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Mee PT, Buultjens AH, Oliver J, Brown K, Crowder JC, Porter JL, Hobbs EC, Judd LM, Taiaroa G, Puttharak N, Williamson DA, Blasdell KR, Tay EL, Feldman R, Muzari MO, Sanders C, Larsen S, Crouch SR, Johnson PDR, Wallace JR, Price DJ, Hoffmann AA, Gibney KB, Stinear TP, Lynch SE. Publisher Correction: Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia. Nat Microbiol 2024:10.1038/s41564-024-01693-y. [PMID: 38622381 DOI: 10.1038/s41564-024-01693-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Affiliation(s)
- Peter T Mee
- Centre for AgriBioscience, AgriBio, Agriculture Victoria, Bundoora, Victoria, Australia.
| | - Andrew H Buultjens
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Oliver
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Karen Brown
- Centre for AgriBioscience, AgriBio, Agriculture Victoria, Bundoora, Victoria, Australia
| | - Jodie C Crowder
- Centre for AgriBioscience, AgriBio, Agriculture Victoria, Bundoora, Victoria, Australia
| | - Jessica L Porter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Emma C Hobbs
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Louise M Judd
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - George Taiaroa
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Natsuda Puttharak
- Centre for AgriBioscience, AgriBio, Agriculture Victoria, Bundoora, Victoria, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, Doherty Institute for Infection and Immunity, Melbourne Health, Melbourne, Victoria, Australia
| | - Kim R Blasdell
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
| | - Ee Laine Tay
- Department of Health, Melbourne, Victoria, Australia
| | | | - Mutizwa Odwell Muzari
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital and Health Services, Cairns, Queensland, Australia
| | - Chris Sanders
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stuart Larsen
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Simon R Crouch
- South East Public Health Unit, Monash Health, Clayton, Victoria, Australia
| | - Paul D R Johnson
- North East Public Health Unit, Austin Health, Heidelberg, Victoria, Australia
| | - John R Wallace
- Department of Biology, Millersville University, Millersville, PA, USA
| | - David J Price
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Katherine B Gibney
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
- WHO Collaborating Centre for Mycobacterium ulcerans, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| | - Stacey E Lynch
- Centre for AgriBioscience, AgriBio, Agriculture Victoria, Bundoora, Victoria, Australia
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
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Mee PT, Buultjens AH, Oliver J, Brown K, Crowder JC, Porter JL, Hobbs EC, Judd LM, Taiaroa G, Puttharak N, Williamson DA, Blasdell KR, Tay EL, Feldman R, Muzari MO, Sanders C, Larsen S, Crouch SR, Johnson PDR, Wallace JR, Price DJ, Hoffmann AA, Gibney KB, Stinear TP, Lynch SE. Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia. Nat Microbiol 2024; 9:377-389. [PMID: 38263454 PMCID: PMC10847040 DOI: 10.1038/s41564-023-01553-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/08/2023] [Indexed: 01/25/2024]
Abstract
Buruli ulcer, a chronic subcutaneous infection caused by Mycobacterium ulcerans, is increasing in prevalence in southeastern Australia. Possums are a local wildlife reservoir for M. ulcerans and, although mosquitoes have been implicated in transmission, it remains unclear how humans acquire infection. We conducted extensive field survey analyses of M. ulcerans prevalence among mosquitoes in the Mornington Peninsula region of southeastern Australia. PCR screening of trapped mosquitoes revealed a significant association between M. ulcerans and Aedes notoscriptus. Spatial scanning statistics revealed overlap between clusters of M. ulcerans-positive Ae. notoscriptus, M. ulcerans-positive possum excreta and Buruli ulcer cases, and metabarcoding analyses showed individual mosquitoes had fed on humans and possums. Bacterial genomic analysis confirmed shared single-nucleotide-polymorphism profiles for M. ulcerans detected in mosquitoes, possum excreta and humans. These findings indicate Ae. notoscriptus probably transmit M. ulcerans in southeastern Australia and highlight mosquito control as a Buruli ulcer prevention measure.
