PCR to predict risk of airborne disease

West, Jonathan; Atkins, Simon D.; Emberlin, Jean; Fitt, Bruce D.L.

doi:10.1016/j.tim.2008.05.004

Cited by 99 publications

(74 citation statements)

References 54 publications

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“…S1 in the supplemental material). Airborne particles smaller than 1 m in diameter were collected and directed into 1 liter of phosphate-buffered saline (PBS) buffer (pH 7.4) (61) at 1 m above ground level for 48 h using a modified air sampling device referred to as a connector-linked direct precipitation air sampler with a water jet pump (Eyela) (flow rate, 19 liters min Ϫ1 ), which was different from other commercially available air sampling devices (66,70) (Fig. 1).…”

Section: Methodsmentioning

confidence: 99%

“…Airborne particles of biological origin or activity include atmospheric bacteria, fungal spores, pollen, and allergens (8)(9)(10)26). These particles could be either the direct cause of epidemics and infectious diseases or the indirect cause of noninfectious diseases (e.g., hypersensitivity to aeroallergens, as with asthma) (70). The atmosphere is also known to act as a vehicle for the dispersal of unknown biological particulates, particularly viruses which are regarded as major environmental risk factors in complex disease pathogenesis (17,23,53).…”

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confidence: 99%

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Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

Whon

Kim

Roh

et al. 2012

J Virol

121

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Airborne viruses are expected to be ubiquitous in the atmosphere but they still remain poorly understood. This study investigated the temporal and spatial dynamics of airborne viruses and their genotypic characteristics in air samples collected from three distinct land use types (a residential district [RD], a forest [FR], and an industrial complex [IC]) and from rainwater samples freshly precipitated at the RD site (RD-rain). Viral abundance exhibited a seasonal fluctuation in the range between 1.7 ؋ 10 6 and 4.0 ؋ 10 7 viruses m ؊3 , which increased from autumn to winter and decreased toward spring, but no significant spatial differences were observed. Temporal variations in viral abundance were inversely correlated with seasonal changes in temperature and absolute humidity. Metagenomic analysis of air viromes amplified by rolling-circle phi29 polymerase-based random hexamer priming indicated the dominance of plant-associated single-stranded DNA (ssDNA) geminivirus-related viruses, followed by animal-infecting circovirus-related sequences, with low numbers of nanoviruses and microphages-related genomes. Particularly, the majority of the geminivirus-related viruses were closely related to ssDNA mycoviruses that infect plant-pathogenic fungi. Phylogenetic analysis based on the replication initiator protein sequence indicated that the airborne ssDNA viruses were distantly related to known ssDNA viruses, suggesting that a high diversity of viruses were newly discovered. This research is the first to report the seasonality of airborne viruses and their genetic diversity, which enhances our understanding of viral ecology in temperate regions.

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

Whon

Kim

Roh

et al. 2012

J Virol

121

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“…Woody discs were used to catch the conidia of Heterobasidion irregulare in pine plantations (18,19), while paper filters were used to trap the inoculum of Fusarium circinatum in sites infected with pine pitch canker (20). The use of reliable trapping methods, combined with sensitive molecular approaches, such as real-time quantitative PCR (qPCR) assays, allows for rapid and specific detection of fungal pathogens from these samples (21). The advent of this molecular technique has enabled faster and more sensitive diagnostic tools for the identification and quantification of disease-causing agents.…”

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confidence: 99%

“…The advent of this molecular technique has enabled faster and more sensitive diagnostic tools for the identification and quantification of disease-causing agents. The accuracy and reliability of qPCR may also enable the detection of latent fungal infections before symptoms occur (22,23) and the detection of fungal pathogens that are difficult to culture (21).…”

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confidence: 99%

Rapid Detection of Ceratocystis platani Inoculum by Quantitative Real-Time PCR Assay

