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Moreno-Mesonero L, Soler P, Alonso JL, Macián VJ, Moreno Y. Assessment of pathogenic protozoa in a drinking water treatment plant with UV treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 366:121897. [PMID: 39043088 DOI: 10.1016/j.jenvman.2024.121897] [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: 05/06/2024] [Revised: 07/04/2024] [Accepted: 07/14/2024] [Indexed: 07/25/2024]
Abstract
Controlling drinking water treatment processes is essential to address water contamination and the adaptability of certain pathogenic protozoa. Sometimes, standard treatment methods and chlorine disinfection may prove insufficient in eliminating pathogenic protozoa. However, ultraviolet (UV) radiation has proved to be more effective than chlorine. This study aims to characterize the eukaryotic community of a drinking water treatment plant that applies a final UV disinfection treatment, focusing on pathogenic protozoa. Fifty water samples (raw water, before and after UV treatment) were evaluated to comply with regulation parameters and identify relevant protozoa. Despite physicochemical and microbiological parameters meeting the regulation, some potentially pathogenic protozoa, such as Blastocystis or Cryptosporidium, were still detected in very low relative abundances in treated water. It was found for the first time in Spain the pathogenic amoebae Naegleria fowleri in one river water, which was not found after the treatment. Moreover, Blastocystis subtypes ST1-ST6 were detected in this study in raw, before and after UV water samples. Blastocystis was only found in 2 two samples after UV treatment, with a very low abundance (≤0.02%). Obtained results demonstrate the effectiveness of water treatment in reducing the prevalence of pathogenic protozoa.
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Affiliation(s)
- L Moreno-Mesonero
- Research Institute of Water and Environmental Engineering (IIAMA). Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - P Soler
- Research Institute of Water and Environmental Engineering (IIAMA). Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain; Empresa Mixta Valenciana de Aguas, S.A. (EMIVASA). Av. del Regne de València, 28, 46005, Valencia, Spain.
| | - J L Alonso
- Research Institute of Water and Environmental Engineering (IIAMA). Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - V J Macián
- Empresa Mixta Valenciana de Aguas, S.A. (EMIVASA). Av. del Regne de València, 28, 46005, Valencia, Spain.
| | - Y Moreno
- Research Institute of Water and Environmental Engineering (IIAMA). Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
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Lott MJ, Frankham GJ, Eldridge MDB, Alquezar‐Planas DE, Donnelly L, Zenger KR, Leigh KA, Kjeldsen SR, Field MA, Lemon J, Lunney D, Crowther MS, Krockenberger MB, Fisher M, Neaves LE. Reversing the decline of threatened koala ( Phascolarctos cinereus) populations in New South Wales: Using genomics to enhance conservation outcomes. Ecol Evol 2024; 14:e11700. [PMID: 39091325 PMCID: PMC11289790 DOI: 10.1002/ece3.11700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024] Open
Abstract
Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction-based method (DArTSeq), we generated a data set of 3239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned among individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.
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Affiliation(s)
- Matthew J. Lott
- Australian Museum Research InstituteSydneyNew South WalesAustralia
| | | | | | | | - Lily Donnelly
- Molecular Ecology and Evolutionary Laboratory, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Kellie A. Leigh
- Science for Wildlife LtdMount VictoriaNew South WalesAustralia
| | - Shannon R. Kjeldsen
- Molecular Ecology and Evolutionary Laboratory, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityTownsvilleQueenslandAustralia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityTownsvilleQueenslandAustralia
- Immunogenomics LabGarvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
| | - John Lemon
- JML Environmental ConsultantsArmidaleNew South WalesAustralia
- School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNew South WalesAustralia
| | - Daniel Lunney
- Australian Museum Research InstituteSydneyNew South WalesAustralia
- Department of Planning and EnvironmentParramattaNew South WalesAustralia
- School of Life and Environmental SciencesUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mathew S. Crowther
