Metagenomic analysis reveals mixed Mycobacterium tuberculosis infection in a 18th century Hungarian midwife.

The Vác Mummy Collection comprises 265 well documented mummified individuals from the late 16th to the early 18th century that were discovered in 1994 inside a crypt in Vác, Hungary. This collection offers a unique opportunity to study the relationship between humans and pathogens in the pre-antibiotic era, as previous studies have shown a high proportion of tuberculosis (TB) infections among the individuals. In this study, we recovered ancient DNA with shotgun sequencing from a rib bone sample of a 18th century midwife. This individual is part of the collection and shows clear skeletal changes that are associated with tuberculosis and syphilis. To provide molecular proof, we applied a metagenomic approach to screen for ancient pathogen DNA. While we were unsuccessful to recover any ancient Treponema pallidum DNA, we retrieved high coverage ancient TB DNA and identified a mixed infection with two distinct TB strains by detailed single-nucleotide polymorphism and phylogenetic analysis. Thereby, we have obtained comprehensive results demonstrating the long-time prevalence of mixed infections with the sublineages L4.1.2.1/Haarlem and L4.10/PGG3 within the local community in preindustrial Hungary and put them in context of sociohistorical factors.

Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years.

Tuberculosis (TB), usually caused by Mycobacterium tuberculosis bacteria, is the first cause of death from an infectious disease at the worldwide scale, yet the mode and tempo of TB pressure on humans remain unknown. The recent discovery that homozygotes for the P1104A polymorphism of TYK2 are at higher risk to develop clinical forms of TB provided the first evidence of a common, monogenic predisposition to TB, offering a unique opportunity to inform on human co-evolution with a deadly pathogen. Here, we investigate the history of human exposure to TB by determining the evolutionary trajectory of the TYK2 P1104A variant in Europe, where TB is considered to be the deadliest documented infectious disease. Leveraging a large dataset of 1,013 ancient human genomes and using an approximate Bayesian computation approach, we find that the P1104A variant originated in the common ancestors of West Eurasians ∼30,000 years ago. Furthermore, we show that, following large-scale population movements of Anatolian Neolithic farmers and Eurasian steppe herders into Europe, P1104A has markedly fluctuated in frequency over the last 10,000 years of European history, with a dramatic decrease in frequency after the Bronze Age. Our analyses indicate that such a frequency drop is attributable to strong negative selection starting ∼2,000 years ago, with a relative fitness reduction on homozygotes of 20%, among the highest in the human genome. Together, our results provide genetic evidence that TB has imposed a heavy burden on European health over the last two millennia.

'TB or not TB': the conundrum of pre-European contact tuberculosis in the Pacific.

Tuberculosis (TB) is a major global health threat, infecting one-third of the world's population. Despite this prominence, the age, origin and spread of the disease have been topics of contentious debate. Molecular studies suggest that Mycobacterium tuberculosis 'sensu stricto', the most common strain of TB infecting humans today, originated in Africa and from there spread into Europe and Asia. The M. tuberculosis strains most commonly found across the Pacific and the Americas today are most closely related to European strains, supporting a hypothesis that the disease only reached these regions relatively recently via European sailors or settlers. However, this hypothesis is inconsistent with palaeopathological evidence of TB-like lesions in human remains from across the Pacific that predate European contact. Similarly, genetic evidence from pre-European South American mummies challenges the notion of a European introduction of the disease into the Pacific. Here, we review the complex evidence for the age and origin of TB in the Pacific, and discuss key gaps in our knowledge and how these may be addressed. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.

Multi-proxy stable isotope analyses of dentine microsections reveal diachronic changes in life history adaptations, mobility, and tuberculosis-induced wasting in prehistoric Liguria (Finale Ligure, Italy, northwestern Mediterranean).

