Molecular paleoparasitological diagnosis of Ascaris sp. from coprolites: new scenery of ascariasis in pre-Colombian South America times

Paleoparasitology research on ancient helminth eggs and larvae in the Republic of Korea

Paleoparasitology is a discipline that applies existing conventional and molecular techniques to study parasites found in ancient ruins. This review focuses on the history of the discovery of parasites (mostly helminth eggs and larvae) in archaeological soil samples and mummies in Korea from the Three Kingdoms Period to the Joseon Dynasty (100 BCE-1910 CE). We also briefly review important milestones in global paleoparasitology. The helminth species reported so far in Korea included Ascaris lumbricoides, Trichuris trichiura, Strongyloides stercoralis (larva), Trichostrongylus sp. (larva), Paracapillaria philippinensis (syn. Capillaria philippinensis), Enterobius vermicularis, Fasciola hepatica, dicrocoeliids, Paragonimus westermani, Clonorchis sinensis, Metagonimus yokogawai, Pygidiopsis summa, Gymnophalloides seoi, Isthmiophora hortensis, Dibothriocephalus nihonkaiensis (syn. Diphyllobothrium nihonkaiense), and Taenia spp. tapeworms. The findings obtained by Korean paleoparasitologists/archaeologists have brought about deep insight into the status of helminthic infections in Korea's past populations. Continued paleoparasitological research is essential for further understanding of ancient parasites and parasitic diseases in Korea.

Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review

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.

Gastrointestinal parasite burden in 4th-5th c. CE Florence highlighted by microscopy and paleogenetics

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.

Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace

This study evidenced the presence of parasites in a cesspit of an aristocratic palace of nineteenth century in Sardinia (Italy) by the use of classical paleoparasitological techniques coupled with next-generation sequencing. Parasite eggs identified by microscopy included helminth genera pathogenic for humans and animals: the whipworm Trichuris sp., the roundworm Ascaris sp., the flatworm Dicrocoelium sp. and the fish tapeworm Diphyllobothrium sp. In addition, 18S rRNA metabarcoding and metagenomic sequencing analysis allowed the first description in Sardinia of aDNA of the human specific T. trichiura species and Ascaris genus. Their presence is important for understanding the health conditions, hygiene habits, agricultural practices and the diet of the local inhabitants in the period under study.

Advances in paleopathology in context: A focus on soft tissue paleopathology

Skeletal and mummified remains from South America have had a significant impact on the progress of paleopathological research. In 1997, John Verano synthesized the state of paleopathological research, identifying trends and highlighting future potentials. The goal of this contribution is to consider Verano's observations on advances in soft tissue paleopathology within the context of the development of the field of mummy studies. As his article was published near the midpoint between the present and the early 1970s, when the modern form of mummy studies began to form, considering his observations in this context allows researchers the opportunity to consider how the field has progressed since the late 1990s.

African helminth infection out of Africa: Paleoparasitological and paleogenetic investigations in Pretos Novos cemetery, Rio de Janeiro, Brazil (1769-1830)

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.

Mummy studies and the bioarchaeology of care

The bioarchaeology of care is a framework through which researchers can begin to infer the level of care an individual may have required based on the presence of paleopathological evidence. To date, all of the research that has employed the framework has been based on evidence derived from skeletal material. This special issue was organized in order to highlight how the analysis of mummified soft tissue, as well as other sources of data commonly associated with mummified remains, such as coprolites and intestinal contents, has the potential to provide valuable insight into the reconstruction of care in the past.

Tuberculosis in post-contact Native Americans of Brazil: Paleopathological and paleogenetic evidence from the Tenetehara-Guajajara

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.

DNA barcoding of ancient parasites

Ancient 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.

Palaeoparasitology and palaeogenetics: review and perspectives for the study of ancient human parasites

While 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.

Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles

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.

Migrating microbes: what pathogens can tell us about population movements and human evolution

BACKGROUND

The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen's genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases.

METHODS

This study explores which pathogens leave traces in the archaeological record, and whether there are realistic prospects that these pathogens can be recovered from sub-Saharan African archaeological contexts.

RESULTS

Three stories are then presented of germs on a journey. The first is the story of HIV's spread on the back of colonialism and the railway networks over the last 150 years. The second involves the spread of Schistosoma mansoni, a parasite which shares its history with the trans-Atlantic slave trade and the origins of fresh-water fishing. Finally, we discuss the tantalising hints of hominin migration and interaction found in the genome of human herpes simplex virus 2.

CONCLUSIONS

Evidence from modern African pathogen genomes can provide data on human behaviour and migration in deep time and contribute to the improvement of human quality-of-life and longevity.

The Paleoparasitology in Brazil and Findings in Human Remains from South America: A Review

The review article presents some of the history of how paleoparasitology started in Brazil, making highlight the great responsible Dr. Luiz Fernando Ferreira and Dr. Adauto Araújo, the trajectory of paleoparasitology in Brazil since 1978 and its performance in science to the present day. In sequence, it is made a presentation of parasitological findings on human remains found in archaeological sites in South America, highlighting Brazil, Argentina, Chile, and Peru, where major discoveries have occurred. Many of the parasites found in archaeological material and mentioned in this review went out of Africa with the peopling of Europe and from there they dispersed around the world, where climatic conditions allow the transmission. However, humans have acquired other parasites of animals, since humans invaded new habitats or creating new habits adopting new technologies, thus expanding its range of influence on the environment. Thus, this review article is finalized with information that explain the importance of these findings in the interaction between parasites, human host, and ambient.

