Molecular methods for the detection and characterization of foodborne pathogens

The surveillance of foodborne pathogens in food industries has shown the urgent need for rapid and dependable methods to detect and characterize the organisms in food and environments of clinical and epidemiologic importance. Recent studies on rapid methods in microbiology have been focused on biochemical characterization, immunoassays, and molecular methods. Many molecular methods have been developed and applied to the detection and characterization of foodborne pathogens in laboratories and food industries. They can be mainly divided into DNA banding pattern-based tests and DNA sequence-based tests. The former includes nucleic acid hybridization, polymerase chain reaction (PCR), amplified restriction length polymorphism, and randomly amplified polymorphic DNA, etc. Most of these methods in commercial applications are based on PCR or hybridization techniques. The principle, characteristics, and application of molecular methods for the detection and characterization of foodborne pathogens were reviewed in this article.

[1]  S. Klemsdal,et al.  Development of a highly sensitive nested‐PCR method using a single closed tube for detection of Fusarium culmorum in cereal samples , 2006, Letters in applied microbiology.

[2]  C. Parker,et al.  Detection and Genotyping of Arcobacter and Campylobacter Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays , 2007, Applied and Environmental Microbiology.

[3]  T. Notomi,et al.  Accelerated reaction by loop-mediated isothermal amplification using loop primers. , 2002, Molecular and cellular probes.

[4]  A. Fernández-Astorga,et al.  Detection of Campylobacter jejuni and Campylobacter coli in chicken meat samples by real-time nucleic acid sequence-based amplification with molecular beacons. , 2007, International journal of food microbiology.

[5]  S. Yamasaki,et al.  Development of a cytolethal distending toxin (cdt) gene-based species-specific multiplex PCR assay for the detection and identification of Campylobacter jejuni, Campylobacter coli and Campylobacter fetus. , 2008, FEMS immunology and medical microbiology.

[6]  Jie Zhang,et al.  Development of reverse transcription loop-mediated isothermal amplification for rapid detection of H9 avian influenza virus. , 2008, Journal of virological methods.

[7]  Simon Kasif,et al.  MuPlex: multi-objective multiplex PCR assay design , 2005, Nucleic Acids Res..

[8]  A. Azzi,et al.  A FRET based melting curve analysis to detect nucleotide variations in HA receptor-binding site of H5N1 virus. , 2010, Molecular and cellular probes.

[9]  Ching-Ho Wang,et al.  Simultaneous detection and differentiation of Newcastle disease and avian influenza viruses using oligonucleotide microarrays. , 2008, Veterinary microbiology.

[10]  Chang-mu Chen,et al.  Detection of porcine parvovirus by loop-mediated isothermal amplification. , 2009, Journal of virological methods.

[11]  V. Sharma.  Real-time reverse transcription-multiplex PCR for simultaneous and specific detection of rfbE and eae genes of Escherichia coli O157:H7. , 2006, Molecular and cellular probes.

[12]  J. Hedlund,et al.  Quantitative detection of Streptococcus pneumoniae from sputum samples with real-time quantitative polymerase chain reaction for etiologic diagnosis of community-acquired pneumonia. , 2008, Diagnostic microbiology and infectious disease.

[13]  S. T. Lambertz,et al.  TaqMan-Based Real-Time PCR Method for Detection of Yersinia pseudotuberculosis in Food , 2008, Applied and Environmental Microbiology.

[14]  Huanchun Chen,et al.  CHARACTERIZATION OF A DUPLEX POLYMERASE CHAIN REACTION ASSAY FOR THE DETECTION OF ENTEROTOXIGENIC STRAINS OF STAPHYLOCOCCUS AUREUS , 2006 .

[15]  H. Iseki,et al.  Development of a multiplex loop-mediated isothermal amplification (mLAMP) method for the simultaneous detection of bovine Babesia parasites. , 2007, Journal of microbiological methods.

