scholarly journals Exploring the Cause of Diarrhoea and Poor Growth in 8–11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1608
Author(s):  
Tarka Raj Bhatta ◽  
Anthony Chamings ◽  
Soren Alexandersen
Keyword(s):  
Growing Pigs ◽  
Clinical Disease ◽  
Porcine Circovirus ◽  
Economic Losses ◽  
Porcine Parvovirus ◽  
Metagenomic Sequencing ◽  
Poor Growth ◽  
Dna Viruses ◽  
Porcine Astrovirus ◽  
Wide Range

Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.

scholarly journals Prevalence of Porcine Pseudorabies Virus and Its Coinfection Rate in Heilongjiang Province in China from 2013 to 2018

2019 ◽  
Author(s):  
Han Zhou ◽  
Yan Pan ◽  
Mengda Liu ◽  
Zifeng Han
Keyword(s):  
Pseudorabies Virus ◽  
Classical Swine Fever ◽  
Porcine Circovirus ◽  
Economic Losses ◽  
Respiratory Syndrome Virus ◽  
Heilongjiang Province ◽  
Serum Samples ◽  
Tissue Samples ◽  
Wide Range ◽  
Pig Farms

Abstract Background Pseudorabies (PR) is a highly contagious disease affecting a wide range of animals worldwide, which causes great annual economic losses in China. In this study, a total number of 18815 serum samples and 1589 tissue samples were tested by ELISA and PCR, which were collected from 311 intensive pig farms (≥350 sows) located in eight cities in Heilongjiang province. Results Overall, 16.3% and 84.5% serum samples were positive for gE- and gB-specified ELISA, respectively. 17.8% of tissue samples were shown as PCR positive for PRV. The co-infection rates of PRV with porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV2), and classical swine fever virus (CSFV) were measured. The rate of PRV co-infected with PRRSV was 36.0% followed by 12.9% with PCV2 and 1.8% with CSFV, respectively. Conclusions These results clearly demonstrate PRV prevalence and its coinfection rate in Heilongjiang province indicating high PR endemic in pig farms in this region. This study provides data for further epidemiological investigations and a reference for developing PRV control strategies in this region and in China.

Effect of porcine circovirus type 2 (PCV2) infection on reproduction: disease, vertical transmission, diagnostics and vaccination

2011 ◽  
Vol 12 (1) ◽  
pp. 47-65 ◽  
Author(s):  
D. M. Madson ◽  
T. Opriessnig
Keyword(s):  
Vertical Transmission ◽  
Current Knowledge ◽  
Clinical Signs ◽  
Porcine Circovirus Type ◽  
Porcine Circovirus Type 2 ◽  
Growing Pigs ◽  
Pcv2 Infection ◽  
Porcine Circovirus ◽  
Economic Losses

AbstractPorcine circovirus type 2 (PCV2) causes great economic losses in growing pigs and there are several reviews on disease manifestations and lesions associated with PCV2 in growing pigs. Reproductive failure in breeding herds, predominately associated with increased numbers of mummies and non-viable piglets at parturition, is one of the disease manifestations of PCV2 infection. Boars shed low amounts of infectious PCV2 in semen for extended time periods, and vertical transmission of PCV2 to fetuses during PCV2 viremia of the dam has been experimentally confirmed. However, intrauterine-infected piglets often are clinically normal. Nevertheless, pigs infected with PCV2 by the intrauterine route can be born viremic, possibly contributing to horizontal spread of PCV2 within the breeding herd and into the nursery. Shedding of PCV2 in semen and prevalence of intrauterine-infected piglets can both be greatly reduced by PCV2 vaccination well ahead of expected PCV2 exposure. This review is a discussion on current knowledge on the effects of PCV2 infection in the dam and inin uterofetuses, including clinical signs, lesions, diagnosis and prevention through vaccination. Infection of boars with PCV2, the potential for PCV2 transmission via semen and prevention of PCV2 shedding are also discussed.

scholarly journals Correlation of Lawsonia intracellularis positivity in quantitative PCR and herd factors in European pig herds

