ABSTRACT
Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia BCE, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.
Subject(s)
DNA, Ancient , Genome, Mitochondrial , Genome, Protozoan , Malaria , Plasmodium , Female , Humans , Male , Altitude , Americas/epidemiology , Asia/epidemiology , Biological Evolution , Disease Resistance/genetics , DNA, Ancient/analysis , Europe/epidemiology , Genome, Mitochondrial/genetics , Genome, Protozoan/genetics , History, Ancient , Malaria/parasitology , Malaria/history , Malaria/transmission , Malaria/epidemiology , Malaria, Falciparum/epidemiology , Malaria, Falciparum/history , Malaria, Falciparum/parasitology , Malaria, Falciparum/transmission , Malaria, Vivax/epidemiology , Malaria, Vivax/history , Malaria, Vivax/parasitology , Malaria, Vivax/transmission , Plasmodium/genetics , Plasmodium/classification , Plasmodium falciparum/genetics , Plasmodium falciparum/isolation & purification , Plasmodium malariae/genetics , Plasmodium malariae/isolation & purification , Plasmodium vivax/genetics , Plasmodium vivax/isolation & purificationABSTRACT
The origin of the medieval Black Death pandemic (AD 1346-1353) has been a topic of continuous investigation because of the pandemic's extensive demographic impact and long-lasting consequences1,2. Until now, the most debated archaeological evidence potentially associated with the pandemic's initiation derives from cemeteries located near Lake Issyk-Kul of modern-day Kyrgyzstan1,3-9. These sites are thought to have housed victims of a fourteenth-century epidemic as tombstone inscriptions directly dated to 1338-1339 state 'pestilence' as the cause of death for the buried individuals9. Here we report ancient DNA data from seven individuals exhumed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium Yersinia pestis in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic's emergence, here dated to the first half of the fourteenth century. Comparisons with present-day diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early fourteenth-century source of the second plague pandemic in central Eurasia.
Subject(s)
Plague , Yersinia pestis , Archaeology , Cemeteries , DNA, Ancient/analysis , DNA, Bacterial/analysis , History, Medieval , Humans , Kyrgyzstan/epidemiology , Pandemics/history , Phylogeny , Plague/epidemiology , Plague/history , Plague/microbiology , Yersinia pestis/classification , Yersinia pestis/pathogenicityABSTRACT
Changes in biodiversity may impact infectious disease transmission through multiple mechanisms. We explored the impact of biodiversity changes on the transmission of Amazonian leishmaniases, a group of wild zoonoses transmitted by phlebotomine sand flies (Psychodidae), which represent an important health burden in a region where biodiversity is both rich and threatened. Using molecular analyses of sand fly pools and blood-fed dipterans, we characterized the disease system in forest sites in French Guiana undergoing different levels of human-induced disturbance. We show that the prevalence of Leishmania parasites in sand flies correlates positively with the relative abundance of mammal species known as Leishmania reservoirs. In addition, Leishmania reservoirs tend to dominate in less diverse mammal communities, in accordance with the dilution effect hypothesis. This results in a negative relationship between Leishmania prevalence and mammal diversity. On the other hand, higher mammal diversity is associated with higher sand fly density, possibly because more diverse mammal communities harbor higher biomass and more abundant feeding resources for sand flies, although more research is needed to identify the factors that shape sand fly communities. As a consequence of these antagonistic effects, decreased mammal diversity comes with an increase of parasite prevalence in sand flies, but has no detectable impact on the density of infected sand flies. These results represent additional evidence that biodiversity changes may simultaneously dilute and amplify vector-borne disease transmission through different mechanisms that need to be better understood before drawing generalities on the biodiversity-disease relationship.
