the genes transfer between different species of bacteria.
Listeria monocytogenes, an important zoonotic pathogen, poses a serious threat to food safety and human health, but the research on its evolution is still relatively limited at present. In this study, we sequenced the genome of L. monocytogenes WaX12 isolated from China by using Illumina technology, and analyzed its microevolution by comparative genome. The results showed that WaX12 strain had the highest similarity in genomic sequences with the Finland 1998 strain, but there were 135 different genes between two genomes, which mainly located on the prophages in WaX12. Further analysis indicated that L. monocytogenes strain WaX12 contained five prophages, of which four prophages didn't exist in Finland 1998 except for prophage 1. In addition,prophage 3 and prophage 5 came from other strains of L. monocytogenes, while prophage 2 and prophage 4 came from Escherichia coli and Enterococcus respectively. Thus, prophages were the major reason of the microevolution of WaX12, and this occurrence not only limited in the same species of L. monocytogenes, but may also result from the genes transfer between different species of bacteria.
引文
Aziz R.K.,Bartels D.,Best A.A.,De Jongh M.,Disz T.,Edward R.A.,Formsma K.,Gerdes S.,Glass E.M.,Kubal M.,Meye F.,Olsen G.J.,Olson R.,Osterman A.L.,Overbeek R.A.Mc Neil L.K.,Paarmann D.,Paczian T.,Parrello B.,Pusch G.D.,Reich C.,Stevens R.,Vassieva O.,Vonstein V.,Wilk A.,and Zagnitko O.,2008,The RAST Server:rapid annota tions using subsystems technology,BMC Genomics,9:75
Cock P.J.,Fields C.J.,Goto N.,Heuer M.L.,and Rice P.M.2010,The Sanger FASTQ file format for sequences with quality scores,and the Solexa/Illumina FASTQ variants,Nu cleic Acids Research,38:1767-1771
Campoccia D.,Testoni F.,Ravaioli S.,Cangini I.,Maso A.Speziale P.,Montanaro L.,Visai L.,and Arciola C.A.2016,Orthopedic implant infections:incompetence o Staphylococcus epidermidis,Staphylococcus lugdunensis and Enterococcusfaecalito invade osteoblasts,Journal o Biomedical Materials Research Part A,104(3):788-801
Denes T.,Vongkamjan K.,Ackermann H.W.,Switt A.I.M.Wiedmann M.,and dan Bakker H.C.,2014,Comparativ genomic and morphological analyses of Listeria phages iso lated from farm environments,Applied and Environmenta Microbiology,80:4616-4625
Dorscht J.,Klumpp J.,Bielmann R.,Schmelcher M.,Born Y.Zimmer M.,Calendar R.,and Loessner M.J.,2009,Compar ative genome analysis of Listeria bacteriophages reveals ex tensive mosaicism,programmed translational frameshifting and a novel prophage insertion site,Journal of Bacteriology191:7206-7215
Farber J.M.,and Peterkin P.I.,1991,Listeria monocytogenes,a foodborne pathogen,Microbiological Reviews,55:476-511
Flelschmann R.D.,Adams M.D.,White O.,Clayton R.A.,Kirkness E.F.,Kerlavage A.R.,Bult C.J.,Tomb J.F.,Dougherty B.A.,and Merrick J.M.,1995,Whole-genome random sequencing and assembly of Haemophilus influenzae Rd,Sci ence,269(5223):496-512
Fortier L.C.,and Sekulovic O.,2013,Importance of prophages to evolution and virulence of bacterial pathogens,Virulence,4354-365
