1
|
Yang LF, Liu YG, Tao YL, Zhang WM, Li JY, Chi SQ, Zhang GF, Chu D. Development of an on-site diagnostic LAMP assay for rapid differentiation of the invasive pest Phthorimaea absoluta (Meyrick) using insect tissues. PEST MANAGEMENT SCIENCE 2024; 80:4069-4073. [PMID: 38563512 DOI: 10.1002/ps.8114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND The tomato leafminer, Phthorimaea absoluta (Meyrick) (Lepidoptera: Gelechiidae), is a destructive invasive pest that originated in South America and has spread within China since 2017. A rapid method for on-site identification of P. absoluta is urgently needed for interception of this pest across China. RESULTS We developed a loop-mediated isothermal amplification (LAMP) technique to differentiate P. absoluta from Liriomyza sativae, Chromatomyia horticola, and Phthorimaea operculella using extracted genomic DNA, which was then refined to create an on-site LAMP diagnostic method that can be performed under field conditions without the need for laboratory equipment. CONCLUSION In the present research, we developed an on-site diagnostic method for rapid differentiation of P. absoluta from other insects with similar morphology or damage characteristics in China. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- Li-Feng Yang
- Shandong Engineering Research Center for Environment-friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Shandong Province Center for Bioinvasions and Eco-security, Qingdao Agricultural University, Qingdao, China
| | - Ya-Ge Liu
- Shandong Engineering Research Center for Environment-friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Shandong Province Center for Bioinvasions and Eco-security, Qingdao Agricultural University, Qingdao, China
| | - Yun-Li Tao
- Shandong Engineering Research Center for Environment-friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Shandong Province Center for Bioinvasions and Eco-security, Qingdao Agricultural University, Qingdao, China
| | - Wan-Min Zhang
- Department of Pest Prediction and Management, Liaoning Technological Center of Green Agriculture, Shenyang, China
| | - Jian-Yong Li
- Tech Center of Jinan Customs District, Jinan, China
| | - Sheng-Qi Chi
- Shandong Engineering Research Center for Environment-friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Shandong Province Center for Bioinvasions and Eco-security, Qingdao Agricultural University, Qingdao, China
| | - Gui-Fen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Integrated Pest Management of Crop, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Chu
- Shandong Engineering Research Center for Environment-friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Shandong Province Center for Bioinvasions and Eco-security, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
2
|
Hulme PE, Beggs JR, Binny RN, Bray JP, Cogger N, Dhami MK, Finlay-Smits SC, French NP, Grant A, Hewitt CL, Jones EE, Lester PJ, Lockhart PJ. Emerging advances in biosecurity to underpin human, animal, plant, and ecosystem health. iScience 2023; 26:107462. [PMID: 37636074 PMCID: PMC10450416 DOI: 10.1016/j.isci.2023.107462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
One Biosecurity is an interdisciplinary approach to policy and research that builds on the interconnections between human, animal, plant, and ecosystem health to effectively prevent and mitigate the impacts of invasive alien species. To support this approach requires that key cross-sectoral research innovations be identified and prioritized. Following an interdisciplinary horizon scan for emerging research that underpins One Biosecurity, four major interlinked advances were identified: implementation of new surveillance technologies adopting state-of-the-art sensors connected to the Internet of Things, deployable handheld molecular and genomic tracing tools, the incorporation of wellbeing and diverse human values into biosecurity decision-making, and sophisticated socio-environmental models and data capture. The relevance and applicability of these innovations to address threats from pathogens, pests, and weeds in both terrestrial and aquatic ecosystems emphasize the opportunity to build critical mass around interdisciplinary teams at a global scale that can rapidly advance science solutions targeting biosecurity threats.