Subject(s)
Leishmania , Leishmaniasis , Psychodidae , Animals , Humans , Leishmania/genetics , Biodiversity , Zoonoses , MammalsABSTRACT
Leishmania kinetoplast DNA contains thousands of small circular molecules referred to as kinetoplast DNA (kDNA) minicercles. kDNA minicircles are the preferred targets for sensitive Leishmania detection, because they are present in high copy number and contain conserved sequence blocks in which polymerase chain reaction (PCR) primers can be designed. On the other hand, the heterogenic nature of minicircle networks has hampered the use of this peculiar genomic region for strain typing. The characterization of Leishmania minicirculomes used to require isolation and cloning steps prior to sequencing. Here, we show that high-throughput sequencing of single minicircle PCR products allows bypassing these laborious laboratory tasks. The 120 bp long minicircle conserved region was amplified by PCR from 18 Leishmania strains representative of the major species complexes found in the Neotropics. High-throughput sequencing of PCR products enabled recovering significant numbers of distinct minicircle sequences from each strain, reflecting minicircle class diversity. Minicircle sequence analysis revealed patterns that are congruent with current hypothesis of Leishmania relationships. Then, we show that a barcoding-like approach based on minicircle sequence comparisons may allow reliable identifications of Leishmania spp. This work opens up promising perspectives for the study of kDNA minicercles and a variety of applications in Leishmania research.
Subject(s)
DNA, Kinetoplast/genetics , DNA, Protozoan/genetics , Genome, Protozoan , High-Throughput Nucleotide Sequencing , Leishmania/genetics , DNA Barcoding, Taxonomic , DNA, Kinetoplast/isolation & purification , DNA, Protozoan/isolation & purification , Genetic Variation , Leishmania/classification , Leishmania/isolation & purification , Polymerase Chain ReactionABSTRACT
Trypanosoma evansi, the causative agent of surra, is widespread in domestic livestock and wildlife in South East Asia. Surra can affect cattle, buffaloes, horses and also Asian elephants (Elephas maximus). Despite the 'threatened to extinction' CITES status of elephant, surra's impact has not been thoroughly assessed yet in this species. This work offers to adapt an antibody enzyme-linked immunosorbent assay (ELISA) protocol, to detect Trypanosoma evansi antibodies in elephant serum. The test was validated with 365 negative-reference samples, which allowed the determination of a 16% positive threshold. The test was applied to a serological survey including 375 individuals. The estimated global seroprevalence was 2·1% (95% CI 1·1-4·2%). Therefore, surra does not appear to be endemic in Thai domestic elephants, but occasional outbreaks were reported to our laboratory during the survey period. These outbreaks seemed to be linked to close proximity to cattle or buffaloes, and led to severe clinical signs in elephants. Frequent relapses were observed after treatment with diminazene aceturate, the only trypanocide drug currently available in Thailand. Therefore, care should be taken to keep elephants away from bovine reservoirs, and to monitor the disease in this endangered species. ELISA proved to be reliable for screening purposes as well as for post-treatment monitoring.
Subject(s)
Antibodies, Protozoan/blood , Enzyme-Linked Immunosorbent Assay/veterinary , Protozoan Infections, Animal/diagnosis , Seroepidemiologic Studies , Trypanosoma/immunology , Trypanosomiasis/veterinary , Acclimatization , Animals , Animals, Domestic/immunology , Animals, Wild/immunology , Animals, Wild/parasitology , Antigens, Protozoan/immunology , Buffaloes/parasitology , Cattle/parasitology , Diminazene/analogs & derivatives , Diminazene/therapeutic use , Disease Reservoirs/parasitology , Disease Reservoirs/veterinary , Elephants/parasitology , Enzyme-Linked Immunosorbent Assay/methods , Protozoan Infections, Animal/blood , Protozoan Infections, Animal/epidemiology , Protozoan Infections, Animal/immunology , Thailand/epidemiology , Trypanosomiasis/drug therapy , Trypanosomiasis/epidemiology , Trypanosomiasis/immunologyABSTRACT
In the current context of global change and human-induced biodiversity decline, there is an urgent need for developing sampling approaches able to accurately describe the state of biodiversity. Traditional surveys of vertebrate fauna involve time-consuming and skill-demanding field methods. Recently, the use of DNA derived from invertebrate parasites (leeches and blowflies) was suggested as a new tool for vertebrate diversity assessment. Bloodmeal analyses of arthropod disease vectors have long been performed to describe their feeding behaviour, for epidemiological purposes. On the other hand, this existing expertise has not yet been applied to investigate vertebrate fauna per se. Here, we evaluate the usefulness of hematophagous dipterans as vertebrate samplers. Blood-fed sand flies and mosquitoes were collected in Amazonian forest sites and analysed using high-throughput sequencing of short mitochondrial markers. Bloodmeal identifications highlighted contrasting ecological features and feeding behaviour among dipteran species, which allowed unveiling arboreal and terrestrial mammals of various body size, as well as birds, lizards and amphibians. Additionally, lower vertebrate diversity was found in sites undergoing higher levels of human-induced perturbation. These results suggest that, in addition to providing precious information on disease vector host use, dipteran bloodmeal analyses may represent a useful tool in the study of vertebrate communities. Although further effort is required to validate the approach and consider its application to large-scale studies, this first work opens up promising perspectives for biodiversity monitoring and eco-epidemiology.
