M Milanese

Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics

ABSTRACT Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a Brucella melitensis genome. Sequence reads from this genome showed signatures typical of ancient or aged DNA. Despite the relatively low coverage, we were able to use information from single-nucleotide polymorphisms to place the medieval pathogen genome within a clade of B. melitensis strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS711 insertions. We conclude that metagenomics stands ready to document past and present infections, shedding light on the emergence, evolution, and spread of microbial pathogens. IMPORTANCE Infectious diseases have shaped human populations and societies throughout history. The recovery of pathogen DNA sequences from human remains provides an opportunity to identify and characterize the causes of individual and epidemic infections. By sequencing DNA extracted from medieval human remains through shotgun metagenomics, without target-specific capture or amplification, we have obtained a draft genome sequence of an ~700-year-old Brucella melitensis strain. Using a variety of bioinformatic approaches, we have shown that this historical strain is most closely related to recent strains isolated from Italy, confirming the continuity of this zoonotic infection, and even a specific lineage, in the Mediterranean region over the centuries. Infectious diseases have shaped human populations and societies throughout history. The recovery of pathogen DNA sequences from human remains provides an opportunity to identify and characterize the causes of individual and epidemic infections. By sequencing DNA extracted from medieval human remains through shotgun metagenomics, without target-specific capture or amplification, we have obtained a draft genome sequence of an ~700-year-old Brucella melitensis strain. Using a variety of bioinformatic approaches, we have shown that this historical strain is most closely related to recent strains isolated from Italy, confirming the continuity of this zoonotic infection, and even a specific lineage, in the Mediterranean region over the centuries.

Metals in bones of the middle-aged inhabitants of Sardinia island (Italy) to assess nutrition and environmental exposure

Metals in bones of 72 subjects lived between the twelfth and eighteenth century AC and collected in four Sardinian (Italian insular region) burial sites (Alghero, Bisarcio, Geridu, and Sassari) were determined and used as biomarkers to evaluate diet and potential social-environmental differences. Concentrations of Ba, Ca, Cd, Cu, Hg, Pb, Sr, and Zn were quantified in different types of compact bone (femur, fibula, humerus, radius, tibia, ulna) by sector field inductively coupled plasma mass spectrometry previous acidic digestion and differences among the various burial sites, centuries, types of bone, gender, and age were explored by univariate and multivariate analyses. Results indicated differences between sites in terms of diet: Bisarcio (inland village) had increased ratios of Ba/Ca and Zn/Ca due to higher incidence of vegetables, cereals, and animal foods in the diet; Geridu (coastal village) showed increased Sr/Ca ratio indicating foods of plant and marine origin that were predominant; Alghero (coastal site) and Sassari (inland site) displayed prevalently a mixed diet reflecting a higher economy and food imports. In addition, these latter sites showed increased levels of Hg/Ca (fish, drugs, cosmetics) and Pb/Ca (coins, utensils, pipeline for water). In conclusion, the elemental Ba/Ca, Sr/Ca, and Zn/Ca ratios were indicative of provenance and diet, while Hg/Ca and Pb/Ca ratios were associated to various forms of environmental exposure.

Atlas occipitalization associated with other anomalies in a 16th century skeleton from Sardinia (Italy).

Archaeological excavations carried out in the plague cemetery of 16th century Alghero (Sardinia) brought to light the skeleton of a male aged 35-45 years, showing anomalies of the atlas. A macroscopic and radiological study has been carried out. The first cervical vertebra is fused with the skull base, resulting in an occipitalisation of the atlas. Absence of the costal element of the left foramen transversarium, resulting in an open anterior foramen transversarium, and posterior arch defect are also observed. The atlanto-occipital junction is a complex structure, susceptible to develop different patterns of congenital defects. These anatomical variations of atlas should be considered in modern clinical practice in order to formulate a correct diagnosis and to conceive an appropriate treatment. Osteoarchaeological cases are important as, beside to ascertain the presence of congenital defects in past populations, allow an in-depth study in dry bones, which can help modern medicine in interpreting anatomical variations. We present an association of congenital anomalies of the atlanto-occipital junction, a condition rarely documented in ancient and modern human skeletal remains.

A Case of brachymetatarsia from Medieval Sardinia (Italy)

Archaeological excavations carried out in the Medieval village of Geridu (Sardinia) uncovered several burials dating to the late 13th or the first half of 14th century. Among these individuals, the skeleton of an adult female showing a bilateral abnormal shortness of the fourth metatarsal bone was identified. Bilaterality and absence of other skeletal anomalies allow to rule out an acquired aetiology of the disease and to support a diagnosis of congenital brachymetatarsia. Such a rare deformity has a clinical incidence of 0.02% to 0.05%, with strong predominance of the female gender. To our knowledge, no other cases of brachymetatarsia have been reported in paleopathology so far. Anat Rec, 297:650–652, 2014.