Loop-mediated isothermal amplification: a rapid molecular technique for early diagnosis of Pseudomonas syringae pv. syringae of stone fruits
Tóm tắt
Pathogenic bacteria cause significant economic damages in agriculture. The detection of such bacteria is considered as a continual interest for plant pathologists to prevent disease dissemination. Pseudomonas syringae pv. syringae is one of the most important bacterial pathogens infecting yield and quality of stone fruits throughout the world. Biochemical assays such as a LOPAT and GATTa are common methods to detect this pathogen. Serological tests and culturing on King’s B selective medium also used to isolate this bacterium. Selective media is composed of specific and effective ingredients to inhibit the growth of certain species of microbes in a mixed culture while allowing others to grow. These are used for the growth of only selected microorganisms. King’s B medium can be used as a general medium for the non-selective isolation cultivation and pigment production of Pseudomonas species from foods, cosmetic samples, plants, etc. Nevertheless, the mentioned methods are not enough accurate to differentiate the strains. On the other hand, PCR-based techniques are sensitive and efficient in detecting plant diseases. However, these techniques are not practicable for those researchers who do not have access to a thermal cycler. We have used loop-mediated isothermal amplification to couple with a target. The amplification of syrD gene using loop and bumper primers can be used to prevent disease dissemination. The outcome of this investigation indicated more sensitivity of LAMP in comparison to PCR. The direct addition of SYBR Gold in microtube is more sensitive than gel in both LAMP and PCR byproducts so we can eliminate gel electrophoresis, while the LAMP showed high sensitivity and high specificity in comparison to results obtained by cultivation. The described molecular test could detect Pseudomonas syringae pv. syringae type in nearly 1 h, and this is the first time that Lamp molecular detection of Pseudomonas syringae pv. syringae particularly on stone fruits is described and introduced. The obtained data confirmed that LAMP is a fast, cheap, and high specific method for the rapid detection of Pseudomonas syringae pv. syringae to the comparison of PCR and culture.
Tài liệu tham khảo
Schaad NW, Jones JB, Chun W (2001) Laboratory guide for identification of plant pathogenic bacteria. USA: American Phytopathological Society Press
Gross DC (1991) Molecular and genetic analysis of toxin production by pathovars of Pseudomonas syringae. Annu Rev Phytopathol 29(1):247–278
Ram V, Bhardwaj L (2004) Stone fruit diseases and their management in diseases of fruits and vegetables: Volume 2. Springer, p. 485–510
Bultreys A, Gheysen I (1999) Biological and molecular detection of toxic lipodepsipeptide-producing Pseudomonas syringae strains and PCR identification in plants. Appl Environ Microbiol 65(5):1904–1909
Little E, Bostock R, Kirkpatrick B (1998) Genetic characterization of Pseudomonas syringae pv. syringae strains from stone fruits in California. Appl Environ Microbiol 64(10):3818–3823
Agrios G (2005) Plant pathology. Elsevier Academic Press, Burlington, Ma. USA, pp 79–103
Young JM, Saddler GS, Takikawa Y, Boer SH, Vauterin L et al (1996) Names of plant pathogenic bacteria 1864-1995. Rev Plant Pathol 75(9):721–763
Berge O, Monteil CL, Bartoli C, Chandeysson Ch, Guilbaud C, Sands DC (2014) A user’s guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex. PloS one 9(9):e105547
Baltrus DA, Nishimura MT, Romanchuk A, Chang JH, Shahid Mukhtar M et al (2011) Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates. PLoS Pathog 7(7):e1002132