Subject(s)
DNA/blood , Insect Vectors/genetics , Vertebrates/classification , Animals , Biodiversity , Culicidae/genetics , Feeding Behavior , French Guiana , Psychodidae/geneticsABSTRACT
SARS-CoV-2 can infect human cells through the recognition of the human angiotensin-converting enzyme 2 receptor. This affinity is given by six amino acid residues located in the variable loop of the receptor binding domain (RBD) within the Spike protein. Genetic recombination involving bat and pangolin Sarbecoviruses, and natural selection have been proposed as possible explanations for the acquisition of the variable loop and these amino acid residues. In this study we employed Bayesian phylogenetics to jointly reconstruct the phylogeny of the RBD among human, bat and pangolin Sarbecoviruses and detect recombination events affecting this region of the genome. A recombination event involving RaTG13, the closest relative of SARS-CoV-2 that lacks five of the six residues, and an unsampled Sarbecovirus lineage was detected. This result suggests that the variable loop of the RBD didn't have a recombinant origin and the key amino acid residues were likely present in the common ancestor of SARS-CoV-2 and RaTG13, with the latter losing five of them probably as the result of recombination.
Subject(s)
COVID-19 , Chiroptera , Animals , Humans , SARS-CoV-2/genetics , Phylogeny , Pangolins , Bayes Theorem , Recombination, Genetic , Amino Acids/geneticsABSTRACT
Hepatitis B virus is a globally distributed pathogen and the history of HBV infection in humans predates 10000 years. However, long-term evolutionary history of HBV in Eastern Eurasia remains elusive. We present 34 ancient HBV genomes dating between approximately 5000 to 400 years ago sourced from 17 sites across Eastern Eurasia. Ten sequences have full coverage, and only two sequences have less than 50% coverage. Our results suggest a potential origin of genotypes B and D in Eastern Asia. We observed a higher level of HBV diversity within Eastern Eurasia compared to Western Eurasia between 5000 and 3000 years ago, characterized by the presence of five different genotypes (A, B, C, D, WENBA), underscoring the significance of human migrations and interactions in the spread of HBV. Our results suggest the possibility of a transition from non-recombinant subgenotypes (B1, B5) to recombinant subgenotypes (B2 - B4). This suggests a shift in epidemiological dynamics within Eastern Eurasia over time. Here, our study elucidates the regional origins of prevalent genotypes and shifts in viral subgenotypes over centuries.
Subject(s)
Hepatitis B virus , Human Migration , Humans , Hepatitis B virus/genetics , Phylogeny , Genotype , Biological Evolution , DNA, Viral/geneticsABSTRACT
BACKGROUND: Plague is a zoonotic disease caused by the bacterium Yersinia pestis, highly prevalent in the Central Highlands, a mountainous region in the center of Madagascar. After a plague-free period of over 60 years in the northwestern coast city of Mahajanga, the disease reappeared in 1991 and caused several outbreaks until 1999. Previous research indicates that the disease was reintroduced to the city of Mahajanga from the Central Highlands instead of reemerging from a local reservoir. However, it is not clear how many reintroductions occurred and when they took place. METHODOLOGY/PRINCIPAL FINDINGS: In this study we applied a Bayesian phylogeographic model to detect and date migrations of Y. pestis between the two locations that could be linked to the re-emergence of plague in Mahajanga. Genome sequences of 300 Y. pestis strains sampled between 1964 and 2012 were analyzed. Four migrations from the Central Highlands to Mahajanga were detected. Two resulted in persistent transmission in humans, one was responsible for most of the human cases recorded between 1995 and 1999, while the other produced plague cases in 1991 and 1992. We dated the emergence of the Y. pestis sub-branch 1.ORI3, which is only present in Madagascar and Turkey, to the beginning of the 20th century, using a Bayesian molecular dating analysis. The split between 1.ORI3 and its ancestor lineage 1.ORI2 was dated to the second half of the 19th century. CONCLUSIONS/SIGNIFICANCE: Our results indicate that two independent migrations from the Central Highlands caused the plague outbreaks in Mahajanga during the 1990s, with both introductions occurring during the early 1980s. They happened over a decade before the detection of human cases, thus the pathogen likely survived in wild reservoirs until the spillover to humans was possible. This study demonstrates the value of Bayesian phylogenetics in elucidating the re-emergence of infectious diseases.