Past Intestinal Parasites

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.

Human Coprolites as a Source for Paleomicrobiology

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.

Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections

Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies.

Insights from paleomicrobiology into the indigenous peoples of pre-colonial America - a review

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.

Human parasites in the Roman World: health consequences of conquering an empire

The archaeological evidence for parasites in the Roman era is presented in order to demonstrate the species present at that time, and highlight the health consequences for people living under Roman rule. Despite their large multi-seat public latrines with washing facilities, sewer systems, sanitation legislation, fountains and piped drinking water from aqueducts, we see the widespread presence of whipworm (Trichuris trichiura), roundworm (Ascaris lumbricoides) and Entamoeba histolytica that causes dysentery. This would suggest that the public sanitation measures were insufficient to protect the population from parasites spread by fecal contamination. Ectoparasites such as fleas, head lice, body lice, pubic lice and bed bugs were also present, and delousing combs have been found. The evidence fails to demonstrate that the Roman culture of regular bathing in the public baths reduced the prevalence of these parasites. Fish tapeworm was noted to be widely present, and was more common than in Bronze and Iron Age Europe. It is possible that the Roman enthusiasm for fermented, uncooked fish sauce (garum) may have facilitated the spread of this helminth. Roman medical practitioners such as Galen were aware of intestinal worms, explaining their existence and planning treatment using the humoural theory of the period.

Evidence of Helminth Infection in Guanche Mummies: Integrating Paleoparasitological and Paleogenetic Investigations

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.

Ancient mitochondrial DNA analyses of ascaris eggs discovered in coprolites from joseon tomb

Analysis of ancient DNA (aDNA) extracted from Ascaris is very important for understanding the phylogenetic lineage of the parasite species. When aDNAs obtained from a Joseon tomb (SN2-19-1) coprolite in which Ascaris eggs were identified were amplified with primers for cytochrome b (cyt b) and 18S small subunit ribosomal RNA (18S rRNA) gene, the outcome exhibited Ascaris specific amplicon bands. By cloning, sequencing, and analysis of the amplified DNA, we obtained information valuable for comprehending genetic lineage of Ascaris prevalent among pre-modern Joseon peoples.

How to optimise the yield of forensic and clinical post-mortem microbiology with an adequate sampling: a proposal for standardisation

Post-mortem microbiology (PMM) is an important tool in forensic pathology, helping to determine the cause and manner of death, especially in difficult scenarios such as sudden unexpected death (SD). Currently, there is a lack of standardization of PMM sampling throughout Europe. We present recommendations elaborated by a panel of European experts aimed to standardize microbiological sampling in the most frequent forensic and clinical post-mortem situations. A network of forensic microbiologists, pathologists and physicians from Spain, England, Belgium, Italy and Turkey shaped a flexible protocol providing minimal requirements for PMM sampling at four practical scenarios: SD, bioterrorism, tissue and cell transplantation (TCT) and paleomicrobiology. Biosafety recommendations were also included. SD was categorized into four subgroups according to the age of the deceased and circumstances at autopsy: (1) included SD in infancy and childhood (0-16 years); (2) corresponded to SD in the young (17-35 years); (3) comprised SD at any age with clinical symptoms; and (4) included traumatic/iatrogenic SD. For each subgroup, a minimum set of samples and general recommendations for microbiological analyses were established. Sampling recommendations for main bioterrorism scenarios were provided. In the TCT setting, the Belgian sampling protocol was presented as an example. Finally, regarding paleomicrobiology, the sampling selection for different types of human remains was reviewed. This proposal for standardization in the sampling constitutes the first step towards a consensus in PMM procedures. In addition, the protocol flexibility to adapt the sampling to the clinical scenario and specific forensic findings adds a cost-benefit value.

DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in Viking-age settlement

Ancient parasite eggs were recovered from environmental samples collected at a Viking-age settlement in Viborg, Denmark, dated 1018-1030 A.D. Morphological examination identified Ascaris sp., Trichuris sp., and Fasciola sp. eggs, but size and shape did not allow species identification. By carefully selecting genetic markers, PCR amplification and sequencing of ancient DNA (aDNA) isolates resulted in identification of: the human whipworm, Trichuris trichiura , using SSUrRNA sequence homology; Ascaris sp. with 100% homology to cox1 haplotype 07; and Fasciola hepatica using ITS1 sequence homology. The identification of T. trichiura eggs indicates that human fecal material is present and, hence, that the Ascaris sp. haplotype 07 was most likely a human variant in Viking-age Denmark. The location of the F. hepatica finding suggests that sheep or cattle are the most likely hosts. Further, we sequenced the Ascaris sp. 18S rRNA gene in recent isolates from humans and pigs of global distribution and show that this is not a suited marker for species-specific identification. Finally, we discuss ancient parasitism in Denmark and the implementation of aDNA analysis methods in paleoparasitological studies. We argue that when employing species-specific identification, soil samples offer excellent opportunities for studies of human parasite infections and of human and animal interactions of the past.

