A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade.

Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14th-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14th CE and suggest that its divergence was due to human and ruminant co-migration.

Exploring the effects of weaning age on adult infectious disease mortality among 18th-19th century Italians.

OBJECTIVES: The developmental origins of health and disease (DOHaD) hypothesis describes how early childhood stress affects morbidity and mortality later in life. The role of early childhood stress in mortality from infectious disease is understudied. Stressors in early childhood that weaken the immune system may result in increased susceptibility to infectious disease in adulthood. Weaning is one of the earliest potential periods of significant stress in early childhood. This research investigates the effect of weaning after ~6 months of age on cholera mortality among 18th-19th-century Italian populations by determining if earlier breastfeeding cessation is associated with earlier mortality, analyzing childhood dietary variation and physiological stress markers, and determining if age-at-weaning completion differs between catastrophic and attritional populations. METHODS: Serial dentin stable carbon and nitrogen isotope analyses from canines are compared between catastrophic (n = 45) and attritional groups (n = 23). Canines are sectioned serially from crown to apex, and the increment's δ15 N and δ13 C are used to estimate age-at-weaning completion. RESULTS: Catastrophic and attritional groups exhibit similar age-at-weaning completion (~2.8 years). Seventy-four percent of individuals lack elevated δ15 N values in dentin that formed during infancy. CONCLUSIONS: Age-at-weaning completion was not a predisposing factor in cholera mortality in adulthood in this sample. Age-at-weaning completion may not be significantly associated with infectious disease mortality because weaning completion likely occurred after infants had adapted to consuming contaminated weanling foods. Individuals without detectable weaning curves may represent infants who received supplementary foods since birth or were weaned before the age of 6-9 months.

Francesco Maria Fiorentini (1603-1673): An Italian physician in 'The Iron Century'.

The aim of this paper is to shed light on the figure of Francesco Maria Fiorentini, a 17th-century physician from Lucca (Tuscany, Italy) and member of the Iatromechanical School, who distinguished himself for his role during the plague and the typhus epidemics that spread throughout Italy in the first half of that century. His work must be contextualized in a precise historical moment, which marked the gradual transition of Western medicine from the archaism of Galenic doctrine to that of the Iatromechanical School, when the foundations started to be laid for an experimental type of medicine that based its assumptions on the direct observation of phenomena concerning the human body. In this work, we mainly focus on the medical biography of Fiorentini and on the reasons why he enjoyed great social prestige among the most prominent figures of his time. However, Fiorentini should also be remembered as a multifaceted scholar, as evidenced by his numerous writings, which underline his erudition in disparate fields of knowledge.

Back to the Middle Ages: Entomological and Botanical Elements Reveal New Aspects of the Burial of Saint Davino of Armenia.

The natural mummy of Saint Davino Armeno (11th century) is preserved in the church of Saint Michele in Foro in the city of Lucca (Tuscany, Central Italy). The body of Davino is one of the oldest Italian mummies of a Saint, and his paleopathological study was performed in 2018. In the present research, we investigated the arthropod fragments and botanical remains collected from the body, coffin, and fabrics of Saint Davino. Entomological analyses outlined the presence of 192 arthropod fragments. Among these, Diptera, Muscidae (Hydrotaea capensis and Muscina sp.), and Phoridae (Conicera sp.) puparia were the most abundant. Regarding Coleoptera, Ptinidae (Anobium punctatum) were the most frequent, followed by Cleridae (Necrobia sp.), Trogidae (Trox scaber), Curculionidae (Sitophilus granarius), and Histeridae (Gnathoncus). Cocoons of Tineidae and Pyralidae moths were found, along with a propodeum joined to the petiole and a mesopleuron of an Ichneumoninae parasitoid. Numerous metamera of Julida and three scorpion fragments were also found. Botanical samples indicated the presence of a quite broad botanical community, including gramineous species, olives, evergreen oaks, and grapevine. Overall, entomological data allow us to argue that Saint Davino was first buried into the soil, probably in a wooden coffin, thus supporting the historical-hagiographic tradition according to which he was buried sub divo in the cemetery of Saint Michele. The preservation of the body as a natural mummy may have been facilitated by burial in a coffin that prevented direct contact of the corpse with the earth. Botanical remains offer confirmation of a late medieval urban environment rich in horticultural areas and trees, giving us a landscape that is very different from the current Tuscan city.

Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis.