- School of Life and Environmental SciencesUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mark B. Krockenberger
- Sydney School of Veterinary ScienceUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mark Fisher
- 3D Ecology MappingEmerald BeachNew South WalesAustralia
| | - Linda E. Neaves
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
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3
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Zhou X, Wang Z, Zhu P, Gu X, He R, Xu J, Jing B, Wang L, Chen S, Xie Y. Eimeria zuernii (Eimeriidae: Coccidia): mitochondrial genome and genetic diversity in the Chinese yak. Parasit Vectors 2023; 16:312. [PMID: 37661262 PMCID: PMC10475197 DOI: 10.1186/s13071-023-05925-8] [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: 05/24/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
BACKGROUND Coccidiosis caused by Eimeria zuernii (Eimeriidae: Coccidia) represents a significant economic threat to the bovine industry. Understanding the evolutionary and genetic biology of E. zuernii can assist in new interaction developments for the prevention and control of this protozoosis. METHODS We defined the evolutionary and genetic characteristics of E. zuernii by sequencing the complete mitogenome and analyzing the genetic diversity and population structure of 51 isolates collected from eight yak breeding parks in China. RESULTS The 6176-bp mitogenome of E. zuernii was linear and encoded typical mitochondrial contents of apicomplexan parasites, including three protein-coding genes [PCGs; cytochrome c oxidase subunits I and III (cox1 and cox3), and cytochrome b (cytb)], seven fragmented small subunit (SSU) and 12 fragmented large subunit (LSU) rRNAs. Genome-wide comparative and evolutionary analyses showed cytb and cox3 to be the most and least conserved Eimeria PCGs, respectively, and placed E. zuernii more closely related to Eimeria mephitidis than other Eimeria species. Furthermore, cox1-based genetic structure defined 24 haplotypes of E. zuernii with high haplotype diversities and low nucleotide diversities across eight geographic populations, supporting a low genetic structure and rapid evolutionary rate as well as a previous expansion event among E. zuernii populations. CONCLUSIONS To our knowledge, this is the first study presenting the phylogeny, genetic diversity, and population structure of the yak E. zuernii, and such information, together with its mitogenomic data, should contribute to a better understanding of the genetic and evolutionary biological studies of apicomplexan parasites in bovines.
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Affiliation(s)
- Xuan Zhou
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Zhao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Pengchen Zhu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Bo Jing
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
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Rana AK, Kumar N. Current wildlife crime (Indian scenario): major challenges and prevention approaches. BIODIVERSITY AND CONSERVATION 2023; 32:1473-1491. [PMID: 37063172 PMCID: PMC10025790 DOI: 10.1007/s10531-023-02577-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 02/11/2023] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
UNLABELLED The constant depletion of wild flora and fauna in India due to uncontrolled human activities, natural habitat destruction and covert poaching activities is threatening the ecological balance. The poaching and trafficking of wild species in the lure of money as well as fashion has wiped out a range of wildlife species that call for critical attention to tackle this menace. There are many transit routes through the states of Uttar Pradesh, Karnataka, West Bengal, Rajasthan, Madhya Pradesh, and Assam, which are major hubs for wildlife trafficking in India, in both domestic and international markets. The poaching of wild animals and plants slowly erases biodiversity, which in turn affects the survival of humans and other living species. Therefore, there is an urgent need to check ongoing wildlife crimes, raise the number of endangered species, rehabilitate exotic/extinct species and restore natural ecosystems. In this article, we collected wildlife crime data from web portals of various stakeholders, government agencies and authentic news sources, and discuss the current crime trends, challenges, and prevention approaches required to control and restore wildlife biodiversity in India. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10531-023-02577-z.