Luchi¹,

Ghelardini²,

Belbahri

et al. 2013

Appl Environ Microbiol

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Ceratocystis platani is the causal agent of canker stain of plane trees, a lethal disease able to kill mature trees in one or two successive growing seasons. The pathogen is a quarantine organism and has a negative impact on anthropogenic and natural populations of plane trees. Contaminated sawdust produced during pruning and sanitation fellings can contribute to disease spread. The goal of this study was to design a rapid, real-time quantitative PCR assay to detect a C. platani airborne inoculum. Airborne inoculum traps (AITs) were placed in an urban setting in the city of Florence, Italy, where the disease was present. Primers and TaqMan minor groove binder (MGB) probes were designed to target cerato-platanin (CP) and internal transcribed spacer 2 (ITS2) genes. The detection limits of the assay were 0.05 pg/l and 2 fg/l of fungal DNA for CP and ITS, respectively. Pathogen detection directly from AITs demonstrated specificity and high sensitivity for C. platani, detecting DNA concentrations as low as 1.2 ؋ 10 ؊2 to 1.4 ؋ 10 ؊2 pg/l, corresponding to ϳ10 conidia per ml. Airborne inoculum traps were able to detect the C. platani inoculum within 200 m of the closest symptomatic infected plane tree. The combination of airborne trapping and real-time quantitative PCR assay provides a rapid and sensitive method for the specific detection of a C. platani inoculum. This technique may be used to identify the period of highest risk of pathogen spread in a site, thus helping disease management.

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“…PCR-based methods allow precise spore identification s of many fungal species, including the most dangerous plant pathogens (West et al 2008a). Moreover, recent introduction of Realtime PCR is designed to quantify the numbers of spores or gene copies (Kaczmarek et al 2009.…”

Section: Identification Of Fungal Spores In Air With Molecular Toolsmentioning

confidence: 99%

Aeromycology: studies of fungi in aeroplankton

Jędryczka

2014

biologica

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Air is a natural environment for spores of many genera and species of fungi. Despite its small size and a significant dispersion they have a great impact on human health and different areas of our activities, such as agricultural production. The study on spores of fungi that belong to aeroplankton or bioaerosole is called aeromycology. The most frequent fungi present in the air are Cladosporium and Alternaria species. Their numbers are abundant regardless of latitude and height above the sea level and above the ground. They mostly originate from agricultural environment. Other frequently listed species of fungi, whose spores are present in the air include of Aspergillus, Penicillium, Fusarium, Sclerotinia and Ganoderma. The concentration of spores in the air strongly depends on the abundance of their formation during the studied period. This in turn relates to geobotanical region, vegetation, degree of urbanization, climatic conditions, season, current weather, wind force and direction, local microclimate, and many other factors. Changes in humidity affect the concentration of different types of fungal spores. In general they are divided to ‘dry’ (Alternaria, Cladosporium, Puccinia, Ustilago, Melampsora, Epicoccum, Drechslera) and ‘wet’ (Didymella, Fusarium, Ganoderma, Gliocladium, Leptosphaeria, Verticillium). Study of the composition of species and genera are being done using different types of spore samplers, mostly volumetric instruments. Visual identification is based on colony morphology of the fungus and the shape and size of spores. The identification at the species level is possible with molecular tools. Methods based on DNA/RNA amplification are very sensitive and accurate. They allow the identification below the species level, e.g. chemotypes, mating types or isolates with genes or alleles of interest. Aerobiological monitoring is widely used in the epidemiology of human diseases (inhalant allergies) and infections of arable crops (decision support systems for the protection of cultivated plants). Aeromycology is interconnected with such diverse areas as industrial aerobiology, bioterrorism, ecology, climatology or even speleology and cultural heritage.

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PCR to predict risk of airborne disease

Cited by 99 publications

References 54 publications

Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

Rapid Detection of Ceratocystis platani Inoculum by Quantitative Real-Time PCR Assay

Aeromycology: studies of fungi in aeroplankton

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