1887
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.

Molecular Tools To Study Preharvest Food Safety Challenges

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
Buy this Microbiology Spectrum Article
Price Non-Member $15.00
  • Authors: Deepak Kumar1, Siddhartha Thakur2
  • Editors: Kalmia E. Kniel3, Siddhartha Thakur4
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Veterinary Public Health & Epidemiology, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture & Technology, Pantnagar, Uttarakhand-263145, India; 2: Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607; 3: Department of Animal and Food Science, University of Delaware, Newark, DE; 4: North Carolina State University, College of Veterinary Medicine, Raleigh, NC
  • Source: microbiolspec February 2018 vol. 6 no. 1 doi:10.1128/microbiolspec.PFS-0019-2017
  • Received 06 October 2017 Accepted 02 January 2018 Published 23 February 2018
  • Siddhartha Thakur, sthakur@ncsu.edu
image of Molecular Tools To Study Preharvest Food Safety Challenges
    Preview this microbiology spectrum article:
    Zoom in
    Zoomout

    Molecular Tools To Study Preharvest Food Safety Challenges, Page 1 of 2

    | /docserver/preview/fulltext/microbiolspec/6/1/PFS-0019-2017-1.gif /docserver/preview/fulltext/microbiolspec/6/1/PFS-0019-2017-2.gif
  • Abstract:

    Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization–time of flight mass spectrometry and whole-genome sequencing.

  • Citation: Kumar D, Thakur S. 2018. Molecular Tools To Study Preharvest Food Safety Challenges. Microbiol Spectrum 6(1):PFS-0019-2017. doi:10.1128/microbiolspec.PFS-0019-2017.

References

1. Blaha T. 1997. Public health and pork: pre-harvest food safety and slaughter perspectives. Rev Sci Tech 16:489–495. [PubMed]
2. Blaha TH. 1996. What’s coming in food safety and pork quality, p 136–138. Proceedings of the 23rd Allen D. Leman Conference, 21–24 September, St Paul, MN.
3. Buntain B. 1997. The role of the food animal veterinarian in the HACCP era. J Am Vet Med Assoc 210:492–495. [PubMed]
4. Food and Drug Administration (FDA). 2015. Summary report on antimicrobials sold or distributed for use in food-producing animals. https://www.fda.gov/downloads/forindustry/userfees/animaldruguserfeeactadufa/ucm534243.pdf. Accessed July 22, 2017.
5. Turnidge J. 2004. Antibiotic use in animals: prejudices, perceptions and realities. J Antimicrob Chemother 53:26–27. [PubMed]
6. Singer RS, Finch R, Wegener HC, Bywater R, Walters J, Lipsitch M. 2003. Antibiotic resistance: the interplay between antibiotic use in animals and human beings. Lancet Infect Dis 3:47–51. [PubMed]
7. Angeletti S. 2017. Matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology. J Microbiol Methods 138:20–29. [PubMed]
8. Dixon P, Davies P, Hollingworth W, Stoddart M, MacGowan A. 2015. A systematic review of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry compared to routine microbiological methods for the time taken to identify microbial organisms from positive blood cultures. Eur J Clin Microbiol Infect Dis 34:863–876. [PubMed]
9. Lupo A, Papp-Wallace KM, Sendi P, Bonomo RA, Endimiani A. 2013. Non-phenotypic tests to detect and characterize antibiotic resistance mechanisms in Enterobacteriaceae. Diagn Microbiol Infect Dis 77:179–194. [PubMed]
