高通量测序技术在食源性病原体快速检测中的应用进展
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摘要
探讨高通量测序技术在食源性致病病原体早期检测方面的应用,以充分显示高通量测序技术在食品快速检测、预防食源性疾病传播、疫情调查及作为精细化食品安全管理手段等方面的巨大潜力。评价该技术的优势及缺陷,同时对其在食源性病原体快速检测的应用前景进行展望,以期推动、完善高通量技术在食品安全领域的应用。
The applications of high-throughput sequencing technology(HTS)in the rapid detection of foodborne pathogens were discussed.The great potential of HTS in managing food safety,preventing of foodborne disease spreading,investigating outbreak,and refining food safety management was fully demonstrated.The limitations and advantages of the technique were appraised.The application prospect in rapid detection of foodborne pathogens was prospected.The future prospects of the rapid detection of foodborne pathogens were presented as well,with a view to promoting and improving the application of HTS in food safety.
The applications of high-throughput sequencing technology(HTS)in the rapid detection of foodborne pathogens were discussed.The great potential of HTS in managing food safety,preventing of foodborne disease spreading,investigating outbreak,and refining food safety management was fully demonstrated.The limitations and advantages of the technique were appraised.The application prospect in rapid detection of foodborne pathogens was prospected.The future prospects of the rapid detection of foodborne pathogens were presented as well,with a view to promoting and improving the application of HTS in food safety.
引文
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[3]钟俊良,魏彩姣,赵喜红.食源性致病菌活的不可培养状态研究进展[J].食品科学,2017,38(1):269-275
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[5]胡汝源.我国食源性疾病现状及控制策略[J].公共卫生与预防医学,2007,18(3):55-56
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[7]HENAO O L,JONES T F,VUGIA D J,et al.Foodborne Diseases Active Surveillance Network-2 Decades of Achievements,1996-2015[J].Emerging Infectious Diseases,2015,21(9):1529-1536
[8]ZHAO X,LIN C W,WANG J,et al.Advances in rapid detection methods for foodborne pathogens[J].Journal of Microbiology&Biotechnology,2014,24(3):297-312
[9]PARK S H,AYDIN M,KHATIWARA A,et al.Current and emerging technologies for rapid detection and characterization of Salmonella in poultry and poultry products[J].Food Microbiology,2014,38(4):250-262
[10]EMOND-RHEAULT J G,JEUKENS J,FRESCHI L,et al.A SystOMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis[J].Front Microbiol,2017,8:996-1014
[11]MARCHESI J R,RAVEL J.The vocabulary of microbiome research:a proposal[J].Microbiome,2015,3(1):31-33
[12]DIJK V,ERWIN L,HELENE,et al.Ten years of next-generation sequencing technology[J].Trends in Genetics,2014,30(9):418-426
[13]ONDOV B D,VARADARAJAN A,PASSALACQUA K D,et al.Efficient mapping of Applied BiosystemsSOLiD sequence data to a reference genome for functional genomic applications[J].Bioinformatics,2008,24(23):2776-2777
[14]RHOADS A,AU K F.PacBio Sequencing and Its Applications[J].Genomics,Proteomics&Bioinformatics,2015,13(5):278-289
[15]DOYLE C J,GLEESON D,O'TOOLE P W,et al.High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions[J].International Journal of Food Microbiology,2017,255:1-6
[16]张敏,张艳,兰国伟,等.高通量测序技术在乳制品微生物多样性中的研究进展[J].中国农学通报,2016,32(32):48-52
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[22]UNDERWOOD A P,TIM D,THOMSON N R,et al.Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak[J].Journal of Clinical Microbiology,2013,51(1):232-237
