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Huang F, Li X, Zhou Y, Tang W, Dang Z, Kui J, Zhang C, Zhang X. Optimization of CRISPR/Cas12a detection assay and its application in the detection of Echinococcus granulosus. Vet Parasitol 2024; 331:110276. [PMID: 39089176 DOI: 10.1016/j.vetpar.2024.110276] [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: 02/03/2024] [Revised: 07/25/2024] [Accepted: 07/28/2024] [Indexed: 08/03/2024]
Abstract
Cystic echinococcosis, resulting from infection with Echinococcus granulosus, poses a significant challenge as a neglected tropical disease owing to the lack of any known effective treatment. Primarily affecting under-resourced, remote, and conflict-ridden regions, the disease is compounded by the limitations of current detection techniques, such as microscopy, physical imaging, ELISA, and qPCR, which are unsuitable for application in these areas. The emergence of CRISPR/Cas12a as a promising tool for nucleic acid detection, characterized by its unparalleled specificity, heightened sensitivity, and rapid detection time, offers a potential solution. In this study, we present a one-pot CRISPR/Cas12a detection method for E. granulosus (genotype G1, sheep strain) integrating recombinase polymerase amplification (RPA) with suboptimal protospacer adjacent motif (PAM) and structured CRISPR RNA (crRNA) to enhance reaction efficiency. The evaluation of the assay's performance using hydatid cyst spiked dog feces and the examination of 62 dog fecal samples collected from various regions of Western China demonstrate its efficacy. The assay permits visual observation of test results about 15 minutes under blue light and displays superior portability and reaction speed relative to qPCR, achieving a sensitivity level of 10 copies of standard plasmids of the target gene. Analytic specificity was verified against four tapeworm species (E. multilocularis, H. taeniaeformis, M. benedeni, and D. caninum) and two other helminths (T. canis and F. hepatica), with negative results also noted for Mesocestoides sp. This study presents a rapid, sensitive, and time-efficient DNA detection method for E. granulosus of hydatid cyst spiked and clinical dog feces, potential serving as an alternative tool for field detection. This novel assay is primarily used to diagnose the definitive host of E. granulosus. Further validation using a larger set of clinical fecal samples is warranted, along with additional exploration of more effective approaches for nucleic acid release.
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Affiliation(s)
- Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Foshan, China.
| | - Xin Li
- School of Life Science and Engineering, Foshan University, Foshan, China; College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yule Zhou
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Wenqiang Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China; Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases at China CDC/Chinese Center for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory for Parasite and Vector Biology, Shanghai, China
| | - Jun Kui
- Huangzhong District Animal Husbandry and Veterinary Station, Xining, China
| | - Chunxia Zhang
- Qinghai Agri-animal Husbandry Vocational College, Huangyuan, China
| | - Xu Zhang
- School of Life Science and Engineering, Foshan University, Foshan, China
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2
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Yu M, Li W, He X, He G, Yao Y, Wang Y, Shao M, Xiong T, Xu H, Zhao J. Metabarcoding of protozoa and helminth in black-necked cranes: a high prevalence of parasites and free-living amoebae. Parasite 2024; 31:28. [PMID: 38819296 PMCID: PMC11141520 DOI: 10.1051/parasite/2024028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/04/2024] [Indexed: 06/01/2024] Open
Abstract
Parasites and free-living amoebae (FLA) are common pathogens that pose threats to wildlife and humans. The black-necked crane (Grus nigricollis) is a near-threatened species and there is a shortage of research on its parasite diversity. Our study aimed to use noninvasive methods to detect intestinal parasites and pathogenic FLA in G. nigricollis using high-throughput sequencing (HTS) based on the 18S rDNA V9 region. A total of 38 fresh fecal samples were collected in Dashanbao, China, during the overwintering period (early-, middle I-, middle II-, and late-winter). Based on the 18S data, eight genera of parasites were identified, including three protozoan parasites: Eimeria sp. (92.1%) was the dominant parasite, followed by Tetratrichomonas sp. (36.8%) and Theileria sp. (2.6%). Five genera of helminths were found: Echinostoma sp. (100%), Posthodiplostomum sp. (50.0%), Euryhelmis sp. (26.3%), Eucoleus sp. (50.0%), and Halomonhystera sp. (2.6%). Additionally, eight genera of FLA were detected, including the known pathogens Acanthamoeba spp. (n = 13) and Allovahlkampfia spp. (n = 3). Specific PCRs were used to further identify the species of some parasites and FLA. Furthermore, the 18S data indicated significant changes in the relative abundance and genus diversity of the protozoan parasites and FLA among the four periods. These results underscore the importance of long-term monitoring of pathogens in black-necked cranes to protect this near-endangered species.