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Mirjam Arnold ◽  
Annelies Crienen ◽  
Hanny Swam ◽  
Stephan v. Berg ◽  
Rika Jolie ◽  
...  
Keyword(s):  
Direct Detection ◽  
Quantitative Polymerase Chain Reaction ◽  
Median Number ◽  
Growing Pigs ◽  
Economic Losses ◽  
Lawsonia Intracellularis ◽  
Poor Growth ◽  
Nursery Pigs ◽  
Potential Risk Factors ◽  
Polymerase Chain

Abstract Background Lawsonia intracellularis is causing diarrhea, poor growth and sudden death in pigs. It can be found in most pig populations leading to large economic losses worldwide. Many potential risk factors for the occurrence of disease or seropositivity have been described. The current study therefore focused on herd characteristics in European countries associated with direct detection of the pathogen determined by quantitative polymerase chain reaction. Results A median number of less than 30 nursery pigs per pen was correlated to less positive nursery pigs (p < 0.01) and generally less samples positive per herd (p < 0.05) as well as a lower median of genome equivalents determined per herd (p < 0.05). Routine use of zinc oxide at/ around weaning, which was mentioned by 41.0% of all farmers, was correlated to higher number of positive nursery pigs (p < 0.01) as well as higher median genome equivalents determined per herd (p < 0.05). Slatted flooring of more than 78.0% of the surface in nursery units was correlated to lower number of positive animals (p < 0.05) and a lower median of genome equivalents per herd (p < 0.05). A weight of more than 7.8 kg at weaning was correlated to a higher number of positive growing pigs (p < 0.05) as well as general higher number of positive samples/ herd (p < 0.01). Conclusions Weaning and subsequent accommodation of nursery pigs seem to be of particular importance in prevention of infection with Lawsonia intracellularis and the spread of the pathogen within the herd.

scholarly journals Toxin Production in Soybean (Glycine max L.) Plants with Charcoal Rot Disease and by Macrophomina phaseolina, the Fungus that Causes the Disease

Toxins ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 645 ◽  
Author(s):  
Hamed K. Abbas ◽  
Nacer Bellaloui ◽  
Cesare Accinelli ◽  
James R. Smith ◽  
W. Thomas Shier
Keyword(s):  
Culture Media ◽  
Leaf Disc ◽  
Toxin Production ◽  
Macrophomina Phaseolina ◽  
Economic Losses ◽  
Limit Of Quantification ◽  
Charcoal Rot ◽  
Wide Range ◽  
Soybean Plants ◽  
Rot Disease

Charcoal rot disease, caused by the fungus Macrophomina phaseolina, results in major economic losses in soybean production in southern USA. M. phaseolina has been proposed to use the toxin (-)-botryodiplodin in its root infection mechanism to create a necrotic zone in root tissue through which fungal hyphae can readily enter the plant. The majority (51.4%) of M. phaseolina isolates from plants with charcoal rot disease produced a wide range of (-)-botryodiplodin concentrations in a culture medium (0.14–6.11 µg/mL), 37.8% produced traces below the limit of quantification (0.01 µg/mL), and 10.8% produced no detectable (-)-botryodiplodin. Some culture media with traces or no (-)-botryodiplodin were nevertheless strongly phytotoxic in soybean leaf disc cultures, consistent with the production of another unidentified toxin(s). Widely ranging (-)-botryodiplodin levels (traces to 3.14 µg/g) were also observed in the roots, but not in the aerial parts, of soybean plants naturally infected with charcoal rot disease. This is the first report of (-)-botryodiplodin in plant tissues naturally infected with charcoal rot disease. No phaseolinone was detected in M. phaseolina culture media or naturally infected soybean tissues. These results are consistent with (-)-botryodiplodin playing a role in the pathology of some, but not all, M. phaseolina isolates from soybeans with charcoal rot disease in southern USA.

scholarly journals Integration of early disease-resistance phenotyping, histological characterization, and transcriptome sequencing reveals insights into downy mildew resistance in impatiens

