scholarly journals Validation of an eDNA-based method for the detection of wildlife pathogens in water

2020 ◽  
Vol 141 ◽  
pp. 171-184
Author(s):  
N Sieber ◽  
H Hartikainen ◽  
C Vorburger
Keyword(s):  
Water Samples ◽  
Pathogen Detection ◽  
Batrachochytrium Dendrobatidis ◽  
Tap Water ◽  
Pathogenic Fungus ◽  
Environmental Dna ◽  
Detection Sensitivity ◽  
Detection Rates ◽  
Filtration Step ◽  
Wildlife Pathogens

Monitoring the occurrence and density of parasites and pathogens can identify high infection-risk areas and facilitates disease control and eradication measures. Environmental DNA (eDNA) techniques are increasingly used for pathogen detection due to their relative ease of application. Since many factors affect the reliability and efficacy of eDNA-based detection, rigorous validation and assessment of method limitations is a crucial first step. We evaluated an eDNA detection method using in situ filtration of large-volume water samples, developed to detect and quantify aquatic wildlife parasites by quantitative PCR (qPCR). We assessed method reliability using Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid proliferative kidney disease, in a controlled experimental setup. Different amounts of parasite spores were added to tanks containing either clean tap water or water from a semi-natural mesocosm community. Overall detection rates were higher than 80%, but detection was not consistent among replicate samples. Within-tank variation in detection emphasises the need for increased site-level replication when dealing with parasites and pathogens. Estimated parasite DNA concentrations in water samples were highly variable, and a significant increase with higher spore concentrations was observed only for B. dendrobatidis. Despite evidence for PCR inhibition in DNA extractions from mesocosm water samples, the type of water did not affect detection rates significantly. Direct spiking controls revealed that the filtration step reduced detection sensitivity. Our study identifies sensitive quantification and sufficient replication as major remaining challenges for the eDNA-based methods for detection of parasites in water.

Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi

2019 ◽  
Vol 40 (1) ◽  
pp. 29-39 ◽  
Author(s):  
Joana Sabino-Pinto ◽  
E. Tobias Krause ◽  
Molly C. Bletz ◽  
An Martel ◽  
Frank Pasmans ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Pathogen Detection ◽  
Batrachochytrium Dendrobatidis ◽  
Quantitative Polymerase Chain Reaction ◽  
Large Fraction ◽  
Work Load ◽  
Detection Sensitivity ◽  
Pooled Dna ◽  
Reaction Volumes ◽  
User Friendly

Abstract Epidemiology relies on understanding the distribution of pathogens which often can be detected through DNA-based techniques, such as quantitative Polymerase Chain Reaction (qPCR). Typically, the DNA of each individual sample is separately extracted and undergoes qPCR analysis. However, when performing field surveys and long-term monitoring, a large fraction of the samples is generally expected to be negative, especially in geographical areas still considered free of the pathogen. If pathogen detection within a population – rather than determining its individual prevalence – is the focus, work load and monetary costs can be reduced by pooling samples for DNA extraction. We test and refine a user-friendly technique where skin swabs can be pooled during DNA extraction to detect the amphibian chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans (Bsal). We extracted pools with different numbers of samples (from one to four swabs), without increasing reaction volumes, and each pool had one sample inoculated with a predetermined zoospore amount. Pool size did not reduce the ability to detect the two fungi, except if inoculated with extremely low zoospore amounts (one zoospore). We confirm that pooled DNA extraction of cutaneous swabs can substantially reduce processing time and costs without minimizing detection sensitivity. This is of relevance especially for the new emerging pathogen Bsal, for which pooled DNA extraction had so far not been tested and massive monitoring efforts in putatively unaffected regions are underway.

scholarly journals Occurrence and distribution of pharmaceuticals in raw, finished, and drinking water from seven large river basins in China

2019 ◽  
Vol 17 (3) ◽  
pp. 477-489 ◽  
Author(s):  
Jia Lv ◽  
Lan Zhang ◽  
Yongyan Chen ◽  
Bixiong Ye ◽  
Jiayi Han ◽  
...  
Keyword(s):  
Drinking Water ◽  
Water Treatment ◽  
Water Samples ◽  
Solid Phase ◽  
Tap Water ◽  
River Basins ◽  
Large River ◽  
Mass Spectrometry Analysis ◽  
Detection Rates ◽  
Large River Basins

