scholarly journals Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens

2021 ◽  
Vol 9 (1) ◽  
pp. 188
Author(s):  
Edoardo Piombo ◽  
Ahmed Abdelfattah ◽  
Samir Droby ◽  
Michael Wisniewski ◽  
Davide Spadaro ◽  
...  
Keyword(s):  
Plant Material ◽  
Plant Pathogens ◽  
Fruits And Vegetables ◽  
High Throughput Sequencing ◽  
Diagnostic Techniques ◽  
Current Status ◽  
Economic Losses ◽  
Shotgun Metagenomics ◽  
Precise Tool ◽  
Critical Aspects

Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegetables, with a corresponding increase in economic losses caused by the introduction of transboundary plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance protocols regarding specific organisms, but this approach is strictly targeted, while metabarcoding and shotgun metagenomics could be used to simultaneously detect all known pathogens and potentially new ones. This review aims to present the current status of high-throughput sequencing (HTS) diagnostics of fungal and bacterial plant pathogens, discuss the challenges that need to be addressed, and provide direction for the development of methods for the detection of a restricted number of related taxa (specific surveillance) or all of the microorganisms present in a sample (general surveillance). HTS techniques, particularly metabarcoding, could be useful for the surveillance of soilborne, seedborne and airborne pathogens, as well as for identifying new pathogens and determining the origin of outbreaks. Metabarcoding and shotgun metagenomics still suffer from low precision, but this issue can be limited by carefully choosing primers and bioinformatic algorithms. Advances in bioinformatics will greatly accelerate the use of metagenomics to address critical aspects related to the detection and surveillance of plant pathogens in plant material and foodstuffs.

scholarly journals Genome Resources for the Ex-type of Phytophthora citricola, and well-authenticated isolates of P. hibernalis, P. nicotianae and P. syringae

2021 ◽  
Author(s):  
Subodh K. Srivastava ◽  
Leandra M. Knight ◽  
Mark K. Nakhla ◽  
Z. Gloria Abad
Keyword(s):  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Economic Losses ◽  
Biological Research ◽  
Type Specimens ◽  
High Coverage ◽  
Oxford Nanopore ◽  
Long Read ◽  
Basic And Applied Research ◽  
Diagnostic Applications

Phytophthora is one of the most important genera of plant pathogens with many members causing high economic losses world-wide. To build robust molecular identification systems, it is very important to have information from well-authenticated specimens and in preference the ex-type specimens. The reference genomes of well-authenticated specimens form a critical foundation for genetics, biological research, and diagnostic applications. In this study, we describe four draft Phytophthora genomes resources for the Ex-type of P. citricola BL34 (P0716 WPC) (118 contigs for 50 Mb), and well-authenticated specimens of P. syringae BL57G (P10330 WPC) (591 contigs for 75 Mb), P. hibernalis BL41G (P3822 WPC) (404 contigs for 84 Mb), and P. nicotianae BL162 (P6303 WPC) (3984 contigs for 108 Mb) generated with MinION long-read High-Throughput Sequencing (HTS) technology (Oxford Nanopore Technologies, ONT). Using the quality reads we assembled high coverage genomes of P. citricola with 291X coverage and 16,662 annotated genes; P. nicotianae with 205X coverage and 29,271 annotated genes; P. syringae with 76X coverage and 23,331 annotated genes, and P. hibernalis with 42X coverage and 21,762 annotated genes. With the availability of genomes sequences and its annotations, we predict that these draft genomes will be accommodating for various basic and applied research including diagnostics to protect global agriculture.

scholarly journals High-Throughput Sequencing to Investigate Phytopathogenic Fungal Propagules Caught in Baited Insect Traps

2019 ◽  
Vol 5 (1) ◽  
pp. 15 ◽  
Author(s):  
Émilie D. Tremblay ◽  
Troy Kimoto ◽  
Jean A. Bérubé ◽  
Guillaume J. Bilodeau
Keyword(s):  
High Throughput ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Morphological Characteristics ◽  
Diagnostic Techniques ◽  
Phytopathogenic Fungi ◽  
Personal Genome ◽  
Annual Survey ◽  
Fungal Propagules ◽  
Wood Boring