Bultreys A, Kaluzna M (2010) Bacterial cankers caused by Pseudomonas syringae on stone fruit species with special emphasis on the pathovars syringae and morsprunorum race 1 and race 2. J Plant Pathol:S21–S33
Benedict AA, Alvarez AM, Berestecky J, Imanaka W, Mizumoto CY et al (1989) Pathovar-specific monoclonal antibodies for Xanthomonas campestris pv. oryzae and for Xanthomonas campestris pv. oryzicola. Phytopathology 79(3):322–328
Stead D Evaluation of cellular fatty acid profiles for rapid identification of plant pathogenic bacteria. in proceedings 7th International Conference on Plant Pathogenic Bacteria, Budapest. 1990
Berthier Y, Verdier V, Guesdon JL, Chevrier D, Denis JB et al (1993) Characterization of Xanthomonas campestris pathovars by rRNA gene restriction patterns. Appl Environ Microbiol 59(3):851–859
Van Zyl E, Steyn P (1990) Differentiation of phytopathogenic Pseudomonas and Xanthomonas species and pathovars by numerical taxonomy and protein gel electrophoregrams. Syst Appl Microbiol 13(1):60–71
Henson JM, French R (1993) The polymerase chain reaction and plant disease diagnosis. Annu Rev Phytopathol 31(1):81–109
King EO, Ward MK, Raney DE (1954) Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 44(2):301–307
Ménard M, Sutra L, Luisetti K, Prunie JP, Gardan L (2003) Pseudomonas syringae pv. avii (pv. nov.), the causal agent of bacterial canker of wild cherries (Prunus avium) in France. Eur J Plant Pathol 109(6):565–576
Marques AS, Corbière R, Gardan R, Tourte C, Manceau Ch et al (2000) Multiphasic approach for the identification of the different classification levels of Pseudomonas savastanoi pv. phaseolicola. Eur J Plant Pathol 106(8):715–734
Gašić K, Prokić A, Ivanovic MM, Kuzmanović N, Obradović A (2012) Differentiation of Pseudomonas syringae pathovars originating from stone fruits. Pestic Fitomed 27(3):219–229
Kaluzna M, Puławska J, Sobiczewski P (2010) The use of PCR melting profile for typing of Pseudomonas syringae isolates from stone fruit trees. Eur J Plant Pathol 126(4):437–443
Kaluzna M, Ferrante P, Sobiczewski P, Scortichini M (2010) Characterization and genetic diversity of Pseudomonas syringae from stone fruits and hazelnut using repetitive-PCR and MLST. J Plant Pathol p.781–787
Konavko D, Morocko-Bicevska I, Bankina B (2014) Pseudomonas syringae as important pathogen of fruit trees with emphasis on plum and cherry. Res Rural Devel p.19–25
Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K et al (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28(12):e63–e63
Quigley NB, Mo YY, Gross DC (1993) SyrD is required for syringomycin production by Pseudomonas syringae pathovar syringae and is related to a family of ATP-binding secretion proteins. Mol Microbiol 9(4):787–801
Grgurina I, Gross DC, Lacobellis NS, Paola Lavermicocca P, Takemoto JY, Benincasa M (1996) Phytotoxin production by Pseudomonas syringae pv. syringae: Syringopeptin production by syr mutants defective in biosynthesis or secretion of syringomycin. FEMS Microbiol Lett 138(1):35–39
Guilbaud C, Morris CE, Barakat M, Ortet P, Berge O (2016) Isolation and identification of Pseudomonas syringae facilitated by a PCR targeting the whole P. syringae group. FEMS Microbiol Ecol 92(1)
Sorensen KN, Kim KH, Takemoto JY (1998) PCR detection of cyclic lipodepsinonapeptide-producing Pseudomonas syringae pv. syringae and similarity of strains. Appl Environ Microbiol 64(1):226–230
Mullis KB (1990) The unusual origin of the polymerase chain reaction. Sci Am 262(4):56–65
Lee PY, Costumbrado J, Hsu C, Kim YM (2012) Agarose gel electrophoresis for the separation of DNA fragments. JoVE (62): p. e3923
