#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida


Autoři: Richard C. Winkworth aff001;  Briana C. W. Nelson aff002;  Stanley E. Bellgard aff003;  Chantal M. Probst aff003;  Patricia A. McLenachan aff002;  Peter J. Lockhart aff001
Působiště autorů: Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand aff001;  School of Fundamental Sciences, Massey University, Palmerston North, New Zealand aff002;  Manaaki Whenua–Landcare Research, Auckland, New Zealand aff003
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0224007

Souhrn

The root rot causing oomycete, Phytophthora agathidicida, threatens the long-term survival of the iconic New Zealand kauri. Currently, testing for this pathogen involves an extended soil bioassay that takes 14–20 days and requires specialised staff, consumables, and infrastructure. Here we describe a loop-mediated isothermal amplification (LAMP) assay for the detection of P. agathidicida that targets a portion of the mitochondrial apocytochrome b coding sequence. This assay has high specificity and sensitivity; it did not cross react with a range of other Phytophthora isolates and detected as little as 1 fg of total P. agathidicida DNA or 116 copies of the target locus. Assay performance was further investigated by testing plant tissue baits from flooded soil samples using both the extended soil bioassay and LAMP testing of DNA extracted from baits. In these comparisons, P. agathidicida was detected more frequently using the LAMP test. In addition to greater sensitivity, by removing the need for culturing, the hybrid baiting plus LAMP approach is more cost effective than the extended soil bioassay and, importantly, does not require a centralised laboratory facility with specialised staff, consumables, and equipment. Such testing will allow us to address outstanding questions about P. agathidicida. For example, the hybrid approach could enable monitoring of the pathogen beyond areas with visible disease symptoms, allow direct evaluation of rates and patterns of spread, and allow the effectiveness of disease control to be evaluated. The hybrid LAMP bioassay also has the potential to empower local communities to evaluate the pathogen status of local kauri stands, providing information for disease management and conservation initiatives.

Klíčová slova:

DNA extraction – DNA isolation – Forests – Mitochondria – Phytophthora – Polymerase chain reaction – Sequence databases – Oomycetes


Zdroje

1. Beever RE, Coffey MD, Ramsfield TD, Dick M, Horner IJ. Kauri (Agathis australis) under threat from Phytophthora? Proceedings of the Fourth Meeting of the International Union of Forest Research Organizations Working Party S07.02.09. 2011;74–85.

2. Gadgil PD. Phytophthora heveae, a pathogen of kauri. New Zealand Journal of Forestry Science. 1974; 4:59–63.

3. Waipara N, Hill S, Hill L, Hough E, Horner I. Surveillance methods to determine tree health, distribution of kauri dieback disease and associated pathogens. New Zealand Plant Protection. 2013; 66:235–41.

4. Blair JE, Coffey MD, Park SY, Geiser DM, Kang SA. multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Fungal Genetics and Biology. 2008; 45, 266–77. doi: 10.1016/j.fgb.2007.10.010 18039586

5. Martin FN, Blair JE, Coffey MD. A combined mitochondrial and nuclear multilocus phylogeny of the genus Phytophthora. Fungal Genetics and Biology. 2014; 66:19–32. doi: 10.1016/j.fgb.2014.02.006 24603058

6. McArthy CGP, Fitzpatrick DA. Phylogenomic reconstruction of the Oomycete phylogeny derived from 37 genomes. mSphere. 2017; 2:e00095–17. doi: 10.1128/mSphere.00095-17 28435885

7. Bourret TB, Choudhury RA, Mehl HK, Blomquist CL, McRoberts N, Rizzo DM. Multiple origins of downy mildews and mitonuclear discordance within the paraphyletic genus Phytophthora. PLOS ONE. 2018; 13: e0192502. doi: 10.1371/journal.pone.0192502 29529094

8. Weir BS, Paderes EP, Anand N, Uchida JY, Pennycook SR, Bellgard SE, et al. A taxonomic revision of Phytophthora Clade 5 including two new species, Phytophthora agathidicida and P. cocois. Phytotaxa. 2015; 205:21–38.