OBJECTIVE: To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual MATERIALS: 14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 th century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis. METHODS: Shotgun sequencing data from was examined to determine the presence of Brucella DNA. RESULTS: Three of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7-169), but for many the data quality was insufficient to withstand our identification and authentication criteria. CONCLUSIONS: We identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification. SIGNIFICANCE: Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease. LIMITATIONS: Study focuses on pathogen recovery in a single individual. SUGGESTIONS FOR FURTHER RESEARCH: Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples.

A 16th century Escherichia coli draft genome associated with an opportunistic bile infection.

Escherichia coli - one of the most characterized bacteria and a major public health concern - remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16th century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past.

A 13th-century cystic echinococcosis from the cemetery of the monastery of Badia Pozzeveri (Lucca, Italy).

OBJECTIVE: To differentially diagnose a calcified formation recovered from a 13th century AD grave from the Tuscan monastery of Badia Pozzeveri, Lucca, Italy. MATERIALS: A calcified formation from the thoraco-abdominal region of a skeleton buried in the monastery cemetery. METHODS: Cone Beam Computed Tomography, Scanning Electron Microscope and Energy Dispersive X-Ray Spectroscopy. RESULTS: A hollow, calcified ovoid formation was identified as typical of a hydatid cyst, permitting the diagnosis of cystic echinococcosis in a 35-45year-old female. CONCLUSIONS: The study reveals the circulation of the parasite Echinococcus granulosus in the region of Lucca in late medieval Tuscany. SIGNIFICANCE: This finding is the fourth case of cystic echinococcosis from an archaeological context in Italy and provides insight into environmental conditions that appear to have affected members of a community, irrespective of social status. LIMITATIONS: Caution and the application of multiple analyses must be exercised in the differential diagnosis to discriminate among calcified formations. SUGGESTIONS FOR FURTHER RESEARCH: Analysis of stable isotopes of the calcified formation, such as 15N and 13C, in order to compare them with isotopic values of the host individual and to further confirm the parasitic origin of the find.

A human MMTV-like betaretrovirus linked to breast cancer has been present in humans at least since the copper age.

The betaretrovirus Mouse Mammary Tumor Virus (MMTV) is the well characterized etiological agent of mammary tumors in mice. In contrast, the etiology of sporadic human breast cancer (BC) is unknown, but accumulating data indicate a possible viral origin also for these malignancies. The presence of MMTVenv-like sequences (MMTVels) in the human salivary glands and saliva supports the latter as possible route of inter-human dissemination. In the absence of the demonstration of a mouse-man transmission of MMTV, we considered the possibility that a cross-species transmission could have occurred in ancient times. Therefore, we investigated MMTVels in the ancient dental calculus, which originates from saliva and is an excellent material for paleovirology. The calculus was collected from 36 ancient human skulls, excluding any possible mouse contamination. MMTV-like sequences were identified in the calculus of 6 individuals dated from the Copper Age to the 17th century. The MMTV-like sequences were compared with known human endogenous betaretroviruses and with animal exogenous betaretroviruses, confirming their exogenous origin and relation to MMTV. These data reveal that a human exogenous betaretrovirus similar to MMTV has existed at least since 4,500 years ago and indirectly support the hypothesis that it could play a role in human breast cancer.

The 1918/19 Spanish Flu in Pisa (Tuscany, Italy): Clinical, Epidemiological and Autoptic Considerations

The Spanish flu pandemic spread in 1918-19 and infected about 500 million people, killing 50 to 100 million of them. People were suffering from severe poverty and malnutrition, especially in Europe, due to the First World War, and this contributed to the diffusion of the disease. In Italy, Spanish flu appeared in April 1918 with several cases of pulmonary congestion and bronchopneumonia; at the end of the epidemic, about 450.000 people died, causing one of the highest mortality rates in Europe. From the archive documents and the autoptic registers of the Hospital of Pisa, we can express some considerations on the impact of the pandemic on the population of the city and obtain some information about the deceased. In the original necroscopic registers, 43 autopsies were reported with the diagnosis of grippe (i.e. Spanish flu), of which the most occurred from September to December 1918. Most of the dead were young individuals, more than half were soldiers, and all of them showed confluent hemor agic lung bronchopneumonia, which was the typical feature of the pandemic flu. We believe that the study of the autopsy registers represents an incomparable instrument for the History of Medicine and a useful resource to understand the origin and the evolution of the diseases.

Insights on Funeral Practices and Insects Associated With the Tombs of King Ferrante II d'Aragona and Other Renaissance Nobles.