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Affiliation(s)
- Mengshi Yu
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Wenhao Li
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Xin He
- Sichuan Academy of Grassland Sciences Chengdu 610000 PR China
| | - Guiwen He
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University Zhaotong 657000 PR China
| | - Yonfang Yao
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Yuanjian Wang
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province Zhaotong 657000 Yunnan PR China
| | - Mingcui Shao
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province Zhaotong 657000 Yunnan PR China
| | - Tingsong Xiong
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province Zhaotong 657000 Yunnan PR China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Junsong Zhao
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University Zhaotong 657000 PR China
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Woo C, Bhuiyan MIU, Eo KY, Lee WS, Kimura J, Yamamoto N. Diversity of fecal parasitomes of wild carnivores inhabiting Korea, including zoonotic parasites and parasites of their prey animals, as revealed by 18S rRNA gene sequencing. Int J Parasitol Parasites Wildl 2023; 21:179-184. [PMID: 37323131 PMCID: PMC10267430 DOI: 10.1016/j.ijppaw.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023]
Abstract
Consisting of diverse groups of organisms, parasites are among the least studied pathogens despite their enormous impacts on humans, livestock, and wildlife. In particular, little is known about their host specificity and diversity in wildlife. Here, using multiple primer pairs and sequencing 18S rRNA genes of diverse groups of parasites, we aimed to investigate fecal parasitomes of carnivorous wildlife in Korea, namely, the raccoon dog (Nyctereutes procyonoides), the leopard cat (Prionailurus bengalensis), and the Eurasian otter (Lutra lutra). A total of 5 host-specific parasite species were identified, including 2 from raccoon dogs, 2 from leopard cats, and 1 from Eurasian otters. In addition, numerous parasite species of their prey animals were detected in their feces. It was found that the parasitome composition varied between host animals, and it was thought that the difference was attributed to the difference in prey animals, as numerous small mammal parasites were detected from feces of leopard cats inhabiting inland areas and fish parasites from feces of Eurasian otters and raccoon dogs inhabiting waterside areas. Furthermore, 5 zoonotic parasites known to infect humans were identified at the species level. Wildlife-associated zoonoses are expected to increase as the proximity between humans and wildlife increases due to urbanization. Vigilance may be necessary, such as by monitoring parasites in wildlife feces, as was done in this study.
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Affiliation(s)
- Cheolwoon Woo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Mohammad Imtiaj Uddin Bhuiyan
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyung Yeon Eo
- Department of Animal Health and Welfare, College of Healthcare and Biotechnology, Semyung University, Jecheon, 27136, Republic of Korea
| | - Woo-Shin Lee
- Department of Forest Sciences, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Junpei Kimura
- College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
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4
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Papaiakovou M, Fraija-Fernández N, James K, Briscoe AG, Hall A, Jenkins TP, Dunn J, Levecke B, Mekonnen Z, Cools P, Doyle SR, Cantacessi C, Littlewood DTJ. Evaluation of genome skimming to detect and characterise human and livestock helminths. Int J Parasitol 2023; 53:69-79. [PMID: 36641060 DOI: 10.1016/j.ijpara.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/13/2023]
Abstract
The identification of gastrointestinal helminth infections of humans and livestock almost exclusively relies on the detection of eggs or larvae in faeces, followed by manual counting and morphological characterisation to differentiate species using microscopy-based techniques. However, molecular approaches based on the detection and quantification of parasite DNA are becoming more prevalent, increasing the sensitivity, specificity and throughput of diagnostic assays. High-throughput sequencing, from single PCR targets through to the analysis of whole genomes, offers significant promise towards providing information-rich data that may add value beyond traditional and conventional molecular approaches; however, thus far, its utility has not been fully explored to detect helminths in faecal samples. In this study, low-depth whole genome sequencing, i.e. genome skimming, has been applied to detect and characterise helminth diversity in a set of helminth-infected human and livestock faecal material. The strengths and limitations of this approach are evaluated using three methods to characterise and differentiate metagenomic sequencing data based on (i) mapping to whole mitochondrial genomes, (ii) whole genome assemblies, and (iii) a comprehensive internal transcribed spacer 2 (ITS2) database, together with validation using quantitative PCR (qPCR). Our analyses suggest that genome skimming can successfully identify most single and multi-species infections reported by qPCR and can provide sufficient coverage within some samples to resolve consensus mitochondrial genomes, thus facilitating phylogenetic analyses of selected genera, e.g. Ascaris spp. Key to this approach is both the availability and integrity of helminth reference genomes, some of which are currently contaminated with bacterial and host sequences. The success of genome skimming of faecal DNA is dependent on the availability of vouchered sequences of helminths spanning both taxonomic and geographic diversity, together with methods to detect or amplify minute quantities of parasite nucleic acids in mixed samples.