[16]  I. Ross,et al.  Use of AFLP and PFGE to discriminate between Salmonella enterica serovar Typhimurium DT126 isolates from separate food-related outbreaks in Australia , 2005, Epidemiology and Infection.

[17]  S. Y. Lee,et al.  Diagnosis of pathogens using DNA microarray. , 2008, Recent patents on biotechnology.

[18]  C. Clark,et al.  Subtyping of Salmonella enterica Serotype Enteritidis Strains by Manual and Automated PstI-SphI Ribotyping , 2003, Journal of Clinical Microbiology.

[19]  Arun K Bhunia,et al.  Biosensors and bio-based methods for the separation and detection of foodborne pathogens. , 2008, Advances in food and nutrition research.

[20]  G. Greening,et al.  Effect of heat treatment on hepatitis A virus and norovirus in New Zealand greenshell mussels (Perna canaliculus) by quantitative real-time reverse transcription PCR and cell culture. , 2006, Journal of food protection.

[21]  Q. Wu,et al.  New target tissue for food‐borne virus detection in oysters , 2008, Letters in applied microbiology.

[22]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[23]  S. Dowd,et al.  Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing , 2008, BMC Microbiology.

[24]  D. van Beers,et al.  Fast Multiplex polymerase chain reaction on boiled clinical samples for rapid viral diagnosis. , 1990, Journal of virological methods.

[25]  Jean-Yves Coppée,et al.  Do DNA microarrays have their future behind them? , 2008, Microbes and infection.

[26]  X. X. Peng,et al.  Immunocapture UPPCR combined with DGGE for rapid detection of Shigella species , 2006, Journal of applied microbiology.

[27]  E. Threlfall,et al.  Combination of pulsed-field gel electrophoresis (PFGE) and single-enzyme amplified fragment length polymorphism (SAFLP) for differentiation of multiresistant Salmonella enterica serotype typhimurium. , 2002, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[28]  K. Mullis,et al.  Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. , 1986, Cold Spring Harbor symposia on quantitative biology.

[29]  Etsuko N. Moriyama,et al.  GenomeBlast: a web tool for small genome comparison , 2006, First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06).

[30]  Q. Qin,et al.  Development of a SYBR Green I real‐time PCR for quantitative detection of Vibrio alginolyticus in seawater and seafood , 2007, Journal of applied microbiology.

[31]  Y. Hara-Kudo,et al.  Loop-mediated isothermal amplification for the rapid detection of Salmonella. , 2005, FEMS microbiology letters.

[32]  C. Corbett,et al.  Comparison of parasitological, immunological and molecular methods for the diagnosis of leishmaniasis in dogs with different clinical signs. , 2007, Veterinary parasitology.

[33]  Nigel Cook,et al.  The use of NASBA for the detection of microbial pathogens in food and environmental samples. , 2003, Journal of microbiological methods.

[34]  A. DePaola,et al.  Development of a Multiplex Real-Time PCR Assay with an Internal Amplification Control for the Detection of Total and Pathogenic Vibrio parahaemolyticus Bacteria in Oysters , 2007, Applied and Environmental Microbiology.

[35]  M. Bullido,et al.  SNP genotyping with FRET probes. Optimizing the resolution of heterozygotes. , 2004, Molecular and cellular probes.

[36]  Weida Tong,et al.  Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential. , 2008, Current opinion in biotechnology.

[37]  N. Casas,et al.  Evaluation of an extracting method for the detection of Hepatitis A virus in shellfish by SYBR-Green real-time RT-PCR. , 2007, International journal of food microbiology.

[38]  Hanlee P. Ji,et al.  The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. , 2006, Nature biotechnology.

[39]  J. Frye,et al.  Rapid Multiplex PCR and Real-Time TaqMan PCR Assays for Detection of Salmonella enterica and the Highly Virulent Serovars Choleraesuis and Paratyphi C , 2008, Journal of Clinical Microbiology.