10. Mullis KB, Faloona FA. 1987. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 155:335–350.
11. Predari SC, Ligozzi M, Fontana R. 1991. Genotypic identification of methicillin-resistant coagulase-negative staphylococci by polymerase chain reaction. Antimicrob Agents Chemother 35:2568–2573. [PubMed]
12. Keelara S, Scott HM, Morrow WM, Gebreyes WA, Correa M, Nayak R, Stefanova R, Thakur S. 2013. Longitudinal study of distributions of similar antimicrobial-resistant Salmonella serovars in pigs and their environment in two distinct swine production systems. Appl Environ Microbiol 79:5167–5178. [PubMed]
13. Paião FG, Arisitides LGA, Murate LS, Vilas-Bôas GT, Vilas-Boas LA, Shimokomaki M. 2013. Detection of Salmonella spp, Salmonella Enteritidis and Typhimurium in naturally infected broiler chickens by a multiplex PCR-based assay. Braz J Microbiol 44:37–41. [PubMed]
14. Frana TS, Beahm AR, Hanson BM, Kinyon JM, Layman LL, Karriker LA, Ramirez A, Smith TC. 2013. Isolation and characterization of methicillin-resistant Staphylococcus aureus from pork farms and visiting veterinary students. PLoS One 8:e53738. [PubMed]
15. Markoulatos P, Siafakas N, Moncany M. 2002. Multiplex polymerase chain reaction: a practical approach. J Clin Lab Anal 16:47–51. [PubMed]
16. Radhika M, Saugata M, Murali HS, Batra HV. 2014. A novel multiplex PCR for the simultaneous detection of Salmonella enterica and Shigella species. Braz J Microbiol 45:667–676. [PubMed]
17. Alvarez J, Sota M, Vivanco AB, Perales I, Cisterna R, Rementeria A, Garaizar J. 2004. Development of a multiplex PCR technique for detection and epidemiological typing of Salmonella in human clinical samples. J Clin Microbiol 42:1734–1738. [PubMed]
18. Kawasaki S, Horikoshi N, Okada Y, Takeshita K, Sameshima T, Kawamoto S. 2005. Multiplex PCR for simultaneous detection of Salmonella spp., Listeria monocytogenes, and Escherichia coli O157:H7 in meat samples. J Food Prot 68:551–556. [PubMed]
19. Park SH, Hanning I, Jarquin R, Moore P, Donoghue DJ, Donoghue AM, Ricke SC. 2011. Multiplex PCR assay for the detection and quantification of Campylobacter spp., Escherichia coli O157:H7, and Salmonella serotypes in water samples. FEMS Microbiol Lett 316:7–15. [PubMed]
20. Klena JD, Parker CT, Knibb K, Ibbitt JC, Devane PM, Horn ST, Miller WG, Konkel ME. 2004. Differentiation of Campylobacter coli, Campylobacter jejuni, Campylobacter lari, and Campylobacter upsaliensis by a multiplex PCR developed from the nucleotide sequence of the lipid A gene lpxA. J Clin Microbiol 42:5549–5557. [PubMed]
21. Persoons D, Van Hoorebeke S, Hermans K, Butaye P, de Kruif A, Haesebrouck F, Dewulf J. 2009. Methicillin-resistant Staphylococcus aureus in poultry. Emerg Infect Dis 15:452–453. [PubMed]
22. Chen J, Tang J, Liu J, Cai Z, Bai X. 2012. Development and evaluation of a multiplex PCR for simultaneous detection of five foodborne pathogens. J Appl Microbiol 112:823–830. [PubMed]
23. Rawool DB, Doijad SP, Poharkar KV, Negi M, Kale SB, Malik SV, Kurkure NV, Chakraborty T, Barbuddhe SB. 2016. A multiplex PCR for detection of Listeria monocytogenes and its lineages. J Microbiol Methods 130:144–147. [PubMed]
24. Akiba M, Kusumoto M, Iwata T. 2011. Rapid identification of Salmonella enterica serovars, Typhimurium, Choleraesuis, Infantis, Hadar, Enteritidis, Dublin and Gallinarum, by multiplex PCR. J Microbiol Methods 85:9–15. [PubMed]
25. Kralik P, Ricchi M. 2017. A basic guide to real time PCR in microbial diagnostics: definitions, parameters, and everything. Front Microbiol 8:108.
26. Higuchi R, Dollinger G, Walsh PS, Griffith R. 1992. Simultaneous amplification and detection of specific DNA sequences. Biotechnology (N Y) 10:413–417.
27. Malorny B, Paccassoni E, Fach P, Bunge C, Martin A, Helmuth R. 2004. Diagnostic real-time PCR for detection of Salmonella in food. Appl Environ Microbiol 70:7046–7052. [PubMed]
28. Alemu K. 2014. Real-time PCR and its application in plant disease diagnostics. Adv Life Sci Technol 27:39–49.
29. Navarro E, Serrano-Heras G, Castaño MJ, Solera J. 2015. Real-time PCR detection chemistry. Clin Chim Acta 439:231–250. [PubMed]
30. Hein I, Lehner A, Rieck P, Klein K, Brandl E, Wagner M. 2001. Comparison of different approaches to quantify Staphylococcus aureus cells by real-time quantitative PCR and application of this technique for examination of cheese. Appl Environ Microbiol 67:3122–3126. [PubMed]
31. Fukushima H, Tsunomori Y, Seki R. 2003. Duplex real-time SYBR green PCR assays for detection of 17 species of food- or waterborne pathogens in stools. J Clin Microbiol 41:5134–5146. [PubMed]
32. Singh J, Batish VK, Grover S. 2009. A molecular beacon-based duplex real-time polymerase chain reaction assay for simultaneous detection of Escherichia coli O157:H7 and Listeria monocytogenes in milk and milk products. Foodborne Pathog Dis 6:1195–1201. [PubMed]
33. Jamnikar Ciglenecki U, Grom J, Toplak I, Jemersić L, Barlič-Maganja D. 2008. Real-time RT-PCR assay for rapid and specific detection of classical swine fever virus: comparison of SYBR Green and TaqMan MGB detection methods using novel MGB probes. J Virol Methods 147:257–264.
