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Coba-Males MA, Medrano-Vizcaíno P, Enríquez S, Brito-Zapata D, Martin-Solano S, Ocaña-Mayorga S, Carrillo-Bilbao GA, Narváez W, Salas JA, Arrivillaga-Henríquez J, González-Suárez M, Poveda A. From roads to biobanks: Roadkill animals as a valuable source of genetic data. PLoS One 2023; 18:e0290836. [PMID: 38060478 PMCID: PMC10703236 DOI: 10.1371/journal.pone.0290836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/15/2023] [Indexed: 12/18/2023] Open
Abstract
To protect biodiversity we must understand its structure and composition including the bacteria and microparasites associated with wildlife, which may pose risks to human health. However, acquiring this knowledge often presents challenges, particularly in areas of high biodiversity where there are many undescribed and poorly studied species and funding resources can be limited. A solution to fill this knowledge gap is sampling roadkill (animals that die on roads as a result of collisions with circulating vehicles). These specimens can help characterize local wildlife and their associated parasites with fewer ethical and logistical challenges compared to traditional specimen collection. Here we test this approach by analyzing 817 tissue samples obtained from 590 roadkill vertebrate specimens (Amphibia, Reptilia, Aves and Mammalia) collected in roads within the Tropical Andes of Ecuador. First, we tested if the quantity and quality of recovered DNA varied across roadkill specimens collected at different times since death, exploring if decomposition affected the potential to identify vertebrate species and associated microorganisms. Second, we compared DNA stability across taxa and tissues to identify potential limitations and offer recommendations for future work. Finally, we illustrate how these samples can aid in taxonomic identification and parasite detection. Our study shows that sampling roadkill can help study biodiversity. DNA was recovered and amplified (allowing species identification and parasite detection) from roadkill even 120 hours after death, although risk of degradation increased overtime. DNA was extracted from all vertebrate classes but in smaller quantities and with lower quality from amphibians. We recommend sampling liver if possible as it produced the highest amounts of DNA (muscle produced the lowest). Additional testing of this approach in areas with different environmental and traffic conditions is needed, but our results show that sampling roadkill specimens can help detect and potentially monitor biodiversity and could be a valuable approach to create biobanks and preserve genetic data.
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Affiliation(s)
- Manuel Alejandro Coba-Males
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Zoonosis (CIZ), Facultad de Ciencias Químicas (FCQ), Universidad Central del Ecuador, Quito, Ecuador
| | - Pablo Medrano-Vizcaíno
- Ecology and Evolutionary Biology, School of Biological Sciences, University of Reading, Reading, United Kingdom
- Universidad Regional Amazónica IKIAM, Grupo de Investigación Población y Ambiente, Tena, Ecuador
- Red Ecuatoriana para el Monitoreo de Fauna Atropellada-REMFA, Quito, Ecuador
| | - Sandra Enríquez
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Zoonosis (CIZ), Facultad de Ciencias Químicas (FCQ), Universidad Central del Ecuador, Quito, Ecuador
| | - David Brito-Zapata
- Red Ecuatoriana para el Monitoreo de Fauna Atropellada-REMFA, Quito, Ecuador
- Instituto iBIOTROP, Museo de Zoología & Laboratorio de Zoología Terrestre, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sarah Martin-Solano
- Grupo de Investigación en Sanidad Animal y Humana (GISAH), Carrera Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas—ESPE, Sangolquí, Ecuador
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Gabriel Alberto Carrillo-Bilbao
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Zoonosis (CIZ), Facultad de Ciencias Químicas (FCQ), Universidad Central del Ecuador, Quito, Ecuador
| | - Wilmer Narváez
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Zoonosis (CIZ), Facultad de Ciencias Químicas (FCQ), Universidad Central del Ecuador, Quito, Ecuador
| | - Jaime Antonio Salas
- Facultad de Ciencias Naturales, Carrera de Biología, Universidad de Guayaquil, Guayaquil, Ecuador
| | - Jazzmín Arrivillaga-Henríquez
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Zoonosis (CIZ), Facultad de Ciencias Químicas (FCQ), Universidad Central del Ecuador, Quito, Ecuador
| | - Manuela González-Suárez
- Ecology and Evolutionary Biology, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Ana Poveda
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Zoonosis (CIZ), Facultad de Ciencias Químicas (FCQ), Universidad Central del Ecuador, Quito, Ecuador
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First Molecular Identification of Trypanosomes and Absence of Babesia sp. DNA in Faeces of Non-Human Primates in the Ecuadorian Amazon. Pathogens 2022; 11:pathogens11121490. [PMID: 36558823 PMCID: PMC9785249 DOI: 10.3390/pathogens11121490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/20/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Trypanosomes are a group of pathogens distributed in the continents of Africa, America, Asia and Europe, and they affect all vertebrates including the neotropical primate group. Information about the trypanosome's diversity, phylogeny, ecology and pathology in non-human primates (NHPs) from the neotropical region is scarce. The objective of the study was to identify Trypanosoma and Babesia molecularly in NHPs under the phylogenetic species concept. We extracted DNA from a total of 76 faecal samples collected between 2019 and 2021, from a total of 11 non-human primate species of which 46 are from captive NHPs and 30 are free-living NHPs in the Western Amazon region of Ecuador. We did not detect DNA of Babesia sp. by polymerase chain reaction test in any of the faecal samples. However, the nested-PCR-based method revealed Trypanosoma parasites by ITS gene amplification in two faecal samples; one for the species Leontocebus lagonotus (from the captive population) and a second one for Cebus albifrons (from the free-ranging population). Maximum parsimony and likelihood methods with the Kimura2+G+I model inferred the evolutionary history of the two records, which showed an evolutionary relationship with the genus Trypanosoma. Two sequences are monophyletic with Trypanosoma. However, the number of sequences available in GenBank for their species identification is limited. The two samples present different molecular identifications and evolutionary origins in the tree topology. We are most likely referring to two different species, and two different localities of infection. We suggest that health management protocols should be implemented to prevent the transmission of blood-borne pathogens such as Trypanosoma sp. among captive populations. In addition, these protocols also protect the personnel of wildlife rehabilitation centers working in close proximity to NHPs and vice versa.