Molecular paleoparasitological hybridization approach as effective tool for diagnosing human intestinal parasites from scarce archaeological remains

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.

Paleoparasitological studies on mummies of the Joseon Dynasty, Korea

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.

Evolutionary History of Terrestrial Pathogens and Endoparasites as Revealed in Fossils and Subfossils

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.

Insights about echinostomiasis by paleomolecular diagnosis

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.

Palaeopathology and genes: investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations

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.

Are Ascaris lumbricoides and Ascaris suum a single species?

Since the original description and naming of Ascaris lumbricoides from humans by Linnaeus in 1758 and later of Ascaris suum from pigs by Goeze 1782, these species have been considered to be valid. Four hypotheses relative to the conspecificity or lack thereof (and thus origin of these species) are possible: 1) Ascaris lumbricoides (usually infecting humans) and Ascaris suum (recorded mostly from pigs) are both valid species, with the two species originating via a speciation event from a common ancestor sometime before the domestication of pigs by humans, or 2) Ascaris lumbricoides in humans is derived directly from the species A. suum found in pigs with A. suum then existing as a persistent ancestor after formation of A. lumbricoides, or 3) Ascaris suum is derived directly from A. lumbricoides with the persistent ancestor being A. lumbricoides and A. suum being the newly derived species, and finally, 4) Ascaris lumbricoides and A. suum are the same species, this hypothesis being supported by studies showing both low morphological and low genetic divergence at several genes. We present and discuss paleoparasitological and genetic evidence that complement new data to evaluate the origin and evolution of Ascaris spp. in humans and pigs, and the uniqueness of the species in both hosts. Finally, we conclude that Ascaris lumbricoides and A. suum are a single species and that the name A. lumbricoides Linnaeus 1758 has taxonomic priority; therefore A. suum Goeze 1782 should be considered a synonym of A. lumbricoides.

Discovery of taeniid eggs from a 17th century tomb in Korea

Even though Taenia spp. eggs are occasionally discovered from archeological remains around the world, these eggs have never been discovered in ancient samples from Korea. When we attempted to re-examine the archeological samples maintained in our collection, the eggs of Taenia spp., 5 in total number, were recovered from a tomb of Gongju-si. The eggs had radially striated embryophore, and 37.5-40.0 µm×37.5 µm in size. This is the first report on taeniid eggs from ancient samples of Korea, and it is suggested that intensive examination of voluminous archeological samples should be needed for identification of Taenia spp.

Molecular diagnosis of infections and resistance in veterinary and human parasites

Since 1977, >2000 research papers described attempts to detect, identify and/or quantify parasites, or disease organisms carried by ecto-parasites, using DNA-based tests and 148 reviews of the topic were published. Despite this, only a few DNA-based tests for parasitic diseases are routinely available, and most of these are optional tests used occasionally in disease diagnosis. Malaria, trypanosomiasis, toxoplasmosis, leishmaniasis and cryptosporidiosis diagnosis may be assisted by DNA-based testing in some countries, but there are very few cases where the detection of veterinary parasites is assisted by DNA-based tests. The diagnoses of some bacterial (e.g. lyme disease) and viral diseases (e.g. tick borne encephalitis) which are transmitted by ecto-parasites more commonly use DNA-based tests, and research developing tests for these species makes up almost 20% of the literature. Other important uses of DNA-based tests are for epidemiological and risk assessment, quality control for food and water, forensic diagnosis and in parasite biology research. Some DNA-based tests for water-borne parasites, including Cryptosporidium and Giardia, are used in routine checks of water treatment, but forensic and food-testing applications have not been adopted in routine practice. Biological research, including epidemiological research, makes the widest use of DNA-based diagnostics, delivering enhanced understanding of parasites and guidelines for managing parasitic diseases. Despite the limited uptake of DNA-based tests to date, there is little doubt that they offer great potential to not only detect, identify and quantify parasites, but also to provide further information important for the implementation of parasite control strategies. For example, variant sequences within species of parasites and other organisms can be differentiated by tests in a manner similar to genetic testing in medicine or livestock breeding. If an association between DNA sequence and phenotype has been demonstrated, then qualities such as drug resistance, strain divergence, virulence, and origin of isolates could be inferred by DNA-based tests. No such tests are in clinical or commercial use in parasitology and few tests are available for other organisms. Why have DNA-based tests not had a bigger impact in veterinary and human medicine? To explore this question, technological, biological, economic and sociological factors must be considered. Additionally, a realistic expectation of research progress is needed. DNA-based tests could enhance parasite management in many ways, but patience, persistence and dedication will be needed to achieve this goal.

Ancient dicrocoeliosis: Occurrence, distribution and migration

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.

Paleoparasitological report on Ascaris aDNA from an ancient East Asian sample

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.