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[25]SUN Z,PENG Y,ZHANG M,et al,Simultaneous and highly sensitive detection of six different foodborne pathogens by high-throughput suspension array technology[J].Food Contr,2014,40(2):300-309
[26]LOMAN N J,CONSTANTINIDOU C,CHRISTNER M,et al.A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4[J].Jama the Journal of the American Medical Association,2013,309(14):1502-1510
[27]OTTESEN A R,GONZALEZ A,BELL R,et al.Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere[J].Plos One,2013,8(9):e73079
[28]OTTESEN A,RAMACHANDRAN P,REED E,et al.Enrichment dynamics of Listeria monocytogenesand the associated microbiome from naturally contaminated ice cream linked to a listeriosisoutbreak[J].Bmc Microbiology,2016,16(1):275
[29]LEONARD S R,MAMMEL M K,LACHER D W,et al.Application of Metagenomic Sequencing to Food Safety:Detection of Shiga Toxin-Producing Escherichia coli on Fresh Bagged Spinach[J].Applied&Environmental Microbiology,2015,81(23):8183-8191
[30]FILIPPIS F D,STORIA A L,STELLATO G,et al.A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures[J].Plos One,2014,9(2):e89680
[31]ANDREEVSKAYA M,JOHANSSON P,LAINE P,et al.Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcuspiscium MKFS47[J].Appl Environ Microbiol,2015,81(11):3800-3811
[32]ERCOLINI D,FERROCINO I,NASI A,et al.Monitoring of Microbial Metabolites and Bacterial Diversity in Beef Stored under Different Packaging Conditions[J].Appl Environ Microbiol,2011,77(20):7372-7381
[33]MOREIRA D,L魷PEZ-GARC魱A P.Ten reasons to exclude viruses from the tree of life[J].Nature Reviews Microbiology,2009,7(4):306-311
[34]HAYES S,MAHONY J,NAUTA A,et al.Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches[J].Viruses,2017,9(6):127
[35]NEWELL D G,KOOPMANS M,VERHOEF L,et al.Food-borne diseases-the challenges of 20 years ago still persist while new ones continue to emerge[J].International Journal of Food Microbiology,2010,139(1):S3-S15
[36]SEVERI E,VERHOEF L,THORNTON L,et al.Large and prolonged food-borne multistate hepatitis A outbreak in Europe associated with consumption of frozen berries,2013 to 2014[J].European communicable disease bulletin,2015,20(29):21192
[37]洪志恒,冉陆,杨静,等.2016年12月全国突发公共卫生事件及需关注的传染病风险评估[J].疾病监测,2016,31(12):348-352
[38]高志勇,严寒秋,刘白薇,等.北京地区市售牡蛎轮状病毒污染调查[J].中华实验和临床病毒学杂志,2016(1):41-44
[39]COLLIER M G,KHUDYAKOV Y E,SELVAGE D,et al.Outbreak of hepatitis A in the USA associated with frozen pomegranate arils imported from Turkey:an epidemiological case study[J].Lancet Infectious Diseases,2014,14(10):976-981
[40]MIZUKOSHI F,KURODA M,TSUKAGOSHI H,et al.A food-borne outbreak of gastroenteritis due to genotype G1P[8]rotavirus among adolescents in Japan[J].Microbiology&Immunology,2014,58(9):536-539
[41]张静娜,王译葵,蒋岩,等.高通量测序技术用于丙型肝炎病毒感染溯源调查[J].中华预防医学杂志,2016,50(6):530-534
[42]PIRES S M,FISCHER-WALKER C L,LANATA C F,et al.Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food[J].Plos One,2015,10(12):1-17
[43]SCALLAN E,HOEKSTRA R M,ANGULO F J,et al.Foodborne illness acquired in the United States-major pathogens[J].Emerg Infect Dis,2011,17:7-15
[44]IMAMURA S,HARUNA M,GOSHIMA T,et al.Application of next-generation sequencing to investigation of norovirus diversity in shellfish collected from two coastal sites in Japan from 2013 to 2014[J].Japanese Journal of Veterinary Research,2016,64(2):113-122