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Ze Peng ◽  
Yanhong He ◽  
Saroj Parajuli ◽  
Qian You ◽  
Weining Wang ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Downy Mildew ◽  
Transcriptome Sequencing ◽  
Early Stage ◽  
Economic Losses ◽  
Potential Candidate ◽  
Early Disease ◽  
True Leaf ◽  
Cotyledon Stage ◽  
Wide Range

AbstractDowny mildew (DM), caused by obligate parasitic oomycetes, is a destructive disease for a wide range of crops worldwide. Recent outbreaks of impatiens downy mildew (IDM) in many countries have caused huge economic losses. A system to reveal plant–pathogen interactions in the early stage of infection and quickly assess resistance/susceptibility of plants to DM is desired. In this study, we established an early and rapid system to achieve these goals using impatiens as a model. Thirty-two cultivars of Impatiens walleriana and I. hawkeri were evaluated for their responses to IDM at cotyledon, first/second pair of true leaf, and mature plant stages. All I. walleriana cultivars were highly susceptible to IDM. While all I. hawkeri cultivars were resistant to IDM starting at the first true leaf stage, many (14/16) were susceptible to IDM at the cotyledon stage. Two cultivars showed resistance even at the cotyledon stage. Histological characterization showed that the resistance mechanism of the I. hawkeri cultivars resembles that in grapevine and type II resistance in sunflower. By integrating full-length transcriptome sequencing (Iso-Seq) and RNA-Seq, we constructed the first reference transcriptome for Impatiens comprised of 48,758 sequences with an N50 length of 2060 bp. Comparative transcriptome and qRT-PCR analyses revealed strong candidate genes for IDM resistance, including three resistance genes orthologous to the sunflower gene RGC203, a potential candidate associated with DM resistance. Our approach of integrating early disease-resistance phenotyping, histological characterization, and transcriptome analysis lay a solid foundation to improve DM resistance in impatiens and may provide a model for other crops.

scholarly journals SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

scholarly journals Insecticidal activity of citronella grass essential oil on Frankliniella schultzei and Myzus persicae

2013 ◽  
Vol 37 (2) ◽  
pp. 138-144 ◽  
Author(s):  
Patrícia Fontes Pinheiro ◽  
Vagner Tebaldi de Queiroz ◽  
Vando Miossi Rondelli ◽  
Adilson Vidal Costa ◽  
Tiago de Paula Marcelino ◽  
...  
Keyword(s):  
Essential Oil ◽  
Insecticidal Activity ◽  
Myzus Persicae ◽  
Green Peach Aphid ◽  
Biological Activities ◽  
Chemical Constituents ◽  
Economic Losses ◽  
Frankliniella Schultzei ◽  
Wide Range ◽  
Citronella Grass

The thrips, Frankliniella schultzei, and green peach aphid, Myzus persicae, cause direct damage to plants of economic importance and transmit phytoviruses, causing large economic losses. Chemical constituents of essential oils present a wide range of biological activities. The aim of this work was to evaluate insecticidal activity of essential oil from citronella grass, Cymbopogon winterianus, on F. schultzei and M. persicae. This essential oil was obtained by steam distillation and components were identified by GC/FID and GC/MS. A Potter spray tower was used to spray insects with the essential oil. The major constituents are geraniol (28.62%), citronellal (23.62%) and citronellol (17.10%). Essential oil of C. winterianus at 1% (w v-1) causes mortality in F. schultzei and M. persicae at 34.3% and 96.9%, respectively. The LC50 value for M. persicae was 0.36% and LC90 0.66%. Thus, citronella grass essential oil at 1% (w v-1) is more toxic to M. persicae than F. schultzei. This essential oil shows promise for developing pesticides to manage M. persicae.

scholarly journals Ozone damage, detoxification and the role of isoprenoids – new impetus for integrated models