Subject(s)
Yersinia pestis , Zoonoses , Animals , Humans , Phylogeny , Madagascar/epidemiology , Bayes Theorem , Phylogeography , Yersinia pestis/geneticsABSTRACT
Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.
Subject(s)
Deafness , Famous Persons , Music , Male , Humans , Genetic Predisposition to Disease , Genomics , HairABSTRACT
Infectious diseases are a major burden to global economies, and public and animal health. To date, quantifying the spread of infectious diseases to inform policy making has traditionally relied on epidemiological data collected during epidemics. However, interest has grown in recent phylodynamic techniques to infer pathogen transmission dynamics from genetic data. Here, we provide examples of where this new discipline has enhanced disease management in public health and illustrate how it could be further applied in animal health. In particular, we describe how phylodynamics can address fundamental epidemiological questions, such as inferring key transmission parameters in animal populations and quantifying spillover events at the wildlife-livestock interface, and generate important insights for the design of more effective control strategies.
Subject(s)
Communicable Diseases , Epidemics , Animals , Animals, Wild , Communicable Diseases/epidemiology , Communicable Diseases/veterinary , LivestockABSTRACT
French Guiana is a European ultraperipheric region located on the northern Atlantic coast of South America. It constitutes an important forested region for biological conservation in the Neotropics. Although very sparsely populated, with its inhabitants mainly concentrated on the Atlantic coastal strip and along the two main rivers, it is marked by the presence and development of old and new epidemic disease outbreaks, both research and health priorities. In this review paper, we synthetize 15 years of multidisciplinary and integrative research at the interface between wildlife, ecosystem modification, human activities and sociodemographic development, and human health. This study reveals a complex epidemiological landscape marked by important transitional changes, facilitated by increased interconnections between wildlife, land-use change and human occupation and activity, human and trade transportation, demography with substantial immigration, and identified vector and parasite pharmacological resistance. Among other French Guianese characteristics, we demonstrate herein the existence of more complex multi-host disease life cycles than previously described for several disease systems in Central and South America, which clearly indicates that today the greater promiscuity between wildlife and humans due to demographic and economic pressures may offer novel settings for microbes and their hosts to circulate and spread. French Guiana is a microcosm that crystallizes all the current global environmental, demographic and socioeconomic change conditions, which may favor the development of ancient and future infectious diseases.
Subject(s)
Animals, Wild , Demography , Ecosystem , Vector Borne Diseases , Zoonoses , Animals , French Guiana/epidemiology , Human Activities , Humans , Incidence , Interdisciplinary Research , Prevalence , Vector Borne Diseases/epidemiology , Vector Borne Diseases/transmission , Zoonoses/epidemiology , Zoonoses/etiology , Zoonoses/transmissionABSTRACT
Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.