Glaser P.,Frangeul L.,Buchrieser C.,Rusniok C.,Amend A.Ba quero F.,Berche P.,Bloecker H.,Brandt P.Chakraborty T.,Charbit A.,Chetouani F.,CouvéE.,de Daruvar A.,Dehoux P.,Domann E.,Dominguez-Bernal G.Duchaud E.,Durant L.,Dussurget O.,Entian K.D.,Fsih H.,Garcia-Del Portillo F.,Garrido P.,Gautier L.,Goebe W.,Gómez-López N.,Hain T.,Hauf J.,Jackson D.,Jone L.M.,Kaerst U.,Kreft J.,Kuhn M.,Kunst F.,Kurapkat G.Madue觡o E.,Maitournam A.,Mata Vicente J.,Ng E.,Nedjari H.,Nordsiek G.,Novella S.,de Pablos B.,Pérez-Diaz JC.,Purcell R.,Remmel B.,Rose M.,Schlueter T.,Simoes N.,Tierrez A.,Vázquez-Boland J.A.,Voss H.,Wehland J.and Cossart P.,2001,Comparative genomics of Listeria species,Science,294:849-852
Hu Z.Y.,Wang Y.Z.,Lm W.T.,Wang S.Y.,Zhao G.P.,Zheng H.J.and Quan Z.X.,2014,The first complete genome sequence o the class Fimbriimonadia in the Phylum Armatimonadetes PLo S One,9(6):e100794
Jaimee G.,and Halami P.M.,2016,High level aminoglycoside resistance in Enterococcus,Pediococcus and Lactobacillu species from farm animals and commercial meat products Annals of Micbioligy,66(1):101-110
Liu P.P.,Wang S.H.,Zhao Q.H.,Li B.B.,Shao D.H.,Shi Z.X.Wei J.C.,and Ma Z.Y.,2013,Multilocus sequence typing of Listeria monocytogenes from animal foods in Shanghai Zhongguo Dongwu Chuanranbing Xuebao(Chinese Journa of Animal Infectious Diseases),21(4):18-22(刘萍萍,王少辉,赵秋华,李蓓蓓,邵东华,史子学,魏建超,马志永2013,上海市动物源性食品中单增李斯特菌的MLST分析,中国动物传染病学报,21(4):18-22)
Liu W.F.,Wang X.L.,Zhao Y.H.,Zeng J.Y.,and Geng J.N.2011,The brief introduction of research strategies for bacterial genome and transcripome based on the next-generation sequencing technologies,Weishengwuxue Tongbao(Microbiology China),38(11):1705-1714(刘万飞,王西亮,赵宇慧曾瀞瑶,耿佳宁,胡松年,2011,基于第二代测序技术的细菌基因组与转录组研究策略简介,微生物学通报,38(11)1705-1714)
Loessner M.J.,Inman R.B.,Lauer P.,and Calendar R.,2000,Com plete nucleotide sequence,molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes implications for phage evolution,Molecular Microbiology35:324-340
Lyytikainen O.,Autio T.,Maijala R.,Ruutu P.,Honkanen-Buzal ski T.,Miettinen M.,Hatakka M.,Mikkola J.,Anttila V.J.,Jo hansson T.,Rantala L.,Aalto T.,Korkeala H.,and Siitonen A.2000,An outbreak of Listeria monocytogenesserotype 3a in fections from butter in Finland,Journal of Infectious Disase181:1838-1841
Maidak B.L.,Cole J.R.,Parker Jr C.T.,Garrity G.M.,Larsen N.Li B.,Lilburn T.G.,Mc Caughey M.J.,Olsen G.J.,Overbeek R.,Pramanik S.,Schmidt T.M.,Tiedje J.M.,and Woese C.R.1999,A new version of the RDP(Ribosomal Database Pro ject),Nucleic Acids Research,27(1):171-173
Medema M.H.,Takano E.,and Breitling R.,2013,Detecting se quence homology at the gene cluster level with Multi Gene Blast,Molecular Biology and Evolution,30:1218-1223
Muyzer G.,de Waal E.C.,and Uitterlinden A.G.,1993,Profiling of complex microbial populations by denaturing gradient ge electrophoresis analysis of polymerase chain reaction-ampli fied genes coding for 16S r RNA,Applied and Environmen tal Microbiology,59(3):695-700
Murray E.G.D.,Webb R.A.,and Swann H.B.R.,1926,A disease of rabbits characterized by a large mononuclear leucocyto sis caused by a hitherto undescribed bacillus Bacterium monocytogenes(n.sp.),Journal of Pathology and Bacteriolo gy,29:407-439
Ou H.Y.,Kuang S.N.,He X.Y.,Molgora B.M.,Ewing P.J.,Deng Z.X.,Osby M.,Chen W.X.,and Xu H.H,2015,Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4:epidemiology,re sistance genetic determinants and potential virulence factors Scientific Reports,5:8643