[45]AW T G,WENGERT S,ROSE J B.Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses[J].International Journal of Food Microbiology,2016,223:50-56
[46]FERNANDEZCASSI X,TIMONEDA N,GONZALESGUSTAVSONE,et al.A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water[J].International Journal of Food Microbiology,2017,257:80-90
[47]郑乾明,王壮,彭志军,等.利用高通量测序分析侵染贵州火龙果的病毒[J].植物病理学报,2017,47(3):364-369
[48]刘林,张益,李阿茜,等.应用高通量测序技术鉴别中国输入性黄热病毒野毒株与疫苗株[J].中华实验和临床病毒学杂志,2017,31(4):353-356
[49]QUICK J,LOMAN N J,DURAFFOUR S,et al.Real-time,portable genome sequencing for Ebola surveillance[J].Nature,2016,530(7589):228-232
[50]BENEDICT K,CHILLER T M,MODY R K.Invasive Fungal Infections Acquired from Contaminated Food or Nutritional Supplements:A Review of the Literature[J].Foodborne Pathogens&Disease,2016,13(7):343-349
[51]LEE S C,BILLMYRE R B,LI A,et al.Analysis of a Food-Borne Fungal Pathogen Outbreak:Virulence and Genome of a Mucorcircinelloides Isolate from Yogurt[J].Mbio,2014,5(4):01390-01314
[52]BILLMYRE R B,CROLL D,LI W,et al.Highly recombinant VGIICryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution[J].Mbio,2014,5(4):01494-01509
[53]VAUX S,CRISCUOLO A,DESNOS-OLLIVIER M,et al.Multicenter outbreak of infections by Saprochaeteclavata,an unrecognized opportunistic fungal pathogen[J].Mbio,2014,5(6):2309-2318
[54]KAWAI T,SEKIZUKA T,YAHATA Y,et al.Identification of Kudoaseptempunctata as the causative agent of novel food poisoning outbreaks in Japan by consumption of Paralichthysolivaeusc in raw fish[J].Clin.infect.dis,2012,54(8):1046-1052
[55]CUCCURU G,ORSINI M,PINNA A,et al.Orione,a web-based framework for NGS analysis in microbiology[J].Bioinformatics,2014,30(13):1928-1929
[2]TAYEL A A,EL-TRAS W F.Anticandidal activity of pomegranate peel extract aerosol as an applicable sanitizing method[J].Mycoses,2010,53(2):117-122
[3]钟俊良,魏彩姣,赵喜红.食源性致病菌活的不可培养状态研究进展[J].食品科学,2017,38(1):269-275
[4]MARTINOVIC T,ANDJELKOVIC U,GAJDOSIK M S,et al.Foodborne pathogens and their toxins[J].Journal of Proteomics,2016,147:226-235
[5]胡汝源.我国食源性疾病现状及控制策略[J].公共卫生与预防医学,2007,18(3):55-56
[6]Team E E.ECDC publishes the annual epidemiological report2012[J].Euro Surveill,2013,18(10):20418-20418
[7]HENAO O L,JONES T F,VUGIA D J,et al.Foodborne Diseases Active Surveillance Network-2 Decades of Achievements,1996-2015[J].Emerging Infectious Diseases,2015,21(9):1529-1536
[8]ZHAO X,LIN C W,WANG J,et al.Advances in rapid detection methods for foodborne pathogens[J].Journal of Microbiology&Biotechnology,2014,24(3):297-312
[9]PARK S H,AYDIN M,KHATIWARA A,et al.Current and emerging technologies for rapid detection and characterization of Salmonella in poultry and poultry products[J].Food Microbiology,2014,38(4):250-262
[10]EMOND-RHEAULT J G,JEUKENS J,FRESCHI L,et al.A SystOMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis[J].Front Microbiol,2017,8:996-1014
[11]MARCHESI J R,RAVEL J.The vocabulary of microbiome research:a proposal[J].Microbiome,2015,3(1):31-33
[12]DIJK V,ERWIN L,HELENE,et al.Ten years of next-generation sequencing technology[J].Trends in Genetics,2014,30(9):418-426
[13]ONDOV B D,VARADARAJAN A,PASSALACQUA K D,et al.Efficient mapping of Applied BiosystemsSOLiD sequence data to a reference genome for functional genomic applications[J].Bioinformatics,2008,24(23):2776-2777
[14]RHOADS A,AU K F.PacBio Sequencing and Its Applications[J].Genomics,Proteomics&Bioinformatics,2015,13(5):278-289