34. Madani M, Subbotin SA, Moens M. 2005. Quantitative detection of the potato cyst nematode, Globodera pallida, and the beet cyst nematode, Heterodera schachtii, using real-time PCR with SYBR green I dye. Mol Cell Probes 19:81–86. [PubMed]
35. Lauri A, Mariani PO. 2009. Potentials and limitations of molecular diagnostic methods in food safety. Genes Nutr 4:1–12. [PubMed]
36. Levin RE. 2005. The application of real-time PCR to food and agricultural systems. A review. Food Biotechnol 18:97–133.
37. Klein D. 2002. Quantification using real-time PCR technology: applications and limitations. Trends Mol Med 8:257–260.
38. Marthaler D, Raymond L, Jiang Y, Collins J, Rossow K, Rovira A. 2014. Rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus. Emerg Infect Dis 20:1347–1350. [PubMed]
39. Marthaler D, Homwong N, Rossow K, Culhane M, Goyal S, Collins J, Matthijnssens J, Ciarlet M. 2014. Rapid detection and high occurrence of porcine rotavirus A, B, and C by RT-qPCR in diagnostic samples. J Virol Methods 209:30–34. [PubMed]
40. Rodriguez-Lazaro D, Cook N, Hernandez M. 2013. Real-time PCR in food science: PCR diagnostics. Curr Issues Mol Biol 15:39–44. [PubMed]
41. O’Regan E, McCabe E, Burgess C, McGuinness S, Barry T, Duffy G, Whyte P, Fanning S. 2008. Development of a real-time multiplex PCR assay for the detection of multiple Salmonella serotypes in chicken samples. BMC Microbiol 8:156. [PubMed]
42. Fukushima H, Kawase J, Etoh Y, Sugama K, Yashiro S, Iida N, Yamaguchi K. 2010. Simultaneous screening of 24 target genes of foodborne pathogens in 35 foodborne outbreaks using multiplex real-time SYBR green PCR analysis. Int J Microbiol 2010:1–18. [PubMed]
43. Fratamico PM, Bagi LK, Cray WC Jr, Narang N, Yan X, Medina M, Liu Y. 2011. Detection by multiplex real-time polymerase chain reaction assays and isolation of Shiga toxin-producing Escherichia coli serogroups O26, O45, O103, O111, O121, and O145 in ground beef. Foodborne Pathog Dis 8:601–607. [PubMed]
44. Denis E, Bielińska K, Wieczorek K, Osek J. 2016. Multiplex real-time PCRs for detection of Salmonella, Listeria monocytogenes, and verotoxigenic Escherichia coli in carcasses of slaughtered animals. J Vet Res (Pulawy) 60:287–292.
45. Kim HJ, Lee HJ, Lee KH, Cho JC. 2012. Simultaneous detection of pathogenic Vibrio species using multiplex real-time PCR. Food Control 23:491–498.
