23 research outputs found

    An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim.

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    BACKGROUND: The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occurrence of serotype b (Hib), the most virulent type of H. influenzae, has since decreased, reports of infections with other serotypes and non-typeable strains are on the rise. While non-typeable strains have been studied in-depth, very little is known of the pathogen's evolutionary history, and no genomes dating prior to 1940 were available. RESULTS: We describe a Hib genome isolated from a 6-year-old Anglo-Saxon plague victim, from approximately 540 to 550 CE, Edix Hill, England, showing signs of invasive infection on its skeleton. We find that the genome clusters in phylogenetic division II with Hib strain NCTC8468, which also caused invasive disease. While the virulence profile of our genome was distinct, its genomic similarity to NCTC8468 points to mostly clonal evolution of the clade since the 6th century. We also reconstruct a partial Yersinia pestis genome, which is likely identical to a published first plague pandemic genome of Edix Hill. CONCLUSIONS: Our study presents the earliest genomic evidence for H. influenzae, points to the potential presence of larger genomic diversity in the phylogenetic division II serotype b clade in the past, and allows the first insights into the evolutionary history of this major human pathogen. The identification of both plague and Hib opens questions on the effect of plague in immunocompromised individuals already affected by infectious diseases

    A genomic and historical synthesis of plague in 18th century Eurasia

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    Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe

    Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

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    Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1’s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 × 10-7Introduction Results - Retrieved genomes are likely from typical infections - Demographic history of HSV-1 in a global context Discussion Material and Methods - Ethics statement - Sampling - Generation of aDNA libraries - Sequencing - aDNA authentication - Metagenomic screening - Targeted capture of HSV-1 - Alignment of viral data to the reference sequence - Genotyping - HSV-1 linkage disequilibrium and population genetic analysis - Compilation of comparative HSV data - Preparation of genome sequences - HSV-1 phylogenetic analysis and recombination filtering - Phylogenetic dating - Alignment of human data to the reference sequence and quality control - Genetic sex estimation, mtDNA, and Y haplotyping - Human variant calling and imputation of genotype

    Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

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    Hansen’s disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease’s complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period

    Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes.

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    Funder: Max-Planck SocietyFunder: St John’s College, CambridgeFunder: Fondation Raoul FollereauFunder: University of Zurich’s University Research Priority Program “Evolution in Action: From Genomes to Ecosystems”Funder: the Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP) at the University of TĂŒbingenBackgroundHansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period.ResultsHere, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria.ConclusionsOur findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions

    Molecular evidence for the etiologic agent of the Tyrolean epidemic of 1636

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    O. Kersten1, M. Guellil1, S. Luciani2, I. Marota2, B. Bramanti1 1University of Oslo, Department of Biosciences, CEES, Oslo, Norway 2University of Camerino, Camerino, Italy Containing major, historical and modern, trans-alpine travel routes, the region of Tyrol has been affected by various epidemics in the past. In August 1636, the Tyrolean village of Naturns (Italy) was struck by a disease referred to as "pest", killing up to 25% of the local population and leading to an increase of burials in the so-called "plague graveyard" of the St. Procolo church on the outskirts of the village. While historical sources indicated that the outbreak was likely a typhus epidemic caused by the bacterium Rickettsia prowazekii and not plague and its bacterial pathogen, Yersinia pestis, molecular evidence for the etiologic agent of this event was missing. To clarify the nature and cause of the outbreaks striking Tyrol in the 17th century, we attempted to identify the pathogen responsible for the epidemic by investigating tooth samples from individuals recovered from multiple burials in the graveyard of the St. Procolo church in Naturns dated to 1636. Human ancient DNA (aDNA) content in teeth from 24 individuals was assessed by quantitative PCR (qPCR). All extracts were screened for the presence of R. prowazekii and Y. pestis via PCR and qPCR, respectively, and samples exhibiting amplifications were further investigated via shotgun sequencing and metagenomic profiles. All teeth (24/24) contained sufficient endogenous DNA for the amplification of the human mitochondrial HVR1 region. qPCR results revealed the presence of Y. pestis pla and caf1 DNA in seven individuals, but no R. prowazekii DNA was detected in any of the 24 teeth over the course of the experiment. The metagenomic analyses are still undergoing. Contrary to historical evidence, which had suggested that the buried individuals had died of epidemic typhus, we have provided clear molecular evidence that the disease having struck Naturns in 1636 was, in fact, plague. Hence, the results of this study have shedded light on the historical past of Naturns and the Tyrolean region in the 17th century, and highlighted the importance of cooperation between archaeologists, historians, and molecular biologists in order to reconstruct the nature of ancient epidemics

