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Williams MR, Telli AE, Telli N, Islam DT, Hashsham SA. Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens. Methods Mol Biol 2025; 2852:3-17. [PMID: 39235733 DOI: 10.1007/978-1-0716-4100-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection of Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.
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Affiliation(s)
- Maggie R Williams
- School of Engineering & Technology, Institute for Great Lakes Research, Central Michigan University, Mt Pleasant, MI, USA
| | - Arife Ezgi Telli
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | - Nihat Telli
- Department of Food Technology, Vocational School of Technical Sciences, Konya Technical University, Konya, Turkey
| | - Dar Tafazul Islam
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
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2
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Candan C, Karatepe M, Karatepe B. Entamoeba histolytica in Different Water Sources of Niğde Province of Turkey. Acta Parasitol 2024; 69:1517-1521. [PMID: 39162924 PMCID: PMC11379735 DOI: 10.1007/s11686-024-00886-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/30/2024] [Indexed: 08/21/2024]
Abstract
PURPOSE This study was carried out to determine the presence of Entamoeba histolytica in water sources of Niğde province in Turkey, between June and November 2021. METHODS A total of 90 water samples were taken from 15 different water sources (drinking water, well water, spring water, wastewater and dam water) every month and the presence of E. histolytica antigens in the samples was examined by ELISA. RESULTS The positivity for E. histolytica was determined in 7 (7.7%) of 90 samples. While no antigens were found in any of the samples in June and September, E. histolytica was positive for three samples (20%) in July, one sample (6.6%) in August and October and two samples in November (13.3%). One of 24 dam samples (4.1%), 1 of 12 wastewater samples (8.3%), 1 of 12 well samples (8.3%), and 4 of 24 fountain samples (16.6%) that examined by ELISA were found positive. On the other hand, none of the examined 18 spring samples were positive. In addition, 4 (8.8%) of 45 samples that examined in summer and 3 (6.6%) of 45 samples that examined in autumn were detected positive by using ELISA. Entamoeba histolytica positivity in samples was statistically insignificant in terms of months, water resources and seasons (P > 0.05). CONCLUSION As a result, the presence of E. histolytica, which is an important public health problem in water sources, was determined for the first time in Niğde province of Türkiye with this study.
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Affiliation(s)
- Cemal Candan
- Graduate School of Natural and Applied Sciences, Department of Biotechnology , Niğde Ömer Halisdemir University, Niğde, Türkiye
| | - Mustafa Karatepe
- Faculty of Science, Department of Biotechnology, Niğde Ömer Halisdemir University, Niğde, Türkiye.
| | - Bilge Karatepe
- Faculty of Science, Department of Biotechnology, Niğde Ömer Halisdemir University, Niğde, Türkiye
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3
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Golomazou E, Mamedova S, Eslahi AV, Karanis P. Cryptosporidium and agriculture: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170057. [PMID: 38242460 DOI: 10.1016/j.scitotenv.2024.170057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
Cryptosporidiosis is a significant contributor to global foodborne and waterborne disease burden. It is a widespread cause of diarrheal diseases that affect humans and animals worldwide. Agricultural environments can become a source of contamination with Cryptosporidium species through faecal material derived from humans and animals. This review aims to report the main findings of scientific research on Cryptosporidium species related to various agricultural sectors, and highlights the risks of cryptosporidiosis in agricultural production, the contamination sources, the importance of animal production in transmission, and the role of farmed animals as hosts of the parasites. Agricultural contamination sources can cause water pollution in groundwater and different surface waters used for drinking, recreational purposes, and irrigation. The application of contaminated manure, faecal sludge management, and irrigation with inadequately treated water are the main concerns associated with foodborne and waterborne cryptosporidiosis related to agricultural activities. The review emphasizes the public health implications of agriculture concerning the transmission risk of Cryptosporidium parasites and the urgent need for a new concept in the agriculture sector. Furthermore, the findings of this review provide valuable information for developing appropriate measures and monitoring strategies to minimize the risk of infection.
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Affiliation(s)
- Eleni Golomazou
- Department of Ichthyology and Aquatic Environment - Aquaculture Laboratory, School of Agricultural Sciences, University of Thessaly, Fytokou str., 38446 Volos, Greece
| | - Simuzer Mamedova
- Institute of Zoology, Ministry of Science and Education Republic of Azerbaijan, Baku, Azerbaijan & Department of Life Sciences, Khazar University, Baku, Azerbaijan
| | - Aida Vafae Eslahi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Panagiotis Karanis
- University of Cologne, Medical Faculty and University Hospital, 50931 Cologne, Germany; University of Nicosia Medical School, Department of Basic and Clinical Sciences, Anatomy Centre, 2408 Nicosia, Cyprus.