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Affiliation(s)
- Ajay Kumar Rana
- Division of Biology, Central Forensic Science Laboratory Hyderabad, Ministry of Home Affairs, Government of India, Amberpet post, Ramanthapur, Hyderabad, Telangana 500013 India
| | - Nishant Kumar
- Quality Control, Bihar, Patna, Department of Agriculture, Government of Bihar, Patna, 800001 India
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5
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Zhou X, Wang L, Zhu P, Yang Z, Wang Z, Chen Y, Gu X, He R, Xu J, Jing B, Yang G, Chen S, Wu S, Xie Y. Comprehensive molecular characterization of complete mitogenome assemblies of 33 Eimeria isolates infecting domestic chickens. Parasit Vectors 2023; 16:109. [PMID: 36935516 PMCID: PMC10026407 DOI: 10.1186/s13071-023-05712-5] [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: 12/29/2022] [Accepted: 02/22/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Coccidiosis caused by Eimeria is one of the most severe chicken diseases and poses a great economic threat to the poultry industry. Understanding the evolutionary biology of chicken Eimeria parasites underpins development of new interactions toward the improved prevention and control of this poultry disease. METHODS We presented an evolutionary blueprint of chicken coccidia by genetically characterizing complete mitogenome assemblies of 33 isolates representing all seven known Eimeria species infecting chickens in China. Further genome- and gene-level phylogenies were also achieved to better understand the evolutionary relationships of these chicken Eimeria at the species level. RESULTS 33 mitogenomes of chicken eimerian parasites ranged from 6148 bp to 6480 bp in size and encoded typical mitochondrial compositions of apicomplexan parasites including three protein-coding genes (PCGs), seven fragmented small subunit (SSU) and 12/13 fragmented large subunit (LSU) rRNAs. Comparative genomics provided an evolutionary scenario for the genetic diversity of PCGs-cytochrome c oxidase subunits 1 and 3 (cox1 and cox3) and cytochrome b (cytb); all were under purifying selection with cox1 and cox3 being the lowest and highest evolutionary rates, respectively. Genome-wide phylogenies classified the 33 Eimeria isolates into seven subgroups, and furthermore Eimeria tenella and Eimeria necatrix were determined to be more closely related to each other than to the other eight congenic species. Single/concatenated mitochondrial protein gene-based phylogenies supported cox1 as the genetic marker for evolutionary and phylogenetic studies for avain coccidia. CONCLUSIONS To our knowledge, these are the first population-level mitogenomic data on the genus Eimeria, and its comprehensive molecular characterization provides valuable resources for systematic, population genetic and evolutionary biological studies of apicomplexan parasites in poultry.
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Affiliation(s)
- Xuan Zhou
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Pengchen Zhu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Zijiang Yang
- Tokyo University of Marine Science and Technology, Konan Minato-Ku, Tokyo, 1088477, Japan
| | - Zhao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Yijun Chen
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Bo Jing
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China.
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030, Vienna, Austria.
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China.
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6
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Next-generation sequencing amplicon analysis of the genetic diversity of Eimeria populations in livestock and wildlife samples from Australia. Parasitol Res 2023; 122:615-624. [PMID: 36544013 DOI: 10.1007/s00436-022-07764-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Eimeria is an important coccidian enteric parasite that infects a wide range of hosts and can cause substantial economic losses in the poultry and livestock industries. It is common for multiple Eimeria species to infect individual hosts, and this can make species identification difficult due to morphological similarities between species and mixed chromatograms when using Sanger sequencing. Relatively few studies have applied next-generation amplicon sequencing (NGS) to determining the genetic diversity of Eimeria species in different hosts. The present study screened 408 faecal samples from a range of hosts including livestock and wildlife using a previously developed quantitative polymerase chain reaction (qPCR) at the 18S locus and conducted amplicon NGS on the positives using a ~ 455-bp fragment of the 18S locus. A total of 41 positives (10.1%) were identified by qPCR from various hosts and NGS was successful for 38 of these positives. Fifteen Eimeria species and three genotypes were detected by NGS: E. ferrisi, E. kanyana, E. potoroi, E. quokka, E. setonicis, E. trichosuri, E. reichenowi, E. angustus, E. ahsata, E. auburnensis, E. bovis, E. brasiliensis, E. christenseni, E. crandallis, E. ovinoidalis, Eimeria sp. (JF419345), Eimeria sp. (JF419349) and Eimeria sp. (JF419351). Mixed infections were detected in 55.3% (21/38) of positive samples. The most striking finding was the identification of the same species in different hosts. This could be due to contamination and/or mechanical transmission or may provide support for previous studies suggesting that Eimeria species can infect not just closely related hosts but different genera and further research is required. This is also the first study to audit Eimeria populations in livestock (sheep and cattle) by NGS and could be applied in the future to determine the extent of pathogenic species and outcomes of Eimeria control strategies.