Reddy A.R.S,Girinathan B.P.,Zapotocny R.,Zapotocny R.,and Govind R.,2013,Identification and characterization o Clostridium sordellii toxin gene regulator,Journal of Bacte riology,195:4246-4254
Rissman A.I.,Mau B.,Biehl B.S.,Darling A.E.,Glasmer J.D.and Perna N.T.,2009,Reorderingcontigs of draft genome using the Mauve aligner,Bioinformatics,25:2071-2073
Schmitz-Esser S.,Müller A.,Stessl B.,and Wagner M.,2015Genomes of sequence type 121 Listeria monocytogene strains harbor highly conserved plasmids and prophages Fronties in Microbiology,6(380):380
Sch覿ferkordt S.,and Chakraborty T.,1997,Identification cloning,and characterization of the Lma operon,whose gene products are unique to Listeria monocytogenes,Journal o Bacteriology,179:2707-2716
Shao Y.C.,He X.Y.,Harrison E.M.,Tai C.,Ou H.Y.,Rajakumar Kand Deng Z.X.,2010,MGenome Subtractor:a web-based too for parallel in silico subtractive hybridization analysis of mul tiple bacterial genomes,Nucleic Acids Research,38:194-200
Valk D.H.,Vaillant V.,Jacquet C.,Rocourt J.,Querrec F.L.Stainer F.,Quelquejet N.,Pierre O.,Pierre V.,Desenclos J.C.and Goulet V.,1999,Two consecutive nationwide outbreak of Listeriosis in France,American Journal of Epidemiology154:944-950
Vukov N.,Moll I.,Bl覿si U.,Scherer S.,and Loessner M.J.,2003,Functional regulation of the Listeria monocytogenes bacteriophag A118 holin by an intragenic inhibitor lacking the first trans membrane domain,Molecular Microbiology,48:173-186
Wang I.N.,Smith D.L.,and Young R.,2000,Holins:the protein clocks of bacteriophage infections,Annual Review of Mi crobiology,54:799-825
Wang X.X.,Kim Y.,Ma Q.,Hong S.H.,Pokusaeva K.,Sturino J.M.,and Wood T.K.,2010,Cryptic prophages help bacteri a cope with adverse environments,Nature Communication1(147):1-9
Wang Y.,Zhao Ailian.,Zhu R.F.,Lan R.T.,Jin D.,Cui Z.G.Wang Y.L.,Li Z.C.,Wang Y.T.,Xu J.G.,and Ye C.Y.2012,Genetic diversity and molecular typing of Listeria monocytogenes in China,BMC Microbiology,12:119
Zhou Y.,Liang Y.J.,Lynch K.H.,Dennis J.J.,and Wishart D.S.2011,PHAST:A fast phage search tool,Nucleic Acids Re search,39:347-352
Zhang M.,Ito T.,Li S.S.,Jin J.X.,Takeuchi F.,Yang Lauderdale T.L.,Higashide M.,and Hiramatsu K.,2011,Identification of the third type of PVL phage in ST59 methicillin-resistan Staphylococcus aureus(MRSA)strains,FEMS Microbiology Letters,323:20-28
Cock P.J.,Fields C.J.,Goto N.,Heuer M.L.,and Rice P.M.2010,The Sanger FASTQ file format for sequences with quality scores,and the Solexa/Illumina FASTQ variants,Nu cleic Acids Research,38:1767-1771
Campoccia D.,Testoni F.,Ravaioli S.,Cangini I.,Maso A.Speziale P.,Montanaro L.,Visai L.,and Arciola C.A.2016,Orthopedic implant infections:incompetence o Staphylococcus epidermidis,Staphylococcus lugdunensis and Enterococcusfaecalito invade osteoblasts,Journal o Biomedical Materials Research Part A,104(3):788-801
Denes T.,Vongkamjan K.,Ackermann H.W.,Switt A.I.M.Wiedmann M.,and dan Bakker H.C.,2014,Comparativ genomic and morphological analyses of Listeria phages iso lated from farm environments,Applied and Environmenta Microbiology,80:4616-4625