OBJECTIVE: To reconstruct breastfeeding and weaning practices, metabolic stress including tuberculosis-induced wasting, and residential mobility of children in Neolithic and Metal Ages to infer their local ecologies. MATERIALS: Seven permanent teeth from individuals dated to the Neolithic, Copper, Bronze, and Iron Ages buried in nearby caves in western Liguria, Italy. METHODS: Carbon, nitrogen, and sulfur stable isotope analyses on dentine microsections. Tooth maturation was used to calculate age at death. RESULTS: Two Neolithic children present longer pattern of weaning and appear to have been weaned using animal protein in contrast to the earlier weaning of Metal Ages children, which were probably weaned with vegetable resources. Sulfur isotopes suggest local origin of Neolithic and Cooper Age children, and non-local origins for Bronze and Iron Age children. Intense catabolism in the last two years is apparent in the adolescent with tuberculosis. CONCLUSIONS: Shortening in weaning patterns during the Metal Ages are likely driven by the intensification of agricultural practices and cultivation of new crops during Bronze and Iron Ages. Neolithic food choices and delayed weaning patterns may represent one of the strategies to maximize growth and immune potential in a local economy/ecology with high-infectious load. Tuberculosis was a chronic and long-lasting disease. SIGNIFICANCE: The first combined carbon, nitrogen, and sulfur analysis on prehistoric dentine microsections revealing changing human life history adaptations within the same region. LIMITATIONS: Small sample size. SUGGESTIONS FOR FURTHER RESEARCH: Increase the sulfur isotope dataset, use new EA-IRMS equipment, and provide data on amino acid to better define weaning food composition.

Statistics and Colonial Medicine: A Doubt and Controversy on Tuberculosis Statistics in Colonial Korea.

This paper focuses on the criticism of tuberculosis statistics published by the Japanese Government-general in colonial Korea and a research on the reality of tuberculosis prevalence by medical doctors from the Department of Hygiene and Preventive Medicine at Keijo Imperial University (DHPMK). Recent studies have shown that colonial statistics shape the image of colonial subjects and justify the control to them. Following this perspective, this paper explores the process of producing the statistical knowledge of tuberculosis by medical scientists from DHPMK. Their goal was to find out the resistance to tuberculosis as biological characteristics of Korean race/ethnicity. In order to do so, they demonstrated the existence of errors in tuberculosis statistics by the Korean colonial government and devised a statistical method to correct them based on the conviction that the Western modern medicine was superior than Korean traditional medicine as well as the racist bias against Korean. By analyzing how the statistical concepts reflected these prejudices, this paper argues that the statistical knowledge of tuberculosis created images that Japanese people was healthier and stronger than the Korean people and justified the colonial government's control over Korean.

Análise das políticas de controlo da tuberculose e do perfil epidemiológico da infecção em Moçambique (2009-2017) / Analysing tuberculosis control policies and the epidemiological profile of the infection in Mozambique (2009-2017)

A epidemia da tuberculose em Moçambique tem sido influenciada consideravelmente por factores como as condições económicas, incluindo a pobreza e o desemprego, as condições ambientais, incluindo bairros urbanos superlotados, a epidemia de VIH, as condições sociais, incluindo as migrações por trabalho, e as infraestruturas de saúde deficientes, bem como pela ocorrência de novas infecções por tuberculose, que têm aumentado de forma dramática nos últimos 10 a15 anos. A análise das políticas do Programa Nacional de Controlo da Tuberculose é de extrema importância, pois permite avaliar as suas operações e resultados, tornando-as mais efectivas na consecução da cobertura universal dos cuidados de saúde. Estas políticas, adoptadas na área da tuberculose influenciam o perfil epidemiológico da doença, pelo que a análise desse perfil é fundamental para avaliar o desempenho do programa ao longo dos tempos. Por outro lado, a análise do perfil epidemiológico da tuberculose permite, também, ajustar os objectivos e as respectivas intervenções do programa, contribuindo, desta forma, para a melhoria da resposta e dos indicadores de saúde. A maioria dos estudos realizados em Moçambique sobre as políticas de saúde e, mais especificamente, sobre aquelas relacionadas com a tuberculose, analisam as políticas e o perfil dos indicadores do programa de forma independente, desconhecendo-se, até ao presente momento, estudos que adoptem uma abordagem integrada destas duas vertentes ­ políticas e perfil da infecção. A presente investigação teve como objetivo geral compreender as políticas de controlo de tuberculose e a forma como estas se reflectiram no perfil epidemiológico da doença entre 2009 e 2017. Realizaram-se dois estudos: um qualitativo e outro quantitativo. No primeiro estudo, qualitativo, analisaram-se as políticas do Programa Nacional de Controlo da Tuberculose em Moçambique. Para tal utilizou-se a análise documental para identificar as políticas relevantes e a análise de conteúdo para discernir sobre as mesmas. No segundo estudo, quantitativo, o perfil epidemiológico da tuberculose entre 2009 e 2017 foi analisado utilizando um desenho ecológico descritivo, recorrendo a dados secundários de notificação e de avaliação dos casos, colhidos nos programas provinciais de controlo da tuberculose de Nampula, Sofala e Maputo. Para caracterizar clínica e epidemiológicamente a tuberculose, foram calculados indicadores anuais e a variação 7 percentual ao longo dos anos. De seguida, relacionaram-se as políticas, nomeadamente os seus principais marcos, com o perfil epidemiológico da doença, relacionando-os qualitativamente com os resultados dos indicadores...