9. Jeffers SN, Martin SB. Comparison of two media selective for Phytophthora and Pythium species. Plant Disease. 1986; 70:1038–43.

10. Kato S, Coe R, New L, Dick MW. Sensitivities of various Oomycetes to hymexazol and metalaxyl. Journal of General Microbiology. 1990; 136:2127–34

11. Newhook FJ. The association of Phytophthora spp. with mortality of Pinus radiata and other conifers. New Zealand Journal of Agricultural Research. 1959;2:808–43.

12. Martin FN, Abad ZG, Balci Y, Ivors K. Identification and detection of Phytophthora: reviewing our progress, identifying our needs. Plant Disease. 2012;96:1080–103. doi: 10.1094/PDIS-12-11-1036-FE 30727075

13. Horner IJ, Wilcox WF. Temporal changes in activity and dormant spore population of Phytophthora cactorum in New York apple orchards. Phytopathology. 1996;86:1133–9.

14. Bellgard SE, Pennycook SR, Weir BS, Ho W, Waipara NW Phytophthora agathidicida. Forest Phytophthoras. 2016; doi: 10.5399/osu/fp.5.1.3748

15. Than DJ, Hughes KJD, Boonhan N, Tomlinson JA, Woodhall JW, Bellgard SE. A TaqMan real-time PCR assay for the detection of Phytophthora ‘taxon Agathis’ in soil, pathogen of Kauri in New Zealand. Forest Pathology. 2013;43:324–30.

16. Vashist SK. Point-of-Care Diagnostics: Recent Advances and Trends. Biosensors. 2107; 7:62. doi: 10.3390/bios7040062 29258285

17. Manessis G, Gelasakis AI, Bossis I The challenge of introducing point of care diagnostics in farm animal health management. Biomedical Journal of Scientific & Technical Research. 2019; 14: BJSTR. MS.ID.002601.

18. Miles TD, Martin FN, Coffey MD. Development of rapid isothermal amplification assays for detection of Phytophthora spp. in plant tissue. Phytopathology. 2015; 105:265–78. doi: 10.1094/PHYTO-05-14-0134-R 25208239

19. Cevallos W, Fernández-Soto P, Calvopiña M, Fontecha-Cuenca C, Sugiyama H, Sato H, et al. LAMPhimerus: A novel LAMP assay for detecting Amphimerus sp. DNA in human stool samples. PLOS Neglected Tropical Diseases. 2017; 11: e0005672. doi: 10.1371/journal.pntd.0005672 28628614

20. Seki M, Kilgore PE, Kim EJ, Ohnishi M, Hayakawa S, Kim DW. Loop-mediated isothermal amplification methods for diagnosis of bacterial meningitis. Frontiers in Pediatrics. 2018; 6: 57. doi: 10.3389/fped.2018.00057 29594087

21. Zhang SY, Dai DJ, Wang HD, Zhang CQ. One-step loop-mediated isothermal amplification (LAMP) for the rapid and sensitive detection of Fusarium fujikuroi in bakanae disease through NRPS31, an important gene in the gibberellic acid bio-synthesis. Scientific Reports. 2019;9, Article number: 3726.

22. Aglietti C, Luchi N, Pepori AL, Bartolini P, Pecori F, Raio A, et al. Real-time loop-mediated isothermal amplification: an early-warning tool for quarantine plant pathogen detection. AMB Express. 2019; 9:50 doi: 10.1186/s13568-019-0774-9 31016406

23. Farooq U, Latif A, Irshad H, Ullah A, Zahur AB, Naeem K, et al. Loop-mediated isothermal amplification (RT-LAMP): a new approach for the detection of foot-and-mouth disease virus and its sero-types in Pakistan. Iranian Journal of Veterinary Research. 2015; 16: 331–33. 27175198

