Genome Wide Search for Biomarkers to Diagnose Yersinia Infections

Indian Journal of Microbiology

Volumn 55, Issue 4, 2015, Pages 366-374

  Kalia, Vipin Chandra ^a   Kumar, Prasun ^a  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

Biomarkers; Diagnosis; Genome; In silico; Restriction endonuclease; Yersinia

Indexed keywords

EID: 84946476660     PISSN: 00468991     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12088-015-0552-6     Document Type: Article

References (40)

1. Prakash O, Jangid K, Shouche YS (2013) Carl Woese: from Biophysics to evolutionary microbiology. Indian J Microbiol 53:247–252. doi:10.1007/s12088-013-0401-4
2. Gupta V, Gulati P, Bhagat N, Dhar MS, Virdi JS (2015) Detection of Yersinia enterocolitica in food: an overview. Eur J Clin Microbiol Infect Dis 34:641–650. doi:10.1007/s10096-014-2276-7
3. Santos-Montañez J, Benavides-Montaño JA, Hinz AK, Vadyvaloo V (2015) Yersinia pseudotuberculosis IP32953 survives and replicates in trophozoites and persists in cysts of Acanthamoeba castellanii. FEMS Microbiol Lett. doi:10.1093/femsle/fnv091
4. Laukkanen-Ninios R, Fredriksson-Ahomaa M, Korkeala H (2014) Enteropathogenic Yersinia in the pork production chain: challenges for control. Compr Rev Food Sci Food Saf 13:1165–1191. doi:10.1111/1541-4337.12108
5. Hochel I, Skvor J (2007) Characterization of rabbit antibodies for immunochemical detection of Yersinia enterocolitica. Folia Microbiol (Praha) 52:511–518. doi:10.1007/BF02932112
6. Kapperud G, Vardund T, Skjerve E, Hornes E, Michaelsen TE (1993) Detection of pathogenic Yersinia enterocolitica in foods and water by immunomagnetic separation, nested polymerase chain reactions, and colorimetric detection of amplified DNA. Appl Environ Microbiol 59:2938–2944
7. Thibodeau V, Frost EH, Quessy S (2001) Development of an ELISA procedure to detect swine carriers of pathogenic Yersinia enterocolitica. Vet Microbiol 82:249–259. doi:10.1016/S0378-1135(01)00356-X
8. Oh BK, Lee W, Chun BS, Bae YM, Lee WH, Choi J-W (2005) Surface plasmon resonance immunosensor for the detection of Yersinia enterocolitica. Colloids Surf A Physicochem Eng Asp 257–258:369–374. doi:10.1016/j.colsurfa.2004.10.083
9. Myers KM, Gaba J, Al-Khaldi SF (2006) Molecular identification of Yersinia enterocolitica isolated from pasteurized whole milk using DNA microarray chip hybridization. Mol Cell Probes 20:71–80. doi:10.1016/j.mcp.2005.09.006
10. 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. doi:10.1038/nprot.2008.57
11. Giannino ML, Aliprandi M, Feligini M, Vanoni L, Brasca M, Fracchetti F (2009) A DNA array based assay for the characterization of microbial community in raw milk. J Microbiol Methods 78:181–188. doi:10.1016/j.mimet.2009.05.015
12. Porwal S, Lal S, Cheema S, Kalia VC (2009) Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus. PLoS One 4:e4438. doi:10.1371/journal.pone.0004438
13. Chen J, Miao X, Xu M, He J, Xie J, Wu X, Chen G, Yu L, Zhang W (2015) Intra-genomic heterogeneity in 16S rRNA genes in strictly anaerobic clinical isolates from periodontal abscesses. PLoS One 10:e0130265. doi:10.1371/journal.pone.0130265
14. Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, Jin Z, Lee P, Yang L, Poles M, Brown SM, Sotero S, DeSantis T, Brodie E, Nelson K, Pei Z (2010) Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol 76:3886–3897. doi:10.1128/AEM.02953-09AEM.02953-09
15. Kekre A, Bhushan A, Kumar P, Kalia VC (2015) Genome wide analysis for searching novel markers to rapidly identify Clostridium strains. Indian J Microbiol 55:250–257. doi:10.1007/s12088-015-0535-7
16. Khushiramani R, Shukla J, Tuteja U, Batra HV (2006) Yersinia outer-membrane protein B (YopB): a tool for identification of Yersinia pestis isolates. J Med Microbiol 55:467–469. doi:10.1099/jmm.0.46382-0
17. Paixão R, Moreno LZ, Sena de Gobbi DD, Raimundo DC, Hofer E, Matté MH, Sebastiana T, Ferreira P, de Moura Gomes VT, Costa BLP, Moreno AM (2013) Characterization of Yersinia enterocolitica biotype 1A Strains isolated from swine slaughterhouses and markets. Sci World J 2013:769097. doi:10.1155/2013/769097
18. Garzetti D, Susen R, Fruth A, Tietze E, Heesemann J, Rakin A (2014) A molecular scheme for Yersinia enterocolitica patho-serotyping derived from genome-wide analysis. Int J Med Microbiol 304:275–283. doi:10.1016/j.ijmm.2013.10.007
19. von Altrock A, Seinige D, Kehrenberg C (2015) Yersinia enterocolitica isolates from wild boars hunted in Lower Saxony, Germany. Appl Environ Microbiol 81:4835–4840. doi:10.1128/AEM.00550-15
20. Malorny B, Tassios PT, Rådström P, Cook N, Wagner M, Hoorfar J (2003) Standardization of diagnostic PCR for the detection of foodborne pathogens. Int J Food Microbiol 83:39–48. doi:10.1016/S0168-1605(02)00322-7
