Evaluating the Prevalence of Foodborne Pathogens in Livestock Using Metagenomics Approach |
Kim, Hyeri
(Department of Animal Resources Science, Dankook University)
Cho, Jin Ho (Division of Food and Animal Science, Chungbuk National University) Song, Minho (Division of Animal and Dairy Science, Chungnam National University) Cho, Jae Hyoung (Department of Animal Resources Science, Dankook University) Kim, Sheena (Department of Animal Resources Science, Dankook University) Kim, Eun Sol (Department of Animal Resources Science, Dankook University) Keum, Gi Beom (Department of Animal Resources Science, Dankook University) Kim, Hyeun Bum (Department of Animal Resources Science, Dankook University) Lee, Ju-Hoon (Department of Food Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University) |
1 | Moore JE, Madden RH. 1998. Occurrence of thermophilic Campylobacter spp. in porcine liver in Northern Ireland. J. Food Prot. 61: 409-413. DOI |
2 | Harvey RB, Young CR, Ziprin RL, Hume ME, Genovese KJ, Anderson RC, et al. 1999. Prevalence of Campylobacter spp. isolated from the intestinal tract of pigs raised in an integrated swine production system. J. Am. Vet. Med. Assoc. 215: 1601-1604. |
3 | Brynestad S, Granum PE. 2002. Clostridium perfringens and foodborne infections. Int. J. Food Microbiol. 74: 195-202. DOI |
4 | Suh J PO, Kang Y, Ahn JE, Jung JS, An YS, Park SH, et al. 2013. Risk assessment on nitrate and nitrite in vegetables available in Korean diet. J. Appl. Biol. Chem. 56: 205-211. DOI |
5 | Anonymous. 2018. Foodborne disease outbreak. |
6 | Asghar Arshi SN, Hamidreza Kabiri, Arman Akbarpour, Rassoul Hashemzehi, Behnaz Mansouri, Ayse Kilic, et al. 2017. Incidence of Clostridium perfringens in intestinal contents of domestic livestock detected by PCR. Int. J. Anim. Res. 1: 1-6. |
7 | Jeong D, Kim DH, Kang IB, Chon JW, Kim H, Om AS, et al. 2017. Prevalence and toxin type of Clostridium perfringens in beef from four different types of meat markets in Seoul, Korea. Food Sci. Biotechnol. 26: 545-548. DOI |
8 | Oliver SP, Jayarao BM, Almeida RA. 2005. Foodborne pathogens in milk and the dairy farm environment: food safety and public health implications. Foodborne Pathog. Dis. 2: 115-129. DOI |
9 | Velusamy V, Arshak K, Korostynska O, Oliwa K, Adley C. 2010. An overview of foodborne pathogen detection: in the perspective of biosensors. Biotechnol. Adv. 28: 232-254. DOI |
10 | R.Beuchat L. 1999. Listeria monocytogenes: incidence on vegetables Food Control 7: 6. |
11 | Heiman KE, Garalde VB, Gronostaj M, Jackson KA, Beam S, Joseph L, et al. 2016. Multistate outbreak of listeriosis caused by imported cheese and evidence of cross-contamination of other cheeses, USA, 2012. Epidemiol. Infect. 144: 2698-2708. DOI |
12 | Arnold DL, Preston GM. 2019. Pseudomonas syringae: enterprising epiphyte and stealthy parasite. Microbiology 165: 251-253. DOI |
13 | Burnett SL, Beuchat LR. 2001. Human pathogens associated with raw produce and unpasteurized juices, and difficulties in decontamination. J. Ind. Microbiol. Biotechnol. 27: 104-110. DOI |
14 | Finlay RC, Mann ED, Horning JL. 1986. Prevalence of Salmonella and Campylobacter contamination in manitoba Swine carcasses. Can. Vet. J. 27: 185-187. |
15 | Hu WS, Kim H, Koo OK. 2018. Molecular genotyping, biofilm formation and antibiotic resistance of enterotoxigenic Clostridium perfringens isolated from meat supplied to school cafeterias in South Korea. Anaerobe 52: 115-121. DOI |
16 | Mafart P, Couvert O, Gaillard S, Leguerinel I. 2002. On calculating sterility in thermal preservation methods: application of the Weibull frequency distribution model. Int. J. Food Microbiol. 72: 107-113. DOI |
17 | Hennekinne JA, De Buyser ML, Dragacci S. 2012. Staphylococcus aureus and its food poisoning toxins: characterization and outbreak investigation. FEMS Microbiol. Rev. 36: 815-836. DOI |
18 | Spaulding AR, Salgado-Pabon W, Kohler PL, Horswill AR, Leung DY, Schlievert PM. 2013. Staphylococcal and streptococcal superantigen exotoxins. Clin. Microbiol. Rev. 26: 422-447. DOI |
19 | Cantet F, Magras C, Marais A, Federighi M, Megraud F. 1999. Helicobacter species colonizing pig stomach: molecular characterization and determination of prevalence. Appl. Environ. Microbiol. 65: 4672-4676. DOI |
20 | Fawcett AMSL. 2002. Tracking and traceability in the meat processing industry: a solution. Br. Food J. 104: 13. |
21 | Zhao X, Lin CW, Wang J, Oh DH. 2014. Advances in rapid detection methods for foodborne pathogens. J. Microbiol. Biotechnol. 24: 297-312. DOI |