Ibarra-Meneses AV, Cruz I, Chicharro C, Sánchez C, Biéler B et al (2018) Evaluation of fluorimetry and direct visualization to interpret results of a loop-mediated isothermal amplification kit to detect Leishmania DNA. Parasit Vectors 11(1):1–9
Tuma RS, Beaudet MP, Jin X, Jones LJ, Cheung CY et al (1999) Characterization of SYBR Gold nucleic acid gel stain: a dye optimized for use with 300-nm ultraviolet transilluminators. Anal Biochem 268(2):278–288
Moskowitz CS, Pepe MS (2006) Comparing the predictive values of diagnostic tests: sample size and analysis for paired study designs. Clin Trials 3(3):272–279
Morris CE, Sands DC, Vinatzer BA, Glaux C, Guilbaud C et al (2008) The life history of the plant pathogen Pseudomonas syringae is linked to the water cycle. The ISME J 2(3):321–334
Iwamoto T, Sonobe T, Hayashi K (2003) Loop-mediated isothermal amplification for direct detection of Mycobacterium tuberculosis complex, M. avium, and M. intracellulare in sputum samples. J Clin Microbiol 41 (6): 2616–2622
Misawa Y, Saito R, Moriya K, Koike K, Yoshida A (2007) Application of loop-mediated isothermal amplification technique to rapid and direct detection of methicillin-resistant Staphylococcus aureus (MRSA) in blood cultures. J Infect Chemother 13(3):134–140
Kubota R, Vine BG, Alvarez AM, Jenkins DM (2008) Detection of Ralstonia solanacearum by loop-mediated isothermal amplification. Phytopathology 98(9):1045–1051
Bereswill S, Bugert P, Völksch B, Ullrich M, Bender CL, Geider K (1994) Identification and relatedness of coronatine-producing Pseudomonas syringae pathovars by PCR analysis and sequence determination of the amplification products. Appl Environ Microbiol 60(8):2924–2930
Vicente JG, Roberts SJ (2007) Discrimination of Pseudomonas syringae isolates from sweet and wild cherry using rep-PCR. Eur J of Plant Pathol 117(4):383–392
Raaijmakers JM, Weller DM, Thomashow LS (1997) Frequency of antibiotic-producing Pseudomonas spp. in natural environments. Appl Environ Microbiol 63(3):881–887
Li X, Nie J, Ward L, Madani M, Hsiang T, Zhao Y, De Boer SH (2009) Comparative genomics-guided loop-mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola. J Appl Microbiol 107(3):717–726
Ghosh DK, Bhose S, Warghane A, Motghare M, Kumar Sharma A et al (2016) Loop-mediated isothermal amplification (LAMP) based method for rapid and sensitive detection of ‘Candidatus Liberibacter asiaticus’ in citrus and the psyllid vector, Diaphorina citri Kuwayama. J Plant Biochem Biotech 25(2):219–223
Chandra A, Keizerweerd AT, Grisham MP (2016) Detection of Puccinia kuehnii causing sugarcane orange rust with a loop-mediated isothermal amplification-based assay. Mol Biotechnol 58(3):188–196
Herrera-Vásquez JA, Puchades AV, Elvira-González L, Jaén-Sanjur JN, Carpino C et al (2018) Fast detection by loop-mediated isothermal amplification (LAMP) of the three begomovirus species infecting tomato in Panama. Eur J Plant Pathol 151(1):243–250
Meng XL, Xie XW, Shi YX, Chai AL, Ma ZH, Li BJ (2017) Evaluation of a loop-mediated isothermal amplification assay based on hrpZ gene for rapid detection and identification of Pseudomonas syringae pv. lachrymans in cucumber leaves. J Appl Microbiol 122(2):441–449
Zhao X, Wang L, Li Y, Xu Z, Li L, He X (2011) Development and application of a loop-mediated isothermal amplification method on rapid detection of Pseudomonas aeruginosa strains. World J of Microbiol Biotechnol 27(1):181–184
Sun M, Liu H, Huang J, Peng J, Fei F et al (2019) A loop-mediated isothermal amplification assay for rapid detection of Pectobacterium aroidearum that Causes Soft Rot in Konjac. Int J Mol Sci 20(8): p. 1937
Li GR, Huang GM, Zhu LH, Lv D, Cao B et al (2019) Loop-mediated isothermal amplification (LAMP) detection of Phytophthora hibernalis, P. syringae and P. cambivora. J Plant Pathol 101(1):51–57