Abstract The occurrence of pharmaceuticals in the drinking water is a growing concern in China. In this study, we determined the concentration and distribution of 59 selected pharmaceuticals in raw, finished, and tap water samples from 79 drinking water treatment plants (DWTPs) in 15 cities, encompassing seven large river basins in China, using solid-phase extraction pretreatment and ultra-high-performance liquid chromatography–tandem mass spectrometry analysis. Forty-seven pharmaceuticals were detected in raw water samples, with detection rates of 1.27–96.20% and average concentrations of 0.09–128.87 ng/L. Forty-three pharmaceuticals were detected in finished water samples, with detection rates of 1.27–96.20% and average concentrations of 0.07–59.17 ng/L. Forty-two pharmaceuticals were detected in tap water samples, with detection rates of 1.27–94.94% and average concentrations of 0.07–58.43 ng/L. Purification methods implemented by DWTPs are capable of removing some pharmaceuticals from water treatment systems; however, low concentrations of pharmaceuticals were detected in drinking water, raising concerns about the possible human health implications of long-term exposure to low-dose pharmaceuticals. The detection and quantification of pharmaceuticals in municipal water samples presented in this study represent the most extensive analysis of commonly used pharmaceuticals and personal care products located in Chinese river basins.

scholarly journals Molecular evidence for the ubiquitous presence of Legionella species in Dutch tap water installations

2007 ◽  
Vol 5 (3) ◽  
pp. 375-383 ◽  
Author(s):  
Bram M. W. Diederen ◽  
Caroline M. A. de Jong ◽  
Ingrid Aarts ◽  
Marcel F. Peeters ◽  
Anneke van der Zee
Keyword(s):  
16S Rrna ◽  
Water Samples ◽  
Tap Water ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Specific Probe ◽  
Detection Rates ◽  
Specific Pcr ◽  
Legionella Species ◽  
Species Specific

Our aim was to investigate the occurrence and identity of Legionella spp. in Dutch tap water installations using culture, real-time PCR and sequence analysis. The PCR assays used were a 16S rRNA gene based PCR with both a Legionella species specific probe and a L. pneumophila specific probe and a L. pneumophila-specific PCR based on the sequence of the mip gene. A total of 357 water samples from 250 locations in The Netherlands was investigated. The detection rates of Legionella spp. were 2,2% (8 of 357) by culture, and 87,1% (311 of 357) by PCR. The majority of samples was found to contain Legionella species other than L. pneumophila. These comprised of Legionella Like Amoebal Pathogens (LLAPs), L. busanensis, L. worsliensis and others. Fourteen (3,9%) samples were positive for L. pneumophila by either culture, 16S rRNA based PCR and/or mip based PCR. It is apparent from this study that Legionella spp. DNA is ubiquitous in Dutch potable water samples. Our findings further suggest that LLAPs and viable but nonculturable (VBNC) Legionella represent a large proportion of the population in man-made environments.

scholarly journals An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5871 ◽  
Author(s):  
Robert S. Cornman ◽  
James E. McKenna ◽  
Jennifer Fike ◽  
Sara J. Oyler-McCance ◽  
Robin Johnson
Keyword(s):  
Water Samples ◽  
Stream Water ◽  
Environmental Dna ◽  
Experimental Comparison ◽  
Grab Sampling ◽  
Detection Rates ◽  
Composite Sampling ◽  
Lowest Common Ancestor ◽  
The Impact ◽  
Composite Samples