Dorscht J.,Klumpp J.,Bielmann R.,Schmelcher M.,Born Y.Zimmer M.,Calendar R.,and Loessner M.J.,2009,Compar ative genome analysis of Listeria bacteriophages reveals ex tensive mosaicism,programmed translational frameshifting and a novel prophage insertion site,Journal of Bacteriology191:7206-7215
Farber J.M.,and Peterkin P.I.,1991,Listeria monocytogenes,a foodborne pathogen,Microbiological Reviews,55:476-511
Flelschmann R.D.,Adams M.D.,White O.,Clayton R.A.,Kirkness E.F.,Kerlavage A.R.,Bult C.J.,Tomb J.F.,Dougherty B.A.,and Merrick J.M.,1995,Whole-genome random sequencing and assembly of Haemophilus influenzae Rd,Sci ence,269(5223):496-512
Fortier L.C.,and Sekulovic O.,2013,Importance of prophages to evolution and virulence of bacterial pathogens,Virulence,4354-365
Glaser P.,Frangeul L.,Buchrieser C.,Rusniok C.,Amend A.Ba quero F.,Berche P.,Bloecker H.,Brandt P.Chakraborty T.,Charbit A.,Chetouani F.,CouvéE.,de Daruvar A.,Dehoux P.,Domann E.,Dominguez-Bernal G.Duchaud E.,Durant L.,Dussurget O.,Entian K.D.,Fsih H.,Garcia-Del Portillo F.,Garrido P.,Gautier L.,Goebe W.,Gómez-López N.,Hain T.,Hauf J.,Jackson D.,Jone L.M.,Kaerst U.,Kreft J.,Kuhn M.,Kunst F.,Kurapkat G.Madue觡o E.,Maitournam A.,Mata Vicente J.,Ng E.,Nedjari H.,Nordsiek G.,Novella S.,de Pablos B.,Pérez-Diaz JC.,Purcell R.,Remmel B.,Rose M.,Schlueter T.,Simoes N.,Tierrez A.,Vázquez-Boland J.A.,Voss H.,Wehland J.and Cossart P.,2001,Comparative genomics of Listeria species,Science,294:849-852
Hu Z.Y.,Wang Y.Z.,Lm W.T.,Wang S.Y.,Zhao G.P.,Zheng H.J.and Quan Z.X.,2014,The first complete genome sequence o the class Fimbriimonadia in the Phylum Armatimonadetes PLo S One,9(6):e100794
Jaimee G.,and Halami P.M.,2016,High level aminoglycoside resistance in Enterococcus,Pediococcus and Lactobacillu species from farm animals and commercial meat products Annals of Micbioligy,66(1):101-110
Liu P.P.,Wang S.H.,Zhao Q.H.,Li B.B.,Shao D.H.,Shi Z.X.Wei J.C.,and Ma Z.Y.,2013,Multilocus sequence typing of Listeria monocytogenes from animal foods in Shanghai Zhongguo Dongwu Chuanranbing Xuebao(Chinese Journa of Animal Infectious Diseases),21(4):18-22(刘萍萍,王少辉,赵秋华,李蓓蓓,邵东华,史子学,魏建超,马志永2013,上海市动物源性食品中单增李斯特菌的MLST分析,中国动物传染病学报,21(4):18-22)
Liu W.F.,Wang X.L.,Zhao Y.H.,Zeng J.Y.,and Geng J.N.2011,The brief introduction of research strategies for bacterial genome and transcripome based on the next-generation sequencing technologies,Weishengwuxue Tongbao(Microbiology China),38(11):1705-1714(刘万飞,王西亮,赵宇慧曾瀞瑶,耿佳宁,胡松年,2011,基于第二代测序技术的细菌基因组与转录组研究策略简介,微生物学通报,38(11)1705-1714)
Loessner M.J.,Inman R.B.,Lauer P.,and Calendar R.,2000,Com plete nucleotide sequence,molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes implications for phage evolution,Molecular Microbiology35:324-340
Lyytikainen O.,Autio T.,Maijala R.,Ruutu P.,Honkanen-Buzal ski T.,Miettinen M.,Hatakka M.,Mikkola J.,Anttila V.J.,Jo hansson T.,Rantala L.,Aalto T.,Korkeala H.,and Siitonen A.2000,An outbreak of Listeria monocytogenesserotype 3a in fections from butter in Finland,Journal of Infectious Disase181:1838-1841
Maidak B.L.,Cole J.R.,Parker Jr C.T.,Garrity G.M.,Larsen N.Li B.,Lilburn T.G.,Mc Caughey M.J.,Olsen G.J.,Overbeek R.,Pramanik S.,Schmidt T.M.,Tiedje J.M.,and Woese C.R.1999,A new version of the RDP(Ribosomal Database Pro ject),Nucleic Acids Research,27(1):171-173