Subject(s)
Communicable Diseases, Emerging/history , Evolution, Molecular , Hepatitis B virus/classification , Hepatitis B virus/genetics , Hepatitis B/history , Americas , Asia , Asian People , Communicable Diseases, Emerging/virology , Europe , Genetic Variation , Genomics , Hepatitis B/virology , History, Ancient , Humans , Paleontology , Phylogeny , White People , American Indian or Alaska NativeABSTRACT
The forced relocation of several thousand Africans during Mexico's historic period has so far been documented mostly through archival sources, which provide only sparse detail on their origins and lived experience. Here, we employ a bioarchaeological approach to explore the life history of three 16th century Africans from a mass burial at the San José de los Naturales Royal Hospital in Mexico City. Our approach draws together ancient genomic data, osteological analysis, strontium isotope data from tooth enamel, δ13C and δ15N isotope data from dentine, and ethnohistorical information to reveal unprecedented detail on their origins and health. Analyses of skeletal features, radiogenic isotopes, and genetic data from uniparental, genome-wide, and human leukocyte antigen (HLA) markers are consistent with a Sub-Saharan African origin for all three individuals. Complete genomes of Treponema pallidum sub. pertenue (causative agent of yaws) and hepatitis B virus (HBV) recovered from these individuals provide insight into their health as related to infectious disease. Phylogenetic analysis of both pathogens reveals their close relationship to strains circulating in current West African populations, lending support to their origins in this region. The further relationship between the treponemal genome retrieved and a treponemal genome previously typed in an individual from Colonial Mexico highlights the role of the transatlantic slave trade in the introduction and dissemination of pathogens into the New World. Putting together all lines of evidence, we were able to create a biological portrait of three individuals whose life stories have long been silenced by disreputable historical events.
Subject(s)
DNA, Ancient/analysis , Enslaved Persons/history , Health Status , Hepatitis B/history , Yaws/history , Adult , Archaeology , Black People/history , Hepatitis B virus/isolation & purification , History, 16th Century , Humans , Male , Mexico , Treponema/isolation & purification , Young AdultABSTRACT
Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15th century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood.
Subject(s)
DNA, Ancient/analysis , Genome, Bacterial/genetics , Treponema pallidum/genetics , Archaeology , Europe , Genetic Variation/genetics , History, 15th Century , History, Medieval , Humans , Syphilis/genetics , Syphilis/history , Syphilis/microbiology , Treponema pallidum/metabolism , Yaws/genetics , Yaws/history , Yaws/microbiologyABSTRACT
Surra, caused by Trypanosoma evansi, is a widely distributed animal trypanosomosis; it affects both domestic and wild mammals with high economic impact. Clinical picture is moderate in bovines but severe in equids. Surra is also an important constraint for international animal trade and movements. Despite its impact, surra remains poorly diagnosed because of low sensitivity tests. To improve epidemiological knowledge of the disease and to secure international movement, efficient diagnosis tools are required. Here, we optimized and applied to equids the OIE-recommended indirect ELISA T. evansi that was validated in other species. Based on 96 positive and 1,382 negative horse reference samples from Thailand, a TG-ROC analysis was conducted to define the cutoff value. ELISA's sensitivity and specificity were estimated at 97.5% and 100%, respectively, qualifying the test to provide a reliable immune status of equids. The test was then applied on 1,961 horse samples from 18 Thai Provinces; the only scarce positives suggested that horses do not constitute a reservoir of T. evansi in Thailand. All samples from racing horses were negative. Conversely, two outbreaks of surra reported to our laboratory, originating from a bovine reservoir, exhibited high morbidity and lethality rates in horses. Finally, posttreatment follow-ups of infected animals allowed us to provide outbreak management guidelines.
Subject(s)
Horses/blood , Serologic Tests , Trypanosoma/isolation & purification , Trypanosomiasis/blood , Animals , Antigens, Protozoan/blood , Enzyme-Linked Immunosorbent Assay , Horses/parasitology , Thailand/epidemiology , Trypanosoma/pathogenicity , Trypanosomiasis/epidemiology , Trypanosomiasis/parasitology , Trypanosomiasis/veterinaryABSTRACT
Phlebotomine sand flies are insects that are highly relevant in medicine, particularly as the sole proven vectors of leishmaniasis. Accurate identification of sand fly species is an essential prerequisite for eco-epidemiological studies aiming to better understand the disease. Traditional morphological identification is painstaking and time-consuming, and molecular methods for extensive screening remain expensive. Recent studies have shown that matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a promising tool for rapid and cost-effective identification of arthropod vectors, including sand flies. The aim of this study was to validate the use of MALDI-TOF MS for the identification of Northern Amazonian sand flies. We constituted a MALDI-TOF MS reference database comprising 29 species of sand flies that were field-collected in French Guiana, which are expected to cover many of the more common species of the Northern Amazonian region, including known vectors of leishmaniasis. Carrying out a blind test, all the sand flies tested (n = 157) with a log (score) threshold greater than 1.7 were correctly identified at the species level. We confirmed that MALDI-TOF MS protein profiling is a useful tool for the study of sand flies, including neotropical species, known for their great diversity. An application that includes the spectra generated here will be available to the scientific community in the near future via an online platform.