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Affiliation(s)
- Marina Papaiakovou
- Natural History Museum, Cromwell Road, London, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Natalia Fraija-Fernández
- Natural History Museum, Cromwell Road, London, UK; Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Spain
| | - Katherine James
- Natural History Museum, Cromwell Road, London, UK; Interdisciplinary Computing and Complex BioSystems, School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew G Briscoe
- Natural History Museum, Cromwell Road, London, UK; NatureMetrics, Surrey Research Park, Guildford, UK
| | - Andie Hall
- Natural History Museum, Cromwell Road, London, UK
| | - Timothy P Jenkins
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Dunn
- Department of Infectious Disease Epidemiology, Imperial College, London W2 1PG, UK
| | - Bruno Levecke
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | - Zeleke Mekonnen
- Jimma University Institute of Health (JUIH), Jimma, Ethiopia
| | - Piet Cools
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | | | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Investigation of Parasitic Nematodes Detected in the Feces of Wild Carnivores in the Eastern Qinghai-Tibet Plateau, China. Pathogens 2022; 11:pathogens11121520. [PMID: 36558854 PMCID: PMC9785254 DOI: 10.3390/pathogens11121520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Wildlife shares grazing areas with herders in the eastern Qinghai-Tibet Plateau, and humans can be infected by zoonotic nematodes through direct contact with animals or contaminated water. In this study, fecal samples (n = 296) from wild carnivores were collected to explore the infection rate and molecular genetic characteristics of nematodes by stratified random sampling in the survey areas. Host species and the nematodes they carried were then identified using 16S rRNA and 18S rRNA gene sequencing, respectively. Statistical analysis, neutrality tests, genetic diversity analysis and Bayesian inferred trees were performed to complete the study. In total, 10 species of nematodes were detected in 240 feces from six species of carnivores identified (including dominant Vulpes ferrilata and Vulpes vulpes), namely Uncinaria stenocephala, Toxascaris sp., Crenosoma vulpis, Parapharyngodon bainae, Oesophagostomum muntiacum, Aspiculuris tetraptera, Mastophorus muris, Nematodirus spathiger, Muellerius capillaris, and Molineus patens. Among these nematodes, U. stenocephala (35.83%, 86/240) and Toxascaris sp. (14.58%, 35/240) were detected at higher rates than the other nematodes (χ2 = 516.909, p < 0.05). Of 17 and 18 haplotypes were found based on the ITS1 gene for U. stenocephala and nad1 gene for Toxascaris sp., respectively. For the first time, using molecular methods, we report the infection of V. ferrilata by U. stenocephala, a potential zoonotic parasite, and suggest Toxascaris sp. may be a newly discovered nematode that lives within the fox intestine.
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Zhu J, Huang Q, Peng X, Zhou X, Gao S, Li Y, Luo X, Zhao Y, Rensing C, Su J, Cai P, Liu Y, Chen W, Hao X, Huang Q. MRG Chip: A High-Throughput qPCR-Based Tool for Assessment of the Heavy Metal(loid) Resistome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10656-10667. [PMID: 35876052 DOI: 10.1021/acs.est.2c00488] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial metal detoxification mechanisms have been well studied for centuries in pure culture systems. However, profiling metal resistance determinants at the community level is still a challenge due to the lack of comprehensive and reliable quantification tools. Here, a novel high-throughput quantitative polymerase chain reaction (HT-qPCR) chip, termed the metal resistance gene (MRG) chip, has been developed for the quantification of genes involved in the homeostasis of 9 metals. The MRG chip contains 77 newly designed degenerate primer sets and 9 published primer sets covering 56 metal resistance genes. Computational evaluation of the taxonomic coverage indicated that the MRG chip had a broad coverage matching 2 kingdoms, 29 phyla, 64 classes, 130 orders, 226 families, and 382 genera. Temperature gradient PCR and HT-qPCR verified that 57 °C was the optimal annealing temperature, with amplification efficiencies of over 94% primer sets achieving 80-110%, with R2 > 0.993. Both computational evaluation and the melting curve analysis of HT-qPCR validated a high specificity. The MRG chip has been successfully applied to characterize the distribution of diverse metal resistance determinants in natural and human-related environments, confirming its wide scope of application. Collectively, the MRG chip is a powerful and efficient high-throughput quantification tool for exploring the microbial metal resistome.
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Affiliation(s)
- Jiaojiao Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiong Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyi Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyuan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Shenghan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Zhao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jianqiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
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7
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Guzzo GL, Andrews JM, Weyrich LS. The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease. Inflamm Bowel Dis 2022; 28:1112-1122. [PMID: 35092426 PMCID: PMC9247841 DOI: 10.1093/ibd/izab343] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Indexed: 12/14/2022]
Abstract
The gut microbiome has been implicated in the pathogenesis of inflammatory bowel disease (IBD). Studies suggest that the IBD gut microbiome is less diverse than that of the unaffected population, a phenomenon often referred to as dysbiosis. However, these studies have heavily focused on bacteria, while other intestinal microorganisms-fungi, protozoa, and bacteriophages-have been neglected. Of the nonbacterial microbes that have been studied in relation to IBD, most are thought to be pathogens, although there is evidence that some of these species may instead be harmless commensals. In this review, we discuss the nonbacterial gut microbiome of IBD, highlighting the current biases, limitations, and outstanding questions that can be addressed with high-throughput DNA sequencing methods. Further, we highlight the importance of studying nonbacterial microorganisms alongside bacteria for a comprehensive view of the whole IBD biome and to provide a more precise definition of dysbiosis in patients. With the rise in popularity of microbiome-altering therapies for the treatment of IBD, such as fecal microbiota transplantation, it is important that we address these knowledge gaps to ensure safe and effective treatment of patients.