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7
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Peacock D, Croxford A, Iannella A, Kovaliski J, Lavazza A, Cooke B, Spratt D, Strive T, Taggart D, Campbell S, Robinson S, Sawyers E. Using genetic analysis to determine the distribution, prevalence and diversity of Eimeria species in pest rabbits (Oryctolagus cuniculus) in Australia. Parasitol Int 2022; 91:102642. [DOI: 10.1016/j.parint.2022.102642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022]
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8
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Sweeny AR, Corripio-Miyar Y, Bal X, Hayward AD, Pilkington JG, McNeilly TN, Nussey DH, Kenyon F. Longitudinal dynamics of co-infecting gastrointestinal parasites in a wild sheep population. Parasitology 2022; 149:1-12. [PMID: 35264257 PMCID: PMC10090596 DOI: 10.1017/s0031182021001980] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/09/2021] [Accepted: 11/01/2021] [Indexed: 11/07/2022]
Abstract
Within-year variation in infection is a ubiquitous feature of natural populations, but is determined by a complex interplay of environmental, parasitological and host factors. At the same time, co-infection is the norm in the wild. Longitudinal dynamics of co-infecting parasites may therefore be further complicated by covariation across multiple parasites. Here, we used fecal parasite egg and oocyst counts collected repeatedly from individually marked wild Soay sheep to investigate seasonal dynamics of six gastrointestinal parasite groups. Prevalence and abundance tended to be higher in spring and summer, and abundance was higher in lambs compared to adults. We found that within-year variation in highly prevalent strongyle nematode counts was dependent on adult reproductive status, where reproductive ewes had distinct dynamics compared to males and barren ewes. For similarly prevalent coccidia we found an overall peak in oocyst counts in spring but no differences among males, barren and pregnant ewes. Using multivariate mixed-effects models, we further show that apparent positive correlation between strongyle and coccidia counts was driven by short-term within-individual changes in both counts rather than long-term among-individual covariation. Overall, these results demonstrate that seasonality varies across demographic and parasite groups and highlight the value of investigating co-infection dynamics over time.
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Affiliation(s)
- Amy R. Sweeny
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Xavier Bal
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Jill G. Pilkington
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Daniel H. Nussey
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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An Illumina MiSeq-Based Amplicon Sequencing Method for the Detection of Mixed Parasite Infections Using the Blastocystis SSU rRNA Gene as an Example. Methods Mol Biol 2021. [PMID: 34313984 DOI: 10.1007/978-1-0716-1681-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Parasite mixed infections remain a relatively unexplored field in part due to the difficulties of unraveling complex mixtures of parasite DNA using classical methods of sequencing. Next-generation amplicon sequencing (NGS) is a powerful tool for exploring mixed infections of multiple genetic variants of the same parasite in clinical, environmental (water or soil), or food samples. Here, we provide a method for NGS-based detection of mixed parasite infections which uses the Blastocystis SSU rRNA gene as an example and includes steps for parasite concentration, DNA extraction, sequencing library preparation, and bioinformatic analysis.
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10
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Mthethwa NP, Amoah ID, Reddy P, Bux F, Kumari S. A review on application of next-generation sequencing methods for profiling of protozoan parasites in water: Current methodologies, challenges, and perspectives. J Microbiol Methods 2021; 187:106269. [PMID: 34129906 DOI: 10.1016/j.mimet.2021.106269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 01/23/2023]
Abstract
The advancement in metagenomic techniques has provided novel tools for profiling human parasites in environmental matrices, such as water and wastewater. However, application of metagenomic techniques for the profiling of protozoan parasites in environmental matrices is not commonly reported in the literature. The key factors leading to the less common use of metagenomics are the complexity and large eukaryotic genome, the prevalence of small parasite populations in environmental samples compared to bacteria, difficulties in extracting DNA from (oo)cysts, and limited reference databases for parasites. This calls for further research to develop optimized methods specifically looking at protozoan parasites in the environment. This study reviews the current workflow, methods and provide recommendations for the standardization of techniques. The article identifies and summarizes the key methods, advantages, and limitations associated with metagenomic analysis, like sample pre-processing, DNA extraction, sequencing approaches, and analysis methods. The study enhances the understanding and application of standardized protocols for profiling of protozoan parasite community from highly complexe samples and further creates a resourceful comparison among datasets without any biases.
