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 Diversity, virulence and antibiogram traits of Escherichia coli recovered from potable water sources in Gharbia, Egypt

2020 ◽  
Vol 18 (3) ◽  
pp. 430-438
Author(s):  
Walid Elmonir ◽  
Etab Mohamed Abo Remela ◽  
Yasmine Alwakil
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Water Samples ◽  
Potable Water ◽  
Multiple Drug Resistance ◽  
Tap Water ◽  
Water Sources ◽  
Multiple Drug ◽  
Well Water ◽  
E Coli

Abstract This study aimed to assess the public health risk of coliforms and Escherichia coli contamination of potable water sources in Egypt. A total of 150 water samples (100 tap and 50 well) were collected from five districts in Gharbia governorate, Egypt. High rates of coliforms contamination were recorded in 52 and 76% of examined tap and well water samples, respectively. E. coli strains were detected in 16% of the water samples (15% tap water and 18% well water; 23.7% rural and 8.1% urban). Rural water sources were 3.5 times more likely to be contaminated than urban sources (P = 0.01). Eight (33.3%) E. coli isolates were Shiga toxin-producing E. coli (STEC). Multiple drug resistance (MDR) was observed for 62.5% of the isolates. Seven (29.2%) E. coli isolates harboured at least one of the extended-spectrum beta-lactamase (ESBL) genes. The majority (87.5%) of the STEC isolates were MDRs and harboured ESBL genes. STEC isolates were significantly more likely to resist six classes of antibiotics than non-STEC isolates. This is the first report of potable water contamination with MDR-STEC in Egypt. This study highlights an alarming public health threat that necessitates preventive interventions for public and environmental safety.

scholarly journals AI-based mobile application to fight antibiotic resistance

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Marco Pascucci ◽  
Guilhem Royer ◽  
Jakub Adamek ◽  
Mai Al Asmar ◽  
David Aristizabal ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Infections ◽  
Automatic Measurement ◽  
Smartphone Application ◽  
Measurement Procedure ◽  
Resistance Testing ◽  
Resource Limited Settings ◽  
Resource Limited ◽  
Automatic Reading ◽  
Reading System

AbstractAntimicrobial resistance is a major global health threat and its development is promoted by antibiotic misuse. While disk diffusion antibiotic susceptibility testing (AST, also called antibiogram) is broadly used to test for antibiotic resistance in bacterial infections, it faces strong criticism because of inter-operator variability and the complexity of interpretative reading. Automatic reading systems address these issues, but are not always adapted or available to resource-limited settings. We present an artificial intelligence (AI)-based, offline smartphone application for antibiogram analysis. The application captures images with the phone’s camera, and the user is guided throughout the analysis on the same device by a user-friendly graphical interface. An embedded expert system validates the coherence of the antibiogram data and provides interpreted results. The fully automatic measurement procedure of our application’s reading system achieves an overall agreement of 90% on susceptibility categorization against a hospital-standard automatic system and 98% against manual measurement (gold standard), with reduced inter-operator variability. The application’s performance showed that the automatic reading of antibiotic resistance testing is entirely feasible on a smartphone. Moreover our application is suited for resource-limited settings, and therefore has the potential to significantly increase patients’ access to AST worldwide.

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.

scholarly journals Development and oviposition preferences of field collected Aedes albopictus based on different water characteristics

2019 ◽  
Vol 15 (1) ◽  
pp. 61-64
Author(s):  
Nazri Che Dom ◽  
Megat Azman Megat Mokhtar ◽  
Cornellia Tata Australia
Keyword(s):  
Aedes Albopictus ◽  
Water Samples ◽  
Environmental Changes ◽  
Tap Water ◽  
Pond Water ◽  
Hatching Rate ◽  
Drain Water ◽  
Breeding Sites ◽  
Oviposition Preferences ◽  
Significant Difference