Collapse
Affiliation(s)
- Philip E. Hulme
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Jacqueline R. Beggs
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Rachelle N. Binny
- Manaaki Whenua - Landcare Research, PO Box 69040, Lincoln, New Zealand
| | - Jonathan P. Bray
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Naomi Cogger
- Tāwharau Ora, School of Veterinary Science, Massey University, Palmerston North 4472, New Zealand
| | - Manpreet K. Dhami
- Manaaki Whenua - Landcare Research, PO Box 69040, Lincoln, New Zealand
| | | | - Nigel P. French
- Tāwharau Ora, School of Veterinary Science, Massey University, Palmerston North 4472, New Zealand
| | - Andrea Grant
- Scion, 10 Kyle Street, Riccarton, Christchurch 8011, New Zealand
| | - Chad L. Hewitt
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Eirian E. Jones
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Phil J. Lester
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Peter J. Lockhart
- School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand
| |
Collapse
|
3
|
Rako L, Agarwal A, Eow L, Roberts JMK, Rodoni BC, Blacket MJ. LAMP (Loop-mediated isothermal amplification) assay for rapid identification of Varroa mites. Sci Rep 2023; 13:11931. [PMID: 37488147 PMCID: PMC10366197 DOI: 10.1038/s41598-023-38860-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/16/2023] [Indexed: 07/26/2023] Open
Abstract
Varroa mites are serious pests of European honeybees (Apis mellifera). For detection of Varroa mite, a new molecular LAMP-based assay has been developed, which retains the body of the mite intact for morphological identification. Six novel Varroa LAMP primers were designed from existing DNA sequences of the COI locus to target V. destructor and V. jacobsoni, providing the ability to tell them apart from other non-target beehive associated mite and insect species. This LAMP assay is specific in detecting these Varroa species and has been tested on specimens originating from multiple countries. It produces amplification of V. destructor and V. jacobsoni in 16 ± 3.4 min with an anneal derivative of 78 ± 0.5 °C whilst another Varroa species,V. underwoodi, showed late amplification. A gBlock gene fragment, used here as a positive control has a different anneal derivative of 80 °C. Three non-destructive DNA extraction methods (HotShot, QuickExtract and Xtract) were tested and found to be suitable for use in the field. The LAMP assay was sensitive to very low levels of Varroa DNA, down to 0.24 picogram (~ 1 × 10 copies/µL of Varroa gBlock). This is a new molecular tool for rapid and accurate detection and identification of Varroa mites for pest management, in areas where these mites do not occur.
Collapse
Grants
- 4-8KPXYWM Department of Agriculture, Fisheries and Forestry, Australian Government
- 4-8KPXYWM Department of Agriculture, Fisheries and Forestry, Australian Government
- 4-8KPXYWM Department of Agriculture, Fisheries and Forestry, Australian Government
- 4-8KPXYWM Department of Agriculture, Fisheries and Forestry, Australian Government
- 4-8KPXYWM Department of Agriculture, Fisheries and Forestry, Australian Government
Collapse
Affiliation(s)
- Lea Rako
- Agriculture Victoria Research, AgriBio - Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia.
| | - Arati Agarwal
- Agriculture Victoria Research, AgriBio - Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Lixin Eow
- Agriculture Victoria Research, AgriBio - Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - John M K Roberts
- Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio - Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio - Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| |
Collapse
|
4
|
Agarwal A, Martoni F, Eow L, Rodoni BC, Blacket MJ. LAMP assay for the detection of the Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psylloidea: Psyllidae). Sci Rep 2023; 13:10895. [PMID: 37407637 DOI: 10.1038/s41598-023-37721-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/26/2023] [Indexed: 07/07/2023] Open
Abstract
Diaphorina citri Kuwayama, also known as the Asian citrus psyllid (ACP), can vector the bacterium Candidatus Liberibacter asiaticus (CLas), agent of Huanglongbing (HLB): an incurable disease affecting citrus trees worldwide. In citrus growing regions where ACP and HLB are absent, such as Australia, the risk of an incursion and consequent economic damage to citrus industries make this psyllid one of the top-priority pests. Due to ACP's small dimensions and the generally poorly studied native psylloid fauna worldwide, morphological identification of this insect to distinguish it from harmless species is challenging, especially in the field, and with immature, partial or damaged specimens. To allow rapid and efficient detection of ACP in the field, we designed and optimised a new Loop-mediated isothermal amplification (LAMP) assay for the detection of D. citri based on the mitochondrial 16S locus. The optimised ACP 16S LAMP assay produced amplification from D. citri samples within 13.3 ± 3.6 min, with an anneal derivative of ~ 78.5 °C. A synthetic gBlock gene fragment was also developed to be used as positive control for the new LAMP assay with a different anneal derivative of ~ 83 °C. An existing commercially available LAMP assay for detection of the bacterium CLas was also tested in this study on ACP DNA. The ACP 16S LAMP assay we developed and tested here provides a valuable new in-field compatible tool that can allow early detections of ACP, enabling a quick biosecurity response, and could potentially be adopted by a wide range of users, from farmers to agronomists and from researchers to industry.