Studying the means of dispersal of plant pathogens is crucial to better understand the dynamic interactions involved in plant infections. On one hand, entomologists rely mostly on both traditional molecular methods and morphological characteristics, to identify pests. On the other hand, high-throughput sequencing (HTS) is becoming the go-to avenue for scientists studying phytopathogens. These organisms sometimes infect plants, together with insects. Considering the growing number of exotic insect introductions in Canada, forest pest-management efforts would benefit from the development of a high-throughput strategy to investigate the phytopathogenic fungal and oomycete species interacting with wood-boring insects. We recycled formerly discarded preservative fluids from the Canadian Food Inspection Agency annual survey using insect traps and analysed more than one hundred samples originating from across Canada. Using the Ion Torrent Personal Genome Machine (PGM) HTS technology and fusion primers, we performed metabarcoding to screen unwanted fungi and oomycetes species, including Phytophthora spp. Community profiling was conducted on the four different wood-boring, insect-attracting semiochemicals; although the preservative (contained ethanol) also attracted other insects. Phytopathogenic fungi (e.g., Leptographium spp. and Meria laricis in the pine sawyer semiochemical) and oomycetes (mainly Peronospora spp. and Pythium aff. hypogynum in the General Longhorn semiochemical), solely associated with one of the four types of semiochemicals, were detected. This project demonstrated that the insect traps’ semiochemical microbiome represents a new and powerful matrix for screening phytopathogens. Compared to traditional diagnostic techniques, the fluids allowed for a faster and higher throughput assessment of the biodiversity contained within. Additionally, minimal modifications to this approach would allow it to be used in other phytopathology fields.

scholarly journals Towards Precise Interpretation of Oil Transformers via Novel Combined Techniques Based on DGA and Partial Discharge Sensors

Sensors ◽  
2021 ◽  
Vol 21 (6) ◽  
pp. 2223 ◽  
Author(s):  
Sayed A. Ward ◽  
Adel El-Faraskoury ◽  
Mohamed Badawi ◽  
Shimaa A. Ibrahim ◽  
Karar Mahmoud ◽  
...  
Keyword(s):  
Power Transformer ◽  
Partial Discharge ◽  
Electrical Power ◽  
Diagnostic Techniques ◽  
Gas Analysis ◽  
Economic Losses ◽  
Dissolved Gas ◽  
Electricity Transmission ◽  
Dissolved Gas Analysis ◽  
Precise Interpretation

Power transformers are considered important and expensive items in electrical power networks. In this regard, the early discovery of potential faults in transformers considering datasets collected from diverse sensors can guarantee the continuous operation of electrical systems. Indeed, the discontinuity of these transformers is expensive and can lead to excessive economic losses for the power utilities. Dissolved gas analysis (DGA), as well as partial discharge (PD) tests considering different intelligent sensors for the measurement process, are used as diagnostic techniques for detecting the oil insulation level. This paper includes two parts; the first part is about the integration among the diagnosis results of recognized dissolved gas analysis techniques, in this part, the proposed techniques are classified into four techniques. The integration between the different DGA techniques not only improves the oil fault condition monitoring but also overcomes the individual weakness, and this positive feature is proved by using 532 samples from the Egyptian Electricity Transmission Company (EETC). The second part overview the experimental setup for (66/11.86 kV–40 MVA) power transformer which exists in the Egyptian Electricity Transmission Company (EETC), the first section in this part analyzes the dissolved gases concentricity for many samples, and the second section illustrates the measurement of PD particularly in this case study. The results demonstrate that precise interpretation of oil transformers can be provided to system operators, thanks to the combination of the most appropriate techniques.

scholarly journals Optical Detection and Eradication of Dysplastic Barrett's Esophagus

2003 ◽  
Vol 2 (4) ◽  
pp. 289-302 ◽  
Author(s):  
Louis-Michel Wong Kee Song ◽  
Kenneth K. Wang
Keyword(s):  
Barrett’S Esophagus ◽  
Barrett's Esophagus ◽  
Sampling Error ◽  
Imaging Techniques ◽  
Standard Of Care ◽  
Diagnostic Techniques ◽  
Endoscopic Surveillance ◽  
Current Status ◽  
Delay In Diagnosis ◽  
Multiple Biopsies

Dysplastic Barrett's esophagus is a condition that offers multiple diagnostic and therapeutic challenges. The diagnosis of dysplasia within Barrett's esophagus currently relies on periodic endoscopic surveillance with multiple biopsies, a methodology limited by random sampling error, inconsistent histopathologic interpretation and delay in diagnosis. Optical spectroscopic and imaging techniques have the potential to identify dysplastic or early neoplastic lesions in real-time. These diagnostic modalities are needed to enhance the endoscopic surveillance of Barrett's esophagus in the future as well as help to define lesions for endoscopic therapy. Esophagectomy has been the standard of care for Barrett's esophagus with high-grade dysplasia although it is a procedure associated with significant morbidity and mortality. Minimally invasive endoscopic ablative therapies are attractive and less morbid alternatives to esophagectomy, with promising results obtained from the use of light-activated drugs (i.e., photodynamic therapy). The combination of novel optical diagnostic techniques and therapies will provide the endoscopist with much needed tools that can considerably enhance the management of patients with Barrett's esophagus. This article reviews the current status and future prospects of optical-based modalities for diagnosis and therapy of dysplastic Barrett's esophagus.