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Affiliation(s)
- Gina L Guzzo
- Address correspondence to: Gina L. Guzzo, The University of Adelaide, Adelaide, South Australia, Australia ()
| | - Jane M Andrews
- Inflammatory Bowel Disease Service, Department of Gastroenterology and Hepatology, Royal Adelaide Hospital and School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia,Department of Anthropology and Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, USA
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8
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Bourret V, Gutiérrez López R, Melo M, Loiseau C. Metabarcoding options to study eukaryotic endoparasites of birds. Ecol Evol 2021; 11:10821-10833. [PMID: 34429884 PMCID: PMC8366860 DOI: 10.1002/ece3.7748] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
There is growing interest in the study of avian endoparasite communities, and metabarcoding is a promising approach to complement more conventional or targeted methods. In the case of eukaryotic endoparasites, phylogenetic diversity is extreme, with parasites from 4 kingdoms and 11 phyla documented in birds. We addressed this challenge by comparing different primer sets across 16 samples from 5 bird species. Samples consisted of blood, feces, and controlled mixes with known proportions of bird and nematode DNA. Illumina sequencing revealed that a 28S primer set used in combination with a custom blocking primer allowed detection of various plasmodiid parasites and filarioid nematodes in the blood, coccidia in the feces, as well as two potentially pathogenic fungal groups. When tested on the controlled DNA mixes, these primers also increased the proportion of nematode DNA by over an order of magnitude. An 18S primer set, originally designed to exclude metazoan sequences, was the most effective at reducing the relative number of avian DNA sequences and was the only one to detect Trypanosoma in the blood. Expectedly, however, it did not allow nematode detection and also failed to detect avian malaria parasites. This study shows that a 28S set including a blocking primer allows detection of several major and very diverse bird parasite clades, while reliable amplification of all major parasite groups may require a combination of markers. It helps clarify options for bird parasite metabarcoding, according to priorities in terms of the endoparasite clades and the ecological questions researchers wish to focus on.
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Affiliation(s)
- Vincent Bourret
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Rafael Gutiérrez López
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Martim Melo
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- MHNC‐UP – Natural History and Science Museum of the University of PortoPortoPortugal
- FitzPatrick Institute of African OrnithologyUniversity of Cape TownCape TownSouth Africa
| | - Claire Loiseau
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- CEFEUniversité de MontpellierCNRSMontpellierFrance
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9
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Cannon MV, Bogale HN, Bhalerao D, Keita K, Camara D, Barry Y, Keita M, Coulibaly D, Kone AK, Doumbo OK, Thera MA, Plowe CV, Travassos MA, Irish SR, Yeroshefsky J, Dorothy J, Prendergast B, St. Laurent B, Fritz ML, Serre D. High-throughput detection of eukaryotic parasites and arboviruses in mosquitoes. Biol Open 2021; 10:bio058855. [PMID: 34156069 PMCID: PMC8325944 DOI: 10.1242/bio.058855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022] Open
Abstract
Vector-borne pathogens cause many human infectious diseases and are responsible for high mortality and morbidity throughout the world. They can also cause livestock epidemics with dramatic social and economic consequences. Due to its high costs, vector-borne disease surveillance is often limited to current threats, and the investigation of emerging pathogens typically occurs after the reports of clinical cases. Here, we use high-throughput sequencing to detect and identify a wide range of parasites and viruses carried by mosquitoes from Cambodia, Guinea, Mali and the USA. We apply this approach to individual Anopheles mosquitoes as well as pools of mosquitoes captured in traps; and compare the outcomes of this assay when applied to DNA or RNA. We identified known human and animal pathogens and mosquito parasites belonging to a wide range of taxa, as well as DNA sequences from previously uncharacterized organisms. Our results also revealed that analysis of the content of an entire trap could be an efficient approach to monitor and identify rare vector-borne pathogens in large surveillance studies. Overall, we describe a high-throughput and easy-to-customize assay to screen for a wide range of pathogens and efficiently complement current vector-borne disease surveillance approaches.
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Affiliation(s)
- Matthew V. Cannon
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Haikel N. Bogale
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Devika Bhalerao
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kalil Keita
- Programme National de Lutte contre le Paludisme, Guinea
| | - Denka Camara
- Programme National de Lutte contre le Paludisme, Guinea
| | - Yaya Barry
- Programme National de Lutte contre le Paludisme, Guinea
| | - Moussa Keita
- Programme National de Lutte contre le Paludisme, Guinea
| | - Drissa Coulibaly
- Malaria Research and Training Center, University Science, Techniques and Technologies of Bamako, Mali
| | - Abdoulaye K. Kone
- Malaria Research and Training Center, University Science, Techniques and Technologies of Bamako, Mali
| | - Ogobara K. Doumbo
- Malaria Research and Training Center, University Science, Techniques and Technologies of Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Center, University Science, Techniques and Technologies of Bamako, Mali
| | - Christopher V. Plowe
- Malaria Research Program, Department of Medicine, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Mark A. Travassos
- Malaria Research Program, Department of Medicine, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Seth R. Irish
- U.S. President's Malaria Initiative and Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Joshua Yeroshefsky
- Department of Entomology, University of Maryland College Park, College Park, MD 20742, USA
| | - Jeannine Dorothy
- Mosquito Control Program, Maryland Department of Agriculture, Annapolis, MD 21401, USA
| | - Brian Prendergast
- Mosquito Control Program, Maryland Department of Agriculture, Annapolis, MD 21401, USA
| | - Brandyce St. Laurent
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD 20852, USA
| | - Megan L. Fritz
- Department of Entomology, University of Maryland College Park, College Park, MD 20742, USA
| | - David Serre
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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10
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Walters HA, Temesvari LA. Target acquired: transcriptional regulators as drug targets for protozoan parasites. Int J Parasitol 2021; 51:599-611. [PMID: 33722681 PMCID: PMC8169582 DOI: 10.1016/j.ijpara.2020.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 11/22/2022]
Abstract
Protozoan parasites are single-celled eukaryotic organisms that cause significant human disease and pose a substantial health and socioeconomic burden worldwide. They are responsible for at least 1 million deaths annually. The treatment of such diseases is hindered by the ability of parasites to form latent cysts, develop drug resistance, or be transmitted by insect vectors. Additionally, these pathogens have developed complex mechanisms to alter host gene expression. The prevalence of these diseases is predicted to increase as climate change leads to the augmentation of ambient temperatures, insect ranges, and warm water reservoirs. Therefore, the discovery of novel treatments is necessary. Transcription factors lie at the junction of multiple signalling pathways in eukaryotes and aberrant transcription factor function contributes to the progression of numerous human diseases including cancer, diabetes, inflammatory disorders and cardiovascular disease. Transcription factors were previously thought to be undruggable. However, due to recent advances, transcription factors now represent appealing drug targets. It is conceivable that transcription factors, and the pathways they regulate, may also serve as targets for anti-parasitic drug design. Here, we review transcription factors and transcriptional modulators of protozoan parasites, and discuss how they may be useful in drug discovery. We also provide information on transcription factors that play a role in stage conversion of parasites, TATA box-binding proteins, and transcription factors and cofactors that participate with RNA polymerases I, II and III. We also highlight a significant gap in knowledge in that the transcription factors of some of parasites have been under-investigated. Understanding parasite transcriptional pathways and how parasites alter host gene expression will be essential in discovering innovative drug targets.