46. Hu Q, Lyu D, Shi X, Jiang Y, Lin Y, Li Y, Qiu Y, He L, Zhang R, Li Q. 2014. A modified molecular beacons-based multiplex real-time PCR assay for simultaneous detection of eight foodborne pathogens in a single reaction and its application. Foodborne Pathog Dis 11:207–214. [PubMed]
47. Hanemaaijer NM, Nijhuis RHT, Slotboom BJ, Mascini EM, van Zwet AA. 2014. New screening method to detect carriage of carbapenemase-producing Enterobacteriaceae in patients within 24 hours. J Hosp Infect 87:47–49. [PubMed]
48. Lowman W, Marais M, Ahmed K, Marcus L. 2014. Routine active surveillance for carbapenemase-producing Enterobacteriaceae from rectal swabs: diagnostic implications of multiplex polymerase chain reaction. J Hosp Infect 88:66–71. [PubMed]
49. Chen L, Chavda KD, Mediavilla JR, Zhao Y, Fraimow HS, Jenkins SG, Levi MH, Hong T, Rojtman AD, Ginocchio CC, Bonomo RA, Kreiswirth BN. 2012. Multiplex real-time PCR for detection of an epidemic KPC-producing Klebsiella pneumoniae ST258 clone. Antimicrob Agents Chemother 56:3444–3447. [PubMed]
50. Roschanski N, Fischer J, Guerra B, Roesler U. 2014. Development of a multiplex real-time PCR for the rapid detection of the predominant beta-lactamase genes CTX-M, SHV, TEM and CIT-type AmpCs in Enterobacteriaceae. PLoS One 9:e100956. [PubMed]
51. Guo D, Liu B, Liu F, Cao B, Chen M, Hao X, Feng L, Wang L. 2013. Development of a DNA microarray for molecular identification of all 46 Salmonella O serogroups. Appl Environ Microbiol 79:3392–3399. [PubMed]
52. Sibley CD, Peirano G, Church DL. 2012. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. Infect Genet Evol 12:505–521. [PubMed]
53. Law JW, Ab Mutalib NS, Chan KG, Lee LH. 2015. Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations. Front Microbiol 5:770. [PubMed]
54. Wang XW, Zhang L, Jin LQ, Jin M, Shen ZQ, An S, Chao FH, Li JW. 2007. Development and application of an oligonucleotide microarray for the detection of food-borne bacterial pathogens. Appl Microbiol Biotechnol 76:225–233. [PubMed]
55. Li Y, Liu D, Cao B, Han W, Liu Y, Liu F, Guo X, Bastin DA, Feng L, Wang L. 2006. Development of a serotype-specific DNA microarray for identification of some Shigella and pathogenic Escherichia coli strains. J Clin Microbiol 44:4376–4383. [PubMed]
56. Bang J, Beuchat LR, Song H, Gu MB, Chang HI, Kim HS, Ryu JH. 2013. Development of a random genomic DNA microarray for the detection and identification of Listeria monocytogenes in milk. Int J Food Microbiol 161:134–141. [PubMed]
57. Scaria J, Palaniappan RUM, Chiu D, Phan JA, Ponnala L, McDonough P, Grohn YT, Porwollik S, McClelland M, Chiou CS, Chu C, Chang YF. 2008. Microarray for molecular typing of Salmonella enterica serovars. Mol Cell Probes 22:238–243. [PubMed]
58. Porwollik S, Boyd EF, Choy C, Cheng P, Florea L, Proctor E, McClelland M. 2004. Characterization of Salmonella enterica subspecies I genovars by use of microarrays. J Bacteriol 186:5883–5898. [PubMed]
59. Braun SD, Ziegler A, Methner U, Slickers P, Keiling S, Monecke S, Ehricht R. 2012. Fast DNA serotyping and antimicrobial resistance gene determination of Salmonella enterica with an oligonucleotide microarray-based assay. PLoS One 7:e46489. [PubMed]
60. Keramas G, Bang DD, Lund M, Madsen M, Bunkenborg H, Telleman P, Christensen CBV. 2004. Use of culture, PCR analysis, and DNA microarrays for detection of Campylobacter jejuni and Campylobacter coli from chicken feces. J Clin Microbiol 42:3985–3991. [PubMed]
61. Keramas G, Bang DD, Lund M, Madsen M, Rasmussen SE, Bunkenborg H, Telleman P, Christensen CBV. 2003. Development of a sensitive DNA microarray suitable for rapid detection of Campylobacter spp. Mol Cell Probes 17:187–196.
62. Laksanalamai P, Jackson SA, Mammel MK, Datta AR. 2012. High density microarray analysis reveals new insights into genetic footprints of Listeria monocytogenes strains involved in listeriosis outbreaks. PLoS One 7:e32896. [PubMed]
63. Chiang YC, Yang CY, Li C, Ho YC, Lin CK, Tsen HY. 2006. Identification of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with 16S ribosomal DNA-based oligonucleotide array hybridization. Int J Food Microbiol 107:131–137. [PubMed]
64. Perreten V, Vorlet-Fawer L, Slickers P, Ehricht R, Kuhnert P, Frey J. 2005. Microarray-based detection of 90 antibiotic resistance genes of Gram-positive bacteria. J Clin Microbiol 43:2291–2302. [PubMed]
65. De Boer SH, López MM. 2012. New grower-friendly methods for plant pathogen monitoring. Annu Rev Phytopathol 50:197–218. [PubMed]
66. Everett KR, Rees-George J, Pushparajah IPS, Janssen BJ, Luo Z. 2010. Advantages and disadvantages of microarrays to study microbial population dynamics: a mini review. N Z Plant Prot 63:1–6.
67. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T. 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28:E63. [PubMed]
68. Mori Y, Nagamine K, Tomita N, Notomi T. 2001. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Biophys Res Commun 289:150–154. [PubMed]
69. Tomita N, Mori Y, Kanda H, Notomi T. 2008. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat Protoc 3:877–882. [PubMed]
70. Liu N, Zou D, Dong D, Yang Z, Ao D, Liu W, Huang L. 2017. Development of a multiplex loop-mediated isothermal amplification method for the simultaneous detection of Salmonella spp. and Vibrio parahaemolyticus. Sci Rep 7:45601. [PubMed]
71. Chen HT, Zhang J, Sun DH, Ma LN, Liu XT, Cai XP, Liu YS. 2008. Development of reverse transcription loop-mediated isothermal amplification for rapid detection of H9 avian influenza virus. J Virol Methods 151:200–203. [PubMed]
72. Wang D, Wang Y, Xiao F, Guo W, Zhang Y, Wang A, Liu Y. 2015. A comparison of in-house real-time LAMP assays with a commercial assay for the detection of pathogenic bacteria. Molecules 20:9487–9495. [PubMed]
73. Shao Y, Zhu S, Jin C, Chen F. 2011. Development of multiplex loop-mediated isothermal amplification-RFLP (mLAMP-RFLP) to detect Salmonella spp. and Shigella spp. in milk. Int J Food Microbiol 148:75–79. [PubMed]
74. Wang Y, Wang Y, Ma A, Li D, Luo L, Liu D, Hu S, Jin D, Liu K, Ye C. 2015. The novel multiple inner primers-loop-mediated isothermal amplification (MIP-LAMP) for rapid detection and differentiation of Listeria monocytogenes. Molecules 20:21515–21531. [PubMed]
75. Ye Y, Wang B, Huang F, Song Y, Yan H, Alam MJ, Yamasaki S, Shi L. 2011. Application of in situ loop-mediated isothermal amplification method for detection of Salmonella in foods. Food Control 22:438–444.
76. Xu Z, Li L, Chu J, Peters BM, Harris ML, Li B, Shi L, Shirtliff ME. 2012. Development and application of loop-mediated isothermal amplification assays on rapid detection of various types of staphylococci strains. Food Res Int 47:166–173. [PubMed]
77. Frickmann H, Masanta WO, Zautner AE. 2014. Emerging rapid resistance testing methods for clinical microbiology laboratories and their potential impact on patient management. Biomed Res Int 2014:375681. doi:10.1155/2014/375681. [PubMed]
78. Hordijk J, Wagenaar JA, Kant A, van Essen-Zandbergen A, Dierikx C, Veldman K, Wit B, Mevius D. 2013. Cross-sectional study on prevalence and molecular characteristics of plasmid mediated ESBL/AmpC-producing Escherichia coli isolated from veal calves at slaughter. PLoS One 8:e65681. [PubMed]
79. Dong HJ, Cho AR, Hahn TW, Cho S. 2014. Development of a loop-mediated isothermal amplification assay for rapid, sensitive detection of Campylobacter jejuni in cattle farm samples. J Food Prot 77:1593–1598. [PubMed]
80. Yamazaki W, Taguchi M, Kawai T, Kawatsu K, Sakata J, Inoue K, Misawa N. 2009. Comparison of loop-mediated isothermal amplification assay and conventional culture methods for detection of Campylobacter jejuni and Campylobacter coli in naturally contaminated chicken meat samples. Appl Environ Microbiol 75:1597–1603. [PubMed]
81. Tang MJ, Zhou S, Zhang XY, Pu JH, Ge QL, Tang XJ, Gao YS. 2011. Rapid and sensitive detection of Listeria monocytogenes by loop-mediated isothermal amplification. Curr Microbio 63:511–516. [PubMed]
82. Koide Y, Maeda H, Yamabe K, Naruishi K, Yamamoto T, Kokeguchi S, Takashiba S. 2010. Rapid detection of mecA and spa by the loop-mediated isothermal amplification (LAMP) method. Lett Appl Microbiol 50:386–392. [PubMed]
83. Chen C, Zhao Q, Guo J, Li Y, Chen Q. 2017. Identification of methicillin-resistant Staphylococcus aureus (MRSA) using simultaneous detection of mecA, nuc, and femB by loop-mediated isothermal amplification (LAMP). Curr Microbiol 74:965–971. [PubMed]
84. Croxatto A, Prod’hom G, Greub G. 2012. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 36:380–407. [PubMed]
85. Fenselau C, Demirev PA. 2001. Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom Rev 20:157–171. [PubMed]
86. Singhal N, Kumar M, Kanaujia PK, Virdi JS. 2015. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 6:791. [PubMed]
87. Freiwald A, Sauer S. 2009. Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc 4:732–742. [PubMed]