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Affiliation(s)
- N P Mthethwa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa; Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - I D Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - P Reddy
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - F Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - S Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
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11
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Maloney JG, Molokin A, Santin M. Assessment of next generation amplicon sequencing of the beta-giardin gene for the detection of Giardia duodenalis assemblages and mixed infections. Food Waterborne Parasitol 2020; 21:e00098. [PMID: 33294649 PMCID: PMC7691155 DOI: 10.1016/j.fawpar.2020.e00098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Giardia duodenalis is an enteric protozoan parasite commonly found in humans and many other animals around the world. The parasite is grouped into genetically related strains called assemblages which display differing degrees of host specificity. Although mixed assemblage infections have been documented the full extent of the occurrence and importance of mixed infections remains to be characterized as current sequencing technologies lack the sensitivity to readily detect mixed infections. Here we have developed a next generation amplicon sequencing (NGS) protocol and analysis pipeline for detecting Giardia assemblages using the beta-giardin gene. NGS was validated using 37 isolates that included Giardia muris and six assemblages (A-F) of Giardia duodenalis obtained from seven different hosts. NGS was compared to traditional PCR and direct Sanger sequencing for its ability to detect Giardia species, assemblages, and mixed assemblage infections. We demonstrate that NGS works as well as PCR and Sanger sequencing for assemblage detection as the same assemblage was observed in all samples by both methods. NGS has the further benefit of detecting mixed assemblage infections, low abundance assemblages, and intra-assemblage variation in samples which would have been missed using direct Sanger sequencing alone. NGS represents a powerful new tool for exploring Giardia infections not only in infected hosts but also in environmental specimens which may aide in understanding Giardia epidemiology. Developed a next generation sequencing (NGS) protocol to detect Giardia Comparison of NGS to Sanger sequencing for sensitivity and accuracy NGS improved detection of mixed assemblages and detects low abundance assemblages NGS allowed detection of intra-assemblage variabilities Mixed assemblages may be far more common than previously thought
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Affiliation(s)
- Jenny G Maloney
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Ave, Beltsville, MD 20705, United States
| | - Aleksey Molokin
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Ave, Beltsville, MD 20705, United States
| | - Monica Santin
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Ave, Beltsville, MD 20705, United States
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12
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Blake DP, Worthing K, Jenkins MC. Exploring Eimeria Genomes to Understand Population Biology: Recent Progress and Future Opportunities. Genes (Basel) 2020; 11:E1103. [PMID: 32967167 PMCID: PMC7564333 DOI: 10.3390/genes11091103] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022] Open
Abstract
Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control.
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Affiliation(s)
- Damer P. Blake
- Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms AL9 7TA, UK
| | - Kate Worthing
- Animal Parasitic Diseases Laboratory, Building 1040, Agricultural Research Service, USDA, Beltsville, MD 20705, USA; (K.W.); (M.C.J.)
| | - Mark C. Jenkins
- Animal Parasitic Diseases Laboratory, Building 1040, Agricultural Research Service, USDA, Beltsville, MD 20705, USA; (K.W.); (M.C.J.)
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13
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Glidden CK, Koehler AV, Hall RS, Saeed MA, Coppo M, Beechler BR, Charleston B, Gasser RB, Jolles AE, Jabbar A. Elucidating cryptic dynamics of Theileria communities in African buffalo using a high-throughput sequencing informatics approach. Ecol Evol 2020; 10:70-80. [PMID: 31988717 PMCID: PMC6972817 DOI: 10.1002/ece3.5758] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/31/2022] Open
Abstract
Increasing access to next-generation sequencing (NGS) technologies is revolutionizing the life sciences. In disease ecology, NGS-based methods have the potential to provide higher-resolution data on communities of parasites found in individual hosts as well as host populations.Here, we demonstrate how a novel analytical method, utilizing high-throughput sequencing of PCR amplicons, can be used to explore variation in blood-borne parasite (Theileria-Apicomplexa: Piroplasmida) communities of African buffalo at higher resolutions than has been obtained with conventional molecular tools.Results reveal temporal patterns of synchronized and opposite fluctuations of prevalence and relative abundance of Theileria spp. within the host population, suggesting heterogeneous transmission across taxa. Furthermore, we show that the community composition of Theileria spp. and their subtypes varies considerably between buffalo, with differences in composition reflected in mean and variance of overall parasitemia, thereby showing potential to elucidate previously unexplained contrasts in infection outcomes for host individuals.Importantly, our methods are generalizable as they can be utilized to describe blood-borne parasite communities in any host species. Furthermore, our methodological framework can be adapted to any parasite system given the appropriate genetic marker.The findings of this study demonstrate how a novel NGS-based analytical approach can provide fine-scale, quantitative data, unlocking opportunities for discovery in disease ecology.
