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Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review. Genes (Basel) 2023; 14:genes14020303. [PMID: 36833230 PMCID: PMC9957072 DOI: 10.3390/genes14020303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/25/2023] Open
Abstract
Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.
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Mas-Coma S, Valero MA, Bargues MD. Human and Animal Fascioliasis: Origins and Worldwide Evolving Scenario. Clin Microbiol Rev 2022; 35:e0008819. [PMID: 36468877 PMCID: PMC9769525 DOI: 10.1128/cmr.00088-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fascioliasis is a plant- and waterborne zoonotic parasitic disease caused by two trematode species: (i) Fasciola hepatica in Europe, Asia, Africa, the Americas, and Oceania and (ii) F. gigantica, which is restricted to Africa and Asia. Fasciolid liver flukes infect mainly herbivores as ruminants, equids, and camelids but also omnivore mammals as humans and swine and are transmitted by freshwater Lymnaeidae snail vectors. Two phases may be distinguished in fasciolid evolution. The long predomestication period includes the F. gigantica origin in east-southern Africa around the mid-Miocene, the F. hepatica origin in the Near-Middle East of Asia around the latest Miocene to Early Pliocene, and their subsequent local spread. The short postdomestication period includes the worldwide spread by human-guided movements of animals in the last 12,000 years and the more recent transoceanic anthropogenic introductions of F. hepatica into the Americas and Oceania and of F. gigantica into several large islands of the Pacific with ships transporting livestock in the last 500 years. The routes and chronology of the spreading waves followed by both fasciolids into the five continents are redefined on the basis of recently generated knowledge of human-guided movements of domesticated hosts. No local, zonal, or regional situation showing disagreement with historical records was found, although in a few world zones the available knowledge is still insufficient. The anthropogenically accelerated evolution of fasciolids allows us to call them "peridomestic endoparasites." The multidisciplinary implications for crucial aspects of the disease should therefore lead the present baseline update to be taken into account in future research studies.
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Affiliation(s)
- Santiago Mas-Coma
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - M. Adela Valero
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - M. Dolores Bargues
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
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3
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Ummarino A, Caputo M, Tucci FA, Pezzicoli G, Piepoli A, Gentile A, Latiano T, Panza A, Calà N, Ceglia AP, Pistoio G, Troiano V, Pucatti M, Latiano A, Andriulli A, Tucci A, Palmieri O. A PCR-based method for the diagnosis of Enterobius vermicularis in stool samples, specifically designed for clinical application. Front Microbiol 2022; 13:1028988. [PMID: 36466657 PMCID: PMC9712443 DOI: 10.3389/fmicb.2022.1028988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/31/2022] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Enterobius vermicularis (E. vermicularis) is a nematode that infects up to 200 million people worldwide, despite effective medications being available. Conventional diagnostic tests are hindered by low sensitivity and poor patient compliance. Furthermore, no biomolecular techniques are available for clinical application. The aim of this study was to develop a procedure specifically designed for clinical application to detect E. vermicularis by means of PCR. MATERIALS AND METHODS Two subject groups were taken into account: a group of 27 infected patients and a control group of 27 healthy subjects. A nested-PCR was performed on fecal samples to detect E. vermicularis. Due to the intrinsic difficulties of the fecal matrix, several countermeasures were adopted to ensure the efficient performance of the method: (a) a large amount of feces for the extraction process (20 g instead of 200 mg); (b) a combination of chemical and physical treatments to grind the fecal matrix; (c) an additional purification process for the negative samples after the first nested-PCR; and (d) the selection of a very specific target region for the PCR. RESULTS Due to the lack of overlap with other organisms, a sequence of the 5S ribosomal DNA (rDNA) spacer region including the tract SL1 was chosen to design appropriate external and internal primers. The first nested-PCR detected E.vermicularis in 19/27 samples from infected patients. After further purification, 5/8 of the negative samples resulted positive at the second PCR. Conversely, all the samples from healthy controls resulted negative to both PCRs. Sensitivity and specificity of the method were, respectively, 88.9% and 100%. CONCLUSION The results prove the high diagnostic accuracy of the proposed method, addressing and overcoming the challenges posed by both conventional tests and PCR-based approaches. Therefore, the method can be proposed for clinical application.
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Affiliation(s)
- Aldo Ummarino
- Agorà Biomedical Sciences, Etromapmacs Pole, Lesina (FG), Italy
| | - Michele Caputo
- Agorà Biomedical Sciences, Etromapmacs Pole, Lesina (FG), Italy
| | | | | | - Ada Piepoli
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Annamaria Gentile
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Tiziana Latiano
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Anna Panza
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Nicholas Calà
- Agorà Biomedical Sciences, Etromapmacs Pole, Lesina (FG), Italy
| | | | | | | | - Michela Pucatti
- Agorà Biomedical Sciences, Etromapmacs Pole, Lesina (FG), Italy
| | - Anna Latiano
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Angelo Andriulli
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
| | - Antonio Tucci
- Agorà Biomedical Sciences, Etromapmacs Pole, Lesina (FG), Italy
| | - Orazio Palmieri
- Gastroenterology Unit, Fondazione IRCCS “Casa Sollievo Della Sofferenza” Hospital, Viale Cappuccini, Italy
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Pessanha TS, Pires M, Iñiguez AM. Molecular detection of blood meal source up to three months since the last meal: Experimental starvation resistance in triatomines. Acta Trop 2022; 232:106507. [PMID: 35568070 DOI: 10.1016/j.actatropica.2022.106507] [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: 12/16/2021] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/28/2022]
Abstract
The identification of Blood Meal Source (BMS) in hematophagous vectors contributes to a better understanding of the ecology of hemoparasite transmission. Those insects can endure long periods without feeding, waiting for a favorable setting. Although this represents an important behavior observed in those groups, such as triatomines, little is known about how time can affect BMS detection, especially considering extended periods. To comprehend to which extent this behavioral phenomenon can impact molecular detection, we submitted two groups of Rhodnius robustus to increasing periods of starvation under experimental conditions. It was possible to recover the BMS until the 12th week of the starvation process. Nymphs were more resistant to prolonged periods of starvation (up to more than 189 days) than adults (maximum of 137 days), with no significant difference between their weights after being fed. The study brought new insights to the understanding of Trypanosoma cruzi transmission by R. robustus in the nature, with a temporal perspective.
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Affiliation(s)
- Thaila Santos Pessanha
- Laboratorio de Biologia de Tripanosomatideos, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil 4365, 21040-360, Rio de Janeiro, RJ, Brazil
| | - Marcelo Pires
- Laboratorio de Biologia de Tripanosomatideos, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil 4365, 21040-360, Rio de Janeiro, RJ, Brazil
| | - Alena Mayo Iñiguez
- Laboratorio de Biologia de Tripanosomatideos, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil 4365, 21040-360, Rio de Janeiro, RJ, Brazil.