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Affiliation(s)
- H A Walters
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, United States; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, United States
| | - L A Temesvari
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, United States; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, United States.
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11
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Messaoud M, Abbes S, Gnaien M, Rebai Y, Kallel A, Jemel S, Cherif G, Skhairia MA, Marouen S, Fakhfekh N, Mardassi H, Belhadj S, Znaidi S, Kallel K. High Frequency of Enterocytozoon bieneusi Genotype WL12 Occurrence among Immunocompromised Patients with Intestinal Microsporidiosis. J Fungi (Basel) 2021; 7:jof7030161. [PMID: 33668221 PMCID: PMC7996336 DOI: 10.3390/jof7030161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 11/25/2022] Open
Abstract
Microsporidiosis is an emerging opportunistic infection causing severe digestive disorders in immunocompromised patients. The aim of this study was to investigate the prevalence of intestinal microsporidia carriage among immunocompromised patients hospitalized at a major hospital complex in the Tunis capital area, Tunisia (North Africa), and perform molecular epidemiology and population structure analyses of Enterocytozoon bieneusi, which is an emerging fungal pathogen. We screened 250 stool samples for the presence of intestinal microsporidia from 171 patients, including 81 organ transplant recipients, 73 Human Immunodeficiency Virus (HIV)-positive patients, and 17 patients with unspecified immunodeficiency. Using a nested PCR-based diagnostic approach for the detection of E. bieneusi and Encephalitozoon spp., we identified 18 microsporidia-positive patients out of 171 (10.5%), among which 17 were infected with E. bieneusi. Microsporidia-positive cases displayed chronic diarrhea (17 out of 18), which was associated more with HIV rather than with immunosuppression other than HIV (12 out of 73 versus 6 out of 98, respectively, p = 0.02) and correlated with extended hospital stays compared to microsporidia-negative cases (60 versus 19 days on average, respectively; p = 0.001). Strikingly, internal transcribed spacer (ITS)-based genotyping of E. bieneusi strains revealed high-frequency occurrence of ITS sequences that were identical (n = 10) or similar (with one single polymorphic site, n = 3) to rare genotype WL12. Minimum-spanning tree analyses segregated the 17 E. bieneusi infection cases into four distinct genotypic clusters and confirmed the high prevalence of genotype WL12 in our patient population. Phylogenetic analyses allowed the mapping of all 17 E. bieneusi strains to zoonotic group 1 (subgroups 1a and 1b/1c), indicating loose host specificity and raising public health concern. Our study suggests a probable common source of E. bieneusi genotype WL12 transmission and prompts the implementation of a wider epidemiological investigation.
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Affiliation(s)
- Mariem Messaoud
- Laboratoire de Parasitologie et Mycologie, UR17SP03, La Rabta Hospital, Tunis 1007, Tunisia; (M.M.); (S.A.); (A.K.); (S.J.); (G.C.); (S.M.); (N.F.); (S.B.)
| | - Salma Abbes
- Laboratoire de Parasitologie et Mycologie, UR17SP03, La Rabta Hospital, Tunis 1007, Tunisia; (M.M.); (S.A.); (A.K.); (S.J.); (G.C.); (S.M.); (N.F.); (S.B.)
| | - Mayssa Gnaien
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique, Tunis 1002, Tunisia; (M.G.); (Y.R.); (M.A.S.); (H.M.)
| | - Yasmine Rebai
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique, Tunis 1002, Tunisia; (M.G.); (Y.R.); (M.A.S.); (H.M.)
| | - Aicha Kallel
- Laboratoire de Parasitologie et Mycologie, UR17SP03, La Rabta Hospital, Tunis 1007, Tunisia; (M.M.); (S.A.); (A.K.); (S.J.); (G.C.); (S.M.); (N.F.); (S.B.)