Collapse
Affiliation(s)
- Arati Agarwal
- Agriculture Victoria Research, AgriBio - Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Francesco Martoni
- Agriculture Victoria Research, AgriBio - Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Lixin Eow
- Agriculture Victoria Research, AgriBio - Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio - Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio - Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia.
| |
Collapse
|
5
|
Shimbori EM, Querino RB, Costa VA, Zucchi RA. Taxonomy and Biological Control: New Challenges in an Old Relationship. NEOTROPICAL ENTOMOLOGY 2023; 52:351-372. [PMID: 36656493 PMCID: PMC9851596 DOI: 10.1007/s13744-023-01025-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/03/2023] [Indexed: 05/13/2023]
Abstract
Biological control and taxonomy are continuously developing fields with remarkable impacts on society. At least 80 years of literature have documented this relationship, which remains essentially the same in its mutualistic nature, as well as in its major challenges. From the perspective of Brazilian taxonomists, we discuss the impacts of important scientific and social developments that directly affect research in these areas, posing new challenges for this lasting relationship. The increasing restrictions and concerns regarding the international transit of organisms require improvements in research related to risk assessment for exotic biological control agents and also stimulate prospecting within the native biota. In our view, this is a positive situation that can foster a closer relationship between taxonomists and applied entomologists, as well as local surveys and taxonomic studies that are necessary before new programs and agents can be implemented. We discuss the essential role of molecular biology in this context, as an iconic example of the synergy between applied sciences and natural history. As our society comes to need safer and more sustainable solutions for food security and the biodiversity crisis, scientific progress will build upon this integration, where biological control and taxonomy play an essential role.
Collapse
Affiliation(s)
- Eduardo Mitio Shimbori
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), São Paulo Piracicaba, Brazil
| | - Ranyse Barbosa Querino
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Cerrados, Planaltina, Distrito Federal Brazil
| | - Valmir Antonio Costa
- Centro Avançado de Pesquisa e Desenvolvimento em Sanidade Agropecuária, Instituto Biológico, São Paulo Campinas, Brazil
| | - Roberto Antonio Zucchi
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), São Paulo Piracicaba, Brazil
| |
Collapse
|
6
|
Fowler EV, Starkie ML, Zhu X, Piper AM, Agarwal A, Rako L, Gardiner A, Oczkowicz S, Gopurenko D, Schutze MK, Blacket MJ. Development of a cost-effective, morphology-preserving method for DNA isolation from bulk invertebrate trap catches: Tephritid fruit flies as an exemplar. PLoS One 2023; 18:e0281759. [PMID: 36791141 PMCID: PMC9931127 DOI: 10.1371/journal.pone.0281759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Abstract
Insect identification and preservation of voucher specimens is integral to pest diagnostic and surveillance activities; yet bulk-trapped insects are a diagnostic challenge due to high catch numbers and the susceptibility of samples to environmental damage. Many insect trap catches rely on examination of morphological characters for species identifications, which is a time consuming and highly skilled task, hence there is a need for more efficient molecular approaches. Many bulk DNA extraction methods require destructive sampling of specimens, resulting in damaged, or fully destroyed, voucher specimens. We developed an inexpensive, rapid, bulk DNA isolation method that preserves specimens as pinned vouchers to a standard that allows for post-extraction morphological examination and inclusion in insect reference collections. Our protocol was validated using a group of insects that are time-consuming to identify when trapped in large numbers-the dacine fruit flies (Diptera: Tephritidae: Dacinae). In developing our method, we evaluated existing protocols against the following criteria: effect on morphology; suitability for large trap catches; cost; ease of handling; and application to downstream molecular diagnostic analyses such as real-time PCR and metabarcoding. We found that the optimum method for rapid isolation of DNA extraction was immersing flies in a NaOH:TE buffer at 75°C for 10 minutes, without the need for proteinase K or detergents. This HotSOAK method produced sufficient high-quality DNA whilst preserving morphological characters suitable for species-level identification with up to 20,000 flies in a sample. The lysates performed well in down-stream analyses such as loop-mediated isothermal amplification (LAMP) and real-time PCR applications, while for metabarcoding PCR the lysate required an additional column purification step. Development of this method is a key step required for upscaling our capacity to accurately detect insects captured in bulk traps, whether for biodiversity, biosecurity, or pest management objectives.