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Carrillo-Bilbao G, Martin-Solano S, Saegerman C. Zoonotic Blood-Borne Pathogens in Non-Human Primates in the Neotropical Region: A Systematic Review. Pathogens 2021; 10:1009. [PMID: 34451473 PMCID: PMC8400055 DOI: 10.3390/pathogens10081009] [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: 07/04/2021] [Revised: 07/29/2021] [Accepted: 08/05/2021] [Indexed: 01/17/2023] Open
Abstract
Background: Understanding which non-human primates (NHPs) act as a wild reservoir for blood-borne pathogens will allow us to better understand the ecology of diseases and the role of NHPs in the emergence of human diseases in Ecuador, a small country in South America that lacks information on most of these pathogens. Methods and principal findings: A systematic review was carried out using PRISMA guidelines from 1927 until 2019 about blood-borne pathogens present in NHPs of the Neotropical region (i.e., South America and Middle America). Results: A total of 127 publications were found in several databases. We found in 25 genera (132 species) of NHPs a total of 56 blood-borne pathogens in 197 records where Protozoa has the highest number of records in neotropical NHPs (n = 128) compared to bacteria (n = 12) and viruses (n = 57). Plasmodium brasilianum and Trypanosoma cruzi are the most recorded protozoa in NHP. The neotropical primate genus with the highest number of blood-borne pathogens recorded is Alouatta sp. (n = 32). The use of non-invasive samples for neotropical NHPs remains poor in a group where several species are endangered or threatened. A combination of serological and molecular techniques is common when detecting blood-borne pathogens. Socioecological and ecological risk factors facilitate the transmission of these parasites. Finally, a large number of countries remain unsurveyed, such as Ecuador, which can be of public health importance. Conclusions and significance: NHPs are potential reservoirs of a large number of blood-borne pathogens. In Ecuador, research activities should be focused on bacteria and viruses, where there is a gap of information for neotropical NHPs, in order to implement surveillance programs with regular and effective monitoring protocols adapted to NHPs.
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Affiliation(s)
- Gabriel Carrillo-Bilbao
- Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULiège), Fundamental and Applied Research for Animal and Health (FARAH) Center, Department of Infections and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium;
- Facultad de Filosofía y Letras y Ciencias de la Educación, Universidad Central del Ecuador, 170521 Quito, Ecuador
- Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, 170521 Quito, Ecuador;
| | - Sarah Martin-Solano
- Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, 170521 Quito, Ecuador;
- Grupo de Investigación en Sanidad Animal y Humana (GISAH), Carrera Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas—ESPE, 171103 Sangolquí, Ecuador
| | - Claude Saegerman
- Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULiège), Fundamental and Applied Research for Animal and Health (FARAH) Center, Department of Infections and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium;
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de Groot N, Stanbury K, de Vos-Rouweler AJM, de Groot NG, Poirier N, Blancho G, de Luna C, Doxiadis GGM, Bontrop RE. A quick and robust MHC typing method for free-ranging and captive primate species. Immunogenetics 2017; 69:231-240. [PMID: 28084496 PMCID: PMC5350218 DOI: 10.1007/s00251-016-0968-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/27/2016] [Indexed: 12/21/2022]
Abstract
Gene products of the major histocompatibility complex (MHC) of human and non-human primates play a crucial role in adaptive immunity, and most of the relevant genes not only show a high degree of variability (polymorphism) but also copy number variation (CNV) is observed. Due to this diversity, MHC proteins influence the capability of individuals to cope with various pathogens. MHC and/or MHC-linked gene products such as odorant receptor genes are thought to influence mate choice and reproductive success. Therefore, MHC typing of wild and captive primate populations is considered to be useful in conservation biology, which is, however, often hampered by the need of invasive and time-consuming methods. All intact Mhc-DRB genes in primates appear to possess a complex and highly divergent microsatellite, DRB-STR. A panel of 154 pedigreed olive baboons (Papio anubis) was examined for their DRB content by DRB-STR analysis of genomic DNA. Using the same methodology on DNA of feces samples, DRB variability of a silvery gibbon population (Hylobates moloch) (N = 24), an endangered species, could successfully be studied. In both species, length determination of the DRB-STR resulted in the definition of unique genotyping patterns that appeared to be specific for a certain chromosome. Moreover, the different STR lengths were shown to segregate with the allelic variation of the respective gene. The results obtained expand data gained previously on DRB-STR typing in macaques, great apes, and humans and strengthen the conclusion that this protocol is applicable in molecular ecology, conservation biology, and colony management, especially of endangered primate species.