Subject(s)
Phlebotomus/genetics , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Animals , Female , French Guiana , Gene Library , Male , Species SpecificityABSTRACT
Phlebotomine sand flies are haematophagous dipterans of primary medical importance. They represent the only proven vectors of leishmaniasis worldwide and are involved in the transmission of various other pathogens. Studying the ecology of sand flies is crucial to understand the epidemiology of leishmaniasis and further control this disease. A major limitation in this regard is that traditional morphological-based methods for sand fly species identifications are time-consuming and require taxonomic expertise. DNA metabarcoding holds great promise in overcoming this issue by allowing the identification of multiple species from a single bulk sample. Here, we assessed the reliability of a short insect metabarcode located in the mitochondrial 16S rRNA for the identification of Neotropical sand flies, and constructed a reference database for 40 species found in French Guiana. Then, we conducted a metabarcoding experiment on sand flies mixtures of known content and showed that the method allows an accurate identification of specimens in pools. Finally, we applied metabarcoding to field samples caught in a 1-ha forest plot in French Guiana. Besides providing reliable molecular data for species-level assignations of phlebotomine sand flies, our study proves the efficiency of metabarcoding based on the mitochondrial 16S rRNA for studying sand fly diversity from bulk samples. The application of this high-throughput identification procedure to field samples can provide great opportunities for vector monitoring and eco-epidemiological studies.
Subject(s)
DNA Barcoding, Taxonomic/methods , Insect Vectors , Metagenomics/methods , Psychodidae/classification , Psychodidae/genetics , Animals , Cluster Analysis , DNA, Mitochondrial/chemistry , DNA, Mitochondrial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , French Guiana , Phylogeny , Psychodidae/growth & development , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNAABSTRACT
The nearly complete mitochondrial genome of Lutzomyia umbratilis Ward & Fraiha, 1977 (Psychodidae: Phlebotominae), considered as the main vector of Leishmania guyanensis, is presented. The sequencing has been performed on an Illumina Hiseq 2500 platform, with a genome skimming strategy. The full nuclear ribosomal RNA segment was also assembled. The mitogenome of L. umbratilis was determined to be at least 15,717 bp-long and presents an architecture found in many mitogenomes of insect (13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one non-coding region also referred as the control region). The control region contains a large repeated element of c. 370 bp and a poly-AT region of unknown length. This is the first mitogenome of Psychodidae to be described.
Subject(s)
Genome, Mitochondrial , Insect Vectors/genetics , Psychodidae/genetics , Animals , Insect Proteins/genetics , Insect Vectors/parasitology , Leishmania guyanensis , Mitochondrial Proteins/genetics , Psychodidae/parasitology , RNA/genetics , RNA, Mitochondrial , RNA, Ribosomal/genetics , RNA, Transfer/geneticsABSTRACT
Lace bugs (Tingidae) are a family of phytophagous heteropterans, some of which are important agricultural and forestry pests. They currently comprise around 2500 species distributed worldwide, for which only one mitochondrial genome has been described so far. We sequenced the complete mitochondrial genome and the nuclear ribosomal gene segment of the avocado lace bug Pseudacysta perseae using a genome skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including the one of the sycamore lace bug Corythucha ciliata, were retrieved to allow for comparisons and phylogenetic analyses. P. perseae mitochondrial genome was determined to be 15,850 bp long, and presented the typical organisation of insect mitogenomes. The phylogenetic analysis placed P. perseae as a sister to C. ciliata but did not confirm the monophyly of Miroidae including Tingidae. Our results contradicted widely accepted phylogenetic hypothesis, which highlights the limits of analyses based on mitochondrial data only. Shotgun sequencing approaches should provide substantial improvements in harmonizing mitochondrial and nuclear databases.