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Affiliation(s)
| | - Anson V. Koehler
- Department of Veterinary BiosciencesMelbourne Veterinary SchoolUniversity of MelbourneWerribeeVic.Australia
| | - Ross S. Hall
- Department of Veterinary BiosciencesMelbourne Veterinary SchoolUniversity of MelbourneWerribeeVic.Australia
| | - Muhammad A. Saeed
- Department of Veterinary BiosciencesMelbourne Veterinary SchoolUniversity of MelbourneWerribeeVic.Australia
| | - Mauricio Coppo
- Department of Veterinary BiosciencesMelbourne Veterinary SchoolUniversity of MelbourneWerribeeVic.Australia
| | | | | | - Robin B. Gasser
- Carlson College of Veterinary MedicineOregon State UniversityCorvallisORUSA
| | - Anna E. Jolles
- Department of Integrative BiologyOregon State UniversityCorvallisORUSA
- Carlson College of Veterinary MedicineOregon State UniversityCorvallisORUSA
| | - Abdul Jabbar
- Department of Veterinary BiosciencesMelbourne Veterinary SchoolUniversity of MelbourneWerribeeVic.Australia
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14
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Abstract
Coccidiosis is an antagonistic poultry disease which negatively impacts animal welfare and productivity. The disease is caused by an obligate, intracellular protozoon known as Eimeria. Several Eimeria species known to infect chickens have been well documented. However, recent studies have elucidated the emergence of three novel genetic variants or operational taxonomic units (OTUs). The discovery of OTUx, OTUy and OTUz complicates the identification and diagnosis of coccidiosis. OTUs are clusters of unknown or uncultivated organisms that are grouped according to a similarity in DNA sequence to a set of specific gene markers. OTUs have been reported in the Earth's Southern Hemisphere, including Australia, Venezuela, India, Zambia, Uganda, Tanzania, China and Ghana. Elucidating their impact on the poultry industry is fundamental in preventing anticoccidial resistance and to access the potential of OTUs as vaccine candidates to provide cross-protection against similar Eimeria species. The identification of OTUs further decreases the risk of false negative coccidial diagnosis. Therefore, this article reviews the importance and risk imposed by OTUs, coupled with their prevalence and geographical distribution in chickens globally.
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15
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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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16
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Hinsu AT, Thakkar JR, Koringa PG, Vrba V, Jakhesara SJ, Psifidi A, Guitian J, Tomley FM, Rank DN, Raman M, Joshi CG, Blake DP. Illumina Next Generation Sequencing for the Analysis of Eimeria Populations in Commercial Broilers and Indigenous Chickens. Front Vet Sci 2018; 5:176. [PMID: 30105228 PMCID: PMC6077195 DOI: 10.3389/fvets.2018.00176] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/10/2018] [Indexed: 01/04/2023] Open
Abstract
Eimeria species parasites can cause the enteric disease coccidiosis, most notably in chickens where the economic and welfare implications are significant. Seven Eimeria species are recognized to infect chickens, although understanding of their regional occurrence, abundance, and population structure remains limited. Reports of Eimeria circulating in chickens across much of the southern hemisphere with cryptic genotypes and the capacity to escape current anticoccidial vaccines have revealed unexpected levels of complexity. Consequently, it is important to supplement validated species-specific molecular diagnostics with new genus-level tools. Here, we report the application of Illumina MiSeq deep sequencing to partial 18S rDNA amplicons generated using Eimeria genus-specific primers from chicken caecal contents collected in India. Commercial Cobb400 broiler and indigenous Kadaknath type chickens were sampled under field conditions after co-rearing (mixed type farms, n = 150 chickens for each) or separate rearing (single type farms, n = 150 each). Comparison of MiSeq results with established Internal Transcribed Spacer (ITS) and Sequence Characterised Amplified Region (SCAR) quantitative PCR assays suggest greater sensitivity for the MiSeq approach. The caecal-dwelling Eimeria tenella and E. necatrix dominated each sample set, although all seven species which infect chickens were detected. Two of the three cryptic Eimeria genotypes were detected including OTU-X and OTU-Y, the most northern report for the latter to date. Low levels of DNA representing other Eimeria species were detected, possibly representing farm-level contamination with non-replicating oocysts or Eimeria DNA, or false positives, indicating a requirement for additional validation. Next generation deep amplicon sequencing offers a valuable resource for future Eimeria studies.