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Oh CS, Seo M, Lee HJ, Kim MJ, Lim DS, Shin DH. Genetic Analysis of Ancient Clonorchis sinensis Eggs Attained from Goryeong Mummy of Joseon Dynasty Period. J Parasitol 2022; 108:70-78. [DOI: 10.1645/21-49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Chang Seok Oh
- Department of Mortuary Science, College of Bio-convergence, Eulji University, 553, Sanseong-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13135, Korea
| | - Min Seo
- Department of Parasitology, Dankook University College of Medicine, 119, Dandae-ro, Dongnam-gu, Cheonan-si, Chungcheongnam-do 31116, Korea
| | - Hye Jin Lee
- Ministry of National Defense Agency for KIA Recovery & Identification, 250, Hyeonchung-ro, Dongjak-gu, Seoul 06984, Korea
| | - Myeung Ju Kim
- Department of Anatomy, Dankook University College of Medicine, 119, Dandae-ro, Dongnam-gu, Cheonan-si, Chungcheongnam-do 31116, Korea
| | - Do-Seon Lim
- Department of Dental Hygiene, College of Health Science, Eulji University, 553, Sanseong-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13135, Korea
| | - Dong Hoon Shin
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine, 103, Daehak-ro, Chongno-gu, Seoul 03080, Korea
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Cardia DFF, Bertini RJ, Camossi LG, Richini-Pereira VB, Losnak DO, Francischini H, Dentzien-Dias P. Paleoparasitological analysis of a coprolite assigned to a carnivoran mammal from the Upper Pleistocene Touro Passo Formation, Rio Grande do Sul, Brazil. AN ACAD BRAS CIENC 2021; 93:e20190876. [PMID: 34105692 DOI: 10.1590/0001-3765202120190876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/06/2020] [Indexed: 11/21/2022] Open
Abstract
A paleoparasitological analysis was carried out on a large coprolite assigned to a carnivoran mammal, recovered from the Municipality of Uruguaiana, in the western region of the State of Rio Grande do Sul, Brazil, where the Upper Pleistocene Touro Passo Formation crops out. For this, an individual sample was extracted from the specimen using an electric drill, dissociated with 10% hydrochloric acid solution, washed with distilled water, and sifted through a 500 mesh Tyler sieve. After laboratory processing, the sediment retained on the sieve was mixed with glycerin and examined by optical microscopy, which revealed the presence of 14 protozoan oocysts and three nematode eggs. The morphological characteristics of the oocysts (i.e., spherical shape, thick-walled, internal zygote apparently at the beginning of sporulation, as well as their size) and of the eggs (i.e., ovoidal shape, rounded ends, smooth surface, thin-shelled, embryo in their interior, along with their morphometry) suggest that these specimens belong respectively to the orders Eucoccidiorida and Strongylida (Family Ancylostomatidae) represented by several parasitic species of the alimentary tract of modern carnivore. This is the first record of paleoparasites discovered in a vertebrate host from the Touro Passo Formation.
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Affiliation(s)
- Daniel F F Cardia
- UNESP, Núcleo de Evolução e Paleobiologia de Vertebrados, Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Campus Rio Claro, Av. 24 A, 1515, 13506-900 Rio Claro, SP, Brazil
| | - Reinaldo J Bertini
- UNESP, Núcleo de Evolução e Paleobiologia de Vertebrados, Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Campus Rio Claro, Av. 24 A, 1515, 13506-900 Rio Claro, SP, Brazil
| | - Lucilene G Camossi
- UNESP, Núcleo de Evolução e Paleobiologia de Vertebrados, Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Campus Rio Claro, Av. 24 A, 1515, 13506-900 Rio Claro, SP, Brazil
| | - Virgínia B Richini-Pereira
- Instituto Adolfo Lutz, Núcleo de Ciências Biomédicas, CLR II, R. Rubens Arruda, Q6, 17015-110 Bauru, SP, Brazil
| | - Debora O Losnak
- Instituto Adolfo Lutz, Núcleo de Ciências Biomédicas, CLR II, R. Rubens Arruda, Q6, 17015-110 Bauru, SP, Brazil
| | - Heitor Francischini
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Geociências, Instituto de Geociências, UFRGS, Av. Bento Gonçalves, 9500, 91540-000 Porto Alegre, RS, Brazil
| | - Paula Dentzien-Dias
- Universidade Federal do Rio Grande (FURG), Laboratório de Geologia e Paleontologia, Instituto de Oceanografia, Av. Itália, Km 8, 96201-900 Rio Grande, RS, Brazil
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Kévin R, Nicolas C, Elsa P, Paolo L, Pasquino P, Raffaella B, Matthieu LB. Gastrointestinal parasite burden in 4th-5th c. CE Florence highlighted by microscopy and paleogenetics. INFECTION GENETICS AND EVOLUTION 2021; 90:104713. [PMID: 33429070 DOI: 10.1016/j.meegid.2021.104713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/25/2020] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
The study of ancient parasites, named paleoparasitology, traditionally focused on microscopic eggs disseminated in past environments and archaeological structures by humans and other animals infested by gastrointestinal parasites. Since the development of paleogenetics in the early 1980s, few paleoparasitological studies have been based on the ancient DNA (aDNA) of parasites, although such studies have clearly proven their utility and reliability. In this paper, we describe our integrative approach for the paleoparasitological study of an ancient population from Florence in Italy, dated to the 4th-5th c. CE. The first stage consisted in the study of sediment samples from the pelvic area of 18 individuals under light microscopy. This allowed us to detect Ascarid-type eggs belonging very probably to the human-infesting roundworm Ascaris lumbricoides. Ten subsamples were selected corresponding to five individuals, and we extracted their whole DNA following sediment aDNA protocols. A targeted approach allowed us to detect two nematodes and one trematode aDNA fragments, namely Ascaris sp., Trichuris trichiura, and Dicrocoelium dendriticum. Among the five individuals tested for microscopic eggs and aDNA, three of them showed the remains of eggs (only Ascarid-type), but all of them tested positive to the presence of at least one parasite aDNA. Microscopic diagnosis first guided our research for the selection of promising samples while the targeted aDNA approach significantly improved our knowledge in terms of parasitic diversity and frequency in this population subgroup. These results enabled us to discuss the possible impact of latent parasitism in this past population at the time of an epidemic, as suggested in Florence. In particular, the singular case of D. dendriticum detection is discussed in light of the present-day scarcity of genuine human infections. Nevertheless, actual infections are known in the paleoparasitological record, and food habits may have led to false parasitism in this historical context. aDNA leaching from overlying strata may also explain this detection. This study strongly pleads for a systematic integrative approach combining microscopy and aDNA in paleoparasitology.
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Affiliation(s)
- Roche Kévin
- Université Bordeaux Montaigne, CNRS UMR 5607 Ausonius, France; Université de Bourgogne Franche-Comté, CNRS UMR 6249 Chrono-Environnement, France.
| | - Capelli Nicolas
- Université de Bourgogne Franche-Comté, CNRS UMR 6249 Chrono-Environnement, France
| | - Pacciani Elsa
- Soprintendenza Archeologia, Belle Arti e Paesaggio of Firenze, Pistoia and Prato, Italy
| | | | - Pallecchi Pasquino
- Soprintendenza Archeologia, Belle Arti e Paesaggio of Firenze, Pistoia and Prato, Italy
| | - Bianucci Raffaella
- Legal Medicine Section, Department of Public Health and Paediatric Sciences, University of Turin, Italy; Warwick Medical School, Biomedical Sciences, University of Warwick, United Kingdom; ADES (UMR 7268), Laboratoire d'Anthropologie bio-culturelle, Droit, Ethique & Santé (Adés), Faculté de Médecine de Marseille, France
| | - Le Bailly Matthieu
- Université de Bourgogne Franche-Comté, CNRS UMR 6249 Chrono-Environnement, France.