[15]DOYLE C J,GLEESON D,O'TOOLE P W,et al.High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions[J].International Journal of Food Microbiology,2017,255:1-6
[16]张敏,张艳,兰国伟,等.高通量测序技术在乳制品微生物多样性中的研究进展[J].中国农学通报,2016,32(32):48-52
[17]ASTRIDGE K,BARKER M,BELL R,et al.Monitoring the incidence and causes of diseases potentially transmitted by food in Australia:Annual report of the OzFoodNet network,(2011)[J].Communicable Diseases Intelligence Quarterly Report,2015,39,E236-E264
[18]Marder E P,Cieslak P R,Cronquist A B,et al.Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food and the Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance-Foodborne Diseases Active Surveillance Network,10 U.S.Sites,2013-2016[J].Mmwr Morbidity&Mortality Weekly Report,2017,66(15):397-403
[19]JOENSEN K G,SCHEUTZ F,LUND O,et al.Real-time wholegenome sequencing for routine typing,surveillance,and outbreak detection of verotoxigenic Escherichia coli[J].Journal of Clinical Microbiology,2014,52(5):1501-1510
[20]ANNE H,LESLEY A,MELISSA W,et al.Utility of Whole-Genome Sequencing ofEscherichia coliO157 for Outbreak Detection and Epidemiological Surveillance[J].Journal of Clinical Microbiology,2015,53(11):3565-3573
[21]FORBES J D,KNOX N C,RONHOLM J,et al.Metagenomics:The Next Culture-Independent Game Changer[J].Frontiers in Microbiology,2017,8:1069-1089
[22]UNDERWOOD A P,TIM D,THOMSON N R,et al.Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak[J].Journal of Clinical Microbiology,2013,51(1):232-237
[23]GILMOUR M W,GRAHAM M,DOMSELAAR G V,et al.Highthroughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak[J].Bmc Genomics,2010,11(1):120
[24]郭启新,张蕾,张柏棋,等.液相基因芯片法同时检测3种食源性病原菌[J].食品科学,2013,34(16):191-195
[25]SUN Z,PENG Y,ZHANG M,et al,Simultaneous and highly sensitive detection of six different foodborne pathogens by high-throughput suspension array technology[J].Food Contr,2014,40(2):300-309
[26]LOMAN N J,CONSTANTINIDOU C,CHRISTNER M,et al.A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4[J].Jama the Journal of the American Medical Association,2013,309(14):1502-1510
[27]OTTESEN A R,GONZALEZ A,BELL R,et al.Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere[J].Plos One,2013,8(9):e73079
[28]OTTESEN A,RAMACHANDRAN P,REED E,et al.Enrichment dynamics of Listeria monocytogenesand the associated microbiome from naturally contaminated ice cream linked to a listeriosisoutbreak[J].Bmc Microbiology,2016,16(1):275
[29]LEONARD S R,MAMMEL M K,LACHER D W,et al.Application of Metagenomic Sequencing to Food Safety:Detection of Shiga Toxin-Producing Escherichia coli on Fresh Bagged Spinach[J].Applied&Environmental Microbiology,2015,81(23):8183-8191
[30]FILIPPIS F D,STORIA A L,STELLATO G,et al.A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures[J].Plos One,2014,9(2):e89680
[31]ANDREEVSKAYA M,JOHANSSON P,LAINE P,et al.Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcuspiscium MKFS47[J].Appl Environ Microbiol,2015,81(11):3800-3811
[32]ERCOLINI D,FERROCINO I,NASI A,et al.Monitoring of Microbial Metabolites and Bacterial Diversity in Beef Stored under Different Packaging Conditions[J].Appl Environ Microbiol,2011,77(20):7372-7381
[33]MOREIRA D,L魷PEZ-GARC魱A P.Ten reasons to exclude viruses from the tree of life[J].Nature Reviews Microbiology,2009,7(4):306-311