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Affiliation(s)
- Ankit T Hinsu
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, India
| | - Jalpa R Thakkar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, India
| | - Vladimir Vrba
- Eimeria Pty Ltd, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Werribee, VIC, Australia
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, India
| | - Androniki Psifidi
- Department of Clinical Science and Services, Royal Veterinary College, North Mymms, Hertfordshire, United Kingdom.,The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Javier Guitian
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hertfordshire, United Kingdom
| | - Fiona M Tomley
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hertfordshire, United Kingdom
| | - Dharamsibhai N Rank
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, India
| | - Muthusamy Raman
- Department of Veterinary Parasitology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India.,Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, India
| | - Damer P Blake
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hertfordshire, United Kingdom
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17
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Thines M, Crous PW, Aime MC, Aoki T, Cai L, Hyde KD, Miller AN, Zhang N, Stadler M. Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon. IMA Fungus 2018; 9:177-183. [PMID: 30018878 PMCID: PMC6048572 DOI: 10.5598/imafungus.2018.09.01.11] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 11/08/2022] Open
Abstract
The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.
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Affiliation(s)
- Marco Thines
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60483 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Pedro W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, 59 Dudley Road, Foran Hall 201, New Brunswick, New Jersey 08901, USA
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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18
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Sharma D, Singh NK, Singh H, Joachim A, Rath SS, Blake DP. Discrimination, molecular characterisation and phylogenetic comparison of porcine Eimeria spp. in India. Vet Parasitol 2018; 255:43-48. [DOI: 10.1016/j.vetpar.2018.03.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 11/26/2022]
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19
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Cooper C, Keatley S, Northover A, Gofton AW, Brigg F, Lymbery AJ, Pallant L, Clode PL, Thompson RCA. Next generation sequencing reveals widespread trypanosome diversity and polyparasitism in marsupials from Western Australia. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2018; 7:58-67. [PMID: 29988778 PMCID: PMC6031965 DOI: 10.1016/j.ijppaw.2018.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/29/2017] [Accepted: 01/16/2018] [Indexed: 01/22/2023]
Abstract
In Western Australia a number of indigenous Trypanosoma spp. infect susceptible native marsupials, such as the woylie (Bettongia penicillata), brushtail possum (Trichosurus vulpecula), and chuditch (Dasyurus geoffroii). Two genotypes of Trypanosoma copemani (identified as G1 and G2) have been found in the woylie, and G2 has been implicated in the decline of this host species, making its presence of particular interest. Here we used targeted amplicon next generation sequencing (NGS) of the Trypanosoma 18S rDNA loci on 70 Trypanosoma-positive marsupial blood samples, to identify T. copemani genotypes and multiple Trypanosoma infections (polyparasitism) in woylies and cohabiting species in Western Australia. Polyparasitism with Trypanosoma spp. was found in 50% of the wildlife sampled, and within species diversity was high, with 85 zero-radius operational taxonomic units (ZOTUs) identified in nine putative parasite species. Trypanosoma copemani was assigned 17 ZOTUs and was identified in 80% of samples. The most abundant ZOTU isolated (63%) differed slightly from the published genotype of G1, and G2 was the second most abundant ZOTU (14%). Trypanosome diversity was significantly greater in woylies than in brushtail possums, and parasite community composition also differed significantly between these host species. One novel Trypanosoma spp. genotype (Trypanosoma sp. ANU2) was found in 20% of samples. A species of Crithidia was detected in a woylie, and two avian trypanosomes (Trypanosoma avium and Trypanosoma sp. AAT) were identified in woylies for the first time. Extensive trypanosome diversity and polyparasitism in south Western Australia. A significant difference between trypanosomes infecting woylies and brushtail possums. Evidence that the current species-level taxonomy of Australian trypanosomes may need revision.