88. Kang L, Li N, Li P, Zhou Y, Gao S, Gao H, Xin W, Wang J. 2017. MALDI-TOF mass spectrometry provides high accuracy in identification of Salmonella at species level but is limited to type or subtype Salmonella serovars. Eur J Mass Spectrom 23:70–82. [PubMed]
89. Dieckmann R, Malorny B. 2011. Rapid screening of epidemiologically important Salmonella enterica subsp. enterica serovars by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 77:4136–4146. [PubMed]
90. Mandrell RE, Harden LA, Bates A, Miller WG, Haddon WF, Fagerquist CK. 2005. Speciation of Campylobacter coli, C. jejuni, C. helveticus, C. lari, C. sputorum, and C. upsaliensis by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 71:6292–6307. [PubMed]
91. Cameron M, Barkema HW, De Buck J, De Vliegher S, Chaffer M, Lewis J, Keefe GP. 2017. Identification of bovine-associated coagulase-negative staphylococci by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a direct transfer protocol. J Dairy Sci 100:2137–2147. [PubMed]
92. Wolters M, Rohde H, Maier T, Belmar-Campos C, Franke G, Scherpe S, Aepfelbacher M, Christner M. 2011. MALDI-TOF MS fingerprinting allows for discrimination of major methicillin-resistant Staphylococcus aureus lineages. Int J Med Microbiol 301:64–68. [PubMed]
93. Egli A, Tschudin-Sutter S, Oberle M, Goldenberger D, Frei R, Widmer AF. 2015. Matrix-assisted laser desorption/ionization time of flight mass-spectrometry (MALDI-TOF MS) based typing of extended-spectrum β-lactamase producing E. coli: a novel tool for real-time outbreak investigation. PLoS One 10:e0120624. [PubMed]
94. Carbonnelle E, Beretti JL, Cottyn S, Quesne G, Berche P, Nassif X, Ferroni A. 2007. Rapid identification of staphylococci isolated in clinical microbiology laboratories by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 45:2156–2161. [PubMed]
95. Emonet S, Shah HN, Cherkaoui A, Schrenzel J. 2010. Application and use of various mass spectrometry methods in clinical microbiology. Clin Microbiol Infect 16:1604–1613. [PubMed]
96. Urwyler SK, Glaubitz J. 2016. Advantage of MALDI-TOF-MS over biochemical-based phenotyping for microbial identification illustrated on industrial applications. Lett Appl Microbiol 62:130–137. [PubMed]
97. Tran A, Alby K, Kerr A, Jones M, Gilligan PH. 2015. Cost savings realized by implementation of routine microbiological identification by matrix-assisted laser desorption ionization–time of flight mass spectrometry. J Clin Microbiol 53:2473–2479. [PubMed]
98. Trindade PA, McCulloch JA, Oliveira GA, Mamizuka EM. 2003. Molecular techniques for MRSA typing: current issues and perspectives. Braz J Infect Dis 7:32–43. [PubMed]
99. Chroma M, Kolar M. 2010. Genetic methods for detection of antibiotic resistance: focus on extended-spectrum β-lactamases. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 154:289–296. [PubMed]
100. Mohran ZS, Guerry P, Lior H, Murphy JR, el-Gendy AM, Mikhail MM, Oyofo BA. 1996. Restriction fragment length polymorphism of flagellin genes of Campylobacter jejuni and/or C. coli isolates from Egypt. J Clin Microbiol 34:1216–1219. [PubMed]
101. Babalola OO. 2003. Molecular techniques: an overview of methods for the detection of bacteria. Afr J Biotechnol 2:710–713.
102. Chen Y, Son I. 2014. Polymerase chain reaction-based subtyping methods, p 3–26. In Oyarzabal OA, Kathariou S (ed), DNA Methods in Food Safety. Molecular Typing of Foodborne and Waterborne Bacterial Pathogens. Wiley-Blackwell, Oxford, United Kingdom.
103. Lin AW, Usera MA, Barrett TJ, Goldsby RA. 1996. Application of random amplified polymorphic DNA analysis to differentiate strains of Salmonella enteritidis. J Clin Microbiol 34:870–876. [PubMed]
104. Shangkuan YH, Lin HC. 1998. Application of random amplified polymorphic DNA analysis to differentiate strains of Salmonella typhi and other Salmonella species. J Appl Microbiol 85:693–702.
105. Yoshida T, Takeuchi M, Sato M, Hirai K. 1999. Typing Listeria monocytogenes by random amplified polymorphic DNA (RAPD) fingerprinting. J Vet Med Sci 61:857–860. [PubMed]
106. Hernandez J, Fayos A, Ferrus MA, Owen RJ. 1995. Random amplified polymorphic DNA fingerprinting of Campylobacter jejuni and C. coli isolated from human faeces, seawater and poultry products. Res Microbiol 146:685–696.