Use of environmental DNA (eDNA) to assess distributions of aquatic and semi-aquatic macroorganisms is promising, but sampling schemes may need to be tailored to specific objectives. Given the potentially high variance in aquatic eDNA among replicate grab samples, compositing smaller water volumes collected over a period of time may be more effective for some applications. In this study, we compared eDNA profiles from composite water samples aggregated over three hours with grab water samples. Both sampling patterns were performed with identical autosamplers paired at two different sites in a headwater stream environment, augmented with exogenous fish eDNA from an upstream rearing facility. Samples were filtered through 0.8 μm cellulose nitrate filters and DNA was extracted with a cetyl trimethylammonium bromide procedure. Eukaryotic and bacterial community profiles were derived by amplicon sequencing of 12S ribosomal, 16S ribosomal, and cytochrome oxidase I loci. Operational taxa were assigned to genus with a lowest common ancestor approach for eukaryotes and to family with the RDP Classifier software for prokaryotes. Eukaryotic community profiles were more consistent with composite sampling than grab sampling. Downstream, rarefaction curves suggested faster taxon accumulation for composite samples, and estimated richness was higher for composite samples as a set than for grab samples. Upstream, composite sampling produced lower estimated richness than grab samples, but with overlapping standard errors. Furthermore, a bimodal pattern of richness as a function of sequence counts suggested the impact of clumped particles on upstream samples. Bacterial profiles were insensitive to sample method, consistent with the more even dispersion expected for bacteria compared with eukaryotic eDNA. Overall, samples composited over 3 h performed equal to or better than triplicate grab sampling for quantitative community metrics, despite the higher total sequencing effort provided to grab replicates. On the other hand, taxon-specific detection rates did not differ appreciably and the two methods gave similar estimates of the ratio of the common fish genera Salmo and Coregonus at each site. Unexpectedly, Salmo eDNA dropped out substantially faster than Coregonus eDNA between the two sites regardless of sampling method, suggesting that differential settling affects the estimation of relative abundance. We identified bacterial patterns that were associated with eukaryotic diversity, suggesting potential roles as biomarkers of sample representativeness.

scholarly journals Comparison of supervised machine learning algorithms for waterborne pathogen detection using mobile phone fluorescence microscopy

Nanophotonics ◽  
2017 ◽  
Vol 6 (4) ◽  
pp. 731-741 ◽  
Author(s):  
Hatice Ceylan Koydemir ◽  
Steve Feng ◽  
Kyle Liang ◽  
Rohan Nadkarni ◽  
Parul Benien ◽  
...  
Keyword(s):  
Machine Learning ◽  
Water Samples ◽  
Pathogen Detection ◽  
Potable Water ◽  
Tap Water ◽  
Pond Water ◽  
Smartphone Application ◽  
Automated Detection ◽  
Resource Limited Settings ◽  
Resource Limited

AbstractGiardia lambliais a waterborne parasite that affects millions of people every year worldwide, causing a diarrheal illness known as giardiasis. Timely detection of the presence of the cysts of this parasite in drinking water is important to prevent the spread of the disease, especially in resource-limited settings. Here we provide extended experimental testing and evaluation of the performance and repeatability of a field-portable and cost-effective microscopy platform for automated detection and counting ofGiardiacysts in water samples, including tap water, non-potable water, and pond water. This compact platform is based on our previous work, and is composed of a smartphone-based fluorescence microscope, a disposable sample processing cassette, and a custom-developed smartphone application. Our mobile phone microscope has a large field of view of ~0.8 cm2and weighs only ~180 g, excluding the phone. A custom-developed smartphone application provides a user-friendly graphical interface, guiding the users to capture a fluorescence image of the sample filter membrane and analyze it automatically at our servers using an image processing algorithm and training data, consisting of >30,000 images of cysts and >100,000 images of other fluorescent particles that are captured, including, e.g. dust. The total time that it takes from sample preparation to automated cyst counting is less than an hour for each 10 ml of water sample that is tested. We compared the sensitivity and the specificity of our platform using multiple supervised classification models, including support vector machines and nearest neighbors, and demonstrated that a bootstrap aggregating (i.e. bagging) approach using raw image file format provides the best performance for automated detection ofGiardiacysts. We evaluated the performance of this machine learning enabled pathogen detection device with water samples taken from different sources (e.g. tap water, non-potable water, pond water) and achieved a limit of detection of 12 cysts per 10 ml, an average cyst capture efficiency of ~79%, and an accuracy of ~95%. Providing rapid detection and quantification of waterborne pathogens without the need for a microbiology expert, this field-portable imaging and sensing platform running on a smartphone could be very useful for water quality monitoring in resource-limited settings.

scholarly journals High frequency of Helicobacter pylori DNA in drinking water in Kermanshah, Iran, during June–November 2012