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8
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Sabin S, Yeh HY, Pluskowski A, Clamer C, Mitchell PD, Bos KI. Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190576. [PMID: 33012229 PMCID: PMC7702797 DOI: 10.1098/rstb.2019.0576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ancient latrine sediments, which contain the concentrated collective biological waste of past whole human communities, have the potential to be excellent proxies for human gastrointestinal health on the population level. A rich body of literature explores their use to detect the presence of gut-associated eukaryotic parasites through microscopy, immunoassays and genetics. Despite this interest, a lack of studies have explored the whole genetic content of ancient latrine sediments through consideration not only of gut-associated parasites, but also of core community gut microbiome signals that remain from the group that used the latrine. Here, we present a metagenomic analysis of bulk sediment from medieval latrines in Riga (Latvia) and Jerusalem. Our analyses reveal survival of microbial DNA representative of intestinal flora as well as numerous parasites. These data are compared against parasite taxon identifications obtained via microscopy and ELISA techniques. Together, these findings provide a first glimpse into the rich prokaryotic and eukaryotic intestinal flora of pre-industrial agricultural populations, which may give a better context for interpreting the health of modern microbiomes. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- Susanna Sabin
- Max Planck Institute for the Science of Human History, Jena, Germany.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, 48 Nanyang Avenue, Singapore 639818, Singapore
| | - Aleks Pluskowski
- Department of Archaeology, University of Reading, Whiteknights, Reading RG6 6AB, UK
| | - Christa Clamer
- École Biblique de Jérusalem, PO Box 19053, IL9119001, Jerusalem
| | - Piers D Mitchell
- Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge CB2 1QH, UK
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
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9
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Flammer PG, Smith AL. Intestinal helminths as a biomolecular complex in archaeological research. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190570. [PMID: 33012232 DOI: 10.1098/rstb.2019.0570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enteric helminths are common parasites in many parts of the world and in the past were much more widespread both geographically and socially. Many enteric helminths are relatively long-lived in the human host, often benign or of low pathogenicity while producing large numbers of environmentally resistant eggs voided in the faeces or found associated with individual remains (skeletons and mummies). The combination of helminth characters offers opportunities to the field of historical pathogen research that are quite different to that of some of the more intensively studied high impact pathogens. Historically, a wealth of studies has employed microscopic techniques to diagnose infection using the morphology of the helminth eggs. More recently, various ancient DNA (aDNA) approaches have been applied in the archaeoparasitological context and these are revolutionizing the field, allowing much more specific diagnosis as well as interrogating the epidemiology of helminths. These advances have enhanced the potential for the field to provide unique information on past populations including using diseases to consider many aspects of life (e.g. sanitation, hygiene, diet, culinary practices and other aspects of society). Here, we consider the impact of helminth archaeoparasitology and more specifically the impact and potential for application of aDNA technologies as a part of the archaeologists' toolkit. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
| | - Adrian L Smith
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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10
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Guedes L, Borba VH, Camacho M, Neto J, Dias O, Iñiguez AM. African helminth infection out of Africa: Paleoparasitological and paleogenetic investigations in Pretos Novos cemetery, Rio de Janeiro, Brazil (1769-1830). Acta Trop 2020; 205:105399. [PMID: 32081659 DOI: 10.1016/j.actatropica.2020.105399] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023]
Abstract
Pretos Novos cemetery (PNC), Rio de Janeiro, Brazil (1769-1830) was created exclusively to bury enslaved Africans who died upon arrival at the city or before being sold in the slave market. The PNC site may be unique in the Americas in allowing the study of African parasite infections acquired in Africa. We aimed to identify parasites infecting PNC individuals through paleoparasitological and paleogenetic analyses. The bodies had been dismembered, placed in mass graves, and burned, and most human remains collected from the site are highly fragmented and show extensive degradation. Sacrum and pelvic sediments were collected from five individuals along with seven samples of sediment from other areas of the body, as controls. Samples were submitted to three parasitological techniques and, in paleogenetic analysis, to four molecular targets. Larvae, mites, pollen grains, and structure suggestive of plants and fungus were observed, but we found no evidence of helminth infection. Ascaris sp. cytb sequence was recovered in one individual. We emphasize that, even with the extensive degradation of PNC human remains and the process of curation of samples, it was possible to recover helminth aDNA. The origin of PNC individuals confirms that these infections were brought to Brazil from western and central Africa during the colonial era.
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Affiliation(s)
- Lucélia Guedes
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (LABTRIP/IOC/FIOCRUZ). Avenida Brasil, 4365, Pavilhão Rocha Lima, Manguinhos, Rio de Janeiro, CEP: 21045-900, Brazil
| | - Victor Hugo Borba
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (LABTRIP/IOC/FIOCRUZ). Avenida Brasil, 4365, Pavilhão Rocha Lima, Manguinhos, Rio de Janeiro, CEP: 21045-900, Brazil
| | - Morgana Camacho
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (LABTRIP/IOC/FIOCRUZ). Avenida Brasil, 4365, Pavilhão Rocha Lima, Manguinhos, Rio de Janeiro, CEP: 21045-900, Brazil
| | - Jandira Neto
- Instituto de Arqueologia Brasileira (IAB). Estr. Cruz Vermelha, 45 - Vila Santa Teresa, Belford Roxo, Rio de Janeiro, CEP: 26193-415, Brazil
| | - Ondemar Dias
- Instituto de Arqueologia Brasileira (IAB). Estr. Cruz Vermelha, 45 - Vila Santa Teresa, Belford Roxo, Rio de Janeiro, CEP: 26193-415, Brazil
| | - Alena Mayo Iñiguez
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (LABTRIP/IOC/FIOCRUZ). Avenida Brasil, 4365, Pavilhão Rocha Lima, Manguinhos, Rio de Janeiro, CEP: 21045-900, Brazil.
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11
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Kistler L, Bieker VC, Martin MD, Pedersen MW, Ramos Madrigal J, Wales N. Ancient Plant Genomics in Archaeology, Herbaria, and the Environment. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:605-629. [PMID: 32119793 DOI: 10.1146/annurev-arplant-081519-035837] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA;
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Jazmín Ramos Madrigal
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Nathan Wales
- Department of Archaeology, University of York, York YO1 7EP, United Kingdom;
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Borba VH, Machado-Silva JR, Le Bailly M, Iñiguez AM. Worldwide paleodistribution of capillariid parasites: Paleoparasitology, current status of phylogeny and taxonomic perspectives. PLoS One 2019; 14:e0216150. [PMID: 31039193 PMCID: PMC6490956 DOI: 10.1371/journal.pone.0216150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/15/2019] [Indexed: 11/18/2022] Open
Abstract
Introduction Paleoparasitology, the study of parasites in the past, brings the knowledge of where and when they occurred in preterit populations. Some groups of parasites, as capillariids, have a complex and controversial systematic, hindering the paleoparasitological diagnosis. In this article, we synthesized the occurrence of capillariids in both the New and the Old World in ancient times, and discussed the difficulty of the diagnosis of species and the strategies for identification. The present review also shows the current status of the phylogeny in capillariids and indicates the necessity to try new approaches for a better understanding of capillariid paleodistribution. Methods For the systematic review, a predefined guideline defined by PRISMA was used. The articles collected were identified, screened, and included in the review following criteria for eligibility. The current status of the phylogeny of capillariids was accessed using MUSCLE, Bioedit v.7.0.5 and MEGA v. 7.0.21 programs. Results The review discussed 38 articles that presented information about capillariids in past populations. Most of capillariid eggs found in the New and Old World were not identified. However, Calodium hepaticum eggs were the most identified, as some from Eucoleus genus. It was observed that sites from the New World had a better chance for capillariid egg identification, due to previous knowledge of its host, when compared to the Old World. In the 18S rDNA phylogenetic analyses, two datasets were constructed, one including sequences from 7 Moravec’s genera, where 3 genus-specific clusters, with high bootstrap values, could be observed for Capillaria (ML = 99%, NJ = 96%), Eucoleus (ML / NJ = 100%) and Paratrichosoma (ML / NJ = 100%). A fourth cluster of 18S rDNA dataset I revealed lack of definition of Pearsonema and Aonchotheca genera. The 18S rDNA dataset II comprised 8 Moravec’s genera and defined 3 clusters, 2 genus-specific for Eucoleus (ML = 99%, NJ = 100%) and Capillaria (ML / NJ = 98%). The third 18S rDNA dataset II cluster included 6 genera and exhibited, once again, Pearsonema and Aonchotheca poor discrimination. The cox1 gene data consist of 4 Moravec’s genera, and in spite of grouping some species-specific clusters, did not show genera-specific definition. Conclusions Despite the numerous archaeological findings, both in the New and the Old Worlds, the identification of capillariid species based on the morphology and morphometry of eggs remains imprecise, often resulting in a generic diagnosis of a group or morphotype of capillariid. Capillariid is one of the most diverse group of helminths recovered in archaeological sites. The phylogenetic trees produced in this study showed limited genetic information available, unresolved genera and incongruence with the classical taxonomy. The elucidation of the paleodistribution of capillariids can give insights of the ancient host-parasite associations but also in modern sceneries.