107. Açik MN, Cetinkaya B. 2006. Random amplified polymorphic DNA analysis of Campylobacter jejuni and Campylobacter coli isolated from healthy cattle and sheep. J Med Microbiol 55:331–334. [PubMed]
108. Barbut F, Mario N, Delmée M, Gozian J, Petit JC. 1993. Genomic fingerprinting of Clostridium difficile isolates by using a random amplified polymorphic DNA (RAPD) assay. FEMS Microbiol Lett 114:161–166. [PubMed]
109. Roussel S, Félix B, Grant K, Dao TT, Brisabois A, Amar C. 2013. Fluorescence amplified fragment length polymorphism compared to pulsed field gel electrophoresis for Listeria monocytogenes subtyping. BMC Microbiol 13:14. [PubMed]
110. Singh DV, Mohapatra H. 2008. Application of DNA-based methods in typing Vibrio cholerae strains. Future Microbiol 3:87–96. [PubMed]
111. Guerra MM, Bernardo F, McLauchlin J. 2002. Amplified fragment length polymorphism (AFLP) analysis of Listeria monocytogenes. Syst Appl Microbiol 25:456–461. [PubMed]
112. Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau M. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414. [PubMed]
113. Savelkoul PHM, Aarts HJM, de Haas J, Dijkshoorn L, Duim B, Otsen M, Rademaker JL, Schouls L, Lenstra JA. 1999. Amplified-fragment length polymorphism analysis: the state of an art. J Clin Microbiol 37:3083–3091. [PubMed]
114. Duim B, Vandamme PA, Rigter A, Laevens S, Dijkstra JR, Wagenaar JA. 2001. Differentiation of Campylobacter species by AFLP fingerprinting. Microbiology 147:2729–2737. [PubMed]
115. Aarts HJ, Hakemulder LE, Van Hoef AM. 1999. Genomic typing of Listeria monocytogenes strains by automated laser fluorescence analysis of amplified fragment length polymorphism fingerprint patterns. Int J Food Microbiol 49:95–102.
116. Ross IL, Heuzenroeder MW. 2005. Use of AFLP and PFGE to discriminate between Salmonella enterica serovar Typhimurium DT126 isolates from separate food-related outbreaks in Australia. Epidemiol Infect 133:635–644.
117. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145. [PubMed]
118. Cooper JE, Feil EJ. 2004. Multilocus sequence typing: what is resolved? Trends Microbiol 12:373–377. [PubMed]
119. Enright MC, Spratt BG. 1999. Multilocus sequence typing. Trends Microbiol 7:482–487.
120. Knabel J. 2014. Multilocus sequence typing: an adaptable tool for understanding the global epidemiology of bacterial pathogens, p 47–64. In Oyarzabal OA, Kathariou S (ed), DNA Methods in Food Safety. Molecular Typing of Foodborne and Waterborne Bacterial Pathogens. Wiley-Blackwell, Oxford, United Kingdom.
121. Thakur S, Morrow WE, Funk JA, Bahnson PB, Gebreyes WA. 2006. Molecular epidemiologic investigation of Campylobacter coli in swine production systems, using multilocus sequence typing. Appl Environ Microbiol 72:5666–5669. [PubMed]
122. Thakur S, White DG, McDermott PF, Zhao S, Kroft B, Gebreyes W, Abbott J, Cullen P, English L, Carter P, Harbottle H. 2009. Genotyping of Campylobacter coli isolated from humans and retail meats using multilocus sequence typing and pulsed-field gel electrophoresis. J Appl Microbiol 106:1722–1733. [PubMed]
123. Zhao X, Gao Y, Ye C, Yang L, Wang T, Chang W. 2016. Prevalence and Characteristics of Salmonella isolated from free-range chickens in Shandong Province, China. BioMed Res Int 2016:8183931. [PubMed]
124. Thakur S, Gebreyes WA. 2010. Phenotypic and genotypic heterogeneity of Campylobacter coli within individual pigs at farm and slaughter in the US. Zoonoses Public Health 57(Suppl 1):100–106. [PubMed]
125. Stone D, Davis M, Baker K, Besser T, Roopnarine R, Sharma R. 2013. MLST genotypes and antibiotic resistance of Campylobacter spp. isolated from poultry in Grenada. BioMed Res Int 2013:794643. [PubMed]
126. Vidal AB, Colles FM, Rodgers JD, McCarthy ND, Davies RH, Maiden MC, Clifton-Hadley FA. 2016. Genetic diversity of Campylobacter jejuni and Campylobacter coli isolates from conventional broiler flocks and the impacts of sampling strategy and laboratory method. Appl Environ Microbiol 82:2347–2355. [PubMed]
127. Molla B, Byrne M, Abley M, Mathews J, Jackson CR, Fedorka-Cray P, Sreevatsan S, Wang P, Gebreyes WA. 2012. Epidemiology and genotypic characteristics of methicillin-resistant Staphylococcus aureus strains of porcine origin. J Clin Microbiol 50:3687–3693. [PubMed]
128. Quintana-Hayashi MP, Thakur S. 2012. Phylogenetic analysis reveals common antimicrobial resistant Campylobacter coli population in antimicrobial-free (ABF) and commercial swine systems. PLoS One 7:e44662. [PubMed]
129. Ray M, Schwartz DC. 2014. Pulsed-field gel electrophoresis and the molecular epidemiology of foodborne pathogens, p 27–46. In Oyarzabal OA, Kathariou S (ed), DNA Methods in Food Safety. Molecular Typing of Foodborne and Waterborne Bacterial Pathogens. Wiley-Blackwell, Oxford, United Kingdom.