Swine influenza vaccines: current status and future perspectives

2010 ◽  
Vol 11 (1) ◽  
pp. 81-96 ◽  
Author(s):  
Wenjun Ma ◽  
Jürgen A. Richt
Keyword(s):  
Influenza A ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Current Status ◽  
Economic Losses ◽  
Influenza A Viruses ◽  
Swine Industry ◽  
Effective Strategies ◽  
Swine Disease ◽  
And Control

AbstractSwine influenza is an important contagious disease in pigs caused by influenza A viruses. Although only three subtypes of influenza A viruses, H1N1, H1N2 and H3N2, predominantly infect pigs worldwide, it is still a big challenge for vaccine manufacturers to produce efficacious vaccines for the prevention and control of swine influenza. Swine influenza viruses not only cause significant economic losses for the swine industry, but are also important zoonotic pathogens. Vaccination is still one of the most important and effective strategies to prevent and control influenza for both the animal and human population. In this review, we will discuss the current status of swine influenza worldwide as well as current and future options to control this economically important swine disease.

scholarly journals Draft Genome Sequence of “ Candidatus Phytoplasma oryzae” Strain Mbita1, the Causative Agent of Napier Grass Stunt Disease in Kenya

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Anne Fischer ◽  
Ivette Santana-Cruz ◽  
Lillian Wambua ◽  
Cassandra Olds ◽  
Charles Midega ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Agricultural Production ◽  
Plant Pathogens ◽  
Genomic Organization ◽  
Draft Genome ◽  
Napier Grass ◽  
Eastern Africa ◽  
Draft Genome Sequence ◽  
Economic Losses ◽  
Insight Into

Phytoplasmas are bacterial plant pathogens with devastating impact on agricultural production worldwide. In eastern Africa, Napier grass stunt disease causes serious economic losses in the smallholder dairy industry. This draft genome sequence of “ Candidatus Phytoplasma oryzae” strain Mbita1 provides insight into its genomic organization and the molecular basis of pathogenicity.

scholarly journals Methods for management of soilborne plant pathogens

2017 ◽  
Vol 32 (1) ◽  
pp. 9-24 ◽  
Author(s):  
Milica Mihajlovic ◽  
Emil Rekanovic ◽  
Jovana Hrustic ◽  
Mila Grahovac ◽  
Brankica Tanovic
Keyword(s):  
Methyl Bromide ◽  
Agricultural Production ◽  
Plant Pathogens ◽  
Current Knowledge ◽  
Montreal Protocol ◽  
Economic Losses ◽  
Simultaneous Application ◽  
Soilborne Disease ◽  
Single Chemical ◽  
Soil Disinfection

Soilborne pathogens cause significant economic losses in agricultural production all over the world. These species can survive for many years in the absence of a host plant by forming persistent structures such as microsclerotia, sclerotia, chlamydospores or oospores. Consequently, soilborne diseases are particularly difficult to predict, detect, diagnose and successfully control. Over the past 30 years, a fumigant, methyl bromide, has been widely used for their control in many crops. In 1992, methyl bromide was listed as an ozone-depleting substance under the Montreal Protocol ? an international treaty to protect the ozone layer. During the phaseout of methyl bromide, problems generated in agricultural production made it clear that dependence on a single method or a single chemical should be avoided. The objective of this review paper was to summarize the current knowledge about different methods of soilborne disease control including: crop rotation, steam soil disinfection, soil amendments, hydroponics and soilless growing systems, soil solarization, grafting, biological control and use of natural compounds, and chemical control. Positive and negative aspects of all available methods were reviewed. Benefits, achieved by simultaneous application of several methods based on different mechanisms of actions, are discussed.

scholarly journals The Diversity of Bacteria Associated with the Invasive Gall Wasp Dryocosmus kuriphilus, Its Galls and a Specialist Parasitoid on Chestnuts

Insects ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 86
Author(s):  
Xiaohui Yang ◽  
Yu Hui ◽  
Daohong Zhu ◽  
Yang Zeng ◽  
Lvquan Zhao ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Gall Wasp ◽  
Potential Vector ◽  
Dryocosmus Kuriphilus ◽  
Torymus Sinensis ◽  
Galling Insects ◽  
First Time