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Affiliation(s)
- Victor Hugo Borba
- Laboratório de Helmintologia Romero Lascasas Porto, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (FCM/UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Roberto Machado-Silva
- Laboratório de Helmintologia Romero Lascasas Porto, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (FCM/UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matthieu Le Bailly
- University of Bourgogne Franche-Comte, CNRS UMR 6249 Chrono-environment, Besançon, France
| | - Alena Mayo Iñiguez
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Abstract
Enterobiasis, caused by the nematode Enterobius vermicularis, is a common health problem among schoolchildren in Thailand. We provide the first molecular identification of this nematode from Thai schoolchildren and document genetic variation among E. vermicularis eggs using sequence analyses of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene and the nuclear ribosomal DNA second internal transcribed spacer (ITS2). A cross-sectional parasitological survey was conducted in schoolchildren (n = 491) in five regions of Thailand between May 2015 and December 2016. The diagnosis of Enterobius infection was made using the adhesive tape perianal swab technique. Enterobius eggs were recovered from 43 participants (8.75%). DNA was extracted from these eggs and the cox1 gene and partial ITS2 region amplified using the polymerase chain reaction (PCR). Nineteen amplified PCR products of the cox1 gene (441 bp) and 18 of the ITS2 region (623 bp) were subsequently sequenced. All sequences were identified as belonging to E. vermicularis based on database searches. Phylogenetic analysis and a median-joining network of available E. vermicularis cox1 sequences showed 66 haplotypes. We found haploclusters (types A and B) represented among the Thai sequences. Six haplotypes from Thailand fell into type A (of Nakano et al., 2006) (along with sequences from Japan and Korea) and five haplotypes into type B (with sequences from Japan, Iran, Czech Republic, Greece, Denmark and Sudan). The overall haplotype diversity (Hd) was 0.9888. Transmission of worms with type B haplotypes from primates to humans in Asia or from humans in Europe possibly occurs in Thailand.
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Guedes L, Dias O, Neto J, Ribeiro da Silva LDP, Mendonça de Souza SMF, Iñiguez AM. First Paleogenetic Evidence of Probable Syphilis and Treponematoses Cases in the Brazilian Colonial Period. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8304129. [PMID: 30406142 PMCID: PMC6199871 DOI: 10.1155/2018/8304129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/25/2018] [Accepted: 09/12/2018] [Indexed: 12/28/2022]
Abstract
Despite interest in the origins of syphilis, paleopathological analysis has not provided answers, and paleogenetic diagnosis remains a challenge. Even venereal syphilis has low infectivity which means there are few circulating bacteria for most of the individual's life. Human remains recovered from the Nossa Senhora do Carmo Church (17th to 19th centuries) and the Praça XV Cemetery (18th to 19th centuries), Rio de Janeiro, Brazil, were subjected to Treponema paleogenetic analysis. Historical data point to endemic treponemal infections in the city, including venereal syphilis. Based on the physiopathology of Treponema pallidum infection, 25 samples, mostly from skull remains of young adults, with no visible paleopathological evidence of treponematoses, were analyzed. PCR with three molecular targets, tpp47, polA, and tpp15, were applied. Ancient DNA tpp15 sequences were recovered from two young adults from each archaeological site and revealed the polymorphism that characterizes T. p. subsp. pallidum in a female up to 18 years old, suggesting a probable case of syphilis infection. The results indicated that the epidemiological context and the physiopathology of the disease should be considered in syphilis paleogenetic detection. The findings of Treponema sp. aDNA are consistent with historical documents that describe venereal syphilis and yaws as endemic diseases in Rio de Janeiro. Data on the epidemiological characteristics of the disease and its pathophysiology offer new perspectives in paleopathology.
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Affiliation(s)
- Lucélia Guedes
- Laboratório de Biologia de Tripanosomatídeos (LABTRIP), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365 – Manguinhos, Rio de Janeiro, RJ 21040-900, Brazil
| | - Ondemar Dias
- Instituto de Arqueologia Brasileira, Estr. Cruz Vermelha, 45 – Vila Santa Teresa, Belford Roxo, Rio de Janeiro, RJ 26193-415, Brazil
| | - Jandira Neto
- Instituto de Arqueologia Brasileira, Estr. Cruz Vermelha, 45 – Vila Santa Teresa, Belford Roxo, Rio de Janeiro, RJ 26193-415, Brazil
| | - Laura da Piedade Ribeiro da Silva
- Instituto de Arqueologia Brasileira, Estr. Cruz Vermelha, 45 – Vila Santa Teresa, Belford Roxo, Rio de Janeiro, RJ 26193-415, Brazil
| | - Sheila M. F. Mendonça de Souza
- Departamento de Endemias Samuel Pessoa, Escola Nacional de Saúde Pública Sérgio Arouca, Fundação Oswaldo Cruz, R. Leopoldo Bulhões, 1480 Bonsucesso, Rio de Janeiro, RJ 21041-210, Brazil
| | - Alena Mayo Iñiguez
- Laboratório de Biologia de Tripanosomatídeos (LABTRIP), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365 – Manguinhos, Rio de Janeiro, RJ 21040-900, Brazil
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Tuberculosis in post-contact Native Americans of Brazil: Paleopathological and paleogenetic evidence from the Tenetehara-Guajajara. PLoS One 2018; 13:e0202394. [PMID: 30183732 PMCID: PMC6124704 DOI: 10.1371/journal.pone.0202394] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/02/2018] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) has been described in Native American populations prior to the arrival of European explorers, and in Brazilian populations dating from the Colonial Period. There are no studies demonstrating TB infection in native Brazilians, and the history and epidemiological scenario of TB in Brazil is still unknown. The aim of this study was to verify the presence of TB infection among the native Tenetehara-Guajajara population from Maranhão State, Brazil, 210 ± 40 years ago. A Tenetehara-Guajajara skeleton collection was submitted to paleopathological analysis, and rib bone samples (n = 17) were used for paleogenetic analysis based on Mycobacterium tuberculosis complex (MTC) targets. Porotic hyperostosis and cribra orbitalia were found in 10 and 13 individuals, respectively. Maternal ancestry analysis revealed Native American mtDNA haplogroups A and C1 in three individuals. Three samples showed osteological evidence suggestive of TB. katG and mtp40 sequences were detected in three individuals, indicating probable TB infection by two MTC lineages. Tuberculosis infection in the Tenetehara-Guajajara population since the 18th century points to a panorama of the disease resulting, most probably, from European contact. However, the important contribution of African slaves in the population of Maranhão State, could be also considered as a source of the disease. This study provides new data on TB during the Brazilian Colonial Period. This is the first report integrating paleopathological and paleogenetic data for the study of TB in Brazil.
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Abstract
SUMMARYAncient samples present a number of technical challenges for DNA barcoding, including damaged DNA with low endogenous copy number and short fragment lengths. Nevertheless, techniques are available to overcome these issues, and DNA barcoding has now been used to successfully recover parasite DNA from a wide variety of ancient substrates, including coprolites, cesspit sediment, mummified tissues, burial sediments and permafrost soils. The study of parasite DNA from ancient samples can provide a number of unique scientific insights, for example: (1) into the parasite communities and health of prehistoric human populations; (2) the ability to reconstruct the natural parasite faunas of rare or extinct host species, which has implications for conservation management and de-extinction; and (3) the ability to view in ‘real-time’ processes that may operate over century- or millenial-timescales, such as how parasites responded to past climate change events or how they co-evolved alongside their hosts. The application of DNA metabarcoding and high-throughput sequencing to ancient specimens has so far been limited, but in future promises great potential for gaining empirical data on poorly understood processes such as parasite co-extinction.