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique, Tunis 1002, Tunisia; (M.G.); (Y.R.); (M.A.S.); (H.M.)
| | - Sana Jemel
- Laboratoire de Parasitologie et Mycologie, UR17SP03, La Rabta Hospital, Tunis 1007, Tunisia; (M.M.); (S.A.); (A.K.); (S.J.); (G.C.); (S.M.); (N.F.); (S.B.)
| | - Ghaya Cherif
- Laboratoire de Parasitologie et Mycologie, UR17SP03, La Rabta Hospital, Tunis 1007, Tunisia; (M.M.); (S.A.); (A.K.); (S.J.); (G.C.); (S.M.); (N.F.); (S.B.)
| | - Mohamed Amine Skhairia
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique, Tunis 1002, Tunisia; (M.G.); (Y.R.); (M.A.S.); (H.M.)
| | - Sonia Marouen
- Laboratoire de Parasitologie et Mycologie, UR17SP03, La Rabta Hospital, Tunis 1007, Tunisia; (M.M.); (S.A.); (A.K.); (S.J.); (G.C.); (S.M.); (N.F.); (S.B.)
| | - Najla Fakhfekh
- Laboratoire de Parasitologie et Mycologie, UR17SP03, La Rabta Hospital, Tunis 1007, Tunisia; (M.M.); (S.A.); (A.K.); (S.J.); (G.C.); (S.M.); (N.F.); (S.B.)
| | - Helmi Mardassi
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique, Tunis 1002, Tunisia; (M.G.); (Y.R.); (M.A.S.); (H.M.)
| | - Slaheddine Belhadj
- Laboratoire de Parasitologie et Mycologie, UR17SP03, La Rabta Hospital, Tunis 1007, Tunisia; (M.M.); (S.A.); (A.K.); (S.J.); (G.C.); (S.M.); (N.F.); (S.B.)
| | - Sadri Znaidi
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique, Tunis 1002, Tunisia; (M.G.); (Y.R.); (M.A.S.); (H.M.)
- Institut Pasteur, INRA, Département Mycologie, Unité Biologie et Pathogénicité Fongiques, 75015 Paris, France
- Correspondence: (S.Z.); (K.K.)
| | - Kalthoum Kallel
- Laboratoire de Parasitologie et Mycologie, UR17SP03, La Rabta Hospital, Tunis 1007, Tunisia; (M.M.); (S.A.); (A.K.); (S.J.); (G.C.); (S.M.); (N.F.); (S.B.)
- Correspondence: (S.Z.); (K.K.)
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12
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Flaherty BR, Barratt J, Lane M, Talundzic E, Bradbury RS. Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing. MICROBIOME 2021; 9:1. [PMID: 33388088 PMCID: PMC7778815 DOI: 10.1186/s40168-020-00939-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/14/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Targeted amplicon deep sequencing (TADS) has enabled characterization of diverse bacterial communities, yet the application of TADS to communities of parasites has been relatively slow to advance. The greatest obstacle to this has been the genetic diversity of parasitic agents, which include helminths, protozoa, arthropods, and some acanthocephalans. Meanwhile, universal amplification of conserved loci from all parasites without amplifying host DNA has proven challenging. Pan-eukaryotic PCRs preferentially amplify the more abundant host DNA, obscuring parasite-derived reads following TADS. Flaherty et al. (2018) described a pan-parasitic TADS method involving amplification of eukaryotic 18S rDNA regions possessing restriction sites only in vertebrates. Using this method, host DNA in total DNA extracts could be selectively digested prior to PCR using restriction enzymes, thereby increasing the number of parasite-derived reads obtained following NGS. This approach showed promise though was only as sensitive as conventional PCR. RESULTS Here, we expand on this work by designing a second set of pan-eukaryotic primers flanking the priming sites already described, enabling nested PCR amplification of the established 18S rDNA target. This nested approach facilitated introduction of a second restriction digestion between the first and second PCR, reducing the proportional mass of amplifiable host-derived DNA while increasing the number of PCR amplification cycles. We applied this method to blood specimens containing Babesia, Plasmodium, various kinetoplastids, and filarial nematodes and confirmed its limit of detection (LOD) to be approximately 10-fold lower than previously described, falling within the range of most qPCR methods. CONCLUSIONS The assay detects and differentiates the major malaria parasites of humans, along with several other clinically important blood parasites. This represents an important step towards a TADS-based universal parasite diagnostic (UPDx) test with a sufficient LOD for routine applications. Video Abstract.
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Affiliation(s)
- Briana R Flaherty
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Joel Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.
| | - Meredith Lane
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Synergy America Inc., Duluth, GA, USA
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Richard S Bradbury
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
- School of Health and Life Sciences, Federation University, Ballarat, Australia.