2013 ◽  
Vol 12 (3) ◽  
pp. 504-512 ◽  
Author(s):  
Alvandi Amirhooshang ◽  
Abiri Ramin ◽  
Aryan Ehsan ◽  
Rezaei Mansour ◽  
Bagherabadi Shahram
Keyword(s):  
Helicobacter Pylori ◽  
Drinking Water ◽  
Water Samples ◽  
Tap Water ◽  
Piping System ◽  
Detection Rates ◽  
High Prevalence ◽  
Polymerase Chain ◽  
H Pylori ◽  
Drinking Water Samples

To gain a better understanding of transmission and selecting appropriate measures for preventing the spread of Helicobacter pylori, the aim of this study was to investigate the prevalence of H. pylori in drinking water samples in Kermanshah, Iran. Drinking water samples were collected from around Kermanshah and filtered through 0.45 μm nitrocellulose filters. The bacterial sediment was subjected to DNA extraction and polymerase chain reaction (PCR) for H. pylori detection using newly designed primers targeted at the conserved region of the ureC gene. The overall detection rates for H. pylori DNA in the water samples were 56% (66/118) with a frequency of 36% (25/70) in tap water samples and 85% (41/48) in wells. The detection limit was 50 bacteria per liter of filtered water and a pure H. pylori DNA copy number of 6 per reaction. Based on the evidence we may suggest that recontamination occurred and H. pylori entered into the water piping system through cracked or broken pipes or was released from established H. pylori biofilms on pipes. In conclusion, a high prevalence of H. pylori was detected in drinking water samples that strengthens the evidence of H. pylori transmission through drinking water.

Acanthamoeba Species in Tap Water, Egypt

2017 ◽  
Vol 9 (1) ◽  
Author(s):  
Ahmad Z Al-Herrawy ◽  
Mohamed A Marouf ◽  
Mahmoud A. Gad
Keyword(s):  
Water Samples ◽  
Tap Water ◽  
Pcr Analysis ◽  
Pulmonary Infections ◽  
Clinical Syndromes ◽  
Acanthamoeba Species ◽  
Amebic Encephalitis ◽  
Acanthamoeba Culbertsoni ◽  
Autumn And Winter

Genus Acanthamoeba causes 3 clinical syndromes amebic keratitis, granulomatous amebic encephalitis and disseminated granulomatous amebic disease (eg, sinus, skin and pulmonary infections). A total of 144 tap water samples were collected from Giza governorate, Egypt. Samples were processed for detection of Acanthamoeba species using non-nutrient agar (NNA) and were incubated at 30oC. The isolates of Acanthamoeba were identified to species level based on the morphologic criteria. Molecular characterization of the Acanthamoeba isolates to genus level was performed by using PCR. The obtained results showed that the highest occurrence percentage of Acanthamoeba species in water samples was observed in summer season (38.9%), then it decreased to be 30.6% in spring and 25% in each of autumn and winter. PCR analysis showed that 100% of 43 Acanthamoeba morphologically positive samples were positive by genus specific primer. In the present study eight species of Acanthamoeba can be morphologically recognized namely Acanthamoeba triangularis, Acanthamoeba echinulata, Acanthamoeba astronyxis, Acanthamoeba comandoni, Acanthamoeba griffini, Acanthamoeba culbertsoni, Acanthamoeba quina and Acanthamoeba lenticulata. In conclusion, the most common Acanthamoeba species in tap water was Acanthamoeba comandoni

ECOLOGICAL AND PHYSIOLOGICAL ASSESSMENT OF CHEMICAL COMPOSITION OF DRINKING TAP WATER IN KHANTY-MANSIYSK AND SALEKHARD

2020 ◽  
pp. 159-167
Author(s):  
V.V. Lapenko ◽  
L.N. Bikbulatova ◽  
E.M. Ternikova
Keyword(s):  
Drinking Water ◽  
Chemical Composition ◽  
Water Samples ◽  
Tap Water ◽  
Iron Concentration ◽  
Absorption Spectrometry ◽  
Northern Region ◽  
Transport Processes ◽  
Magnesium Concentration ◽  
Geochemical Environment