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Affiliation(s)
- Peter T Mee
- Centre for AgriBioscience, AgriBio, Agriculture Victoria, Bundoora, Victoria, Australia.
| | - Andrew H Buultjens
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Oliver
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Karen Brown
- Centre for AgriBioscience, AgriBio, Agriculture Victoria, Bundoora, Victoria, Australia
| | - Jodie C Crowder
- Centre for AgriBioscience, AgriBio, Agriculture Victoria, Bundoora, Victoria, Australia
| | - Jessica L Porter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Emma C Hobbs
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Louise M Judd
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - George Taiaroa
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Natsuda Puttharak
- Centre for AgriBioscience, AgriBio, Agriculture Victoria, Bundoora, Victoria, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, Doherty Institute for Infection and Immunity, Melbourne Health, Melbourne, Victoria, Australia
| | - Kim R Blasdell
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
| | - Ee Laine Tay
- Department of Health, Melbourne, Victoria, Australia
| | | | - Mutizwa Odwell Muzari
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital and Health Services, Cairns, Queensland, Australia
| | - Chris Sanders
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stuart Larsen
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Simon R Crouch
- South East Public Health Unit, Monash Health, Clayton, Victoria, Australia
| | - Paul D R Johnson
- North East Public Health Unit, Austin Health, Heidelberg, Victoria, Australia
| | - John R Wallace
- Department of Biology, Millersville University, Millersville, PA, USA
| | - David J Price
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Katherine B Gibney
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
- WHO Collaborating Centre for Mycobacterium ulcerans, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| | - Stacey E Lynch
- Centre for AgriBioscience, AgriBio, Agriculture Victoria, Bundoora, Victoria, Australia
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
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Batovska J, Mee PT, Sawbridge TI, Rodoni BC, Lynch SE. Enhanced Arbovirus Surveillance with High-Throughput Metatranscriptomic Processing of Field-Collected Mosquitoes. Viruses 2022; 14:v14122759. [PMID: 36560765 PMCID: PMC9782886 DOI: 10.3390/v14122759] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022] Open
Abstract
Surveillance programs are essential for the prevention and control of mosquito-borne arboviruses that cause serious human and animal diseases. Viral metatranscriptomic sequencing can enhance surveillance by enabling untargeted, high-throughput arbovirus detection. We used metatranscriptomic sequencing to screen field-collected mosquitoes for arboviruses to better understand how metatranscriptomics can be utilised in routine surveillance. Following a significant flood event in 2016, more than 56,000 mosquitoes were collected over seven weeks from field traps set up in Victoria, Australia. The traps were split into samples of 1000 mosquitoes or less and sequenced on the Illumina HiSeq. Five arboviruses relevant to public health (Ross River virus, Sindbis virus, Trubanaman virus, Umatilla virus, and Wongorr virus) were detected a total of 33 times in the metatranscriptomic data, with 94% confirmed using reverse transcription quantitative PCR (RT-qPCR). Analysis of metatranscriptomic cytochrome oxidase I (COI) sequences enabled the detection of 12 mosquito and two biting midge species. Screening of the same traps by an established public health arbovirus surveillance program corroborated the metatranscriptomic arbovirus and mosquito species detections. Assembly of genome sequences from the metatranscriptomic data also led to the detection of 51 insect-specific viruses, both known and previously undescribed, and allowed phylogenetic comparison to past strains. We have demonstrated how metatranscriptomics can enhance surveillance by enabling untargeted arbovirus detection, providing genomic epidemiological data, and simultaneously identifying vector species from large, unsorted mosquito traps.