he tuberculosis epidemic in Mozambique has been considerably influenced by factors such as economic conditions, including poverty and unemployment, environmental conditions, including overcrowded urban neighborhoods, the HIV epidemic, social conditions, including migrations by work, and poor health infrastructure; as well as the occurrence of new tuberculosis infections that have increased dramatically in the last 10 to 15 years. The analysis of the policies of the National Tuberculosis Control Program is extremely important, as it allows to evaluate its operations and results, making them more effective in achieving universal health care coverage. These policies adopted in the area of tuberculosis influence the epidemiological profile of the disease, so the analysis of this profile is essential to assess the performance of the program over time. On the other hand, the analysis of the epidemiological profile of tuberculosis also allows to adjust the objectives and respective interventions of the program, thus contributing to the improvement of the response and health indicators. Most of the studies carried out in Mozambique on health policies and, more specifically, on those related to tuberculosis, analyze the policies and the profile of the program indicators independently, and at the moment, studies that adopt an integrated analyze of these two policy approaches and infection profile are unknown. This research aimed to understand the tuberculosis control policies and the way they were reflected in the epidemiological profile of the disease between 2009 and 2017. Two studies were carried out: one qualitative and other quantitative. In the qualitative study, the policies of the National Tuberculosis Control Program in Mozambique were analyzed. To this end, document analysis was used to identify relevant policies and content analysis to discern them. In the seconda, quantitative study, the epidemiological profile of tuberculosis between 2009 and 2017 was analyzed using a descriptive ecological design, using secondary data for notification and case assessment, collected in the provincial tuberculosis control programs of Nampula, Sofala and Maputo. In order to clinically and epidemiologically characterize tuberculosis, annual indicators and percentage change over the years were calculated. Then, the policies, namely their main milestones, were related to the epidemiological profile of the disease, qualitatively relating them to the results of the indicators...

Sanatoria revisited: sunlight and health.

Since the 18th century tuberculosis has been a major cause of death throughout the world. It is a highly infectious disease that spreads by droplet infection and finding effective treatment to combat tuberculosis took a great deal of time. One of the first treatments to have some real success was a stay in a sanatorium. Sanatoria were homes that provided patients with good food and fresh air (and therefore sunlight). The first sanatorium to use sunlight therapy (heliotherapy) seriously was founded in Leysin, Switzerland, by Auguste Rollier. Patients built up their sun exposure gradually to prevent sunburn or skin damage. We suggest that heliotherapy was more successful in treating tuberculosis than was appreciated once chemotherapy became available. The birth of heliotherapy coincided with an increased appreciation of the association of sunlight and health among the general public. The secret of its success is the combined effects of sunlight on the skin inducing the production of nitric oxide and vitamin. Nitric oxide is not only a messenger in the cardiovascular system and responsible for relaxation of vascular muscle but is also involved in the innate immune system. Vitamin D is responsible for immune system functions and multiple studies have found an association between tuberculosis immunity and high vitamin D levels. Therefore, it is understandable that providing tuberculosis patients with sunlight may have boosted their immune system and aided them in the fight against tuberculosis. In view of the high level of resistance to all drug regimens in some patients, perhaps it is time to revive the use of sanatoria in the fight against tuberculosis.

Paleomicrobiology of Human Tuberculosis.

Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections. These can be recognized in historical and archaeological material, along with nonspecific paleopathology such as new bone formation (periostitis), especially on ribs. Based on such lesions, tuberculosis has been found in ancient Egypt, pre-Columbian America, and Neolithic Europe. The detection of M. tuberculosis ancient DNA (aDNA) by using PCR led to the development of the new field of paleomicrobiology. As a result, a large number of tuberculosis cases were recognized in mummified tissue and bones with nonspecific or no lesions. In parallel with these developments, M. tuberculosis cell wall lipid biomarkers have detected tuberculosis suggested by paleopathology and confirmed aDNA findings. In well-preserved cases, molecular typing has identified M. tuberculosis lineages and genotypes. The current interest in targeted enrichment, shotgun sequencing, and metagenomic analysis reveals ancient mixed infections with different M. tuberculosis strains and other pathogens. Identification of M. tuberculosis lineages from samples of known age enables the date of the emergence of strains and lineages to be calculated directly rather than by making assumptions on the rate of evolutionary change.