21. Mäde D, Reiting R, Strauch E, Ketteritzsch K, Wicke A (2008) A real-time PCR for detection of pathogenic Yersinia enterocolitica in food combined with an universal internal amplification control system. J Consum Prot Food Saf 3:141–151. doi:10.1007/s00003-008-0341-9
22. Ikeda M, Yamaguchi N, Tani K, Nasu M (2006) Detection of food poisoning bacteria in fresh vegetables using DNA microarray. J Health Sci 52:36–42. doi:10.1248/jhs.52.36
23. Bang J, Beuchat LR, Gu MB, Chang HI, Ryu JH (2010) Identification of Yersinia enterocolitica using a random genomic DNA microarray chip. Lett Appl Microbiol 51:665–670. doi:10.1111/j.1472-765X.2010.02954.x
24. Kim DH, Lee BK, Kim YD, Sk Rhee, Kim YC (2010) Detection of representative enteropathogenic bacteria, Vibrio spp., pathogenic Escherichia coli, Salmonella spp., Shigella spp., and Yersinia enterocolitica, using a virulence factor gene-based oligonucleotide microarray. J Microbiol 48:682–688. doi:10.1007/s12275-010-0119-5
25. 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. doi:10.1006/bbrc.2001.5921
26. Gao H, Lei Z, Jia J, Wang S, Chen Y, Sun M, Liang C (2009) Application of loop-mediated isothermal amplification for detection of Yersinia enterocolitica in pork meat. J Microbiol Methods 77:198–201. doi:10.1016/j.mimet.2009.02.001
27. Li Y, Jiang M, Liu W, Zhang L, Zhang S, Zhao X, Xiang R, Liu Y (2010) Loop-mediated isothermal amplification method targets to the phoP gene for detection of Yersinia enterocolitica. Mol Cell Probes 24:68–71. doi:10.1016/j.mcp.2009.10.003
28. Bai S, Zhao J, Zhang Y, Huang W, Xu S, Chen H, Fan L-M, Chen Y, Deng XW (2010) Rapid and reliable detection of 11 food-borne pathogens using thin-film biosensor chips. Appl Microbiol Biotechnol 86:983–990. doi:10.1007/s00253-009-2417-6
29. Kuhm AE, Suter D, Felleisen R, Rau J (2009) Identification of Yersinia enterocolitica at the species and subspecies levels by Fourier transform infrared spectroscopy. Appl Environ Microbiol 75:5809–5813. doi:10.1128/AEM.00206-09
30. Ayyadurai S, Flaudrops C, Raoult D, Drancourt M (2010) Rapid identification and typing of Yersinia pestis and other Yersinia species by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. BMC Microbiol 10:285. doi:10.1186/1471-2180/10/285
31. Stephan R, Cernela N, Ziegler D, Pflüger V, Tonolla M, Ravasi D, Fredriksson-Ahomaa M, Hächler H (2011) Rapid species specific identification and subtyping of Yersinia enterocolitica by MALDI-TOF mass spectrometry. J Microbiol Methods 87:150–153. doi:10.1016/j.mimet.2011.08.016
32. Huma N, Shankar P, Kushwah J, Bhushan A, Joshi J, Mukherjee T, Raju SC, Purohit HJ, Kalia VC (2011) Diversity and polymorphism in AHL-lactonase gene (aiiA) of Bacillus. J Microbiol Biotechnol 21:1001–1011. doi:10.4014/jmb.1105.05056
33. Kalia VC, Mukherjee T, Bhushan A, Joshi J, Shankar P, Huma N (2011) Analysis of the unexplored features of rrs (16S rDNA) of the genus Clostridium. BMC Genom 12:18. doi:10.1186/1471-2164-12-18
34. Lal D, Verma M, Lal R (2011) Exploring internal features of 16S rRNA gene for identification of clinically relevant species of the genus Streptococcus. Ann Clin Microbiol Antimicrob 10:28. doi:10.1186/1476-0711-10-28
35. Bhushan A, Joshi J, Shankar P, Kushwah J, Raju SC, Purohit HJ, Kalia VC (2013) Development of genomic tools for the identification of certain Pseudomonas up to species level. Indian J Microbiol 53:253–263. doi:10.1007/s12088-013-0412-1
36. Kalia VC (2015) Let’s explore the latent features of genes to identify bacteria. J Mol Genet Med 9:e105. doi:10.4172/1747-0862.1000E105
37. Bhushan A, Mukherjee T, Joshi J, Shankar P, Kalia VC (2015) Insights into the origin of Clostridium botulinum strains: evolution of distinct restriction endonuclease sites in rrs (16S rRNA gene). Indian J Microbiol 55:140–150. doi:10.1007/s12088-015-0514-z
38. Shivaji S, Bhanu NV, Aggarwal RK (2000) Identification of Yersinia pestis as the causative organism of plague in India as determined by 16S rDNA sequencing and RAPD-based genomic fingerprinting. FEMS Microbiol Lett 189:247–252. doi:10.1111/j.1574-6968.2000.tb09238.x
39. Bhagat N, Virdi JS (2007) Distribution of virulence associated genes in Yersinia enterocolitica biovar 1A correlates with clonal groups and not the source of isolation. FEMS Microbiol Lett 266:177–183. doi:10.1111/j.1574-6968.2006.00524.x
40. Kishore P, Lalitha KV, Joseph TC, Thampuran N (2012) Biotyping and antibiotic resistance profile of Yersinia enterocolitica associated with seafoods from South-west coast of India. Fish Technol 49:64–71