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Elseadawy R, Abbas I, Al-Araby M, Abu-Elwafa S. Occurrence and molecular characterization of Acanthamoeba, Naegleria fowleri and Blastocystis in water samples from various sources in Egypt. Acta Trop 2022; 237:106733. [DOI: 10.1016/j.actatropica.2022.106733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/26/2022]
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Fradette MS, Culley AI, Charette SJ. Detection of Cryptosporidium spp. and Giardia spp. in Environmental Water Samples: A Journey into the Past and New Perspectives. Microorganisms 2022; 10:microorganisms10061175. [PMID: 35744692 PMCID: PMC9228427 DOI: 10.3390/microorganisms10061175] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 01/27/2023] Open
Abstract
Among the major issues linked with producing safe water for consumption is the presence of the parasitic protozoa Cryptosporidium spp. and Giardia spp. Since they are both responsible for gastrointestinal illnesses that can be waterborne, their monitoring is crucial, especially in water sources feeding treatment plants. Although their discovery was made in the early 1900s and even before, it was only in 1999 that the U.S. Environmental Protection Agency (EPA) published a standardized protocol for the detection of these parasites, modified and named today the U.S. EPA 1623.1 Method. It involves the flow-through filtration of a large volume of the water of interest, the elution of the biological material retained on the filter, the purification of the (oo)cysts, and the detection by immunofluorescence of the target parasites. Since the 1990s, several molecular-biology-based techniques were also developed to detect Cryptosporidium and Giardia cells from environmental or clinical samples. The application of U.S. EPA 1623.1 as well as numerous biomolecular methods are reviewed in this article, and their advantages and disadvantages are discussed guiding the readers, such as graduate students, researchers, drinking water managers, epidemiologists, and public health specialists, through the ever-expanding number of techniques available in the literature for the detection of Cryptosporidium spp. and Giardia spp. in water.
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Affiliation(s)
- Marie-Stéphanie Fradette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.I.C.); (S.J.C.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et Génie, Université Laval, Québec City, QC G1V 0A6, Canada
- Centre de Recherche en Aménagement et Développement du Territoire (CRAD), Université Laval, Québec City, QC G1V 0A6, Canada
- Correspondence:
| | - Alexander I. Culley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.I.C.); (S.J.C.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et Génie, Université Laval, Québec City, QC G1V 0A6, Canada
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de Médecine Dentaire, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.I.C.); (S.J.C.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et Génie, Université Laval, Québec City, QC G1V 0A6, Canada
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec City, QC G1V 0A6, Canada
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eDNA-based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity. Sci Rep 2022; 12:6553. [PMID: 35449180 PMCID: PMC9023534 DOI: 10.1038/s41598-022-10545-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/07/2022] [Indexed: 11/25/2022] Open
Abstract
LAMP assays are becoming increasingly popular in the field of invasive species detection but are still underused in eDNA-based monitoring. Here, we propose a LAMP assay designed to detect the North American crayfish species Pacifastacus leniusculus in water samples from streams. The presence of P. leniusculus was detected through this new LAMP assay in all but one of the nine sites sampled. No correlation was found between ddPCR absolute concentration measurements and the number of LAMP-positive technical replicates. However, we showed that using dependent technical replicates could significantly enhance the detection sensitivity of the LAMP assay. Applied to other assays, it could improve sensitivity and thus allow for a more efficient use of eDNA-based LAMP assays for invasive species detection in aquatic ecosystems.
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Karaman U, Koloren Z, Karanis P. Survey and first report of Acanthamoeba T4 genotype in natural spring water resources in the Black Sea, Turkey. JOURNAL OF WATER AND HEALTH 2022; 20:193-204. [PMID: 35100167 DOI: 10.2166/wh.2021.250] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Infection with Acanthamoeba spp. may result in granulomatous amoebic encephalitis and Acanthamoeba keratitis. Water is an important habitat where Acanthamoeba species thrive. Therefore, studying the occurrence of this free-living amoeba in water sources will help understand the infection dynamics. The aim of the study was to survey and report on the presence of Acanthamoeba spp. in water resources from the Ordu and Giresun provinces in Black Sea. Acanthamoeba spp. was found in 1/17 natural spring water samples from Ordu and in 2/18 from Giresun. Acanthamoeba species were not detected in any of the investigated tap water samples. Sequencing of the (SSU) rDNA gene resulted in the identification of haplotype I (Acanthamoeba genotype: KJ094684). T4 (8.6%) was the only isolated genotype in both Ordu and Giresun provinces. This is the first report of Acanthamoeba T4 genotype in natural spring water resources in the Black Sea. The occurrence of Acanthamoeba species in natural spring water sources should be considered as a potential risk for human infection, especially to high-risk populations.