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de Souza MV, da Silva LGR, Silva-Pinto V, Mendez-Quiros P, de Miranda Chaves SA, Iñiguez AM. New paleoparasitological investigations from the pre-inca to hispanic contact period in northern Chile. Acta Trop 2018; 178:290-296. [PMID: 29191518 DOI: 10.1016/j.actatropica.2017.11.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 11/15/2017] [Accepted: 11/26/2017] [Indexed: 11/19/2022]
Abstract
Paleoparasitological studies have demonstrated that changes in environment or culture are reflected in the patterns of parasitic infection diseases in populations worldwide. The advent of agriculture and animal domestication, with its accompanying reduction in human mobility and expanding population involves changes in or emergence of, parasites, the so-called first epidemiological transition. Cultural processes related to territory occupation contribute to both loss and acquisition of parasites. The archaeological site Lluta 57 in the Lluta Valley, Chile, provides a chronology of the transition from the pre-Inca or Late Intermediate Period (LIP), through the Late or Inca Period (LP), to the Hispanic Contact Period (HCP), providing the possibility of evaluating this epidemiological transition. The aim of this study was to conduct a paleoparasitological investigation of to gain insight into the dynamics of parasitism in Lluta people throughout the Inca expansion. Fourteen human coprolites from the three periods were rehydrated, submitted to spontaneous sedimentation, and examined by light microscopy for the presence of intestinal parasite eggs, pollen grains, and micro-remains. Eggs of four parasites: Enterobius vermicularis, Trichostrongylus sp., Trichuris sp., and Eimeria macusaniensis were recovered. Frequency, diversity, and number of parasite eggs per sample increased over the studied time period. Trichostrongylus sp. and E. macusaniensis were recorded in the region for the first time. Enterobius vermicularis eggs, absent in the LIP, were present as a hyper-infection in LP. The presence of E. macusaniensis is likely related to exploitation of llamas, which were used for food and transport and as sacrificial offerings. The paleobotanical analysis revealed ten families of pollen grains, as well as phytoliths and floral remains. In contrast to parasitological results, a diachronic pattern was not detected. Evolution of the settlements, with the advent of larger, more densely populated, villages, could have influenced the emergence and intensification of transmission of parasites in the region. The study showed that the Inca expansion influenced host-parasite-environment relationships in the Lluta Valley.
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Affiliation(s)
- Mônica Vieira de Souza
- Laboratório de Paleoparasitologia, Escola Nacional de Saúde Pública Sergio Arouca/Fundação Oswaldo Cruz (DENSP/ENSP/FIOCRUZ), Rua Leopoldo Bulhões, 1480, Manguinhos, Rio de Janeiro, RJ, 21041-210, Brazil; LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Av. Brasil 4365, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Lucélia Guedes Ribeiro da Silva
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Av. Brasil 4365, Rio de Janeiro, RJ, 21040-900, Brazil.
| | - Verónica Silva-Pinto
- Área de Antropología, Museo Nacional de Historia Natural, Casilla 787 Santiago de Chile, Chile; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany.
| | - Pablo Mendez-Quiros
- Universidad Autónoma de Barcelona, Departamento de Prehistoria, Programa de Doctorado en Arqueología Prehistórica, Spain.
| | - Sergio Augusto de Miranda Chaves
- Laboratório de Ecologia da Escola Nacional de Saúde Pública da FIOCRUZ, Rua Leopoldo Bulhões 1480, térreo-Manguinhos, 21041-210 Rio de Janeiro, RJ, Brazil.
| | - Alena Mayo Iñiguez
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Av. Brasil 4365, Rio de Janeiro, RJ, 21040-900, Brazil.
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Integrative taxonomy of anisakid nematodes in stranded cetaceans from Brazilian waters: an update on parasite’s hosts and geographical records. Parasitol Res 2017; 116:3105-3116. [DOI: 10.1007/s00436-017-5622-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022]
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Palaeoparasitology and palaeogenetics: review and perspectives for the study of ancient human parasites. Parasitology 2017; 145:656-664. [DOI: 10.1017/s003118201700141x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
SUMMARYWhile some species of parasites can be identified to species level from archaeological remains using microscopy (i.e.Enterobius vermicularis,Clonorchis sinensis), others can only be identified to family or genus level as different species produce eggs with similar morphology (i.e.Tæniasp. andEchinococcussp.). Molecular and immunological approaches offer the possibility to provide more precise determination at the species level. They can also identify taxa when classic parasite markers such as eggs or cysts have been destroyed over time. However, biomolecules can be poorly preserved and modern reference DNA is available only for a limited number of species of parasites, leading to the conclusion that classic microscopic observation should be combined with molecular analyses. Here we present a review of the molecular approaches used over the past two decades to identify human pathogenic helminths (Ascarissp.,Trichurissp.,E. vermicularis,Fasciolasp. etc.) or protists (Giardiasp.,Trypanosomasp.,Leishmaniasp. etc.). We also discuss the prospects for studying the evolution of parasites with genetics and genomics.
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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Reinhard KJ, Araújo A, Morrow JJ. Temporal and Spatial Distribution of Enterobius vermicularis (Nematoda: Oxyuridae) in the Prehistoric Americas. THE KOREAN JOURNAL OF PARASITOLOGY 2016; 54:591-603. [PMID: 27853116 PMCID: PMC5127543 DOI: 10.3347/kjp.2016.54.5.591] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/31/2016] [Accepted: 09/11/2016] [Indexed: 02/06/2023]
Abstract
Investigations of Enterobius sp. infection in prehistory have produced a body of data that can be used to evaluate the geographic distribution of infection through time in the Americas. Regional variations in prevalence are evident. In North America, 119 pinworm positive samples were found in 1,112 samples from 28 sites with a prevalence of 10.7%. Almost all of the positive samples came from agricultural sites. From Brazil, 0 pinworm positive samples were found in 325 samples from 7 sites. For the Andes region, 22 pinworm positive samples were found in 411 samples from 26 sites for a prevalence of 5.3%. Detailed analyses of these data defined several trends. First, preagricultural sites less frequently show evidence of infection compared to agricultural populations. This is especially clear in the data from North America, but is also evident in the data from South America. Second, there is an apparent relationship between the commonality of pinworms in coprolites and the manner of constructing villages. These analyses show that ancient parasitism has substantial value in documenting the range of human behaviors that influence parasitic infections.
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Affiliation(s)
- Karl J Reinhard
- Pathoecology Laboratory, School of Natural Resources, University of Nebraska-Lincoln, Lincoln, Nebraska, 68583-0962, USA
| | - Adauto Araújo
- Laboratório de Paleoparasitologia, Departamento de Endemias Samuel Pessoa/Escola Nacional de Saúde Pública Sergio Arouca/Fundação Oswaldo Cruz (DENSP/ENSP/FIOCRUZ), Rua Leopoldo Bulhões, Rio de Janeiro, RJ, 21041-210, Brazil
| | - Johnica J Morrow
- Pathoecology Laboratory, School of Natural Resources, University of Nebraska-Lincoln, Lincoln, Nebraska, 68583-0962, USA
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Abstract
ABSTRACT
This chapter aims to provide some key points for researchers interested in the study of ancient gastrointestinal parasites. These few pages are dedicated to my colleague and friend, Prof. Adauto Araújo (1951-2015), who participated in the writing of this chapter. His huge efforts in paleoparasitology contributed to the development and promotion of the discipline during more than 30 years.
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Abstract
The paleomicrobiology of coprolites, which are fossilized fecal materials, has already yielded data about various organisms, including micro-eukaryotes, bacteria, and archaea, thus expanding our comprehension of ancient human dietary habits, gut microbiota, and intestinal and systemic infections. This mini-review briefly describes previous works and summarizes the main techniques used in handling coprolites and the findings obtained about ancient gut microbiota. Past intestinal and systemic infections are outlined.
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Darling MI, Donoghue HD. Insights from paleomicrobiology into the indigenous peoples of pre-colonial America - a review. Mem Inst Oswaldo Cruz 2016; 109:131-9. [PMID: 24714964 PMCID: PMC4015261 DOI: 10.1590/0074-0276140589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 02/06/2023] Open
Abstract
This review investigates ancient infectious diseases in the Americas dated to the
pre-colonial period and considers what these findings can tell us about the history
of the indigenous peoples of the Americas. It gives an overview, but focuses on four
microbial pathogens from this period: Helicobacter pylori,
Mycobacterium tuberculosis, Trypanosoma cruzi
and Coccidioides immitis, which cause stomach ulceration and gastric
cancer, tuberculosis, Chagas disease and valley fever, respectively. These pathogens
were selected as H. pylori can give insight into ancient human
migrations into the Americas, M. tuberculosis is associated with
population density and urban development, T. cruzi can elucidate
human living conditions and C. immitis can indicate agricultural
development. A range of methods are used to diagnose infectious disease in ancient
human remains, with DNA analysis by polymerase chain reaction one of the most
reliable, provided strict precautions are taken against cross contamination. The
review concludes with a brief summary of the changes that took place after European
exploration and colonisation.