[40]  Anna Coll,et al.  A molecular beacon-based real time NASBA assay for detection of Listeria monocytogenes in food products: role of target mRNA secondary structure on NASBA design. , 2007, Journal of microbiological methods.

[41]  Xianming Shi,et al.  Development of a quantitative polymerase chain reaction method using a live bacterium as internal control for the detection of Listeria monocytogenes. , 2008, Diagnostic microbiology and infectious disease.

[42]  I. Hwang,et al.  Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene , 2007, Nucleic acids research.

[43]  K. Livak,et al.  Real time quantitative PCR. , 1996, Genome research.

[44]  B. Olgemöller,et al.  Simple technique for internal control of real-time amplification assays. , 2004, Clinical chemistry.

[45]  Pierre Servais,et al.  Detection and enumeration of coliforms in drinking water: current methods and emerging approaches. , 2002, Journal of microbiological methods.

[46]  Kiyoshi Inoue,et al.  Development of a loop-mediated Isothermal amplification assay for sensitive and rapid detection of Vibrio parahaemolyticus , 2008, BMC Microbiology.

[47]  M. Uyttendaele,et al.  Development of a real-time NASBA assay for the detection of Campylobacter jejuni cells. , 2006, Journal of microbiological methods.

[48]  J. Ellis,et al.  Characterization of Escherichia coli populations from gulls, landfill trash, and wastewater using ribotyping. , 2008, Diseases of aquatic organisms.

[49]  F. Strle,et al.  Single-tube nested polymerase chain reaction assay based on flagellin gene sequences for detection ofBorrelia burgdorferi sensu lato , 1996, European Journal of Clinical Microbiology and Infectious Diseases.

[50]  E. Reinoso,et al.  RAPD-PCR analysis of Staphylococcus aureus strains isolated from bovine and human hosts. , 2004, Microbiological research.

[51]  Dongyou Liu.  Molecular Detection of Foodborne Pathogens , 2009 .

[52]  S. Nasim,et al.  Nested polymerase chain reaction assay for the detection of cytomegalovirus overcomes false positives caused by contamination with fragmented DNA , 1990, Journal of medical virology.

[53]  Automated Ribotyping to Distinguish the Different nonSau/ nonSep Staphylococcal Emerging Pathogens in Orthopedic Implant Infections , 2006, The International journal of artificial organs.

[54]  J. Vázquez-Boland,et al.  A Novel Real-Time PCR for Listeria monocytogenes That Monitors Analytical Performance via an Internal Amplification Control , 2005, Applied and Environmental Microbiology.

[55]  S. Kanjilal,et al.  Cloning and development of synthetic internal amplification control for Bacillus anthracis real-time polymerase chain reaction assays. , 2008, Diagnostic microbiology and infectious disease.

[56]  Kozaburo Hayashi,et al.  Loop-Mediated Isothermal Amplification for Direct Detection of Mycobacterium tuberculosis Complex, M. avium, and M. intracellulare in Sputum Samples , 2003, Journal of Clinical Microbiology.

[57]  S. Oliver,et al.  Detection of Campylobacter jejuni in dairy farm environmental samples using SYBR Green real-time polymerase chain reaction. , 2005, Foodborne pathogens and disease.

[58]  J. Arqués,et al.  Combined Effect of High-Pressure Treatments and Bacteriocin-Producing Lactic Acid Bacteria on Inactivation of Escherichia coli O157:H7 in Raw-Milk Cheese , 2005, Applied and Environmental Microbiology.

[59]  S. Lukinmaa,et al.  Diversity of Listeria monocytogenes isolates of human and food origin studied by serotyping, automated ribotyping and pulsed-field gel electrophoresis. , 2004, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[60]  Wayne L. Smith,et al.  Development and evaluation of a real-time FRET probe based multiplex PCR assay for the detection of prohibited meat and bone meal in cattle feed and feed ingredients. , 2006, Foodborne pathogens and disease.