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor.

Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity. We then tried to date their Most Recent Common Ancestor (MRCA) using three calibrations of SNP accumulation rate (long-term=0.03SNP/genome/year, derived from a tuberculosis ancestor of around 70,000years old; intermediate=0.2SNP/genome/year derived from a Peruvian mummy; short-term=0.5SNP/genome/year). To disentangle between these scenarios, we confronted the corresponding divergence times with major human history events and knowledge on human genetic divergence. We identified relatively high intrasublineage diversity for both T3-Osaka and Tur. We definitively proved their monophyly; the corresponding super-sublineage (referred to as "T3-Osa-Tur") shares a common ancestor with T3-Ethiopia and Ural sublineages but is only remotely related to other Euro-American sublineages such as X, LAM, Haarlem and S. The evolutionary scenario based on long-term evolution rate being valid until T3-Osa-Tur MRCA was not supported by Japanese fossil data. The evolutionary scenario relying on short-term evolution rate since T3-Osa-Tur MRCA was contradicted by human history and potential traces of past epidemics. T3-Osaka and Tur sublineages were found likely to have diverged between 800y and 2000years ago, potentially at the time of Mongol Empire. Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional studies are needed to reliably date events corresponding to intermediate depths in tuberculosis phylogeny.

Pestilence, riots, lynchings and desecration of corpses. The sleep of reason produces monsters.

Vampirism has been a component of Central European and Balkan folklore since the Middle Ages and was often believed to be responsible for the transmission of serious infectious diseases such as plague and tuberculosis/consumption. Vampirism was believed to be spread within the same family or village and if the rite of the so-called second burial after death was not performed. The practice of "second burial" entailed exhumation of the body and the removal of the shroud from the mouth of the corpse, and a search for evidence if the corpse had chewed the cloth. If the shroud was chewed, a handful of earth or a brick was put into the body's mouth so that the vampire could no longer harm others. In some cases, the corpse was decapitated and an awl, made of ash, was thrust into its chest. Furthermore, the limbs were nailed down to prevent its movements. Remarkably, these beliefs were not restricted to the popular classes, but were also debated by theologians, political scientists at the height of the eighteenth century (Enlightenment). In the Habsburg Empire, this question attained such important political, social as well as health connotations as to force the Empress Maria Theresa to entrust an ad hoc study to her personal physician Gerard van Swieten with a view to determining what was true about the apparitions of vampires that occurred throughout central Europe and in the Balkans. The result of this investigation led to a ban on the "second burial" rites. Despite this prohibition, the practice of necrophilia on the bodies of suspected people continued, and both a cultured and popular literature on vampirism continued to flourish well into the nineteenth century.

On TB Vaccines, Patients' Demands, and Modern Printed Media in Times of Biomedical Uncertainties: Buenos Aires, 1920-1950.

Reconstructing some of the experiences of people living with tuberculosis in Argentina in the first half of the twentieth century, as reflected not only in written and oral accounts but also in individual and collective actions, this article explores the ways in which patients came to grips with medical expertise in times of biomedical uncertainty. These negotiations, which inevitably included adaptations as well as confrontations, highlight a much less passive and submissive patient-physician relationship than is often assumed. Though patients were certainly subordinate to medical doctors' knowledge and practices, that subordination, far from absolute, was limited and often overthrown. The article focuses on patients' demands to gain access to a vaccine not approved by the medical establishment. By engaging with media organizations, the sick invoked their "right to health" in order to obtain access to experimental treatments when biomedicine was unable to deliver efficient therapies.

Old World tuberculosis: Evidence from human remains with a review of current research and future prospects.

The evidence for TB in archaeological human remains for the Old World is reviewed in published and some unpublished sources. The evidence of Pott's disease was considered specific for TB, with other bone changes, such as rib lesions, as non-specific. Limitations of the data are discussed. Most evidence for TB comes from skeletons from the northern hemisphere, particularly in Europe in the late Medieval period (12(th)-16th centuries AD), but there is early evidence in the Near/Middle East and Egypt. Many parts of Africa, Asia and Australasia have very little or no evidence. aDNA analysis has provided data on species and strains of the Mycobacterium tuberculosis complex organisms affecting people in the past. The extant data suggest the first epidemiological transition (Neolithic agriculture and permanent settlements) led to an increase in TB, with later increases in urban environments of the late Medieval period. A number of causative factors were at play. Future research, particularly using biomolecular analysis, has the potential to further contribute to our understanding of the origin and evolution of TB, thus merging the disciplines of palaeopathology and evolutionary medicine.