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Affiliation(s)
- Millie I Darling
- Division of Biosciences, Centre for Clinical Microbiology, University College London, London, UK
| | - Helen D Donoghue
- Division of Biosciences, Centre for Clinical Microbiology, University College London, London, UK
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Côté NML, Daligault J, Pruvost M, Bennett EA, Gorgé O, Guimaraes S, Capelli N, Le Bailly M, Geigl EM, Grange T. A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites. PLoS One 2016; 11:e0146230. [PMID: 26752051 PMCID: PMC4709038 DOI: 10.1371/journal.pone.0146230] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/14/2015] [Indexed: 11/21/2022] Open
Abstract
Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies.
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Affiliation(s)
- Nathalie M. L. Côté
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
- University of Bourgogne Franche-Comte, CNRS UMR 6249 Chrono-environment, 16 route de Gray, 25030, Besançon cedex, France
| | - Julien Daligault
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
| | - Mélanie Pruvost
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
| | - E. Andrew Bennett
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
| | - Olivier Gorgé
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
| | - Silvia Guimaraes
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
| | - Nicolas Capelli
- University of Bourgogne Franche-Comte, CNRS UMR 6249 Chrono-environment, 16 route de Gray, 25030, Besançon cedex, France
| | - Matthieu Le Bailly
- University of Bourgogne Franche-Comte, CNRS UMR 6249 Chrono-environment, 16 route de Gray, 25030, Besançon cedex, France
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
- * E-mail: (EMG); (TG)
| | - Thierry Grange
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
- * E-mail: (EMG); (TG)
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Jaeger LH, Gijón-Botella H, Del Carmen Del Arco-Aguilar M, Martín-Oval M, Rodríguez-Maffiotte C, Del Arco-Aguilar M, Araújo A, Iñiguez AM. Evidence of Helminth Infection in Guanche Mummies: Integrating Paleoparasitological and Paleogenetic Investigations. J Parasitol 2015; 102:222-8. [PMID: 26641720 DOI: 10.1645/15-866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The Guanches, ancient inhabitants of the Canary Islands, Spain, practiced mummification of their dead. A paleoparasitological and paleogenetic analysis was conducted on mummified bodies (n = 6) (AD 1200, Cal BP 750) belonging to the Guanche culture from Gran Canaria Island. Coprolite and sediment samples (n = 19) were removed from below the abdominal region or sacral foramina. The samples were rehydrated in 0.5% trisodium phosphate solution for 72 hr at 4 C, and the paleoparasitological investigation was conducted by spontaneous sedimentation method and microscopic examination. The results revealed the presence of well-preserved eggs of Ascaris sp., Trichuris trichiura , Enterobius vermicularis , and hookworms. Ancient DNA was extracted from sediment samples to elucidate the ancestry of the mummies and for molecular detection of Ascaris sp. infection. Results of paleogenetic analysis demonstrated Ascaris sp. infection using 2 molecular targets, cytb and nad1. The mtDNA haplotypes U6b, U6b1, and HV were identified, which confirmed records of Guanche ancestry. The excellent preservation of Guanche mummies facilitated the paleoparasitological and paleogenetic study, the results of which contribute to our knowledge of Guanche culture and their health status.
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Affiliation(s)
- Lauren Hubert Jaeger
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Herminia Gijón-Botella
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - María Del Carmen Del Arco-Aguilar
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Mercedes Martín-Oval
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Conrado Rodríguez-Maffiotte
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Mercedes Del Arco-Aguilar
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Adauto Araújo
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Alena Mayo Iñiguez
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
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Freire A, Araújo A, Maldonado A, Lobo A, Garcia J, Fonseca ABM, Leles D. It is needless to rehydrate archeological samples to extract ancient DNA. Parasitol Int 2015; 64:303-4. [PMID: 25863165 DOI: 10.1016/j.parint.2015.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 03/28/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Andressa Freire
- Universidade Federal Fluminense, Instituto Biomédico, Departamento de Microbiologia e Parasitologia, Laboratório de Biologia Molecular de Parasitos, Rua Professor Hernani Melo, 101, São Domingos, CEP 24.210-130 Niterói, RJ, Brazil
| | - Adauto Araújo
- Laboratório de Paleoparasitologia, Escola Nacional de Saúde Pública-Fundação Oswaldo Cruz, Rua Leopoldo Bulhões 1480, CEP 21.041-210 Rio de Janeiro, RJ, Brazil
| | - Arnaldo Maldonado
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Av. Brasil, 4365, CEP 21.045-900 Rio de Janeiro, RJ, Brazil
| | - Amanda Lobo
- Laboratório de Paleoparasitologia, Escola Nacional de Saúde Pública-Fundação Oswaldo Cruz, Rua Leopoldo Bulhões 1480, CEP 21.041-210 Rio de Janeiro, RJ, Brazil
| | - Juberlan Garcia
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Av. Brasil, 4365, CEP 21.045-900 Rio de Janeiro, RJ, Brazil
| | - Ana Beatriz Monteiro Fonseca
- Universidade Federal Fluminense, Instituto de Matemática e Estatística, Centro de Estudos Gerais, Rua Mário Santos Braga s/n, Centro, CEP 24.020-140 Niterói, RJ, Brazil
| | - Daniela Leles
- Universidade Federal Fluminense, Instituto Biomédico, Departamento de Microbiologia e Parasitologia, Laboratório de Biologia Molecular de Parasitos, Rua Professor Hernani Melo, 101, São Domingos, CEP 24.210-130 Niterói, RJ, Brazil.
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Warinner C, Speller C, Collins MJ, Lewis CM. Ancient human microbiomes. J Hum Evol 2015; 79:125-36. [PMID: 25559298 PMCID: PMC4312737 DOI: 10.1016/j.jhevol.2014.10.016] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/06/2014] [Accepted: 10/29/2014] [Indexed: 12/20/2022]
Abstract
Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.
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Affiliation(s)
- Christina Warinner
- Department of Anthropology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK 73019, USA
| | - Camilla Speller
- Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Matthew J Collins
- Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK 73019, USA.
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Jaeger LH, Iñiguez AM. Molecular paleoparasitological hybridization approach as effective tool for diagnosing human intestinal parasites from scarce archaeological remains. PLoS One 2014; 9:e105910. [PMID: 25162694 PMCID: PMC4146586 DOI: 10.1371/journal.pone.0105910] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/24/2014] [Indexed: 11/18/2022] Open
Abstract
Paleoparasitology is the science that uses parasitological techniques for diagnosing parasitic diseases in the past. Advances in molecular biology brought new insights into this field allowing the study of archaeological material. However, due to technical limitations a proper diagnosis and confirmation of the presence of parasites is not always possible, especially in scarce and degraded archaeological remains. In this study, we developed a Molecular Paleoparasitological Hybridization (MPH) approach using ancient DNA (aDNA) hybridization to confirm and complement paleoparasitological diagnosis. Eight molecular targets from four helminth parasites were included: Ascaris sp., Trichuris trichiura, Enterobius vermicularis, and Strongyloides stercoralis. The MPH analysis using 18th century human remains from Praça XV cemetery (CPXV), Rio de Janeiro, Brazil, revealed for the first time the presence E. vermicularis aDNA (50%) in archaeological sites of Brazil. Besides, the results confirmed T. trichiura and Ascaris sp. infections. The prevalence of infection by Ascaris sp. and E. vermicularis increased considerably when MPH was applied. However, a lower aDNA detection of T. trichiura (40%) was observed when compared to the diagnosis by paleoparasitological analysis (70%). Therefore, based on these data, we suggest a combination of Paleoparasitological and MPH approaches to verify the real panorama of intestinal parasite infection in human archeological samples.