[61]  T. Barry,et al.  Development of a real-time multiplex PCR assay for the detection of multiple Salmonella serotypes in chicken samples , 2008, BMC Microbiology.

[62]  Y. Hara-Kudo,et al.  Sensitive and rapid detection of Vero toxin-producing Escherichia coli using loop-mediated isothermal amplification. , 2007, Journal of medical microbiology.

[63]  Guo Qing Zhang,et al.  Multiplex PCR and Oligonucleotide Microarray for Detection of Single-Nucleotide Polymorphisms Associated with Plasmodium falciparum Drug Resistance , 2008, Journal of Clinical Microbiology.

[64]  Xianming Shi,et al.  Species-specific diagnostic marker for rapid identification of Staphylococcus aureus. , 2007, Diagnostic microbiology and infectious disease.

[65]  M. Griffiths,et al.  Rapid and Quantitative Detection of Hepatitis A Virus from Green Onion and Strawberry Rinses by Use of Real-Time Reverse Transcription-PCR , 2005, Applied and Environmental Microbiology.

[66]  D. Y. Wu,et al.  The ligation amplification reaction (LAR)--amplification of specific DNA sequences using sequential rounds of template-dependent ligation. , 1989, Genomics.

[67]  Guizhong Wang,et al.  Universal primer PCR with DGGE for rapid detection of bacterial pathogens. , 2004, Journal of microbiological methods.

[68]  Wilfred Chen,et al.  Molecular beacons: a real-time polymerase chain reaction assay for detecting Escherichia coli from fresh produce and water. , 2008, Analytica chimica acta.

[69]  Avraham Rasooly,et al.  Food microbial pathogen detection and analysis using DNA microarray technologies. , 2008, Foodborne pathogens and disease.

[70]  M. Lund,et al.  Strategies for the inclusion of an internal amplification control in conventional and real time PCR detection of Campylobacter spp. in chicken fecal samples. , 2006, Molecular and cellular probes.

[71]  R. Lempicki,et al.  Evaluation of gene expression measurements from commercial microarray platforms. , 2003, Nucleic acids research.

[72]  J. Hoorfar,et al.  Practical Considerations in Design of Internal Amplification Controls for Diagnostic PCR Assays , 2004, Journal of Clinical Microbiology.

[73]  B. Imbert-Marcille,et al.  Quantification of Hepatitis A Virus in Shellfish by Competitive Reverse Transcription-PCR with Coextraction of Standard RNA , 1999, Applied and Environmental Microbiology.

[74]  P E Klapper,et al.  Multiplex PCR: Optimization and Application in Diagnostic Virology , 2000, Clinical Microbiology Reviews.

[75]  F. Priest,et al.  Molecular typing of Bacillus thuringiensis serovars by RAPD-PCR. , 2003, Systematic and applied microbiology.

[76]  A. Siitonen,et al.  Ribotyping as an epidemiologic tool for Escherichia coli , 1994, Epidemiology and Infection.

[77]  C. Walker,et al.  Detection of Diarrheagenic Escherichia coli by Use of Melting-Curve Analysis and Real-Time Multiplex PCR , 2008, Journal of Clinical Microbiology.

[78]  An electronic DNA microarray technique for detection and differentiation of viable Campylobacter species. , 2006, The Analyst.

[79]  Andrew G. Glen,et al.  APPL , 2001 .

[80]  H. Davies,et al.  Rapid antigen detection testing in diagnosing group A β-hemolytic streptococcal pharyngitis , 2006, Expert review of molecular diagnostics.

[81]  V. Juneja,et al.  Sensitive detection of viable Listeria monocytogenes by reverse transcription-PCR , 1997, Applied and environmental microbiology.