Water is very important for humans, as it is a solvent for metabolic products. Moreover, it is necessary for metabolism, biochemical and transport processes. The elemental status in persons depends on the geochemical environment and consumption of bioelements with food and water. The aim of the paper is to conduct a comprehensive assessment of chemical composition of drinking tap water in Khanty-Mansiysk and Salekhard. Materials and Methods. The chemical composition of 100 samples of drinking tap water was analyzed by atomic absorption spectrometry, spectrophotometry and capillary electrophoresis. All in all, there were 50 samples from Khanty-Mansiysk and 50 samples from Salekhard. The results were compared with Sanitary Rules and Norms 2.1.4.1074-01. Results. Drinking tap water in Salekhard contains a significantly higher concentration of iron, which is much above the maximum allowable concentration, if compared to water samples in Khanty-Mansiysk (p=0.03). In the cities under consideration, the water undergoes high-quality reagent-free treatment. However, the deterioration of the water supply networks in Salekhard is 3 times as high as in Khanty-Mansiysk. Calcium and magnesium concentration in water samples from Khanty-Mansiysk is 5.6 and 3.9 times lower than the MAC; in water samples from Salekhard calcium concentration is 6.3 (p=0.008) and magnesium concentration 4.6 (p<0.001) times lower than the MAC. Conclusion. The consumption of ultra-fresh drinking water leads to low intake of bioelements, which are a part of enzymes contributing to the human antioxidant defense and can result in manifestation of cardiovascular diseases. This is especially true for Salekhard with very soft drinking water and high iron concentration, which excess can exhibit prooxidant properties. Keywords: tap water, bioelements, northern region, antioxidants. Вода является важнейшим соединением для человека: необходима в качестве растворителя продуктов метаболизма и протекания обменных, биохимических и транспортных процессов. Элементный статус организма человека зависит от геохимического окружения и поступления биоэлементов с пищей и водой. Цель. Провести комплексную оценку химического состава водопроводной воды городов Ханты-Мансийск и Салехард. Материалы и методы. Методами атомно-абсорбционной спектрометрии, спектрофотометрии и капиллярного электрофореза проанализирован химический состав 100 проб водопроводной воды: по 50 из Ханты-Мансийска и Салехарда. Результаты сравнивали с СанПиН 2.1.4.1074-01. Результаты. В водопроводной воде Салехарда установлена превышающая ПДК и достоверно более высокая концентрация железа сравнительно с водой Ханты-Мансийска (р=0,03). При условии качественной безреагентной водоподготовки в изучаемых городах это обусловлено изношенностью водопроводных сетей в Салехарде, более чем в 3 раза превышающей этот показатель в Ханты-Мансийске. Концентрация кальция и магния в воде Ханты-Мансийска в 5,6 и 3,9 раза ниже ПДК; в воде Салехарда – в 6,3 (р=0,008) и 4,6 (р<0,001) раза ниже ПДК соответственно. Заключение. Употребление ультрапресной питьевой воды на фоне очень малого поступления с водой биоэлементов, входящих в состав ферментов антиоксидантной защиты организма человека, может привести к манифестации кардиоваскулярных заболеваний. Это особенно актуально для г. Салехарда с очень мягкой питьевой водой с повышенным содержанием железа, избыток которого может проявлять прооксидантные свойства. Ключевые слова: водопроводная вода, биоэлементы, северный регион, антиоксиданты.

scholarly journals Determination of essential and non-essential element contents of drinking water and baby water for infant’s nutrition

2021 ◽  
Vol 44 (1) ◽  
pp. 194-202
Author(s):  
Funda Demir ◽  
Meral Yildirim Ozen ◽  
Emek Moroydor Derun
Keyword(s):  
Water Samples ◽  
Infant Nutrition ◽  
Tap Water ◽  
Essential Element ◽  
Essential Elements ◽  
Local Market ◽  
Drinking Waters ◽  
Significant Difference ◽  
Element Contents

Abstract In this study, essential (Ca, Cr, Cu, Fe, K, Mg, Na, P, Zn), and non-essential (Al, Ni, Pb) element contents of the drinking and baby water samples which are sold in the local market and tap water samples in Istanbul were examined. It was determined that elements of Cr, Cu, Fe, P, Zn, Al, and Ni were below detection limits in all water samples. Among the non-essential elements analyzed in water samples, Pb was the only detected element. At the same time, the percentages that meet the daily element requirements of infants were also calculated. As a result of the evaluations made, there is no significant difference in infant nutrition between baby waters and other drinking waters in terms of the element content.

Sign in / Sign up

Export Citation Format

Share Document