130. Foley SL, White DG, McDermott PF, Walker RD, Rhodes B, Fedorka-Cray PJ, Simjee S, Zhao S. 2006. Comparison of subtyping methods for differentiating Salmonella enterica serovar Typhimurium isolates obtained from food animal sources. J Clin Microbiol 44:3569–3577. [PubMed]
131. Anand R. 1986. Pulsed field gel electrophoresis: a technique for fractionating large DNA molecules. Trends Genet 2:278–283.
132. Gautom RK. 1997. Rapid pulsed-field gel electrophoresis protocol for typing of Escherichia coli O157:H7 and other Gram-negative organisms in 1 day. J Clin Microbiol 35:2977–2980. [PubMed]
133. Bopp DJ, Baker DJ, Thompson L, Saylors A, Root TP, Armstrong L, Mitchell K, Dumas NB, Musser KA. 2016. Implementation of Salmonella serotype determination using pulsed-field gel electrophoresis in a state public health laboratory. Diagn Microbiol Infect Dis 85:416–418. [PubMed]
134. Tsen HY, Hu HH, Lin JS, Huang CH, Wang TK. 2000. Analysis of the Salmonella Typhimurium isolates from food-poisoning cases by molecular subtyping methods. Food Microbiol 17:143–152.
135. McCullagh JJ, McNamee PT, Smyth JA, Ball HJ. 1998. The use of pulsed field gel electrophoresis to investigate the epidemiology of Staphylococcus aureus infection in commercial broiler flocks. Vet Microbiol 63:275–281.
136. Zou W, Lin W-J, Foley SL, Chen C-H, Nayak R, Chen JJ. 2010. Evaluation of pulsed-field gel electrophoresis profiles for identification of Salmonella serotypes. J Clin Microbiol 48:3122–3126. [PubMed]
137. Molla B, Sterman A, Mathews J, Artuso-Ponte V, Abley M, Farmer W, Rajala-Schultz P, Morrow WEM, Gebreyes WA. 2010. Salmonella enterica in commercial swine feed and subsequent isolation of phenotypically and genotypically related strains from fecal samples. Appl Environ Microbiol 76:7188–7193. [PubMed]
138. Refsum T, Heir E, Kapperud G, Vardund T, Holstad G. 2002. Molecular epidemiology of Salmonella enterica serovar Typhimurium isolates determined by pulsed-field gel electrophoresis: comparison of isolates from avian wildlife, domestic animals, and the environment in Norway. Appl Environ Microbiol 68:5600–5606. [PubMed]
139. Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rüsch-Gerdes S, Supply P, Kalinowski J, Niemann S. 2013. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med 10:e1001387. [PubMed]
140. Dark MJ. 2013. Whole-genome sequencing in bacteriology: state of the art. Infect Drug Resist 6:115–123. [PubMed]
141. Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D. 2013. Updating benchtop sequencing performance comparison. Nat Biotechnol 31:294–296. [PubMed]
142. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M. 2012. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:251364. [PubMed]
143. Schürch AC, van Schaik W. 2017. Challenges and opportunities for whole-genome sequencing-based surveillance of antibiotic resistance. Ann N Y Acad Sci 1388:108–120. [PubMed]
144. Dunne WM Jr, Westblade LF, Ford B. 2012. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis 31:1719–1726. [PubMed]
Loading

Article metrics loading...

/content/journal/microbiolspec/10.1128/microbiolspec.PFS-0019-2017
2018-02-23
2018-06-20

Abstract:

Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization–time of flight mass spectrometry and whole-genome sequencing.

Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Supplemental Material

No supplementary material available for this content.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error