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Affiliation(s)
- Jana Batovska
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- Correspondence: (J.B.); (P.T.M.); Tel.: +61-3-9623-1442 (J.B.); +61-3-9032-7143 (P.T.M.)
| | - Peter T. Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- Correspondence: (J.B.); (P.T.M.); Tel.: +61-3-9623-1442 (J.B.); +61-3-9032-7143 (P.T.M.)
| | - Tim I. Sawbridge
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, 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 3086, Australia
| | - Stacey E. Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
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Blasdell KR, McNamara B, O’Brien DP, Tachedjian M, Boyd V, Dunn M, Mee PT, Clayton S, Gaburro J, Smith I, Gibney KB, Tay EL, Hobbs EC, Waidyatillake N, Lynch SE, Stinear TP, Athan E. Environmental risk factors associated with the presence of Mycobacterium ulcerans in Victoria, Australia. PLoS One 2022; 17:e0274627. [PMID: 36099259 PMCID: PMC9469944 DOI: 10.1371/journal.pone.0274627] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/01/2022] [Indexed: 11/18/2022] Open
Abstract
In recent years reported cases of Buruli ulcer, caused by Mycobacterium ulcerans, have increased substantially in Victoria, Australia, with the epidemic also expanding geographically. To develop an understanding of how M. ulcerans circulates in the environment and transmits to humans we analyzed environmental samples collected from 115 properties of recent Buruli ulcer cases and from 115 postcode-matched control properties, for the presence of M. ulcerans. Environmental factors associated with increased odds of M. ulcerans presence at a property included certain native plant species and native vegetation in general, more alkaline soil, lower altitude, the presence of common ringtail possums (Pseudocheirus peregrinus) and overhead powerlines. However, only overhead powerlines and the absence of the native plant Melaleuca lanceolata were associated with Buruli ulcer case properties. Samples positive for M. ulcerans were more likely to be found at case properties and were associated with detections of M. ulcerans in ringtail possum feces, supporting the hypothesis that M. ulcerans is zoonotic, with ringtail possums the strongest reservoir host candidate. However, the disparity in environmental risk factors associated with M. ulcerans positive properties versus case properties indicates the involvement of human behavior or the influence of other environmental factors in disease acquisition that requires further study.
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Affiliation(s)
- Kim R. Blasdell
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
- * E-mail:
| | - Bridgette McNamara
- Department of Infectious Diseases, Barwon Health, Geelong, Victoria, Australia
- Centre of Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel P. O’Brien
- Department of Infectious Diseases, Barwon Health, Geelong, Victoria, Australia
- Department of Health, Victorian State Government, Melbourne, Victoria, Australia
| | - Mary Tachedjian
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
| | - Victoria Boyd
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
| | - Michael Dunn
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
| | - Peter T. Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - Simone Clayton
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
| | - Julie Gaburro
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
| | - Ina Smith
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Katherine B. Gibney
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ee Laine Tay
- Department of Health, Victorian State Government, Melbourne, Victoria, Australia
| | - Emma C. Hobbs
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Stacey E. Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Eugene Athan
- Department of Infectious Diseases, Barwon Health, Geelong, Victoria, Australia
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria, Australia
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de Vries EM, Cogan NOI, Gubala AJ, Mee PT, O'Riley KJ, Rodoni BC, Lynch SE. Rapid, in-field deployable, avian influenza virus haemagglutinin characterisation tool using MinION technology. Sci Rep 2022; 12:11886. [PMID: 35831457 PMCID: PMC9279447 DOI: 10.1038/s41598-022-16048-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
Outbreaks of avian influenza virus (AIV) from wild waterfowl into the poultry industry is of upmost significance and is an ongoing and constant threat to the industry. Accurate surveillance of AIV in wild waterfowl is critical in understanding viral diversity in the natural reservoir. Current surveillance methods for AIV involve collection of samples and transportation to a laboratory for molecular diagnostics. Processing of samples using this approach takes more than three days and may limit testing locations to those with practical access to laboratories. In potential outbreak situations, response times are critical, and delays have implications in terms of the spread of the virus that leads to increased economic cost. This study used nanopore sequencing technology for in-field sequencing and subtype characterisation of AIV strains collected from wild bird faeces and poultry. A custom in-field virus screening and sequencing protocol, including a targeted offline bioinformatic pipeline, was developed to accurately subtype AIV. Due to the lack of optimal diagnostic MinION packages for Australian AIV strains the bioinformatic pipeline was specifically targeted to confidently subtype local strains. The method presented eliminates the transportation of samples, dependence on internet access and delivers critical diagnostic information in a timely manner.