Dryocosmus kuriphilus (Hymenoptera: Cynipidae) induces galls on chestnut trees, which results in massive yield losses worldwide. Torymus sinensis (Hymenoptera: Torymidae) is a host-specific parasitoid that phenologically synchronizes with D. kuriphilus. Bacteria play important roles in the life cycle of galling insects. The aim of this research is to investigate the bacterial communities and predominant bacteria of D. kuriphilus, T. sinensis, D. kuriphilus galls and the galled twigs of Castanea mollissima. We sequenced the V5–V7 region of the bacterial 16S ribosomal RNA in D. kuriphilus, T. sinensis, D. kuriphilus galls and galled twigs using high-throughput sequencing for the first time. We provide the first evidence that D. kuriphilus shares most bacterial species with T. sinensis, D. kuriphilus galls and galled twigs. The predominant bacteria of D. kuriphilus are Serratia sp. and Pseudomonas sp. Furthermore, the bacterial community structures of D. kuriphilus and T. sinensis clearly differ from those of the other groups. Many species of the Serratia and Pseudomonas genera are plant pathogenic bacteria, and we suggest that D. kuriphilus may be a potential vector of plant pathogens. Furthermore, a total of 111 bacteria are common to D. kuriphilus adults, T. sinensis, D. kuriphilus galls and galled twigs, and we suggest that the bacteria may transmit horizontally among D. kuriphilus, T. sinensis, D. kuriphilus galls and galled twigs on the basis of their ecological associations.

scholarly journals Current status of porcine epidemic diarrhoea (PED) in European pigs

2019 ◽  
Vol 63 (4) ◽  
pp. 465-470
Author(s):  
Marta Antas ◽  
Grzegorz Woźniakowski
Keyword(s):  
Rna Virus ◽  
Acute Diarrhoea ◽  
Current Status ◽  
Economic Losses ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus ◽  
The Us ◽  
The Usa ◽  
Suckling Piglets ◽  
Farming Industry

Abstract Porcine epidemic diarrhoea (PED) is a highly contagious and devastating enteric disease of pigs caused by porcine epidemic diarrhoea virus (PEDV), an enveloped, single-stranded RNA virus belonging to the Alphacoronavirus genus of the Coronaviridae family. The disease is clinically similar to other forms of porcine gastroenteritis. Pigs are the only known host of the disease, and the occurrence of PED in wild boars is unknown. The virus causes acute diarrhoea, vomiting, dehydration, and high mortality in suckling piglets reaching 100%. Heavy economic losses in the pig-farming industry were sustained in the USA between 2013 and 2015 when PEDV spread very quickly and resulted in epidemics. The loss in the US pig industry has been estimated at almost seven million pigs. The purpose of this review is a description of the current status of porcine epidemic diarrhoea in European pigs and the risk presented by the introduction of PEDV to Poland in comparison to the epidemics in the USA.

scholarly journals Injectisome T3SS Subunits As Potential Chaperones In The Extracellular Export of Pectobacterium Carotovorum Subsp. Carotovorum Bacteriocins Carocin S1 And Carocin S3 Secreted Via Flagellar T3SS

2021 ◽  
Author(s):  
Hang-Cheng Chen ◽  
Reymund C. Derilo ◽  
Han-Ling Chen ◽  
Tzu-Rung Li ◽  
Ruchi Briam James S. Lagitnay ◽  
...  
Keyword(s):  
Type Iii Secretion ◽  
Insertional Mutagenesis ◽  
Plant Pathogens ◽  
Soft Rot ◽  
Economic Losses ◽  
Pectobacterium Carotovorum ◽  
Secretion Systems ◽  
Unique Type ◽  
Bacterial Flagellum ◽  
Type Iii

Abstract Pectobacterium carotovorum subsp. carotovorum (Pcc) causes soft-rot disease in a wide variety of plants resulting in economic losses worldwide. It produces various types of bacteriocin to compete against related plant pathogens. Studies on how bacteriocins are extracellularly secreted are conducted to understand the mechanism of interbacterial competition. In this study, the secretion of the low-molecular-weight bacteriocins (LMWB) Carocin S1 and Carocin S3 produced by a multiple-bacteriocin producing strain of Pcc, 89-H-4, was investigated. Tn5 insertional mutagenesis was used to generate a mutant, TH22-6, incapable of LMWBs secretion. Sequence and homology analyses of the gene disrupted by transposon Tn5 insertion revealed that the gene sctT, an essential component of the injectisome type III secretion machinery (T3aSS), is required for the secretion of the bacteriocins. This result raised a question regarding the nature of the secretion mechanism of Pcc bacteriocins which was previously discovered to be secreted via T3bSS, a system that utilizes the bacterial flagellum for extracellular secretions. Our previous report has shown that bacteriocin Carocin S1 cannot be secreted by mutants that are defective of T3bSS-related genes such as flhA, flhC, flhD and fliC. We knocked out several genes making up the significant structural components of both T3aSS and T3bSS. The findings led us to hypothesize the potential roles of the T3aSS-related proteins, SctT, SctU and SctV, as flagellar T3SS chaperones in the secretion of Pcc bacteriocins. This current discovery and the findings of our previous study helped us to conceptualize a unique Type III secretion system for bacteriocin extracellular export which is a hybrid of the injectisome and flagellar secretion systems.

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