22 | Ryan KJ, Ray CG, Sherris JC. 2004. Sherris medical microbiology: an introduction to infectious diseases, pp. 997. 4th Ed. McGraw-Hill, New York, USA |
23 | Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, et al. 2012. Defining the core Arabidopsis thaliana root microbiome. Nature 488: 86-90. DOI |
24 | Janda JM, Abbott SL. 2007. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J. Clin. Microbiol. 45: 2761-2764. DOI |
25 | Kim M, Lee KH, Yoon SW, Kim BS, Chun J, Yi H. 2013. Analytical tools and databases for metagenomics in the next-generation sequencing era. Genomics Inform. 11: 102-113. DOI |
26 | Ku HJ, Lee JH. 2014. Development of a novel long-range 16S rRNA universal primer set for metagenomic analysis of gastrointestinal microbiota in newborn infants. J. Microbiol. Biotechnol. 24: 812-822. DOI |
27 | Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, et al. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33: D294-296. DOI |
28 | Freney J, Hansen W, Etienne J, Vandenesch F, Fleurette J. 1988. Postoperative infant septicemia caused by Pseudomonas luteola (CDC group Ve-1) and Pseudomonas oryzihabitans (CDC group Ve-2). J. Clin. Microbiol. 26: 1241-1243. DOI |
29 | Lammerding AM, Garcia MM, Mann ED, Robinson Y, Dorward WJ, Ruscott RB, et al. 1988. Prevalence of Salmonella and thermophilic Campylobacter in fresh pork, beef, veal and poultry in Canada. J. Food Prot. 51: 47-52. DOI |
30 | Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7: 335-336. DOI |
31 | Balaban N, Rasooly A. 2000. Staphylococcal enterotoxins. Int. J. Food Microbiol. 61: 1-10. DOI |
32 | Le Loir Y, Baron F, Gautier M. 2003. Staphylococcus aureus and food poisoning. Genet. Mol. Res. GMR 2: 63-76. |
33 | Lowy FD. 2003. Antimicrobial resistance: the example of Staphylococcus aureus. J. Clin. Invest. 111: 1265-1273. DOI |
34 | Fraser JD, Proft T. 2008. The bacterial superantigen and superantigen-like proteins. Immunol. Revi. 225: 226-243. DOI |
35 | Baele M, Decostere A, Vandamme P, Ceelen L, Hellemans A, Mast J, et al. 2008. Isolation and characterization of Helicobactersuis sp. nov. from pig stomachs. Int. J. Syst. Evol. Microbiol. 58: 1350-1358. DOI |
36 | Haesebrouck F, Pasmans F, Flahou B, Smet A, Vandamme P, Ducatelle R. 2011. Non-Helicobacter pylori Helicobacter species in the human gastric mucosa: a proposal to introduce the terms H. heilmannii sensu lato and sensu stricto. Helicobacter 16: 339-340. DOI |
37 | Lowy FD. 1998. Staphylococcus aureus infections. New Eng. J. Med. 339: 520-532. DOI |
38 | Van Delden C, Iglewski BH. 1998. Cell-to-cell signaling and Pseudomonas aeruginosa infections. Emerg. Infect. Dis. 4: 551-560. DOI |
39 | Hanshew AS, Mason CJ, Raffa KF, Currie CR. 2013. Minimization of chloroplast contamination in 16S rRNA gene pyrosequencing of insect herbivore bacterial communities. J.Microbiol. Methods 95: 149-155. DOI |
40 | Diggle SP, Whiteley M. 2020. Microbe Profile: Pseudomonas aeruginosa: opportunistic pathogen and lab rat. Microbiology 166: 30-33. DOI |
41 | Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P. 2013. Metagenomics for pathogen detection in public health. Genome Med. 5: 81. DOI |
42 | Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200. DOI |
43 | Jose A Navas-Molina JMP-S, Antonio Gonzalez, Paul J McMurdie, Yoshiki Vazquez-Baeza, Zhenjiang Xu, Luke K Ursell, et al. 2013. Advancing our understanding of the human microbiome using QIIME. Methods Enzymol. 531: 371. DOI |
44 | Parks DH, Beiko RG. 2010. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715-721. DOI |
45 | Doyle MP, Erickson MC. 2006. Reducing the carriage of foodborne pathogens in livestock and poultry. Poult. Sci. 85: 960-973. DOI |
46 | Rahn K, De Grandis SA, Clarke RC, McEwen SA, Galan JE, Ginocchio C, et al. 1992. Amplification of an invA gene sequence of Salmonella typhimurium by polymerase chain reaction as a specific method of detection of Salmonella. Mol. Cell. Probes 6: 271-279. DOI |
47 | Friedman CR, Neimann J, Wegener HC, Tauxe RV. 2000. |
48 | Anonymous. 2004. Annual Report on Zoonoses in Denmark 2003. |
49 | Anonymous. 2000. Annual report on zoonoses in Denmark 1999. |
50 | Anonymous. 2002. Annual report on zoonoses in Denmark 2001. |
51 | Weber A, Lembke C, Schafer R. 1985. [Isolation of Campylobacter jejuni and Campylobacter coli in fecal samples of healthy slaughter swine depending on the season]. Zentralbl. Veterinarmed. B. 32: 40-45. DOI |
52 | Van Immerseel F, De Buck J, Pasmans F, Huyghebaert G, Haesebrouck F, Ducatelle R. 2004. Clostridium perfringens in poultry: an emerging threat for animal and public health. Avian Pathol. 33: 537-549. DOI |