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13
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Egan SL, Taylor CL, Austen JM, Banks PB, Northover AS, Ahlstrom LA, Ryan UM, Irwin PJ, Oskam CL. Haemoprotozoan surveillance in peri-urban native and introduced wildlife from Australia. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2021; 1:100052. [PMID: 35284862 PMCID: PMC8906138 DOI: 10.1016/j.crpvbd.2021.100052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/30/2021] [Accepted: 09/22/2021] [Indexed: 01/15/2023]
Affiliation(s)
- Siobhon L. Egan
- Harry Butler Institute, Murdoch University, Murdoch, Western Australia, 6150, Australia
- Corresponding author.
| | - Casey L. Taylor
- School of Life and Environmental Sciences, Camperdown, The University of Sydney, New South Wales, 2006, Australia
| | - Jill M. Austen
- Harry Butler Institute, Murdoch University, Murdoch, Western Australia, 6150, Australia
| | - Peter B. Banks
- School of Life and Environmental Sciences, Camperdown, The University of Sydney, New South Wales, 2006, Australia
| | - Amy S. Northover
- College of Veterinary Medicine, Murdoch University, Murdoch, Western Australia, 6150, Australia
| | - Liisa A. Ahlstrom
- Elanco Animal Health, Macquarie Park, New South Wales, 2113, Australia
| | - Una M. Ryan
- Harry Butler Institute, Murdoch University, Murdoch, Western Australia, 6150, Australia
| | - Peter J. Irwin
- Harry Butler Institute, Murdoch University, Murdoch, Western Australia, 6150, Australia
- College of Veterinary Medicine, Murdoch University, Murdoch, Western Australia, 6150, Australia
| | - Charlotte L. Oskam
- Harry Butler Institute, Murdoch University, Murdoch, Western Australia, 6150, Australia
- Corresponding author.
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14
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Bogale HN, Cannon MV, Keita K, Camara D, Barry Y, Keita M, Coulibaly D, Kone AK, Doumbo OK, Thera MA, Plowe CV, Travassos M, Irish S, Serre D. Relative contributions of various endogenous and exogenous factors to the mosquito microbiota. Parasit Vectors 2020; 13:619. [PMID: 33303025 PMCID: PMC7726613 DOI: 10.1186/s13071-020-04491-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/19/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The commensal microbiota of mosquitoes impacts their development, immunity, and competency, and could provide a target for alternative entomological control approaches. However, despite the importance of the mosquito/microbiota interactions, little is known about the relative contribution of endogenous and exogenous factors in shaping the bacterial communities of mosquitoes. METHODS We used a high-throughput sequencing-based assay to characterize the bacterial composition and diversity of 665 individual field-caught mosquitoes, as well as their species, genotype at an insecticide resistance locus, blood-meal composition, and the eukaryotic parasites and viruses they carry. We then used these data to rigorously estimate the individual effect of each parameter on the bacterial diversity as well as the relative contribution of each parameter to the microbial composition. RESULTS Overall, multivariate analyses did not reveal any significant contribution of the mosquito species, insecticide resistance, or blood meal to the bacterial composition of the mosquitoes surveyed, and infection with parasites and viruses only contributed very marginally. The main driver of the bacterial diversity was the location at which each mosquito was collected, which explained roughly 20% of the variance observed. CONCLUSIONS This analysis shows that when confounding factors are taken into account, the site at which the mosquitoes are collected is the main driver of the bacterial diversity of wild-caught mosquitoes, although further studies will be needed to determine which specific components of the local environment affect bacterial composition.
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Affiliation(s)
- Haikel N. Bogale
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Matthew V. Cannon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Kalil Keita
- Programme National de Lutte contre le Paludisme, Conakry, Guinea
| | - Denka Camara
- Programme National de Lutte contre le Paludisme, Conakry, Guinea
| | - Yaya Barry
- Programme National de Lutte contre le Paludisme, Conakry, Guinea
| | - Moussa Keita
- Programme National de Lutte contre le Paludisme, Conakry, Guinea
| | - Drissa Coulibaly
- Malaria Research and Training Center, University Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye K. Kone
- Malaria Research and Training Center, University Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ogobara K. Doumbo
- Malaria Research and Training Center, University Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Center, University Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Mark Travassos
- Malaria Research Program, Center of Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
| | - Seth Irish
- U.S. President’s Malaria Initiative and Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, US Centers for Disease Prevention, Atlanta, GA USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
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15
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Wang X, Liu Z, Li X, Li D, Cai J, Yan H. SPDB: a specialized database and web-based analysis platform for swine pathogens. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5881264. [PMID: 32761141 PMCID: PMC7409514 DOI: 10.1093/database/baaa063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/07/2020] [Accepted: 07/10/2020] [Indexed: 11/12/2022]
Abstract
The rapid and accurate diagnosis of swine diseases is indispensable for reducing their negative impacts on the pork industry. Next-generation sequencing (NGS) is a promising diagnostic tool for swine diseases. To support the application of NGS in the diagnosis of swine disease, we established the Swine Pathogen Database (SPDB). The SPDB represents the first comprehensive and highly specialized database and analysis platform for swine pathogens. The current version features an online genome search tool, which now contains 26 148 genomes of swine, swine pathogens and phylogenetically related species. This database offers a comprehensive bioinformatics analysis pipeline for the identification of 4403 swine pathogens and their related species in clinical samples, based on targeted 16S rRNA gene sequencing and metagenomic NGS data. The SPDB provides a powerful and user-friendly service for veterinarians and researchers to support the applications of NGS in swine disease research. Database URL: http://spdatabase.com:2080/.