24. Best N, Rodoni B, Rawlin G, Beddoe T. The development and deployment of a field based loop mediated isothermal amplification assay for virulent Dichelobacter nodosus detection on Australian sheep. PLOS ONE. 2018; 13: e0204310. doi: 10.1371/journal.pone.0204310 30260992

25. Li Y, Fan P, Zhou S, Zang L. Loop-mediated isothermal amplification (LAMP): A novel rapid detection platform for pathogens. Microbial Pathogenesis. 2017; 107: 54–61. doi: 10.1016/j.micpath.2017.03.016 28323152

26. Notomi T, Mori Y, Tomita N, Kanda H. Loop-mediated isothermal amplification (LAMP): principle, features and future prospects. Journal of Microbiology. 2015; 53: 1–5.

27. Dong ZM, Liu PQ, Li BJ, Chen GL, Weng QY, Chen QH. Loop-mediated isothermal amplification assay for sensitive and rapid detection of Phytophthora capsici. Canadian Journal of Plant Pathology. 2015; 37, 485–94.

28. Dai TT, Yang X, Hu T, Li ZY, Xu Y, Lu CC. A novel LAMP assay for the detection of Phytophthora cinnamomi utilizing a new target gene identified from genome sequences. Plant Disease. 2019; doi: 10.1094/PDIS-04-19-0781-RE 31613192

29. Hansen ZR, Knaus BJ, Tabima JF, Press CM, Judelson HS, Grunwald NJ, et al. Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, Phytophthora infestans. Journal of Applied Microbiology. 2016; 120: 1010–20. doi: 10.1111/jam.13079 26820117

30. Khan MR, Li BJ, Jiang Y, Weng QY, Chen QH. Evaluation of different PCR-based assays and LAMP method for rapid detection of Phytophthora infestans by targeting the Ypt1 gene. Frontiers in Microbiology. 2017; 8: 1920. doi: 10.3389/fmicb.2017.01920 29051751

31. Chen Q, Li B, Liu P, Lan C, Zhan Z, Weng Q. Development and evaluation of specific PCR and LAMP assays for the rapid detection of Phytophthora melonis. European Journal of Plant Pathology. 2013; 137: 597–607.

32. Li B, Liu P, Xie S, Yin R, Weng Q, Chen Q. Specific and sensitive detection of Phytophthora nicotianae by nested PCR and loop-mediated isothermal amplification assays. Journal of Phytopathology 2015; 163: 185–93.

33. Zhao W, Wang T, Qi RD. Ypt1 gene-based detection of Phytophthora sojae in a loop-mediated isothermal amplification assay. Journal of Plant Diseases and Protection. 2015; 122: 63–73.

34. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 2004; 32: 1792–7. doi: 10.1093/nar/gkh340 15034147

35. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research. 1997: 25: 3389–402. doi: 10.1093/nar/25.17.3389 9254694

36. Jeffers SN. Identifying species of Phytophthora. Clemson University. 2006. Available from: https://fhm.fs.fed.us/sp/sod/misc/culturing_species_phytophthora.pdf

37. Bellgard SE, Padamsee M, Probst CM, Lebel T, Williams SE. Visualising the early infection of Agathis australis by Phytophthora agathidicida, using microscopy and fluorescent in situ hybridizatisation assay. Forest Pathology. 2016; 46:622–31 doi: 10.1111/efp.12280

38. White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ editors. PCR protocols–A guide to methods and applications. San Diego: Academic Press; 1990. pp. 315–322.

39. Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics (Oxford, England). 2012; 28:1420–8 https://doi.org/10.1093/bioinformatics/bts174.

40. Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, et al. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biology. 2010; 11:R73. doi: 10.1186/gb-2010-11-7-r73 20626842

41. Schena L, Hughes KJD, Cooke DEL. Detection and quantification of Phytophthora ramorum, P. kernoviae, P. citricola, and P. quercina in symptomatic leaves by multiplex real‐time PCR. Molecular Plant Pathology. 2006; 7:365–79. doi: 10.1111/j.1364-3703.2006.00345.x 20507453

42. Minerdi D, Moretti M, Li Y, Gaggero L, Garibaldi A, Guillino ML. Conventional PCR and real time quantitative PCR detection of Phytophthora cryptogea on Gebera jamesonii. European Journal of Plant Pathology. 2008; 122:227–37.

43. Williamson D. The curious history of yeast mitochondrial DNA. Nature Reviews Genetics. 2002; 3:475–81. doi: 10.1038/nrg814 12042774

44. Huberli D. Analysis of variability among isolates of Phytophthora cinnamomi Rands from Eucalyptus marginata Donn ex Sm. and E. calophylla R. Br. based on cultural characteristics, sporangia and gametangia morphology, and pathogenicity. Honours thesis, Murdoch University. 1995. Available from: https://researchrepository.murdoch.edu.au/id/eprint/1321/2/HUBERLI_whole_hons_thesis.pdf

45. Guo LY, Ko WH. Two widely accessible media for growth and reproduction of Phytophthora and Pythium species. Applied and Environmental Microbiology. 1993; 59:2323–32. 16349002

46. Beever RE, Bellgard SE, Dick MS, Horner IJ, Ramsfield TD. Detection of Phytophthora taxons Agathis (PTA): Final Report. Landcare Report LC0910/137. 2010. Available from: https://www.kauridieback.co.nz/media/1640/11213-11215-12093-detection-of-phytophthora-taxon-agathis-pta-beever.pdf

47. McDougal R, Bellgard S, Scott P, Ganley B. Comparison of a real-time PCR assay and a soil bioassay technique for detection Phytophthora taxon Agathis from soil. Kauri Dieback Response, MPI Contract Report 53789. 2014. Available from: https://www.kauridieback.co.nz/media/1632/2014-17101-real-time-pcr-as-diagnostic- tool-comparison-of-a-real-time.pdf

48. Khaliq I, Hardy GES, White D, Burgess TI. eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems. FEMS Microbiology Ecology. 2018; 94:fiy048.

49. Zou Y, Mason MG, Wang Y, Wee E, Turni C, Blackall P, et al. Nucleic acid purification from plants, animals and microbes in under 30 seconds. PLOS Biology. 2017; 15:e2003916. doi: 10.1371/journal.pbio.2003916 29161268

50. Labarre P, Gerlach J, Wilmoth J, Beddoe A, Singleton J, Weigl B. Non-instrumented nucleic acid amplification (NINA): instrument- free molecular malaria diagnostics for low- resource settings. Proceedings of the 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society. 2011; 1097–9.

51. Singleton J, Osborn JL, Lillis L, Hawkins K, Guelig D, Price W, et al. Electricity-free amplification and detection for molecular point-of-care diagnosis of HIV-1. PLoS ONE. 2014; 9:e113693. doi: 10.1371/journal.pone.0113693 25426953


Článek vyšel v časopise

PLOS One


2020 Číslo 1
Nejčtenější tento týden
Nejčtenější v tomto čísle
Kurzy

Zvyšte si kvalifikaci online z pohodlí domova

Svět praktické medicíny 1/2024 (znalostní test z časopisu)
nový kurz

Koncepce osteologické péče pro gynekology a praktické lékaře
Autoři: MUDr. František Šenk

Sekvenční léčba schizofrenie
Autoři: MUDr. Jana Hořínková

Hypertenze a hypercholesterolémie – synergický efekt léčby
Autoři: prof. MUDr. Hana Rosolová, DrSc.

Význam metforminu pro „udržitelnou“ terapii diabetu
Autoři: prof. MUDr. Milan Kvapil, CSc., MBA

Všechny kurzy
Kurzy Podcasty Doporučená témata Časopisy
Přihlášení
Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se

#ADS_BOTTOM_SCRIPTS#