[82]  J. Blanco,et al.  Serotypes, virulence genes, and PFGE profiles of Escherichia coli isolated from pigs with postweaning diarrhoea in Slovakia , 2006, BMC veterinary research.

[83]  B. Ge,et al.  Evaluation of a loop-mediated isothermal amplification assay for detecting Vibrio vulnificus in raw oysters. , 2008, Foodborne pathogens and disease.

[84]  Y. Hara-Kudo,et al.  Rapid detection of enterotoxigenic Staphylococcus aureus harbouring genes for four classical enterotoxins, SEA, SEB, SEC and SED, by loop‐mediated isothermal amplification assay , 2007, Letters in applied microbiology.

[85]  K. Failing,et al.  New Triplex Real-Time PCR Assay for Detection of Mycobacterium avium subsp. paratuberculosis in Bovine Feces , 2008, Applied and Environmental Microbiology.

[86]  Hsien-Chang Chang,et al.  Discriminating between Achyranthis Bidentatae Radix and Cyathulae Radix in Chinese Medicine Preparations by Nested PCR and DNA Sequencing Methods , 2007, Planta medica.

[87]  F. Qu,et al.  Sensitive and rapid detection of Aeromonas caviae in stool samples by loop-mediated isothermal amplification. , 2008, Diagnostic microbiology and infectious disease.

[88]  Shingo Inoue,et al.  Real-Time Reverse Transcription Loop-Mediated Isothermal Amplification for Rapid Detection of West Nile Virus , 2004, Journal of Clinical Microbiology.

[89]  Ø. Olsvik,et al.  A nested PCR followed by magnetic separation of amplified fragments for detection of Escherichia coli Shiga-like toxin genes. , 1991, Molecular and cellular probes.

[90]  M. Ghanim,et al.  Oligonucleotide microarray-based detection and genotyping of Plum pox virus. , 2008, Journal of virological methods.

[91]  Lei Wang,et al.  Development of a Serotype-Specific DNA Microarray for Identification of Some Shigella and Pathogenic Escherichia coli Strains , 2006, Journal of Clinical Microbiology.

[92]  C. Batt,et al.  Detection of bovine herpesvirus-1 in bovine semen by a nested PCR assay. , 1993, Journal of virological methods.

[93]  M. Aliyu,et al.  Rapid detection and quantitation of hepatitis B virus DNA by real-time PCR using a new fluorescent (FRET) detection system. , 2004, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[94]  R. Shashidhar,et al.  Rapid, sensitive, and validated method for detection of Salmonella in food by an enrichment broth culture - nested PCR combination assay. , 2008, Molecular and cellular probes.

[95]  M. Oh,et al.  Detection of hepatitis a virus from oyster by nested PCR using efficient extraction and concentration method , 2008, The Journal of Microbiology.

[96]  Kiyoshi Inoue,et al.  Development and evaluation of a loop-mediated isothermal amplification assay for rapid and simple detection of Campylobacter jejuni and Campylobacter coli. , 2008, Journal of medical microbiology.

[97]  L. Beutin,et al.  DNA Microarray-Based Identification of Serogroups and Virulence Gene Patterns of Escherichia coli Isolates Associated with Porcine Postweaning Diarrhea and Edema Disease , 2007, Applied and Environmental Microbiology.

[98]  N. Nakasone,et al.  Sensitive and rapid detection of Shigella and enteroinvasive Escherichia coli by a loop-mediated isothermal amplification method. , 2005, FEMS microbiology letters.

[99]  Satoshi Ikeda,et al.  Detection of gene point mutation in paraffin sections using in situ loop‐mediated isothermal amplification , 2007, Pathology international.

[100]  Tae-Ho Lee,et al.  Microarray detection of food-borne pathogens using specific probes prepared by comparative genomics. , 2008, Biosensors & bioelectronics.

[101]  A. Houde,et al.  Comparative evaluation of new TaqMan real-time assays for the detection of hepatitis A virus. , 2007, Journal of virological methods.