The impressive Sacristy of the Basilica of San Domenico Maggiore contains 38 wooden sarcophagi with the bodies of 10 Aragonese princes and other Neapolitan nobles, who died in the 15th and 16th centuries. To improve the knowledge about the entomofauna associated with bodies in archaeological contexts, herein we provide insights on the funerary practices and the insect community associated to Ferrante II King of Naples and other Italian Renaissance mummies of the Aragonese dynasty buried in the Basilica of St. Domenico Maggiore. We identified 842 insect specimens: 88% were Diptera (Muscidae, Fanniidae, and Phoridae), followed by 9% Lepidoptera (Tineidae) and 3% Coleoptera (Dermestidae and Ptinidae). Ninety-seven percent of the specimens were collected from the coffin of Francesco Ferdinando d'Avalos, which was the best preserved. A lack of fly species characterizing the first colonization waves of exposed bodies was noted. The most common fly was the later colonizing muscid Hydrotaea capensis (Wiedemann); only a few Fanniidae (Fannia spp.) were retrieved. The lack of blowflies, coupled with recording H. capensis as the dominant fly, supports our hypothesis that corpses have been kept indoors for a long time under confined environmental conditions. Other explanations include odorous oils/balms having been used in the embalming process, causing the delay or stopping the arrival of first colonizer flies. Hermetically sealing of the coffin with bitumen may also have played a role in preventing access to the corpses. This scenario describes a historical context characterized by a well-advanced knowledge of body preparation, with specific burial techniques adopted for nobles.

Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries.

The concept of the human oral microbiome was applied to understand health and disease, lifestyles, and dietary habits throughout part of human history. In the present study, we augment the understanding of ancient oral microbiomes by characterizing human dental calculus samples recovered from the ancient Abbey of Badia Pozzeveri (central Italy), with differences in socioeconomic status, time period, burial type, and sex. Samples dating from the Middle Ages (11th century) to the Industrial Revolution era (19th century) were characterized using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. Consistent with previous studies, individuals from Badia Pozzeveri possessed commensal oral bacteria that resembled modern oral microbiomes. These results suggest that members of the oral microbiome are ubiquitous despite differences in geographical regions, time period, sex, and socioeconomic status. The presence of fecal bacteria could be in agreement with poor hygiene practices, consistent with the time period. Respiratory tract, nosocomial, and other rare pathogens detected in the dental calculus samples are intriguing and could suggest subject-specific comorbidities that could be reflected in the oral microbiome.

Severe atherosclerosis in the natural mummy of Girolamo Macchi (1648-1734), "major writer" of Santa Maria della Scala Hospital in Siena (Italy).

BACKGROUND AND AIMS: A small crypt in the Santissima Annunziata Church of Santa Maria della Scala Hospital in Siena (Italy) contained three well-preserved mummies, two of which, dated back to the 15th-16th century, were identified as Salimbene Capacci (1433-1497), Rector of the Hospital, and his wife, Margherita Sozzini (?-1511). The third mummy, dressed in clothes of the 17th century, was not initially identified. METHODS: Accurate bibliographical, taphonomic and anthropological studies allowed the identification of the mummy of Girolamo Macchi, who lived between 1648 and 1734 and worked as "major writer", an accountant, for the Hospital. He was present when the corpses of the Rector and his wife were discovered in 1678 and, impressed by this finding, wanted to be buried in the same chapel after his death, which occurred at the age of 86. A complete study, including macroscopic, radiological, isotopic and histological analyses, was performed on the natural mummy of Girolamo. RESULTS: Macroscopic investigation showed a large inguinoscrotal hernia and a good preservation of the internal organs. The circulatory system revealed severe atherosclerosis, with multiple calcifications stenosing the lumen of the vessels, in particular of the lumbar aorta and the iliac arteries. The diagnosis was confirmed by imaging techniques (3D Cone Beam Scan) and by histology. CONCLUSIONS: This case confirms that atherosclerosis is also a disease of ancient times. The presence of atherosclerosis in pre-contemporary individuals could suggest that the disease may not only be uniquely characteristic of a specific diet or lifestyle, but it could be also an inherent component of human ageing.

Gout in Duke Federico of Montefeltro (1422-1482): a new pearl of the Italian Renaissance.

The article examines the truthfulness of historical accounts claiming that Renaissance Duke Federico of Montefeltro (1422-1482) suffered from gout. By direct paleopathological assessment of the skeletal remains and by the philological investigation of historical and documental sources, primarily a 1461 handwritten letter by the Duke himself to his personal physician, a description of the symptoms and Renaissance therapy is offered and a final diagnosis of gout is formulated. The Duke's handwritten letter offers a rare testimony of ancient clinical self-diagnostics and Renaissance living-experience of gout. Moreover, the article also shows how an alliance between historical, documental and paleopathological methods can greatly increase the precision of retrospective diagnoses, thus helping to shed clearer light onto the antiquity and evolution of diseases.