Medema M.H.,Takano E.,and Breitling R.,2013,Detecting se quence homology at the gene cluster level with Multi Gene Blast,Molecular Biology and Evolution,30:1218-1223
Muyzer G.,de Waal E.C.,and Uitterlinden A.G.,1993,Profiling of complex microbial populations by denaturing gradient ge electrophoresis analysis of polymerase chain reaction-ampli fied genes coding for 16S r RNA,Applied and Environmen tal Microbiology,59(3):695-700
Murray E.G.D.,Webb R.A.,and Swann H.B.R.,1926,A disease of rabbits characterized by a large mononuclear leucocyto sis caused by a hitherto undescribed bacillus Bacterium monocytogenes(n.sp.),Journal of Pathology and Bacteriolo gy,29:407-439
Ou H.Y.,Kuang S.N.,He X.Y.,Molgora B.M.,Ewing P.J.,Deng Z.X.,Osby M.,Chen W.X.,and Xu H.H,2015,Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4:epidemiology,re sistance genetic determinants and potential virulence factors Scientific Reports,5:8643
Reddy A.R.S,Girinathan B.P.,Zapotocny R.,Zapotocny R.,and Govind R.,2013,Identification and characterization o Clostridium sordellii toxin gene regulator,Journal of Bacte riology,195:4246-4254
Rissman A.I.,Mau B.,Biehl B.S.,Darling A.E.,Glasmer J.D.and Perna N.T.,2009,Reorderingcontigs of draft genome using the Mauve aligner,Bioinformatics,25:2071-2073
Schmitz-Esser S.,Müller A.,Stessl B.,and Wagner M.,2015Genomes of sequence type 121 Listeria monocytogene strains harbor highly conserved plasmids and prophages Fronties in Microbiology,6(380):380
Sch覿ferkordt S.,and Chakraborty T.,1997,Identification cloning,and characterization of the Lma operon,whose gene products are unique to Listeria monocytogenes,Journal o Bacteriology,179:2707-2716
Shao Y.C.,He X.Y.,Harrison E.M.,Tai C.,Ou H.Y.,Rajakumar Kand Deng Z.X.,2010,MGenome Subtractor:a web-based too for parallel in silico subtractive hybridization analysis of mul tiple bacterial genomes,Nucleic Acids Research,38:194-200
Valk D.H.,Vaillant V.,Jacquet C.,Rocourt J.,Querrec F.L.Stainer F.,Quelquejet N.,Pierre O.,Pierre V.,Desenclos J.C.and Goulet V.,1999,Two consecutive nationwide outbreak of Listeriosis in France,American Journal of Epidemiology154:944-950
Vukov N.,Moll I.,Bl覿si U.,Scherer S.,and Loessner M.J.,2003,Functional regulation of the Listeria monocytogenes bacteriophag A118 holin by an intragenic inhibitor lacking the first trans membrane domain,Molecular Microbiology,48:173-186
Wang I.N.,Smith D.L.,and Young R.,2000,Holins:the protein clocks of bacteriophage infections,Annual Review of Mi crobiology,54:799-825
Wang X.X.,Kim Y.,Ma Q.,Hong S.H.,Pokusaeva K.,Sturino J.M.,and Wood T.K.,2010,Cryptic prophages help bacteri a cope with adverse environments,Nature Communication1(147):1-9
Wang Y.,Zhao Ailian.,Zhu R.F.,Lan R.T.,Jin D.,Cui Z.G.Wang Y.L.,Li Z.C.,Wang Y.T.,Xu J.G.,and Ye C.Y.2012,Genetic diversity and molecular typing of Listeria monocytogenes in China,BMC Microbiology,12:119
Zhou Y.,Liang Y.J.,Lynch K.H.,Dennis J.J.,and Wishart D.S.2011,PHAST:A fast phage search tool,Nucleic Acids Re search,39:347-352
Zhang M.,Ito T.,Li S.S.,Jin J.X.,Takeuchi F.,Yang Lauderdale T.L.,Higashide M.,and Hiramatsu K.,2011,Identification of the third type of PVL phage in ST59 methicillin-resistan Staphylococcus aureus(MRSA)strains,FEMS Microbiology Letters,323:20-28