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Affiliation(s)
- Lauren Hubert Jaeger
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alena Mayo Iñiguez
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Seo M, Araujo A, Reinhard K, Chai JY, Shin DH. Paleoparasitological studies on mummies of the Joseon Dynasty, Korea. THE KOREAN JOURNAL OF PARASITOLOGY 2014; 52:235-42. [PMID: 25031462 PMCID: PMC4096633 DOI: 10.3347/kjp.2014.52.3.235] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 11/23/2022]
Abstract
Paleoparasitology is the application of conventional or molecular investigative techniques to archeological samples in order to reveal parasitic infection patterns among past populations. Although pioneering studies already have reported key paleoparasitological findings around the world, the same sorts of studies had not, until very recently, been conducted in sufficient numbers in Korea. Mummified remains of individuals dating to the Korean Joseon Dynasty actually have proved very meaningful to concerned researchers, owing particularly to their superb preservation status, which makes them ideal subjects for paleoparasitological studies. Over the past several years, our study series on Korean mummies has yielded very pertinent data on parasitic infection patterns prevailing among certain Joseon Dynasty populations. In this short review, we summarized the findings and achievements of our recent paleoparasitological examinations of Joseon mummies and discussed about the prospects for future research in this vein.
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Affiliation(s)
- Min Seo
- Department of Parasitology, Dankook University College of Medicine, Cheonan 330-714, Korea
| | - Adauto Araujo
- Fundação Oswaldo Cruz, FIOCRUZ, Manguinhos, Rio de Janeiro 21040-360, Brasil
| | - Karl Reinhard
- School of Natural Resouces, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jong Yil Chai
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Dong Hoon Shin
- Institute of Forensic Medicine, Seoul National University College of Medicine, Seoul 110-799, Korea
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Evolutionary History of Terrestrial Pathogens and Endoparasites as Revealed in Fossils and Subfossils. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/181353] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The present work uses fossils and subfossils to decipher the origin and evolution of terrestrial pathogens and endoparasites. Fossils, as interpreted by morphology or specific features of their hosts, furnish minimum dates for the origin of infectious agents, coevolution with hosts, and geographical locations. Subfossils, those that can be C14 dated (roughly under 50,000 years) and are identified by morphology as well as molecular and immunological techniques, provide time periods when humans became infected with various diseases. The pathogen groups surveyed include viruses, bacteria, protozoa, fungi, and select multicellular endoparasites including nematodes, trematodes, cestodes, and insect parasitoids in the terrestrial environment.
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Insights about echinostomiasis by paleomolecular diagnosis. Parasitol Int 2014; 63:646-9. [PMID: 24780138 DOI: 10.1016/j.parint.2014.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 04/01/2014] [Accepted: 04/17/2014] [Indexed: 11/22/2022]
Abstract
Echinostomiasis is a zoonosis caused by intestinal trematodes and transmitted by the ingestion of mollusks, crustaceans, fish, amphibians, and reptiles, either raw or poorly cooked. Today human infection is endemic in Southeast Asia and the Far East, but has been reported more recently in other regions of the world. Interestingly eggs identified as Echinostoma sp. were found in coprolites from a mummified body human in Brazil, dated 560 ± 40 BP (before present). However, the specific diagnosis based on morphology of the eggs has not been resolved at the species level. As a follow-up to the previous finding, the current study now aims to standardize the methodology for molecular diagnosis and apply it to the coprolite, using current Echinostoma paraensei-positive feces as the reference, and also the same fecal material dried in a stove as an experimental coprolite model. Isolated eggs of E. paraensei and adult worm were included to verify the sensibility and as positive control, respectively. An adult worm of E. luisreyi was used for comparison. PCR using primers in-house for ITS1 region (126 bp) and cox1 (123 bp) of Echinostoma spp. and subsequent nucleotide sequencing were performed. This is the first molecular paleoparasitological diagnosis for echinostomiasis. The methodology was able to amplify specific DNA fragments for the genus Echinostoma sp. in all samples: adult worm, feces, and a single egg of the parasite, in both the experimental coprolite and archaeological sample. Additionally we observed that ancient DNA can also be retrieved without rehydrating the material. The nucleotide sequences from E. paraensei and E. luisreyi are very similar in the fragment analyzed that difficult the differentiation these species, but DNA sequence analysis recovered in the parasite found in the mummy showed more similarity with the species E. paraensei.
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Appelt S, Armougom F, Le Bailly M, Robert C, Drancourt M. Polyphasic analysis of a middle ages coprolite microbiota, Belgium. PLoS One 2014; 9:e88376. [PMID: 24586319 PMCID: PMC3938422 DOI: 10.1371/journal.pone.0088376] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 01/06/2014] [Indexed: 11/19/2022] Open
Abstract
Paleomicrobiological investigations of a 14(th)-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by ad hoc PCR--sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coprolite, mixing organisms known to originate from the environment and organisms known to be gut inhabitants. Metagenomic analyses yielded 107,470 reads, of which known sequences (31.9%) comprised 98.98% bacterial, 0.52% eukaryotic, 0.44% archaeal and 0.06% viral assigned reads. Most abundant bacterial phyla were Proteobacteria, Gemmatimonadetes, Actinobacteria and Bacteroidetes. The 16 S rRNA gene dataset yielded 132,000 trimmed reads and 673 Operational Taxonomic Units. Most abundant bacterial phyla observed in the 16 S rRNA gene dataset belonged to Proteobacteria, Firmicutes, Actinobacteria and Chlamydia. The Namur coprolite yielded typical gut microbiota inhabitants, intestinal parasites Trichuris and Ascaris and systemic pathogens Bartonella and Bordetella. This study adds knowledge to gut microbiota in medieval times.
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Affiliation(s)
- Sandra Appelt
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
| | - Fabrice Armougom
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
| | - Matthieu Le Bailly
- Centre national de la recherche scientifique UMR 6249 Chrono-Environnement, Franche-Comté Université, Besançon, France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
- * E-mail:
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Cleeland LM, Reichard MV, Tito RY, Reinhard KJ, Lewis CM. Clarifying Prehistoric Parasitism from a Complementary Morphological and Molecular Approach. JOURNAL OF ARCHAEOLOGICAL SCIENCE 2013; 40:3060-3066. [PMID: 23645967 PMCID: PMC3640563 DOI: 10.1016/j.jas.2013.03.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This paper reports an approach to the identification of prehistoric parasitic infection, which integrates traditional morphological methods with molecular methods. The approach includes the strengths of each method while mitigating the limitations. Demonstrating the efficacy of this approach, we provide a case study from a 1,400 year old desiccated fecal sample from La Cueva de los Muertos Chiquitos, archaeological site, near Rio Zape, Durango, Mexico. Traditionally prepared microscope slides were processed via microscopy and tentative ascarids were identified. Information regarding the parasites' developmental stage was recorded. DNA was then extracted directly from the slide material. From this DNA extract, a small segment of the 18S ribosomal RNA gene variant that is specific to Ascaris, and its phylogenetically close relatives, was targeted for PCR amplification and sequencing. Phylogenetic analysis of the DNA sequence best matched a member of physalopterids, rather than ascarids, with a single exception of a match to Contracaecum spiculigerum. Subsequent extractions, amplifications and sequencing of the original rehydrated coprolite material confirmed these results. The C. spiculigerum sequence represented a phylogenetic anomaly and subsequent analysis determined the sequence was an error in the BLAST database, likely attributable to misidentification of juvenile specimens prior to sequencing and submission. Physaloptera are a difficult genus to identify morphologically and can carry major health burdens. They may be underreported in humans, in part, because of morphological similarities to the more common human parasites belonging to ascarids. We conclude that integrating traditional morphological methods with molecular methods can help resolve this issue, in both contemporary and prehistoric populations.