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Affiliation(s)
- Ulku Karaman
- Faculty of Medicine, Department of Parasitology, University of Ordu, Ordu, Turkey
| | - Zeynep Koloren
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, University of Ordu, Ordu, Turkey E-mail:
| | - Panagiotis Karanis
- Medical Faculty and University Hospital, University of Cologne, 50937 Cologne, Cologne, Germany; Department of Basic and Clinical Sciences, University of Nicosia Medical School, Institute of Anatomy, Nicosia, Cyprus
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Feist SM, Lance RF. Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions. NEOBIOTA 2021. [DOI: 10.3897/neobiota.66.60751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sensitive methods, capable of rapidly and accurately detecting aquatic invasive species, are in demand. Molecular-based approaches, such as environmental DNA (eDNA) surveys, satisfy these requirements and have grown in popularity. As such, eDNA surveys could aid the effort to combat the colonisation and spread of two notoriously invasive freshwater mussel species, the quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (D. polymorpha), through improved surveillance ability. Here, we provide a review of dreissenid eDNA literature (both grey and published), summarising efforts involved in the development of various assays for use in multiple different technologies (e.g. quantitative PCR, high-throughput sequencing and loop-mediated isothermal amplification) and sampling scenarios. We discuss important discoveries made along the way, including novel revelations involving environmental RNA (eRNA), as well as the advantages and limitations of available methods and instrumentation. In closing, we highlight critical remaining gaps, where further investigation could lead to advancements in dreissenid monitoring capacity.
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9
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Koyun İ, Kolören Z, Karaman Ü, Tsiami A, Karanis P. Acanthamoeba spp. in river water samples from the Black Sea region, Turkey. JOURNAL OF WATER AND HEALTH 2020; 18:186-199. [PMID: 32300091 DOI: 10.2166/wh.2020.170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The present study aims to investigate the occurrence of free living amoeba (FLA) in water resources (rivers and tap water) in Samsun in the Black Sea. The presence of Acanthamoeba spp. was confirmed in 98 of 192 water samples collected from 32 sites of Samsun province (Samsun centre, Terme, Carsamba, Tekkekoy, Bafra) by PCR. Acanthamoeba spp. were found in 15/36 river samples from Samsun, in 58/90 from Terme, in 12/30 from Carsamba, in 7/18 from Tekkekoy and in 6/18 from Bafra. No Acanthamoeba species were detected in tap water samples. The highest rate in river waters contaminated with Acanthamoeba species was in Terme followed by Samsun centre (41.7%), Carsamba (40%), Tekkekoy (38.9%) and Bafra districts (33.3%), respectively. The result of the subsequent sequence analysis showed Haplotype I (A. triangularis) in 5%, Haplotype II (A. polyphaga) in 29.6%, Haplotype III (Acanthamoeba spp.) in 62% and Haplotype IV (A. lenticulata) in 3%. The most common genotype was Acanthamoeba T4 (Acanthamoeba spp., A. polyphaga, A. triangularis) and T5 genotype was also found in 3%. The T4 genotype is the most common genotype associated with Acanthamoeba keratitis (AK) worldwide; therefore, humans and animals living in the area are at risk after contact with such waters.
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Affiliation(s)
- İlknur Koyun
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, University of Ordu, Ordu, Turkey E-mail:
| | - Zeynep Kolören
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, University of Ordu, Ordu, Turkey E-mail:
| | - Ülkü Karaman
- Faculty of Medicine, Department of Parasitology, University of Ordu, Ordu, Turkey
| | - Amalia Tsiami
- Food Science and Nutrition Department, London Geller College of Hospitality and Tourism, University of West London, London, UK
| | - Panagiotis Karanis
- Medical Faculty and University Hospital, University of Cologne, 50937 Cologne, Cologne, Germany and Department of Basic and Clinical Sciences, University of Nicosia Medical School, 2408 Nicosia, Cyprus
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10
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Comparative evaluation of Cryptosporidium infection in malnourished and well-nourished children: Parasitic infections are affected by the interaction of nutritional status and socio-demographic characteristics. Comp Immunol Microbiol Infect Dis 2020; 68:101406. [DOI: 10.1016/j.cimid.2019.101406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 02/02/2023]
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11
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Williams MR, Hashsham SA. Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens. Methods Mol Biol 2019; 1918:21-33. [PMID: 30580396 DOI: 10.1007/978-1-4939-9000-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.