Aedes species are rapidly adapting to environmental changes which subsequently changing the preferences for their breeding. In the present study, evaluation of the larval development and oviposition preferences of field collected Aedes albopictus was carried out based on different water characteristic. The eggs of Ae. albopictus and the water samples were collected in UiTM Puncak Alam areas. The types of water samples used in this study were (i) distilled water (WT1), (ii) seasoned tap water (WT2), (iii) pond water (WT3), and (iv) drain water (WT4). Each types of water was sampled and tested by controlling the presence and absence of larvae food in the experiment. Development of immature stages in pond and drain water with the presence of food showed fast growth compared to the other types of water. Hatching rate was observed to be higher in all types of water with the presence of food. Oviposition preferences showed a significant difference between water. The data generated from this study was important as a baseline data in development and oviposition for dengue vector control especially on the possibility and ability of Ae. albopictus to survive in specific water types as breeding sites.

scholarly journals Evaluation of Anatomically Designed Flocked Rectal Swabs for Use with the BioFire FilmArray Gastrointestinal Panel for Detection of Enteric Pathogens in Children Admitted to Hospital with Severe Gastroenteritis

2019 ◽  
Vol 57 (12) ◽  
Author(s):  
Celia R. Walker ◽  
Kwana Lechiile ◽  
Margaret Mokomane ◽  
Andrew P. Steenhoff ◽  
Tonya Arscott-Mills ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Diarrheal Disease ◽  
Rectal Swab ◽  
Resource Limited Settings ◽  
Detection Rates ◽  
Resource Limited ◽  
Infectious Gastroenteritis ◽  
Significant Difference ◽  
Rectal Swabs ◽  
Severe Gastroenteritis

ABSTRACT Diagnosing diarrheal disease is difficult in part due to challenges in obtaining and transporting a bulk stool specimen, particularly in resource-limited settings. We compared the performance of flocked rectal swabs to that of traditional bulk stool samples for enteric pathogen detection using the BioFire FilmArray gastrointestinal panel in children admitted to four hospitals in Botswana with community onset severe gastroenteritis. Of the 117-matched flocked rectal swab/stool pairs, we found no significant difference in pathogen detection rates between the flocked rectal swab samples and traditional bulk stool sampling methods for any bacterial (168 versus 167, respectively), viral (94 versus 92, respectively), or protozoan (18 versus 18, respectively) targets. The combination of flocked rectal swab samples with FilmArray testing allows for the rapid diagnosis of infectious gastroenteritis, facilitating a test-and-treat approach for infections that are life-threatening in many resource-limited settings. The culture recovery rates for bacterial pathogens utilizing this approach need to be assessed.

scholarly journals First report of Pythium ultimum causing crown rot in greenhouse grown Cannabis sativa (L.) in California

Plant Disease ◽  
2020 ◽  
Author(s):  
Tera L Pitman ◽  
Richard N Philbrook ◽  
Maxwell R Vetterli ◽  
Jeremy G Warren
Keyword(s):  
Water Samples ◽  
Mycelial Growth ◽  
Potable Water ◽  
Cannabis Sativa ◽  
Callus Formation ◽  
Irrigation System ◽  
Tap Water ◽  
Pythium Ultimum ◽  
Crown Rot ◽  
Plant Sample