    Artificial Intelligence-Based Teleopthalmology Application for Diagnosis of Diabetics Retinopathy

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    Diabetic Retinopathy (DR) is one of the leading causes of blindness for people who have diabetes in the world. However, early detection of this disease can essentially decrease its effects on the patient. The recent breakthroughs in technologies, including the use of smart health systems based on Artificial intelligence, IoT and Blockchain are trying to improve the early diagnosis and treatment of diabetic retinopathy. In this study, we presented an AI-based smart teleopthalmology application for diagnosis of diabetic retinopathy. The app has the ability to facilitate the analyses of eye fundus images via deep learning from the Kaggle database using Tensor Flow mathematical library. The app would be useful in promoting mHealth and timely treatment of diabetic retinopathy by clinicians. With the AI-based application presented in this paper, patients can easily get supports and physicians and researchers can also mine or predict data on diabetic retinopathy and reports generated could assist doctors to determine the level of severity of the disease among the people

    Bioarchaeological insights into the last plague of Imola (1630–1632)

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    The plague of 1630–1632 was one of the deadliest plague epidemics to ever hit Northern Italy, and for many of the affected regions, it was also the last. While accounts on plague during the early 1630s in Florence and Milan are frequent, much less is known about the city of Imola. We analyzed the full skeletal assemblage of four mass graves (n = 133 individuals) at the Lazaretto dell’Osservanza, which date back to the outbreak of 1630–1632 in Imola and evaluated our results by integrating new archival sources. The skeletons showed little evidence of physical trauma and were covered by multiple layers of lime, which is characteristic for epidemic mass mortality sites. We screened 15 teeth for Yersinia pestis aDNA and were able to confirm the presence of plague in Imola via metagenomic analysis. Additionally, we studied a contemporaneous register, in which a friar recorded patient outcomes at the lazaretto during the last year of the epidemic. Our multidisciplinary approach combining historical, osteological and genomic data provided a unique opportunity to reconstruct an in-depth picture of the last plague of Imola through the city's main lazaretto

    Concepção e avaliação de uma unidade de peneiramento forçado para a redução do tamanho de partículas presentes no esgoto bruto doméstico Design and evaluation of a forced sieving unit (FSU) for the reduction of the particle size present in raw domestic sewage

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    Este trabalho teve como objetivo a concepção e o teste de uma unidade de peneiramento forçado, utilizada para o pré-tratamento do esgoto bruto com vistas à redução do tamanho de partículas de matéria orgùnica. A unidade de peneiramento forçado (UPF) era constituída de uma peneira metålica (abertura de malha de 1 mm) inserida na tubulação de recalque através da qual o esgoto efluente era bombeado. O peneiramento forçado resultou em maior concentração de partículas com diùmetro entre 1,8 e 30 ”m, sem que houvesse retenção de material particulado. Todavia, a UPF não influenciou na redução/retenção de DQO TOTAL do esgoto bruto.<br>The work focused on the conception and test of a forced sieving unit, used for the pre-treatment of raw sewage aiming at the reduction of organic matter particle size. The pre-treatment unit involved the use of a metallic sieve (1 mm cut-off) assembled inside the pipeline through which the influent sewage was pumped. The results indicated that the forced sieving resulted in a higher concentration of particles with range diameter between 1.8 and 30 ”m, without the retention of particulate material. However, the forced sieving unit did not influence the reduction/retention of COD TOTAL of the raw sewage
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