Environmental Microbial Forensics and Archaeology of Past Pandemics.

The development of paleomicrobiology with new molecular techniques such as metagenomics is revolutionizing our knowledge of microbial evolution in human history. The study of microbial agents that are concomitantly active in the same biological environment makes it possible to obtain a picture of the complex interrelations among the different pathogens and gives us the perspective to understand the microecosystem of ancient times. This research acts as a bridge between disciplines such as archaeology, biology, and medicine, and the development of paleomicrobiology forces archaeology to broaden and update its methods. This chapter addresses the archaeological issues related to the identification of cemeteries from epidemic catastrophes (typology of burials, stratigraphy, topography, paleodemography) and the issues related to the sampling of human remains for biomolecular analysis. Developments in the field of paleomicrobiology are described with the example of the plague. Because of its powerful interdisciplinary features, the paleomicrobiological study of Yersinia pestis is an extremely interesting field, in which paleomicrobiology, historical research, and archeology are closely related, and it has important implications for the current dynamics of epidemiology.

On the history of gout: paleopathological evidence from the Medici family of Florence.

OBJECTIVES: Throughout history, gout has been referred to as the "disease of the kings", and has been clearly associated with the lifestyle of the aristocratic social classes. According to the written sources, several members of the famous Medici family of Florence suffered from an arthritic disease that contemporary physicians called "gout". A paleopathological study carried out on the skeletal remains of some members of the family, exhumed from their tombs in the Church of San Lorenzo in Florence, offered a unique opportunity to directly investigate the evidence of the arthritic diseases affecting this elite group. METHODS: The skeletal remains of several members of the family were examined macroscopically and submitted to x-ray investigation. RESULTS: The results of the study allowed us to ascertain that the so-called "gout of the Medici" should be considered the clinical manifestation of three different joint conditions: diffuse idiopathic skeletal hyperostosis, rheumatoid arthritis and uratic gout. In particular, uric acid gout was diagnosed in the Grand Duke Ferdinand I (1549-1609). Recently, a new case of this disease was diagnosed in Anton Francesco Maria (1618-1659), a probable illegitimate member of the family. CONCLUSIONS: With this new case, uratic gout was observed in 2 out of 9 adult males, leading to suppose that the disease should have been a common health problem within the family. The aetiology of the disease has to be searched in environmental factors, since both historical and paleonutritional studies demonstrated that the diet of this aristocratic court was rich in meat and wine.

A Hanged From the Past: Medical Consideration on the Judas Iscariot Fresco-Chapelle Notre-Dame-des-Fontaines, La Brigue (15th Century).

The medieval chapel of Notre Dame-des-Fontaines (Our Lady of the Fountains), in the French Maritime Alps, is entirely covered by the fresco cycle of the Passion (15th century) that depicts the last days of Jesus from the Last Supper to the Resurrection. Under a small window, there is the brutal representation of the suicide of Judas Iscariot, hanging from a tree, with the abdomen quartered from which his soul, represented by a small man, is kidnapped by a devil. The author, Giovanni Canavesio, represented the traitor's death with very detailed anatomical structures, differently thus from other paintings of the same subject; it is therefore possible to assume that the artist had become familiar with the human anatomy. In particular, the realism of the hanged man's posture, neck bent in an unnatural way, allows us to hypothesize that it probably comes from direct observation of the executions of capital punishment, not infrequently imposed by the public authorities in low medieval Italy.

Autoptic practices in 16th-18th century Florence: Skeletal evidences from the Medici family.

During the late Middle Ages and the Renaissance autopsy started to be practised for medico-legal purposes in order to investigate the causes of death. The other reason for dissecting a body was embalming, a diffused custom typical of the elitarian classes. The exploration of the Medici tombs in the Basilica of San Lorenzo in Florence offered the opportunity to investigate the practice of autopsy on these aristocratic personages of the Renaissance and Early Modern Age. A total of 25 currently skeletonized individuals, almost all of whom formerly artificial mummies, were exhumed. Accurate examination of the skeletons revealed evident signs of autoptic practices such as horizontal and oblique craniotomies, longitudinal and transversal cuts of the sternum, and sectioning of the sternal extremities of the ribs. In this group, women were treated differently to men at autopsy, as only men underwent craniotomy; autopsy and embalming were carried out also for the illegitimate members of the family and for subaldults. The extremely rich documentary archives of the Medici family confirm that the corpses were in several cases submitted to autopsy. The present study offers important direct information on the 16-18th century autoptic practices that the court surgeons in Florence performed on the members of the elite class.