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Affiliation(s)
- Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA. .,Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
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12
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Adeyemo FE, Singh G, Reddy P, Stenström TA. Methods for the detection of Cryptosporidium and Giardia: From microscopy to nucleic acid based tools in clinical and environmental regimes. Acta Trop 2018; 184:15-28. [PMID: 29395034 DOI: 10.1016/j.actatropica.2018.01.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 12/21/2017] [Accepted: 01/22/2018] [Indexed: 01/18/2023]
Abstract
The detection and characterization of genotypes and sub genotypes of Cryptosporidium and Giardia is essential for their enumeration, surveillance, prevention, and control. Different diagnostic methods are available for the analysis of Cryptosporidium and Giardia including conventional phenotypic tools that face major limitations in the specific diagnosis of these protozoan parasites. The substantial advancement in the development of genetic signature based molecular tools for the quantification, diagnosis and genetic variation analysis has increased the understanding of the epidemiology and preventive measures of related infections. The conventional methods such as microscopy, antibody and enzyme based approaches, offer better detection results when combined with advanced molecular methods. Gene based approaches increase the precision of identification, for example, many signatures detected in environmental matrices represent species/genotype that are not infectious to humans. This review summarizes the available methods and the advantages and limitations of advance detection techniques like nucleic acid-based approaches for the detection of viable oocysts and cysts of Cryptosporidium and Giardia along with the conventional and widely accepted detection techniques like microscopy, antibody and enzyme based ones. This technical article also encourages the wide application of molecular methods in genetic characterization of distinct species of Cryptosporidium and Giardia, to adopt necessary preventive measures with reliable identification and mapping the source of contamination.
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Affiliation(s)
- Folasade Esther Adeyemo
- SARChI Chair, Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Gulshan Singh
- SARChI Chair, Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
| | - Poovendhree Reddy
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Thor Axel Stenström
- SARChI Chair, Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
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Koloren Z, Gulabi BB, Karanis P. Molecular identification of Blastocystis sp. subtypes in water samples collected from Black sea, Turkey. Acta Trop 2018; 180:58-68. [PMID: 29317171 DOI: 10.1016/j.actatropica.2017.12.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/12/2017] [Accepted: 12/26/2017] [Indexed: 10/18/2022]
Abstract
The aim of this study was to identify the subtypes of Blastocystis sp. and complete a phylogenetic analysis of 268 water samples that were collected from the Samsun, Amasya and Sinop Provinces of the Black Sea in Turkey, between the years 2011 and 2014. Blastocystis sp. was investigated in 48 uncultured sea water samples that were collected from 4 sites within the Sinop Province. A total of 100 river water samples were collected from 37 sites in the Samsun Province and 120 river water samples were collected from 10 sampling sites within the Amasya Province. The small subunit (SSU) rDNA gene Polymerase chain reaction (PCR) were performed for the detection of Blastocytis sp. and the PCR-positive samples were sequenced. Subsequently, the (SSU) rDNA sequences were aligned by Bioedit and phylogenetic trees were constructed for Blastocystis with reference to the genotypes from GenBank. Blastocystis sp. were found in 3 out of the 75 (4%) river water samples that were collected from the Samsun Province. Six of the 120 (5%) river water samples and 1 out of the 48 (2%) seawater samples were positive for Blastocystis in the Amasya and Sinop Provinces. There were two different subtypes (ST; 1 and 3) found from sequencing all of the samples from the investigated sites. Two and one PCR products were found to be positive for ST1 and ST3 from the different samples collected within the Samsun Province. Two and 4 PCR products from the Amasya Province were ST1 and ST3, respectively and only one sample from the Sinop Province was found to be positive for ST1. This is the first report to identify and report the occurrence of Blastocystis subtypes within the Black Sea of Turkey.
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Lateral Flow Loop-Mediated Isothermal Amplification Test with Stem Primers: Detection of Cryptosporidium Species in Kenyan Children Presenting with Diarrhea. J Trop Med 2018; 2018:7659730. [PMID: 29681951 PMCID: PMC5846371 DOI: 10.1155/2018/7659730] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/28/2018] [Indexed: 11/17/2022] Open
Abstract
Background. Cryptosporidium is a protozoan parasite and a major cause of diarrhea in children and immunocompromised patients. Current diagnostic methods for cryptosporidiosis such as microscopy have low sensitivity while techniques such as PCR indicate higher sensitivity levels but are seldom used in developing countries due to their associated cost. A loop-mediated isothermal amplification (LAMP) technique, a method with shorter time to result and with equal or higher sensitivity compared to PCR, has been developed and applied in the detection of Cryptosporidium species. The test has a detection limit of 10 pg/µl (~100 oocysts/ml) indicating a need for more sensitive diagnostic tools. This study developed a more sensitive lateral flow dipstick (LFD) LAMP test based on SAM-1 gene and with the addition of a second set of reaction accelerating primers (stem primers). Results. The stem LFD LAMP test showed analytical sensitivity of 10 oocysts/ml compared to 100 oocysts/ml (10 pg/ul) for each of the SAM-1 LAMP test and nested PCR. The stem LFD LAMP and nested PCR detected 29/39 and 25/39 positive samples of previously identified C. parvum and C. hominis DNA, respectively. The SAM-1 LAMP detected 27/39. On detection of Cryptosporidium DNA in 67 clinical samples, the stem LFD LAMP detected 16 samples and SAM-2 LAMP 14 and nested PCR identified 11. Preheating the templates increased detection by stem LFD LAMP to 19 samples. Time to results from master mix preparation step took ~80 minutes. The test was specific, and no cross-amplification was recorded with nontarget DNA. Conclusion. The developed stem LFD LAMP test is an appropriate method for the detection of C. hominis, C. parvum, and C. meleagridis DNA in human stool samples. It can be used in algorithm with other diagnostic tests and may offer promise as an effective diagnostic tool in the control of cryptosporidiosis.