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Affiliation(s)
- Ellen M de Vries
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
| | - Noel O I Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Aneta J Gubala
- Land Division, Defence Science & Technology Group, Fishermans Bend, VIC, 3207, Australia
| | - Peter T Mee
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Kim J O'Riley
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Brendan C Rodoni
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Stacey E Lynch
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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Mee PT, Wong S, Brown K, Lynch SE. Quantitative PCR assay for the detection of Aedes vigilax in mosquito trap collections containing large numbers of morphologically similar species and phylogenetic analysis of specimens collected in Victoria, Australia. Parasit Vectors 2021; 14:434. [PMID: 34454606 PMCID: PMC8401248 DOI: 10.1186/s13071-021-04923-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022] Open
Abstract
Background Aedes vigilax is one of the most significant arbovirus vector and pest species in Australia’s coastal regions. Occurring in multiple countries, this mosquito species occurs as a species complex which has been separated into three clades with two detected in Australia. Until recently, Ae. vigilax has largely been absent from Victoria, only occasionally caught over the years, with no reported detections from 2010 to 2016. Complicating the detection of Ae. vigilax is the shared sympatric distribution to the morphologically similar Ae. camptorhynchus, which can exceed 10,000 mosquitoes in a single trap night in Victoria. Currently, there are no molecular assays available for the detection of Ae. vigilax. We aim to develop a quantitative PCR (qPCR) for the detection of Ae. vigilax, with the specificity and sensitivity of this assay assessed as well as a method to process whole mosquito traps. Methods Trapping was performed during the 2017–2020 mosquito season in Victoria in two coastal areas across these 3 consecutive years. A qPCR assay was designed to allow rapid identification of Ae. vigilax as well as a whole mosquito trap homogenizing and processing methodology. Phylogenetic analysis was performed to determine which clade Ae. vigilax from Victoria was closest to. Results Aedes vigilax was successfully detected each year across two coastal areas of Victoria, confirming the presence of this species. The qPCR assay was proven to be sensitive and specific to Ae. vigilax, with trap sizes up to 1000 mosquitoes showing no inhibition in detection sensitivity. Phylogenetic analysis revealed that Ae. vigilax from Victoria is associated with clade III, showing high sequence similarity to those previously collected in New South Wales, Queensland and Western Australia. Conclusions Aedes vigilax is a significant vector species that shares an overlapping distribution to the morphologically similar Ae. camptorhynchus, making detection difficult. Here, we have outlined the implementation of a specific and sensitive molecular screening assay coupled with a method to process samples for detection of Ae. vigilax in collections with large numbers of non-target species. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04923-y.
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Affiliation(s)
- Peter T Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia.
| | - Shani Wong
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Karen Brown
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Stacey E Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
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Phillips DE, Mee PT, Lynch SE, da Conceição F, Bendita da Costa Jong J, Rawlin GT. Use of Field Based Loop Mediated Isothermal Amplification (LAMP) Technology for a Prevalence Survey and Proof of Freedom Survey for African Swine Fever in Timor-Leste in 2019. Front Vet Sci 2021; 8:672048. [PMID: 34235203 PMCID: PMC8255686 DOI: 10.3389/fvets.2021.672048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/14/2021] [Indexed: 11/13/2022] Open
Abstract
African Swine Fever (ASF) has been spreading in numerous southeast Asian countries since a major incursion in mainland China in 2018. Timor-Leste confirmed an outbreak of ASF in September 2019 which resulted in high mortalities in affected pigs. Pigs in Timor-Leste are the second most common type of livestock kept by villagers and represent a traditionally important source of income and prestige for householders. In order to understand the extent of ASF infected villages in Timor-Leste a prevalence survey was designed and conducted in November-December 2019. Timor-Leste has limited laboratory facilities and access to qPCR diagnostic tests. Therefore, a loop mediated isothermal amplification (LAMP) assay was used to detect ASF positive blood samples collected during the prevalence survey. The LAMP assay was proven to be a robust, highly specific and sensitive laboratory test for ASF suitable for use in the field and where there are limited laboratory facilities. The results of the prevalence survey allowed the extent of the ASF incursion to be delineated and the introduction of a disease response strategy to limit the spread of ASF and assist in the recovery of the pig population in Timor-Leste.