[34]HAYES S,MAHONY J,NAUTA A,et al.Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches[J].Viruses,2017,9(6):127
[35]NEWELL D G,KOOPMANS M,VERHOEF L,et al.Food-borne diseases-the challenges of 20 years ago still persist while new ones continue to emerge[J].International Journal of Food Microbiology,2010,139(1):S3-S15
[36]SEVERI E,VERHOEF L,THORNTON L,et al.Large and prolonged food-borne multistate hepatitis A outbreak in Europe associated with consumption of frozen berries,2013 to 2014[J].European communicable disease bulletin,2015,20(29):21192
[37]洪志恒,冉陆,杨静,等.2016年12月全国突发公共卫生事件及需关注的传染病风险评估[J].疾病监测,2016,31(12):348-352
[38]高志勇,严寒秋,刘白薇,等.北京地区市售牡蛎轮状病毒污染调查[J].中华实验和临床病毒学杂志,2016(1):41-44
[39]COLLIER M G,KHUDYAKOV Y E,SELVAGE D,et al.Outbreak of hepatitis A in the USA associated with frozen pomegranate arils imported from Turkey:an epidemiological case study[J].Lancet Infectious Diseases,2014,14(10):976-981
[40]MIZUKOSHI F,KURODA M,TSUKAGOSHI H,et al.A food-borne outbreak of gastroenteritis due to genotype G1P[8]rotavirus among adolescents in Japan[J].Microbiology&Immunology,2014,58(9):536-539
[41]张静娜,王译葵,蒋岩,等.高通量测序技术用于丙型肝炎病毒感染溯源调查[J].中华预防医学杂志,2016,50(6):530-534
[42]PIRES S M,FISCHER-WALKER C L,LANATA C F,et al.Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food[J].Plos One,2015,10(12):1-17
[43]SCALLAN E,HOEKSTRA R M,ANGULO F J,et al.Foodborne illness acquired in the United States-major pathogens[J].Emerg Infect Dis,2011,17:7-15
[44]IMAMURA S,HARUNA M,GOSHIMA T,et al.Application of next-generation sequencing to investigation of norovirus diversity in shellfish collected from two coastal sites in Japan from 2013 to 2014[J].Japanese Journal of Veterinary Research,2016,64(2):113-122
[45]AW T G,WENGERT S,ROSE J B.Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses[J].International Journal of Food Microbiology,2016,223:50-56
[46]FERNANDEZCASSI X,TIMONEDA N,GONZALESGUSTAVSONE,et al.A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water[J].International Journal of Food Microbiology,2017,257:80-90
[47]郑乾明,王壮,彭志军,等.利用高通量测序分析侵染贵州火龙果的病毒[J].植物病理学报,2017,47(3):364-369
[48]刘林,张益,李阿茜,等.应用高通量测序技术鉴别中国输入性黄热病毒野毒株与疫苗株[J].中华实验和临床病毒学杂志,2017,31(4):353-356
[49]QUICK J,LOMAN N J,DURAFFOUR S,et al.Real-time,portable genome sequencing for Ebola surveillance[J].Nature,2016,530(7589):228-232
[50]BENEDICT K,CHILLER T M,MODY R K.Invasive Fungal Infections Acquired from Contaminated Food or Nutritional Supplements:A Review of the Literature[J].Foodborne Pathogens&Disease,2016,13(7):343-349
[51]LEE S C,BILLMYRE R B,LI A,et al.Analysis of a Food-Borne Fungal Pathogen Outbreak:Virulence and Genome of a Mucorcircinelloides Isolate from Yogurt[J].Mbio,2014,5(4):01390-01314
[52]BILLMYRE R B,CROLL D,LI W,et al.Highly recombinant VGIICryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution[J].Mbio,2014,5(4):01494-01509
[53]VAUX S,CRISCUOLO A,DESNOS-OLLIVIER M,et al.Multicenter outbreak of infections by Saprochaeteclavata,an unrecognized opportunistic fungal pathogen[J].Mbio,2014,5(6):2309-2318
[54]KAWAI T,SEKIZUKA T,YAHATA Y,et al.Identification of Kudoaseptempunctata as the causative agent of novel food poisoning outbreaks in Japan by consumption of Paralichthysolivaeusc in raw fish[J].Clin.infect.dis,2012,54(8):1046-1052
[55]CUCCURU G,ORSINI M,PINNA A,et al.Orione,a web-based framework for NGS analysis in microbiology[J].Bioinformatics,2014,30(13):1928-1929