Collapse
Affiliation(s)
- Elizabeth V. Fowler
- Queensland Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- * E-mail:
| | - Melissa L. Starkie
- Queensland Department of Agriculture and Fisheries, Brisbane, QLD, Australia
| | - Xiaocheng Zhu
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | | | - Arati Agarwal
- Agriculture Victoria Research, AgriBio Centre, Bundoora, VIC, Australia
| | - Lea Rako
- Agriculture Victoria Research, AgriBio Centre, Bundoora, VIC, Australia
| | - Alexandra Gardiner
- Queensland Department of Agriculture and Fisheries, Brisbane, QLD, Australia
| | - Sybilla Oczkowicz
- Queensland Department of Agriculture and Fisheries, Brisbane, QLD, Australia
| | - David Gopurenko
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Mark K. Schutze
- Queensland Department of Agriculture and Fisheries, Brisbane, QLD, Australia
| | - Mark J. Blacket
- Agriculture Victoria Research, AgriBio Centre, Bundoora, VIC, Australia
| |
Collapse
|
7
|
Starkie ML, Fowler EV, Zhu X, Agarwal A, Rako L, Schneider IC, Schutze MK, Royer JE, Gopurenko D, Gillespie P, Blacket MJ. Loop-mediated isothermal amplification (LAMP) assays for detection of the New Guinea fruit fly Bactrocera trivialis (Drew) (Diptera: Tephritidae). Sci Rep 2022; 12:12602. [PMID: 35871253 PMCID: PMC9308764 DOI: 10.1038/s41598-022-16901-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
The cue-lure-responding New Guinea fruit fly, Bactroceratrivialis, poses a biosecurity risk to neighbouring countries, e.g., Australia. In trapping programs, lure caught flies are usually morphologically discriminated from non-target species; however, DNA barcoding can be used to confirm similar species where morphology is inconclusive, e.g., Bactrocerabreviaculeus and B.rufofuscula. This can take days—and a laboratory—to resolve. A quicker, simpler, molecular diagnostic assay would facilitate a more rapid detection and potential incursion response. We developed LAMP assays targeting cytochrome c oxidase subunit I (COI) and Eukaryotic Translation Initiation Factor 3 Subunit L (EIF3L); both assays detected B.trivialis within 25 min. The BtrivCOI and BtrivEIF3L assay anneal derivatives were 82.7 ± 0.8 °C and 83.3 ± 1.3 °C, respectively, detecting down to 1 × 101 copies/µL and 1 × 103 copies/µL, respectively. Each assay amplified some non-targets from our test panel; however notably, BtrivCOI eliminated all morphologically similar non-targets, and combined, the assays eliminated all non-targets. Double-stranded DNA gBlocks were developed as positive controls; anneal derivatives for the COI and EIF3L gBlocks were 84.1 ± 0.7 °C and 85.8 ± 0.2 °C, respectively. We recommend the BtrivCOI assay for confirmation of suspect cue-lure-trapped B.trivialis, with BtrivEIF3L used for secondary confirmation when required.
Collapse
|
8
|
eDNA-based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity. Sci Rep 2022; 12:6553. [PMID: 35449180 PMCID: PMC9023534 DOI: 10.1038/s41598-022-10545-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/07/2022] [Indexed: 11/25/2022] Open
Abstract
LAMP assays are becoming increasingly popular in the field of invasive species detection but are still underused in eDNA-based monitoring. Here, we propose a LAMP assay designed to detect the North American crayfish species Pacifastacus leniusculus in water samples from streams. The presence of P. leniusculus was detected through this new LAMP assay in all but one of the nine sites sampled. No correlation was found between ddPCR absolute concentration measurements and the number of LAMP-positive technical replicates. However, we showed that using dependent technical replicates could significantly enhance the detection sensitivity of the LAMP assay. Applied to other assays, it could improve sensitivity and thus allow for a more efficient use of eDNA-based LAMP assays for invasive species detection in aquatic ecosystems.