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Fallahi S, Moosavi SF, Karimi A, Chegeni AS, Saki M, Namdari P, Rashno MM, Varzi AM, Tarrahi MJ, Almasian M. An advanced uracil DNA glycosylase-supplemented loop-mediated isothermal amplification (UDG-LAMP) technique used in the sensitive and specific detection of Cryptosporidium parvum, Cryptosporidium hominis, and Cryptosporidium meleagridis in AIDS patients. Diagn Microbiol Infect Dis 2017; 91:6-12. [PMID: 29366630 DOI: 10.1016/j.diagmicrobio.2017.12.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 12/15/2017] [Accepted: 12/16/2017] [Indexed: 11/18/2022]
Abstract
The rapid and accurate detection of Cryptosporidium spp. is critically important for the prevention and timely treatment of cryptosporidiosis in AIDS patients (APs). This study was conducted to examine a UDG-LAMP technique for the first time to diagnose cryptosporidiosis in APs. After collecting demographic and clinical data, three stool samples were collected from the participants (120 volunteering APs). The microscopic examination of stained smears using the acid-fast method and the UDG-LAMP assay were performed for each sample. 10% of APs were infected with Cryptosporidium spp. The number of detected cryptosporidiosis cases using the acid-fast staining and UDG-LAMP methods were significantly different (P < 0.001). Diarrhea and weight loss were found to be significantly associated with cryptosporidiosis in patients (P < 0.05). The pretreatment of LAMP reagents with UDG successfully eliminated the likelihood of product re-amplification remaining from previous reactions. The UDG-LAMP technique could detect cryptosporidiosis in APs with high sensitivity and rapidity without carryover contamination.
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Affiliation(s)
- Shirzad Fallahi
- Razi Herbal Medicine Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran; Department of Medical Parasitology and Mycology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | - Seyedeh Fatemeh Moosavi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Azadeh Karimi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Ali Sharafi Chegeni
- Department of Communicable Disease Control and Prevention, Deputy of Health, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohammad Saki
- Department of Communicable Disease Control and Prevention, Deputy of Health, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Parsa Namdari
- Medical Student, Faculty of Medicine, University of Debrecen, Hungary
| | | | - Ali Mohamad Varzi
- Department of Immunology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohammad Javad Tarrahi
- Department of Epidemiology and Statistics, Behavioral Sciences Research Center, Isfahan University of Medical Science, Isfahan, Iran
| | - Mohammad Almasian
- School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
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Ramos AE, Muñoz M, Cortés-Vecino JA, Barato P, Patarroyo MA. A novel loop-mediated isothermal amplification-based test for detecting Neospora caninum DNA. Parasit Vectors 2017; 10:590. [PMID: 29187255 PMCID: PMC5707868 DOI: 10.1186/s13071-017-2549-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neospora caninum is a cyst-forming, coccidian parasite which is known to cause neurological disorders in dogs and abortion and neonatal mortality in cows and other livestock. This study reports the development of a loop-mediated isothermal amplification (LAMP) assay based on the Neospora caninum Nc-5 gene and compares its efficacy for detecting DNA to that of a semi-nested PCR test. RESULTS Six primers were designed based on the Nc-5 repeat region of N. caninum. Specific LAMP primers led to successful amplification of N. caninum DNA at 63 °C in 30 min. The LAMP assay was highly specific (i.e. it did not reveal cross-reactivity with other parasite species) and had a low N. caninum plasmid DNA limit of detection (1 fg), which is ten times higher than that for the semi-nested PCR. LAMP applicability was evaluated using a set of naturally-infected samples (59 from canine faeces and five from bovine abortions). Thirty-nine percent (25/64) of the naturally-infected samples were positive for N. caninum DNA by LAMP and 36% (23/64) by semi-nested PCR. However, the LAMP assay is much faster to perform than semi-nested PCR and provides results in 30 min. CONCLUSION The optimized reaction conditions described in this study resulted in a sensitive, specific and rapid technique for detecting N. caninum DNA. Considering the advantages of LAMP for detecting N. caninum DNA, further assays aimed at testing its usefulness on a wider range of field samples are recommended.