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Affiliation(s)
- Dianne E Phillips
- Agriculture Victoria, Biosecurity and Agriculture Services, Bairnsdale, VIC, Australia
| | - Peter T Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Stacey E Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC, Australia
| | | | | | - Grant T Rawlin
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC, Australia
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Mee PT, Wong S, O’Riley KJ, da Conceição F, Bendita da Costa Jong J, Phillips DE, Rodoni BC, Rawlin GT, Lynch SE. Field Verification of an African Swine Fever Virus Loop-Mediated Isothermal Amplification (LAMP) Assay During an Outbreak in Timor-Leste. Viruses 2020; 12:v12121444. [PMID: 33334037 PMCID: PMC7765541 DOI: 10.3390/v12121444] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Recent outbreaks of African swine fever virus (ASFV) have seen the movement of this virus into multiple new regions with devastating impact. Many of these outbreaks are occurring in remote, or resource-limited areas, that do not have access to molecular laboratories. Loop-mediated isothermal amplification (LAMP) is a rapid point of care test that can overcome a range of inhibitors. We outline further development of a real-time ASFV LAMP, including field verification during an outbreak in Timor-Leste. To increase field applicability, the extraction step was removed and an internal amplification control (IAC) was implemented. Assay performance was assessed in six different sample matrices and verified for a range of clinical samples. A LAMP detection limit of 400 copies/rxn was determined based on synthetic positive control spikes. A colourmetric LAMP assay was also assessed on serum samples. Comparison of the LAMP assay to a quantitative polymerase chain reaction (qPCR) was performed on clinical ASFV samples, using both serum and oral/rectal swabs, with a substantial level of agreement observed. The further verification of the ASFV LAMP assay, removal of extraction step, implementation of an IAC and the assessment of a range of sample matrix, further support the use of this assay for rapid in-field detection of ASFV.
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Affiliation(s)
- Peter T. Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
- Correspondence: ; Tel.: +61-390-327-143
| | - Shani Wong
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
| | - Kim J. O’Riley
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
| | - Felisiano da Conceição
- Ministry of Agriculture and Fisheries, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili 0332, Timor-Leste; (F.d.C.); (J.B.d.C.J.)
| | - Joanita Bendita da Costa Jong
- Ministry of Agriculture and Fisheries, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili 0332, Timor-Leste; (F.d.C.); (J.B.d.C.J.)
| | - Dianne E. Phillips
- Agriculture Victoria, Biosecurity and Agriculture Services, Bairnsdale, VIC 3857, Australia;
| | - Brendan C. Rodoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
| | - Grant T. Rawlin
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
| | - Stacey E. Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
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Batovska J, Mee PT, Lynch SE, Sawbridge TI, Rodoni BC. Sensitivity and specificity of metatranscriptomics as an arbovirus surveillance tool. Sci Rep 2019; 9:19398. [PMID: 31852942 PMCID: PMC6920425 DOI: 10.1038/s41598-019-55741-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/29/2019] [Indexed: 01/30/2023] Open
Abstract
The ability to identify all the viruses within a sample makes metatranscriptomic sequencing an attractive tool to screen mosquitoes for arboviruses. Practical application of this technique, however, requires a clear understanding of its analytical sensitivity and specificity. To assess this, five dilutions (1:1, 1:20, 1:400, 1:8,000 and 1:160,000) of Ross River virus (RRV) and Umatilla virus (UMAV) isolates were spiked into subsamples of a pool of 100 Culex australicus mosquitoes. The 1:1 dilution represented the viral load of one RRV-infected mosquito in a pool of 100 mosquitoes. The subsamples underwent nucleic acid extraction, mosquito-specific ribosomal RNA depletion, and Illumina HiSeq sequencing. The viral load of the subsamples was also measured using reverse transcription droplet digital PCR (RT-ddPCR) and quantitative PCR (RT-qPCR). Metatranscriptomic sequencing detected both RRV and UMAV in the 1:1, 1:20 and 1:400 subsamples. A high specificity was achieved, with 100% of RRV and 99.6% of UMAV assembled contigs correctly identified. Metatranscriptomic sequencing was not as sensitive as RT-qPCR or RT-ddPCR; however, it recovered whole genome information and detected 19 other viruses, including four first detections for Australia. These findings will assist arbovirus surveillance programs in utilising metatranscriptomics in routine surveillance activities to enhance arbovirus detection.