Collapse
|
9
|
Agarwal A, Rako L, Schutze MK, Starkie ML, Tay WT, Rodoni BC, Blacket MJ. A diagnostic LAMP assay for rapid identification of an invasive plant pest, fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae). Sci Rep 2022; 12:1116. [PMID: 35064176 PMCID: PMC8782856 DOI: 10.1038/s41598-021-04496-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
Fall armyworm (FAW), Spodoptera frugiperda (Lepidoptera: Noctuidae), is a highly polyphagous invasive plant pest that has expanded its global geographic distribution, including recently into much of Australia. Rapid diagnostic tests are required for identification of FAW to assist subsequent management and control. We developed a new loop-mediated isothermal amplification (LAMP) assay based on the mitochondrial cytochrome c oxidase subunit I (COI) gene for accurate and timely diagnosis of FAW in the field. The specificity of the new assay was tested against a broad panel of twenty non-target noctuids, including eight other Spodoptera species. Only S. frugiperda samples produced amplification within 20 min, with an anneal derivative temperature of 78.3 ± 0.3 °C. A gBlock dsDNA fragment was developed and trialled as a synthetic positive control, with a different anneal derivative of 81 °C. The new FAW LAMP assay was able to detect FAW DNA down to 2.4 pg, similar to an existing laboratory-based real-time PCR assay. We also trialled the new FAW assay with a colorimetric master mix and found it could successfully amplify positive FAW samples in half the time compared to an existing FAW colorimetric LAMP assay. Given the high sensitivity and rapid amplification time, we recommend the use of this newly developed FAW LAMP assay in a portable real-time fluorometer for in-field diagnosis of FAW.
Collapse
Affiliation(s)
- Arati Agarwal
- Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Lea Rako
- Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Mark K Schutze
- Biosecurity Queensland, Queensland Department of Agriculture and Fisheries, GPO Box 267, Brisbane, QLD, 4001, Australia
| | - Melissa L Starkie
- Biosecurity Queensland, Queensland Department of Agriculture and Fisheries, GPO Box 267, Brisbane, QLD, 4001, Australia
| | - Wee Tek Tay
- CSIRO, Black Mountain Laboratories, Clunies Ross Street, Canberra, ACT, 2601, Australia.,Applied BioSciences, University of Macquarie, Sydney, NSW, 2109, Australia
| | - Brendan C Rodoni
- Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Mark J Blacket
- Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia.
| |
Collapse
|
10
|
Rako L, Agarwal A, Semeraro L, Broadley A, Rodoni BC, Blacket MJ. A LAMP (loop-mediated isothermal amplification) test for rapid identification of Khapra beetle (Trogoderma granarium). PEST MANAGEMENT SCIENCE 2021; 77:5509-5521. [PMID: 34363302 PMCID: PMC9290502 DOI: 10.1002/ps.6591] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/06/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Khapra beetle (Trogoderma granarium Everts) is a significant pest of food products around the world, causing great losses of stored grain and produce, with export restrictions imposed on countries with established beetle populations. Khapra beetle is a high-priority exotic invertebrate pest in many countries requiring a rapid quarantine/biosecurity response when incursions occur. To address this, we developed a novel Khapra LAMP (loop-mediated isothermal amplification) assay using a portable real-time fluorometer and an additional 18S ribosomal DNA (18S) insect control LAMP assay for confirmation of the presence of insect DNA. Both LAMP tests can be performed either in a portable real-time fluorometer or using simple, visual colorimetric technique. RESULTS Both the Khapra and 18S LAMP tests amplify positive samples within ≤ 25 min, with an anneal derivative temperature of 77.7 ± 0.7 °C for Khapra LAMP test and 88.0 ± 1.0 °C for 18S. The new Khapra LAMP assay is sensitive to very low levels of DNA (1.02 × 10-6 ng μL-1 ). Additionally, we developed a gBlock double stranded DNA fragment for use as positive Khapra control with a different anneal derivative of 80 °C. Both assays are simple to use in the field and are capable of amplifying DNA from target beetles, even when samples are partially degraded which is typically found during surveillance activities. By screening a broad panel of Dermestidae species we demonstrate that our new assay is species-specific, with no detections of false positives. Also, we evaluated multiple DNA extraction methods, with both QuickExtract and HotSHOT extraction methods proving suitable for in-field use. CONCLUSION The novel Khapra and 18S LAMP assays should improve speed, accuracy and confidence of detection of Khapra beetle at incursion points and aid rapid biosecurity responses in any country affected, especially as the assays described here are portable and easy to implement in the field conditions where resources are limited. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Lea Rako
- Agriculture VictoriaAgriBioBundooraVICAustralia
| | | | | | - Adam Broadley
- Department of Agriculture, Water and the EnvironmentScience and Surveillance GroupCanberraACTAustralia
| | | | | |
Collapse
|