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Affiliation(s)
- Andrea Estefanía Ramos
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
| | - Marina Muñoz
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
| | | | - Paola Barato
- Corporación Patología Veterinaria (Corpavet), Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia. .,School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia.
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Williams MR, Stedtfeld RD, Engle C, Salach P, Fakher U, Stedtfeld T, Dreelin E, Stevenson RJ, Latimore J, Hashsham SA. Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp. PLoS One 2017; 12:e0186462. [PMID: 29036210 PMCID: PMC5643059 DOI: 10.1371/journal.pone.0186462] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/02/2017] [Indexed: 02/01/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP) of aquatic invasive species environmental DNA (AIS eDNA) was used for rapid, sensitive, and specific detection of Dreissena sp. relevant to the Great Lakes (USA) basin. The method was validated for two uses including i) direct amplification of eDNA using a hand filtration system and ii) confirmation of the results after DNA extraction using a conventional thermal cycler run at isothermal temperatures. Direct amplification eliminated the need for DNA extraction and purification and allowed detection of target invasive species in grab or concentrated surface water samples, containing both free DNA as well as larger cells and particulates, such as veligers, eggs, or seeds. The direct amplification method validation was conducted using Dreissena polymorpha and Dreissena bugensis and uses up to 1 L grab water samples for high target abundance (e.g., greater than 10 veligers (larval mussels) per L for Dreissena sp.) or 20 L samples concentrated through 35 μm nylon screens for low target abundance, at less than 10 veligers per liter water. Surface water concentrate samples were collected over a period of three years, mostly from inland lakes in Michigan with the help of a network of volunteers. Field samples collected from 318 surface water locations included i) filtered concentrate for direct amplification validation and ii) 1 L grab water sample for eDNA extraction and confirmation. Though the extraction-based protocol was more sensitive (resulting in more positive detections than direct amplification), direct amplification could be used for rapid screening, allowing for quicker action times. For samples collected between May and August, results of eDNA direct amplification were consistent with known presence/absence of selected invasive species. A cross-platform smartphone application was also developed to disseminate the analyzed results to volunteers. Field tests of the direct amplification protocol using a portable device (Gene-Z) showed the method could be used in the field to obtain results within one hr (from sample to result). Overall, the direct amplification has the potential to simplify the eDNA-based monitoring of multiple aquatic invasive species. Additional studies are warranted to establish quantitative correlation between eDNA copy number, veliger, biomass or organismal abundance in the field.
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Affiliation(s)
- Maggie R. Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Robert D. Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Cathrine Engle
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Paul Salach
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Umama Fakher
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Tiffany Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Erin Dreelin
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America
- Center for Water Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - R. Jan Stevenson
- Center for Water Sciences, Michigan State University, East Lansing, Michigan, United States of America
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jo Latimore
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America
| | - Syed A. Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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18
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Williams MR, Stedtfeld RD, Stedtfeld TM, Tiedje JM, Hashsham SA. Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device. Biomed Microdevices 2017; 19:45. [PMID: 28536858 PMCID: PMC5896010 DOI: 10.1007/s10544-017-0191-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
MicroRNAs have been proposed to be a class of biomarkers of disease as expression levels are significantly altered in various tissues and body fluids when compared to healthy controls. As such, the detection and quantification of microRNAs is imperative. While many methods have been established for quantification of microRNAs, they typically rely on time consuming handling such as RNA extraction, purification, or ligation. Here we describe a novel method for quantification of microRNAs using direct amplification in body fluids without upstream sample preparation. Tested with a point-of-care device (termed Gene-Z), the presence of microRNA promotes base-stacking hybridization, and subsequent amplification between two universal strands. The base-stacking approach, which was achieved in <60 min, provided a sensitivity of 1.4 fmol per reaction. Tested in various percentages of whole blood, plasma, and faeces, precision (coefficient of variation = 2.6%) was maintained and comparable to amplification in pristine samples. Overall, the developed method represents a significant step towards rapid, one-step detection of microRNAs.
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Affiliation(s)
- Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA.
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA.