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Affiliation(s)
- Xiaoru Wang
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou, Guangdong Province 510641, China
| | - Zongbao Liu
- Institute for Advanced Study, Shenzhen University, No. 3688, Nanhai Boulevard, Nanshan District, Shenzhen, Guangdong Province 518061, China
| | - Xiaoying Li
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou, Guangdong Province 510641, China
| | - Danwei Li
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou, Guangdong Province 510641, China
| | - Jiayu Cai
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou, Guangdong Province 510641, China
| | - He Yan
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou, Guangdong Province 510641, China
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16
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Betson M, Alonte AJI, Ancog RC, Aquino AMO, Belizario VY, Bordado AMD, Clark J, Corales MCG, Dacuma MG, Divina BP, Dixon MA, Gourley SA, Jimenez JRD, Jones BP, Manalo SMP, Prada JM, van Vliet AHM, Whatley KCL, Paller VGV. Zoonotic transmission of intestinal helminths in southeast Asia: Implications for control and elimination. ADVANCES IN PARASITOLOGY 2020; 108:47-131. [PMID: 32291086 DOI: 10.1016/bs.apar.2020.01.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intestinal helminths are extremely widespread and highly prevalent infections of humans, particularly in rural and poor urban areas of low and middle-income countries. These parasites have chronic and often insidious effects on human health and child development including abdominal problems, anaemia, stunting and wasting. Certain animals play a fundamental role in the transmission of many intestinal helminths to humans. However, the contribution of zoonotic transmission to the overall burden of human intestinal helminth infection and the relative importance of different animal reservoirs remains incomplete. Moreover, control programmes and transmission models for intestinal helminths often do not consider the role of zoonotic reservoirs of infection. Such reservoirs will become increasingly important as control is scaled up and there is a move towards interruption and even elimination of parasite transmission. With a focus on southeast Asia, and the Philippines in particular, this review summarises the major zoonotic intestinal helminths, risk factors for infection and highlights knowledge gaps related to their epidemiology and transmission. Various methodologies are discussed, including parasite genomics, mathematical modelling and socio-economic analysis, that could be employed to improve understanding of intestinal helminth spread, reservoir attribution and the burden associated with infection, as well as assess effectiveness of interventions. For sustainable control and ultimately elimination of intestinal helminths, there is a need to move beyond scheduled mass deworming and to consider animal and environmental reservoirs. A One Health approach to control of intestinal helminths is proposed, integrating interventions targeting humans, animals and the environment, including improved access to water, hygiene and sanitation. This will require coordination and collaboration across different sectors to achieve best health outcomes for all.
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Affiliation(s)
- Martha Betson
- University of Surrey, Guildford, Surrey, United Kingdom.
| | | | - Rico C Ancog
- University of the Philippines Los Baños, Laguna, Philippines
| | | | | | | | - Jessica Clark
- University of Surrey, Guildford, Surrey, United Kingdom
| | | | | | - Billy P Divina
- University of the Philippines Los Baños, Laguna, Philippines
| | | | | | | | - Ben P Jones
- University of Surrey, Guildford, Surrey, United Kingdom
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17
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Improved 18S and 28S rDNA primer sets for NGS-based parasite detection. Sci Rep 2019; 9:15789. [PMID: 31673037 PMCID: PMC6823512 DOI: 10.1038/s41598-019-52422-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 10/07/2019] [Indexed: 12/18/2022] Open
Abstract
The development and application of next-generation sequencing (NGS) have enabled comprehensive analyses of the microbial community through extensive parallel sequencing. Current analyses of the eukaryotic microbial community are primarily based on polymerase chain reaction amplification of 18S rRNA gene (rDNA) fragments. We found that widely-used 18S rDNA primers can amplify numerous stretches of the bacterial 16S rRNA gene, preventing the high-throughput detection of rare eukaryotic species, particularly in bacteria-rich samples such as faecal material. In this study, we employed in silico and NGS-based analyses of faecal samples to evaluated the existing primers targeting eukaryotic 18S and 28S rDNA in terms of avoiding bacterial read contamination and improving taxonomic coverage for eukaryotes, with a particular emphasis on parasite taxa. Our findings revealed that newly selected primer sets could achieve these objectives, representing an alternative strategy for NGS.
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18
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A novel metabarcoding diagnostic tool to explore protozoan haemoparasite diversity in mammals: a proof-of-concept study using canines from the tropics. Sci Rep 2019; 9:12644. [PMID: 31477800 PMCID: PMC6718641 DOI: 10.1038/s41598-019-49118-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/19/2019] [Indexed: 01/07/2023] Open
Abstract
Haemoparasites are responsible for some of the most prevalent and debilitating canine illnesses across the globe, whilst also posing a significant zoonotic risk to humankind. Nowhere are the effects of such parasites more pronounced than in developing countries in the tropics where the abundance and diversity of ectoparasites that transmit these pathogens reaches its zenith. Here we describe the use of a novel next-generation sequencing (NGS) metabarcoding based approach to screen for a range of blood-borne apicomplexan and kinetoplastid parasites from populations of temple dogs in Bangkok, Thailand. Our methodology elucidated high rates of Hepatozoon canis and Babesia vogeli infection, whilst also being able to characterise co-infections. In addition, our approach was confirmed to be more sensitive than conventional endpoint PCR diagnostic methods. Two kinetoplastid infections were also detected, including one by Trypanosoma evansi, a pathogen that is rarely screened for in dogs and another by Parabodo caudatus, a poorly documented organism that has been previously reported inhabiting the urinary tract of a dog with haematuria. Such results demonstrate the power of NGS methodologies to unearth rare and unusual pathogens, especially in regions of the world where limited information on canine vector-borne haemoparasites exist.
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