2016 ◽  
Vol 43 (4) ◽  
pp. 324 ◽  
Author(s):  
Supriya Tiwari ◽  
Rüdiger Grote ◽  
Galina Churkina ◽  
Tim Butler
Keyword(s):  
Stomatal Conductance ◽  
Environmental Conditions ◽  
Economic Losses ◽  
Plant Responses ◽  
Damage Scenarios ◽  
Biochemical Processes ◽  
Wide Range ◽  
Defence Responses ◽  
High Concentrations ◽  
The Impact

High concentrations of ozone (O3) can have significant impacts on the health and productivity of agricultural and forest ecosystems, leading to significant economic losses. In order to estimate this impact under a wide range of environmental conditions, the mechanisms of O3 impacts on physiological and biochemical processes have been intensively investigated. This includes the impact on stomatal conductance, the formation of reactive oxygen species and their effects on enzymes and membranes, as well as several induced and constitutive defence responses. This review summarises these processes, discusses their importance for O3 damage scenarios and assesses to which degree this knowledge is currently used in ecosystem models which are applied for impact analyses. We found that even in highly sophisticated models, feedbacks affecting regulation, detoxification capacity and vulnerability are generally not considered. This implies that O3 inflicted alterations in carbon and water balances cannot be sufficiently well described to cover immediate plant responses under changing environmental conditions. Therefore, we suggest conceptual models that link the depicted feedbacks to available process-based descriptions of stomatal conductance, photosynthesis and isoprenoid formation, particularly the linkage to isoprenoid models opens up new options for describing biosphere-atmosphere interactions.

scholarly journals Remedial Treatment of Corroded Iron Objects by EnvironmentalAeromonasIsolates

2018 ◽  
Vol 85 (3) ◽  
Author(s):  
Wafa M. Kooli ◽  
Thomas Junier ◽  
Migun Shakya ◽  
Mathilde Monachon ◽  
Karen W. Davenport ◽  
...  
Keyword(s):  
Iron Reduction ◽  
Building Materials ◽  
Solid Phase ◽  
Corrosion Products ◽  
Metal Corrosion ◽  
Economic Losses ◽  
Cytotoxic Activities ◽  
Iron Corrosion ◽  
Pathogenic Potential ◽  
Wide Range

ABSTRACTUsing bacteria to transform reactive corrosion products into stable compounds represents an alternative to traditional methods employed in iron conservation. Two environmentalAeromonasstrains (CA23 and CU5) were used to transform ferric iron corrosion products (goethite and lepidocrocite) into stable ferrous iron-bearing minerals (vivianite and siderite). A genomic and transcriptomic approach was used to analyze the metabolic traits of these strains and to evaluate their pathogenic potential. Although genes involved in solid-phase iron reduction were identified, key genes present in other environmental iron-reducing species are missing from the genome of CU5. Several pathogenicity factors were identified in the genomes of both strains, but none of these was expressed under iron reduction conditions. Additionalin vivotests showed hemolytic and cytotoxic activities for strain CA23 but not for strain CU5. Both strains were easily inactivated using ethanol and heat. Nonetheless, given a lesser potential for a pathogenic lifestyle, CU5 is the most promising candidate for the development of a bio-based iron conservation method stabilizing iron corrosion. Based on all the results, a prototype treatment was established using archaeological items. On those, the conversion of reactive corrosion products and the formation of a homogenous layer of biogenic iron minerals were achieved. This study shows how naturally occurring microorganisms and their metabolic capabilities can be used to develop bio-inspired solutions to the problem of metal corrosion.IMPORTANCEMicrobiology can greatly help in the quest for a sustainable solution to the problem of iron corrosion, which causes important economic losses in a wide range of fields, including the protection of cultural heritage and building materials. Using bacteria to transform reactive and unstable corrosion products into more-stable compounds represents a promising approach. The overall aim of this study was to develop a method for the conservation and restoration of corroded iron items, starting from the isolation of iron-reducing bacteria from natural environments. This resulted in the identification of a suitable candidate (Aeromonassp. strain CU5) that mediates the formation of desirable minerals at the surfaces of the objects. This led to the proof of concept of an application method on real objects.

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