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Stedtfeld RD, Stedtfeld TM, Waseem H, Fitschen-Brown M, Guo X, Chai B, Williams MR, Shook T, Logan A, Graham A, Chae JC, Sul WJ, VanHouten J, Cole JR, Zylstra GJ, Tiedje JM, Upham BL, Hashsham SA. Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 198:213-220. [PMID: 28460328 PMCID: PMC5513725 DOI: 10.1016/j.jenvman.2017.04.079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 05/05/2023]
Abstract
Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R2 = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively "untrained" personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Hassen Waseem
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | | | - Xueping Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Trevor Shook
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Amanda Logan
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Ally Graham
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Jong-Chan Chae
- Division of Biotechnology, Chonbuk National University, Iksan, 54596, Republic of Korea
| | - Woo-Jun Sul
- Department of Systems Biotechnology, Chung Ang University, Anseong, 17546, Republic of Korea
| | - Jacob VanHouten
- Science Division, Delta College, University Center, MI, 48710, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Gerben J Zylstra
- Department of Biochemistry & Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Brad L Upham
- Pediatrics and Human Development, Michigan State University, East Lansing, MI, 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA; Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA.
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Koloren Z, Ayaz E. Genotyping of Cryptosporidium spp. in environmental water in Turkey. Acta Parasitol 2016; 61:671-679. [PMID: 27787219 DOI: 10.1515/ap-2016-0094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/23/2016] [Indexed: 11/15/2022]
Abstract
This research was undertaken to study the molecular detection and characterization of Cryptosporidium spp. in environmental water sources at Samsun and Giresun Provinces of The Black Sea in Turkey. Two-hundred forty and one-hundred eighty environmental samples were collected from a total of twenty and twenty-five sampling sites of Giresun and Samsun Provinces. One hundred twenty untreated drinking water samples were also detected for Cryptosporidium spp. in both investigated areas. 101 (%42), 92 (%38.3) of 240 and 74 (41.1%), 70 (38.8%) of 180 environmental samples have been found positive for Cryptosporidium spp. by Loop mediated isothermal amplification (LAMP) targeting the S-adenosyl-L-methionine synthetase (SAM) gene and nested PCR targeting small subunit (SSU)rRNA gene in Samsun and Giresun Provinces, respectively. Of the tested untreated drinking water samples collected from the investigated area, one sample was positive for Cryptosporidium spp. Six and twelve samples were clearly sequenced for the Cryptosporidium (SSU)rRNA gene among the highest positive samples selected from each of the twenty and twenty-five sampling sites of Giresun and Samsun Provinces, respectively. Genetic characterization of Cryptosporidium isolates from water samples represented Cryptosporidium bovis for five samples, Cryptosporidium parvum for six samples and one sample for Cryptosporidium felis in Samsun Province, where C. parvum for five samples and C. bovis for one sample were sequenced in Giresun Province. According to accessible information sources, this is the first research about genotyping of Cryptosporidium spp. in water samples collected from Samsun and Giresun Provinces of Turkey.
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Occurency of Giardia duodenalis assemblages in river water sources of Black Sea, Turkey. Acta Trop 2016; 164:337-344. [PMID: 27697482 DOI: 10.1016/j.actatropica.2016.09.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/23/2016] [Accepted: 09/25/2016] [Indexed: 11/23/2022]
Abstract
A total of 420 environmental water samples and 120 drinking water samples from 45 different sampling sites of the Black Sea in Turkey were collected between 2012 and 2014. Genomic DNA was isolated from all the investigated water samples and comparativelly analyzed by Loop-mediated isothermal amplification (LAMP) of the elongation factor 1 Alfa (EF1α) gene, and by nested Polymerase Chain Reaction (nPCR) of the small subunit (SSU) rRNA and semi-nested PCR (snPCR) of the glutamate dehydrogenase gene (GDH). 141 (58.7%), 125 (52.1%) and 120 (50%) samples respectivelly were positive by each method. Out of 240 environmental samples collected from 25 sites of Samsun Province have been found positive for G. duodenalis by LAMP, nPCR and snPCR, respectively. 55 (30.5%), 50 (27.8%) and 47 (26.1%) of 180 environmental samples collected from 20 other sampling sites of Giresun Province were positive for Giardia by LAMP, nPCR and snPCR, respectively. Five PCR products from different samples of the Giresun Province and 10 other samples from the Samsun Province were found positive for G. duodenalis assemblage B. Five PCR products from Giresun Province and 5 samples from Samsun Province were found positive for G. duodenalis assemblage A. This is the first report about G. duodenalis assemblages A and B from water samples investigations in Black Sea of Turkey.