Mycobacterium tuberculosis phylogeography in the context of human migration and pathogen's pathobiology: Insights from Beijing and Ural families.

Here, I review the population structure and phylogeography of the two contrasting families of Mycobacterium tuberculosis, Beijing and Ural, in the context of strain pathobiology and human history and migration. Proprietary database (12-loci MIRU-VNTR profiles of 3067 Beijing genotype isolates) was subjected to phylogenetic and statistical analysis. The highest rate (90%) and diversity (HGI 0.80-0.95) of the Beijing genotype in North China suggest it to be its area of origin. Under VNTR-based MDS analysis the interpopulation genetic distances correlated with geography over uninterrupted landmasses. In contrast, large water distances together with long time generated remarkable outliers. Weak and less expected affinities of the distant M. tuberculosis populations may reflect hidden epidemiological links due to unknown migration. Association with drug-resistance or increased virulence/transmissibility along with particular human migration flows shape global dissemination of some Beijing clones. The paucity of data on the Ural genotype prevents from high-resolution analysis that was mainly based on the available spoligotyping data. The North/East Pontic area marked with the highest prevalence of the Ural family may have been the area of its origin and primary dispersal in Eurasia. Ural strains are not marked by increased pathogenic capacities, increased transmissibility and association with drug resistance (but most recent reports describe an alarming increase of MDR Ural strains in some parts of eastern Europe and northwestern Russia). Large-scale SNP or WGS population-based studies targeting strains from indigenous populations and, eventually, analysis of ancient DNA will better test these hypotheses. Host genetics factors likely play the most prominent role in differential dissemination of particular M. tuberculosis genotypes.

The ancient city of Rome, its empire, and the spread of tuberculosis in Europe.

The formation of the Roman Empire constituted an unprecedented joining of Mediterranean and European lands and peoples, centering on the capital of Rome. During the late Roman Republic and early Roman Empire (ca. 200B.C.-ca. 200 A.D.) urbanization and population growth led to conditions favorable to the spread of tuberculosis throughout Italy and especially within Rome itself. Trade and military expansion would have acted as vehicles for the further extension of tuberculosis to the provinces via direct transmission from Italian-born Romans to the native populations. However, an alternative explanation may better explain the increase in the number of archeological cases of tuberculosis with the start of the Roman era. A literature review of Roman-era cases and their locations suggests that the development of an urban, Roman way of life resulted in significant increases in prevalence in regions where tuberculosis had previously been endemic only at a low level.

La recepción de la teoría bacteriológica en Cataluña a través de la Revista Homeopática (1890-1913) / The bacterial theory in Catalonia through Revista Homeopática (1890-1913)

El cambio de paradigma médico que provocaron los descubrimientos en bacteriología aceleró la necesidad por parte de la homeopatía de recibir y adaptar su doctrina a las nuevas tendencias científicas. Las estrategias de legitimación son un instrumento de gran importancia en el posicionamiento de las disciplinas dentro del mundo científico. La homeopatía, como disciplina médica, también utilizó sus recursos para apropiarse de una teoría que se estaba introduciendo con fuerza. En este trabajo se estudiarán las estrategias legitimadoras utilizadas por la Academia Médico Homeopática de Barcelona, a fin de que los nuevos descubrimientos de koch no derrumbasen la doctrina Hahnemanniana, a partir del análisis de la Revista Homeopática, órgano de difusión de esta institución. Con el estudio de estas estrategias, se intenta demostrar que la teoría bacteriana no representó el principio del fin, de un movimiento que todavía hoy sobrevive al pensamiento hegemónico (AU)

The discoveries in bacteriology led to a paradigm shift in medical homeopathy, accelerating the need to receive and adapt its teaching to new scientific trends. Legitimisation strategies are an important tool in the positioning of the disciplines within the scientific world. Homeopathy is a medicaldiscipline that also uses its resources to take on a theory that was being introduced to great effect. this paper exa mines the legitimisation strategies that the Acadèmia Médico-Homeopàtica de Barcelona used so that koch’s new discoveries did not demolish the Hahnemanniana doctrine, from the analysis of the Revista Homeopática. The study of these strategies tries to show that the bacterial theory did not represent the beginning of the end of a movement that still survives today (AU)

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis.

Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean.

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.