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Affiliation(s)
- Jana Batovska
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
| | - Peter T Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Stacey E Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia.
| | - Tim I Sawbridge
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
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Abstract
The bacterial pathogen Elizabethkingia is known to exist in certain species of mosquito but was unknown in other arthropods. We report the detection and identification of Elizabethkingia in species of Culicoides biting midge in Australia, raising the possibility of bacterial transmission via this species.
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Duchemin JB, Mee PT, Lynch SE, Vedururu R, Trinidad L, Paradkar P. Zika vector transmission risk in temperate Australia: a vector competence study. Virol J 2017; 14:108. [PMID: 28599659 PMCID: PMC5466793 DOI: 10.1186/s12985-017-0772-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/01/2017] [Indexed: 11/23/2022] Open
Abstract
Background Zika virus is an emerging pathogen of global importance. It has been responsible for recent outbreaks in the Americas and in the Pacific region. This study assessed five different mosquito species from the temperate climatic zone in Australia and included Aedes albopictus as a potentially invasive species. Methods Mosquitoes were orally challenged by membrane feeding with Zika virus strain of Cambodia 2010 origin, belonging to the Asian clade. Virus infection and dissemination were assessed by quantitative PCR on midgut and carcass after dissection. Transmission was assessed by determination of cytopathogenic effect of saliva (CPE) on Vero cells, followed by determination of 50% tissue culture infectious dose (TCID50) for CPE positive samples. Additionally, the presence of Wolbachia endosymbiont infection was assessed by qPCR and standard PCR. Results Culex mosquitoes were found unable to present Zika virus in saliva, as demonstrated by molecular as well as virological methods. Aedes aegypti, was used as a positive control for Zika infection and showed a high level of virus infection, dissemination and transmission. Local Aedes species, Ae. notoscriptus and, to a lesser degree, Ae. camptorhynchus were found to expel virus in their saliva and contained viral nucleic acid within the midgut. Molecular assessment identified low or no dissemination for these species, possibly due to low virus loads. Ae. albopictus from Torres Strait islands origin was shown as an efficient vector. Cx quinquefasciatus was shown to harbour Wolbachia endosymbionts at high prevalence, whilst no Wolbachia was found in Cx annulirostris. The Australian Ae. albopictus population was shown to harbour Wolbachia at high frequency. Conclusions The risk of local Aedes species triggering large Zika epidemics in the southern parts of Australia is low. The potentially invasive Ae. albopictus showed high prevalence of virus in the saliva and constitutes a potential threat if this mosquito species becomes established in mainland Australia. Complete risk analysis of Zika transmission in the temperate zone would require an assessment of the impact of temperature on Zika virus replication within local and invasive mosquito species.
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Affiliation(s)
- Jean-Bernard Duchemin
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Peter T Mee
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Stacey E Lynch
- BioScience Research, Agriculture Victoria, AgriBio, The Centre for AgriBioscience, 5 Ring Rd, La Trobe University Campus, Bundoora, VIC, 3083, Australia
| | - Ravikiran Vedururu
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.,School of Applied Sciences, RMIT University, Bundoora, VIC, 3083, Australia
| | - Lee Trinidad
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Prasad Paradkar
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
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