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Affiliation(s)
- Lauren M. Cleeland
- University of Oklahoma, Department of Anthropology, 455 West Lindsey, Dale Hall Tower 521, Norman, OK 73019
| | - Mason V. Reichard
- Oklahoma State University, Center for Veterinary Health Sciences, Veterinary Pathobiology Laboratory, 250 McElroy Hall Stillwater, Oklahoma 74078
| | - Raul Y. Tito
- University of Oklahoma, Department of Anthropology, 455 West Lindsey, Dale Hall Tower 521, Norman, OK 73019
| | - Karl J. Reinhard
- University of Nebraska-Lincoln, School of Natural Resources, 719 Hardin Hall, Lincoln, Nebraska 68583-0987
| | - Cecil M. Lewis
- University of Oklahoma, Department of Anthropology, 455 West Lindsey, Dale Hall Tower 521, Norman, OK 73019
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Anastasiou E, Mitchell PD. Palaeopathology and genes: investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations. Gene 2013; 528:33-40. [PMID: 23792062 DOI: 10.1016/j.gene.2013.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 05/23/2013] [Accepted: 06/01/2013] [Indexed: 01/11/2023]
Abstract
The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future.
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Affiliation(s)
- Evilena Anastasiou
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge CB2 1QH, UK
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Shin DH, Oh CS, Chai JY, Lee HJ, Seo M. Enterobius vermicularis eggs discovered in coprolites from a medieval Korean mummy. THE KOREAN JOURNAL OF PARASITOLOGY 2011; 49:323-6. [PMID: 22072838 PMCID: PMC3210855 DOI: 10.3347/kjp.2011.49.3.323] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/04/2011] [Accepted: 08/08/2011] [Indexed: 11/23/2022]
Abstract
While the presence of pinworm eggs in archaeological samples has been reported by many researchers in the New World, those have been detected very scarcely in the Old World, especially in East Asian countries. In fact, many parasite species were recovered from the archeological remains in Korea, eggs of Enterobius vermicularis had not been found. Recently, a female mummy buried in the 17th century was discovered in the Joseon tomb from Dangjin-gun, Chungcheongnam-do, Korea. After rehydration process for 12 days, investigations were carried on the luminal surface of the colon. From them, 3 eggs of E. vermicularis were recovered. They were elliptical, transparent with a thin egg shell, 50.3±5.2 µm (length) and 28.2±3.9 µm (width) in size. This is the first discovery of E. vermicularis eggs in East Asia.
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Affiliation(s)
- Dong Hoon Shin
- Department of Anatomy, Seoul National University College of Medicine, Seoul 110-799, Korea
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Characterization of Enterobius vermicularis in a human population, employing a molecular-based method from adhesive tape samples. Mol Cell Probes 2011; 25:121-5. [PMID: 21458560 DOI: 10.1016/j.mcp.2011.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 03/23/2011] [Accepted: 03/23/2011] [Indexed: 01/04/2023]
Abstract
Human infection with the parasitic nematode Enterobius vermicularis occurs worldwide, particularly in children. Although its prevalence may exceed 35% in some parts of the world, molecular studies of E. vermicularis in humans are limited. The aim of the present study was to investigate the genetic variation within E. vermicularis in a human population. For this purpose, 77 adhesive tape samples taken from Greek children infested with E. vermicularis were tested. New primers were designed to amplify a segment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of E. vermicularis from adhesive tape samples. Thirty-six amplicons were sequenced and eleven different haplotypes were identified. All sequences clustered within the type previously characterized (type B), only reported to date from captive chimpanzees. To the best of our knowledge, this is the first study of E. vermicularis genotypes from a human population.
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Botella HG, Vargas JAA, de la Rosa MA, Leles D, Reimers EG, Vicente ACP, Iñiguez AM. Paleoparasitologic, paleogenetic and paleobotanic analysis of XVIII century coprolites from the church La Concepción in Santa Cruz de Tenerife, Canary Islands, Spain. Mem Inst Oswaldo Cruz 2010; 105:1054-6. [DOI: 10.1590/s0074-02762010000800017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 09/21/2010] [Indexed: 11/22/2022] Open
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Le Bailly M, Bouchet F. Ancient dicrocoeliosis: Occurrence, distribution and migration. Acta Trop 2010; 115:175-80. [PMID: 20363205 DOI: 10.1016/j.actatropica.2010.03.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 02/22/2010] [Accepted: 03/13/2010] [Indexed: 10/19/2022]
Abstract
This paper focuses on the lancet fluke, Dicrocoelium sp., and includes a complete review of the literature as well as numerous new research results. The compilation of all these data led to a global overview of ancient dicrocoeliosis history. The presence of the lancet fluke in Western Europe was attested from 550,000 years BP to the 16th century AD Moreover, the parasite was identified in the New World around the 17th century AD following the colonization of Canada by Europeans. The role of human and animal migrations is discussed.
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40
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Oh CS, Seo M, Lim NJ, Lee SJ, Lee EJ, Lee SD, Shin DH. Paleoparasitological report on Ascaris aDNA from an ancient East Asian sample. Mem Inst Oswaldo Cruz 2010; 105:225-8. [PMID: 20428686 DOI: 10.1590/s0074-02762010000200020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 02/09/2010] [Indexed: 11/21/2022] Open
Abstract
In this study, Ascaris DNA was extracted and sequenced from a medieval archaeological sample in Korea. While Ascaris eggs were confirmed to be of human origin by archaeological evidence, it was not possible to pinpoint the exact species due to close genetic relationships among them. Despite this shortcoming, this is the first Ascaris ancient DNA (aDNA) report from a medieval Asian country and thus will expand the scope of Ascaris aDNA research.
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Affiliation(s)
- Chang Seok Oh
- Institute of Forensic Medicine, Seoul National University College of Medicine, Chongno-Gu, Seoul, Korea
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Geographical aspects of enterobiasis in Estonia. Health Place 2010; 16:291-300. [DOI: 10.1016/j.healthplace.2009.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 10/13/2009] [Accepted: 10/20/2009] [Indexed: 11/19/2022]
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Parasites as probes for prehistoric human migrations? Trends Parasitol 2008; 24:112-5. [PMID: 18262843 DOI: 10.1016/j.pt.2007.11.007] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 10/26/2007] [Accepted: 11/27/2007] [Indexed: 11/23/2022]
Abstract
Host-specific parasites of humans are used to track ancient migrations. Based on archaeoparasitology, it is clear that humans entered the New World at least twice in ancient times. The archaeoparasitology of some intestinal parasites in the New World points to migration routes other than the Bering Land Bridge. Helminths have been found in mummies and coprolites in North and South America. Hookworms (Necator and Ancylostoma), whipworms (Trichuris trichiura) and other helminths require specific conditions for life-cycle completion. They could not survive in the cold climate of the northern region of the Americas. Therefore, humans would have lost some intestinal parasites while crossing Beringia. Evidence is provided here from published data of pre-Columbian sites for the peopling of the Americas through trans-oceanic or costal migrations.
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Leles D, Araújo A, Ferreira LF, Vicente ACP, Iñiguez AM. Molecular paleoparasitological diagnosis of Ascaris sp. from coprolites: new scenery of ascariasis in pre-Colombian South America times. Mem Inst Oswaldo Cruz 2008; 103:106-8. [PMID: 18327505 DOI: 10.1590/s0074-02762008005000004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 12/27/2007] [Indexed: 11/22/2022] Open
Abstract
Paleoparasitological studies using microscopy showed that Ascarisand Trichuris trichiura are the human intestinal parasites most found in archaeological sites. However, in pre-Columbian South American archaeological sites, Ascaris is rare. In this work we standardized a molecular methodology for Ascaris diagnosis directly from ancient DNA retrieved from coprolites. Using cythochrome b gene (142 bp) target, ancient DNA sequences were retrieved from South American samples, negative by microscopy. Moreover, the methodology applied was sensitive enough to detect ancient DNA extracted from 30 Ascaris eggs from an European coprolite. These results revealed a new scenery for the paleodistribution of Ascaris in South America.
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Affiliation(s)
- Daniela Leles
- Escola Nacional de Saúde Pública, FiocruzRio de Janeiro, Brasil
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