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Affiliation(s)
- Crystal Cooper
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Stirling HWY, Crawley, WA 6009, Australia
| | - Sarah Keatley
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Amy Northover
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Alex W Gofton
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Frances Brigg
- State Agriculture and Biotechnology Institute, School of Veterinary and Life Sciences, Murdoch University, WA 6150, Australia
| | - Alan J Lymbery
- Fish Health Unit, School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia
| | - Louise Pallant
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Peta L Clode
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Stirling HWY, Crawley, WA 6009, Australia
| | - R C Andrew Thompson
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
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20
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Moreno Y, Moreno-Mesonero L, Amorós I, Pérez R, Morillo JA, Alonso JL. Multiple identification of most important waterborne protozoa in surface water used for irrigation purposes by 18S rRNA amplicon-based metagenomics. Int J Hyg Environ Health 2017; 221:102-111. [PMID: 29066287 DOI: 10.1016/j.ijheh.2017.10.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/04/2017] [Accepted: 10/18/2017] [Indexed: 10/18/2022]
Abstract
Understanding waterborne protozoan parasites (WPPs) diversity has important implications in public health. In this study, we evaluated a NGS-based method as a detection approach to identify simultaneously most important WPPs using 18S rRNA high-throughput sequencing. A set of primers to target the V4 18S rRNA region of WPPs such as Cryptosporidium spp., Giardia sp., Blastocystis sp., Entamoeba spp, Toxoplasma sp. and free-living amoebae (FLA) was designed. In order to optimize PCR conditions before sequencing, both a mock community with a defined composition of representative WPPs and a real water sample inoculated with specific WPPs DNA were prepared. Using the method proposed in this study, we have detected the presence of Giardia intestinalis, Acanthamoeba castellanii, Toxoplasma gondii, Entamoeba histolytica and Blastocystis sp. at species level in real irrigation water samples. Our results showed that untreated surface irrigation water in open fields can provide an important source of WPPs. Therefore, the methodology proposed in this study can establish a basis for an accurate and effective diagnostic of WPPs to provide a better understanding of the risk associated to irrigation water.
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Affiliation(s)
- Y Moreno
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - L Moreno-Mesonero
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - I Amorós
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - R Pérez
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - J A Morillo
- Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas (EEZA-CSIC), Carretera de Sacramento s/n, La Cañada, Almería, Spain
| | - J L Alonso
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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21
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Barbosa AD, Gofton AW, Paparini A, Codello A, Greay T, Gillett A, Warren K, Irwin P, Ryan U. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS). PLoS One 2017; 12:e0181279. [PMID: 28704541 PMCID: PMC5509321 DOI: 10.1371/journal.pone.0181279] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/28/2017] [Indexed: 01/19/2023] Open
Abstract
Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus), particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS)-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani) removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2–39.8%) were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2–39.8%), T. gilletti (25%, 95% CI: 18.7–32.3%), T. copemani (27.4%, 95% CI: 20.8–34.8%) and T. vegrandis (10.1%, 95% CI: 6.0–15.7%). Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0–3.3%), and a novel species (Trypanosoma sp. AB-2017) was identified at a prevalence of 4.8% (95% CI: 2.1–9.2%). Mixed infections with up to five species were present in 27.4% (95% CI: 21–35%) of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2–9%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS) within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides new insights on the natural genetic diversity of Trypanosoma communities infecting koalas and constitutes a benchmark for future clinical and epidemiological studies required to quantify the contribution of trypanosome infections on koala survival rates.
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Affiliation(s)
- Amanda D. Barbosa
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Distrito Federal, Brazil
- * E-mail:
| | - Alexander W. Gofton
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Andrea Paparini
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Annachiara Codello
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Telleasha Greay
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Amber Gillett
- Australia Zoo Wildlife Hospital, Beerwah, Queensland, Australia
- School of Veterinary Science, University of Queensland, Saint Lucia, Australia
| | - Kristin Warren
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Peter Irwin
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Una Ryan
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
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Vermeulen ET, Power ML, Nipperess DA, Beveridge I, Eldridge MDB. Biodiversity of parasite assemblages in the genus Petrogale and its relation to the phylogeny and biogeography of their hosts. AUST J ZOOL 2016. [DOI: 10.1071/zo16023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Parasites form an integral part of overall biodiversity although they are often overlooked in conservation management, where emphasis is primarily directed towards the host. Parasites are often highly specialised to particular hosts, and thus may be just as threatened as the host they inhabit. For many of Australia’s wildlife species, little is known about their associated parasite communities. To begin to address this knowledge gap, we documented the parasite fauna described in the genetically diverse marsupial genus Petrogale, which contains seven species of conservation concern. The literature evaluation showed parasites of Petrogale to be highly diverse, with 17 species of protozoa, 8 species of cestodes, 102 species of nematodes and 30 species of ectoparasites identified in 16 of 17 Petrogale host species. A comparison of the parasite communities amongst Petrogale host species indicated a highly significant correlation between the parasite community similarity, and the phylogeny (P = 0.008) and biogeography (P = 0.0001) of their Petrogale hosts, suggesting high host specificity within their associated parasite assemblages. Five Petrogale species have established species recovery programs and their parasite communities should also be considered threatened, and management of parasite diversity required as part of these conservation programs.
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