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Affiliation(s)
- N de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - K Stanbury
- Writtle College, Essex University, Lordship Road, Writtle, Chelmsford, Essex, CM1 3RR, UK
| | - A J M de Vos-Rouweler
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - N G de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - N Poirier
- Institut National de la Sante et de la Recherche Medicale (INSERM) UMR1064, Institut de Transplantation-Urologie-Nephrologie (ITUN), 30 Bd Jean Monnet, 44093, Nantes, France
| | - G Blancho
- Institut National de la Sante et de la Recherche Medicale (INSERM) UMR1064, Institut de Transplantation-Urologie-Nephrologie (ITUN), 30 Bd Jean Monnet, 44093, Nantes, France
| | - C de Luna
- Writtle College, Essex University, Lordship Road, Writtle, Chelmsford, Essex, CM1 3RR, UK
| | - G G M Doxiadis
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.
| | - R E Bontrop
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Zarzoso-Lacoste D, Corse E, Vidal E. Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances. Mol Ecol Resour 2012; 13:117-27. [PMID: 23134438 DOI: 10.1111/1755-0998.12029] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 09/16/2012] [Accepted: 09/20/2012] [Indexed: 11/28/2022]
Abstract
While the morphological identification of prey remains in predators' faeces is the most commonly used method to study trophic interactions, many studies indicate that this method does not detect all consumed prey. Polymerase chain reaction-based methods are increasingly used to detect prey DNA in the predator food bolus and have proven efficient, delivering highly accurate results. When studying complex diet samples, the extraction of total DNA is a critical step, as polymerase chain reaction (PCR) inhibitors may be co-extracted. Another critical step involves a careful selection of suitable group-specific primer sets that should only amplify DNA from the targeted prey taxon. In this study, the food boluses of five Rattus rattus and seven Rattus exulans were analysed using both morphological and molecular methods. We tested a panel of 31 PCR primer pairs targeting bird, invertebrate and plant sequences; four of them were selected to be used as group-specific primer pairs in PCR protocols. The performances of four DNA extraction protocols (QIAamp(®) DNA stool mini kit, DNeasy(®) mericon food kit and two of cetyltrimethylammonium bromide-based methods) were compared using four variables: DNA concentration, A(260) /A(280) absorbance ratio, food compartment analysed (stomach or faecal contents) and total number of prey-specific PCR amplification per sample. Our results clearly indicate that the A(260) /A(280) absorbance ratio, which varies between extraction protocols, is positively correlated to the number of PCR amplifications of each prey taxon. We recommend using the DNeasy(®) mericon food kit (QIAGEN), which yielded results very similar to those achieved with the morphological approach.
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Affiliation(s)
- Diane Zarzoso-Lacoste
- Aix-Marseille Université, CNRS, IRD, IMBE - UMR 7263, Aix-en-Provence Cedex 04, France.
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Martinelli AB, DE Moraes-Barros N, Alvarenga CS, Chaves PB, Santos LAD, Fagundes V. A PCR-RFLP assay for gender assignment in the three-toed sloths (Bradypus, Pilosa, Bradypodidae). Mol Ecol Resour 2011; 10:732-4. [PMID: 21565080 DOI: 10.1111/j.1755-0998.2009.02820.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The three-toed sloths (Bradypus) are slow-moving arboreal neotropical mammals. Understanding demographic variables (such as sex ratio) of populations is a key for conservation purposes. Nevertheless, gender assignment of Bradypus is particularly challenging because of the lack of sexual dimorphism in infants and in adults, particularly B. torquatus, the most endangered of the three-toed sloths, in which sex is attributed by visual observation of the reproductively active males. Here, we standardized a method for sexing Bradypus individuals using PCR-RFLP of sex-linked genes ZFX/ZFY. This assay was validated with known-gender animals and proved accurate to assign gender on three Bradypus species.
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Affiliation(s)
- Arturo B Martinelli
- Laboratório de Genética Animal (LGA), Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo, Av. Fernando Ferrari, 514, Vitória, Espírito Santo, Brazil, 29075-910 Laboratório de Biologia Evolutiva e Conservação de Vertebrados (Labec), Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão. 277, São Paulo, São Paulo, Brazil, 05508-090
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