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Stedtfeld RD, Stedtfeld TM, Samhan F, Kanitkar YH, Hatzinger PB, Cupples AM, Hashsham SA. Direct loop mediated isothermal amplification on filters for quantification of Dehalobacter in groundwater. J Microbiol Methods 2016; 131:61-67. [PMID: 27720723 DOI: 10.1016/j.mimet.2016.09.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 09/30/2016] [Accepted: 09/30/2016] [Indexed: 12/12/2022]
Abstract
Nucleic acid amplification of biomarkers is increasingly used to monitor microbial activity and assess remedial performance in contaminated aquifers. Previous studies described the use of filtration, elution, and direct isothermal amplification (i.e. no DNA extraction and purification) as a field-able means to quantify Dehalococcoides spp. in groundwater. This study expands previous work with direct loop mediated isothermal amplification (LAMP) for the detection and quantification of Dehalobacter spp. in groundwater. Experiments tested amplification of DNA with and without crude lysis and varying concentrations of humic acid. Three separate field-able methods of biomass concentration with eight aquifer samples were also tested, comparing direct LAMP with traditional DNA extraction and quantitative PCR (qPCR). A new technique was developed where filters were amplified directly within disposable Gene-Z chips. The direct filter amplification (DFA) method eliminated an elution step and provided a detection limit of 102Dehalobacter cells per 100mL. LAMP with crudely lysed Dehalobacter had a negligible effect on threshold time and sensitivity compared to lysed samples. The LAMP assay was more resilient than traditional qPCR to humic acid in sample, amplifying with up to 100mg per L of humic acid per reaction compared to 1mg per L for qPCR. Of the tested field-able concentrations methods, DFA had the lowest coefficient of variation among Dehalobacter spiked groundwater samples and lowest threshold time indicating high capture efficiency and low inhibition. While demonstrated with Dehalobacter, the DFA method can potentially be used for a number of applications requiring field-able, rapid (<60min) and highly sensitive quantification of microorganisms in environmental water samples.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Farag Samhan
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA; Department of Water Pollution Control, National Research Centre, 33 El-Bohouth, P.O. 12622, Ad-Doqi, Giza, Egypt
| | - Yogendra H Kanitkar
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | | | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
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Stedtfeld RD, Stedtfeld TM, Kronlein M, Seyrig G, Steffan RJ, Cupples AM, Hashsham SA. DNA extraction-free quantification of Dehalococcoides spp. in groundwater using a hand-held device. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13855-63. [PMID: 25360694 DOI: 10.1021/es503472h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nucleic acid amplification of biomarkers is increasingly used to measure microbial activity and predict remedial performance in sites with trichloroethene (TCE) contamination. Field-based genetic quantification of microorganisms associated with bioremediation may help increase accuracy that is diminished through transport and processing of groundwater samples. Sterivex cartridges and a previously undescribed mechanism for eluting biomass was used to concentrate cells. DNA extraction-free loop mediated isothermal amplification (LAMP) was monitored in real-time with a point of use device (termed Gene-Z). A detection limit of 10(5) cells L(–1) was obtained, corresponding to sensitivity between 10 to 100 genomic copies per reaction for assays targeting the Dehalococcoides spp. specific 16S rRNA gene and vcrA gene, respectively. The quantity of Dehalococcoides spp. genomic copies measured from two TCE contaminated groundwater samples with conventional means of quantification including filtration, DNA extraction, purification, and qPCR was comparable to the field ready technique. Overall, this method of measuring Dehalococcoides spp. and vcrA genes in groundwater via direct amplification without intentional DNA extraction and purification is demonstrated, which may provide a more accurate mechanism of predicting remediation rates.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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Koloren Z. Sensitive and Cost-Effective Detection ofToxoplasma Gondiiin Water Supplies of the Black Sea in Turkey by Loop-Mediated Isothermal Amplification (LAMP). BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2012.0119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Koloren Z, Kaya D, Avsar C. Detection of Cryptosporidium species in the sea and tap water samples of Black Sea, Turkey. J Parasitol 2012; 99:554-7. [PMID: 23145771 DOI: 10.1645/ge-3232.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The aim of this study was to evaluate Cryptosporidium spp. contamination of sea and tap water samples from Sinop and Ordu Provinces, Black Sea, Turkey. The samples (10 L) were collected in spring, summer, autumn, and winter in 2011. A total of 128 water samples was analyzed using an immunofluorescence test (IFT), as well as loop-mediated isothermal amplification (LAMP) and nested polymerase chain reaction (PCR). Cryptosporidium spp. oocysts were detected by IFT in 43 of the 70 samples (61.4%; 1-40 oocysts per 0.5 L) and 35 of the 58 samples (60.3%; 1-23 oocysts per 0.5 L) in the sea water samples from Ordu and Sinop, respectively. The highest number of oocysts by IFT were detected in spring and winter in Ordu and Sinop, respectively. The results of the S-adenosylmethionine synthetase (SAM) gene LAMP assays were 65.5% positive for Cryptosporidium parvum , Cryptosporidium hominis , and Cryptosporidium meleagridis in all examined samples, while the SSUrRNA gene nested PCR assay was 31.0% positive. Six C. parvum nested PCR products from all positive samples were successfully sequenced.
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Affiliation(s)
- Zeynep Koloren
- Department of Biology, Faculty of Arts and Sciences, University of Ordu, Ordu, Turkey.
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