In April of 2020 cuttings of Cannabis sativa (L.) in a greenhouse in San Mateo County, CA were observed collapsing, and further observation revealed: water-soaked stems, tan discoloration to the cortex, and discolored roots. The greenhouse irrigation system was supplied by a local stream. We collected one-liter water samples from: intake pond, reservoir tank, irrigation lines, and local potable water tap. Water samples were filtered and plated as described previously (Rollins et al., 2016). Filter papers were removed after 24 hours. Crown sections from four symptomatic plants and one asymptomatic plant were surfaced sterilized in 10% bleach for five minutes, rinsed in sterile deionized water, cut into four-millimeter long sections, and plated onto V8 media, then incubated at room temperature for three days. White mycelial growth was observed from foci within the print of the filter paper from all irrigation water samples but not the potable water supply sample. Similar mycelial growth was observed from plated crown tissue from symptomatic plants only. Observation under light microscope revealed characteristics congruent with P. ultimum, including aseptate hyphae and globose sporangia (Watanabe, 2002). Mycelia was collected for DNA extraction from each of the water and plant sample plates with DNA extractions performed using Quick DNA Fungi/Bacterial Kit (Zymo Research Irvine, CA, USA) and PCR amplified using primers ITS100/ITS4 as described by Riit et al. (2016). All amplicons were Sanger sequenced, aligned using SnapGene software (from GSL Biotech; available at snapgene.com), and compared to barcode referencPe sequences to identify the species using the BarCode of Life Database (BOLDsystems) within the National Center for Biotechnology Information nucleotide database. After trimming and aligning, all amplicons were found to be identical, yielding the 810-nucleotide long consensus ITS amplicon (accession MW114807), which aligned with Pythium ultimum ITS sequences (e.g., accession HQ643886.1) with 100% identity and homology. We then completed Koch’s postulates by using pure cultures from root sections of P. ultimum to stem inoculate C. sativa plants. We used a three-millimeter corer to remove a disc of epidermis and applied a plug of pure culture to the wound. We inoculated 10 plants, with two plants mock-inoculated using clean V8 agar. Inoculation sites were wrapped in parafilm, and plants were grown in the greenhouse for 20 days. Stems of mock and oomycete inoculated plants were examined for callus formation and 30 centimeters of stem were excised from each plant. The mock inoculated plants had fully callused inoculation sites and were discolored only where wounded. P. ultimum inoculated plant inoculation sites were partially callused over and had tan discoloration of the cortex that extended 6.0 mm +/- 2.0 mm above and below the inoculation site. Stem segments above and below inoculation sites were surface sterilized and plated on V8 media as previously described and P. ultimum recovered from inoculated plants, confirmed as identical to the inoculum by ITS amplification and sequencing. Mock inoculated plant stem cultures yielded no oomycete growth. Together, these results indicate that P. ultimum has the ability to cause crown rot in C. sativa in greenhouse cultivation.

Determination of Malachite Green and Its Leuco Form in Water

1992 ◽  
Vol 75 (4) ◽  
pp. 646-649 ◽  
Author(s):  
John L Allen ◽  
Jeffery R Meinertz ◽  
Jane E Gofus
Keyword(s):  
Malachite Green ◽  
Water Samples ◽  
Tap Water ◽  
Pond Water ◽  
Reversed Phase ◽  
Leuco Form ◽  
Malachite Green Oxalate ◽  
Liquid Chromatographic ◽  
Leuco Malachite Green

Abstract Liquid chromatographic (LC) analysis can detect malachite green residues in water at less than 10µg/L. Water samples were concentrated on disposable diol columns, eluted with 0.05M p-toluenesulfonic acid in methanol, and determined by reversed- phase LC. When combined with a lead oxide postcolumn reactor, the LC method can simultaneously determine both leuco and chromatic forms of malachite green. Recoveries averaged 95.4% for the chromatic form and 57.3% for the leuco form of malachite green oxalate and leuco malachite green in spiked pond water samples. Recoveries of the carbinol form of malachite green (an equilibrium product of the dye in water) from spiked tap water samples averaged 98.6%. Recoveries of leuco malachite green were low and pH-dependent.

scholarly journals Assessment of Potable Water Quality in Baghdad City, Iraq

2017 ◽  
Vol 10 ◽  
pp. 117862211773344 ◽  
Author(s):  
Ghassan Adham AL-Dulaimi ◽  
Mohammad Khairi Younes
Keyword(s):  
Water Quality ◽  
Water Samples ◽  
Potable Water ◽  
Tap Water ◽  
Water Source ◽  
Well Being ◽  
Bottled Water ◽  
Water Levels ◽  
World Health

Safe drinking water is crucial for the well-being of current and future generations. This study aims to evaluate the quality of potable water in Baghdad city. Furthermore, this study compares the quality of tap and bottled water. Baghdad city was divided into 4 districts based on the water source, and 40 water samples were collected from each district. Moreover, the most popular bottled water brands were sampled and compared with the tap water samples. The quality of the analyzed potable water samples varied based on the water source. The total dissolved solid (TDS) levels exceed the palatable (>600 ppm) water levels in some districts. In addition, the concentration of sulfate was relatively high in both tap and bottled water and ranged from 200 to 330 ppm. The bottled water quality was within the acceptable limits set by the World Health Organization, but the TDS levels were relatively high. The hardness, Cl−, Pb2+, and bacteria contents in both tap and bottled water were within the standard limits. Finally, it is important to conduct radiological analyses in the future to investigate the effect of wars on Iraqi water resources.

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