Five millennia of Bartonella quintana bacteraemia.

During the two World Wars, Bartonella quintana was responsible for trench fever and is now recognised as an agent of re-emerging infection. Many reports have indicated widespread B. quintana exposure since the 1990s. In order to evaluate its prevalence in ancient populations, we used real-time PCR to detect B. quintana DNA in 400 teeth collected from 145 individuals dating from the 1st to 19th centuries in nine archaeological sites, with the presence of negative controls. Fisher's exact test was used to compare the prevalence of B. quintana in civil and military populations. B. quintana DNA was confirmed in a total of 28/145 (19.3%) individuals, comprising 78 citizens and 67 soldiers, 20.1% and 17.9% of which were positive for B. quintana bacteraemia, respectively. This study analysed previous studies on these ancient samples and showed that the presence of B. quintana infection followed the course of time in human history; a total of 14/15 sites from five European countries had a positive prevalence. The positive rate in soldiers was higher than those of civilians, with 20% and 18.8%, respectively, in the 18th and 19th centuries, but the difference in frequency was not significant. These results confirmed the role of dental pulp in diagnosing B. quintana bacteraemia in ancient populations and showed the incidence of B. quintana in both civilians and soldiers.

Cervical ribs in human early life: morphological variability and first identification as a morbidity criterion in a past population.

Despite the medical literature on supernumerary cervical ribs in extant adult samples, little is known about their development and occurrence in early infancy. The documentation of cervical ribs in modern samples of fetuses and neonates is indeed affected by ethical as well as technical limitations. The aim of the present study was to investigate their frequencies and morphological variability in the first known archaeological collection of very young children with this anatomical variant. The study sample comes from the 8B-51 necropolis on the Saï island (Sudan) and dates to the Classic Kerma Period (XVIIIe-XVIe centuries BC). It consists of 64 individuals deceased between 24 weeks of amenorrhoea and 2 years of age. Bilateral or unilateral cervical ribs were found in 27 individuals. A total of 43 cervical ribs were identified, 38 of which are fully preserved. According to these observations, at least 42% of the individuals have unilateral or bilateral cervical ribs, with an average maximum length of < 1 cm. This frequency is very high compared to those observed in contemporary adult samples (up to 3%). First, the comparison of our results with biological and genetic research demonstrating the link between the occurrence of cervical ribs and a reduced chance of survival during infancy allows the first identification of this trait as an indicator of morbidity in an archaeological collection, a morbidity to which a genetic homogeneity or even endogamy could contribute. Second, the number of ribs studied makes it possible to propose a morphological classification based on the general shape and the shape of the articular facets, classification that can be used tos refine the analyses of the trait in future samples.

Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes.

The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541-750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750).

The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.

Normal growth, altered growth? Study of the relationship between harris lines and bone form within a post-medieval plague cemetery (Dendermonde, Belgium, 16th Century).

OBJECTIVES: Harris lines (HLs) are defined as transverse, mineralized lines associated with temporary growth arrest. In paleopathology, HLs are used to reconstruct health status of past populations. However, their etiology is still obscure. The aim of this article is to test the reliability of HLs as an arrested growth marker by investigating their incidence on human metrical parameters. METHODS: The study was performed on 69 individuals (28 adults, 41 subadults) from the Dendermonde plague cemetery (Belgium, 16th century). HLs were rated on distal femora and both ends of tibiae. Overall prevalence and age-at-formation of each detected lines were calculated. ANOVA analyses were conducted within subadult and adult samples to test if the presence of HLs did impact size and shape parameters of the individuals. RESULTS: At Dendermonde, 52% of the individuals had at least one HL. The age-at-formation was estimated between 5 and 9 years old for the subadults and between 10 and 14 years old for the adults. ANOVA analyses showed that the presence of HLs did not affect the size of the individuals. However, significant differences in shape parameters were highlighted by HL presence. Subadults with HLs displayed slighter shape parameters than the subadults without, whereas the adults with HLs had larger measurements than the adults without. CONCLUSIONS: The results suggest that HLs can have a certain impact on shape parameters. The underlying causes can be various, especially for the early formed HLs. However, HLs deposited around puberty are more likely to be physiological lines reflecting hormonal secretions. Am. J. Hum. Biol. 29:e22885, 2017. © 2016 Wiley Periodicals, Inc.

Demographic Patterns Distinctive of Epidemic Cemeteries in Archaeological Samples.

The analysis of biological parameters such as age and sex is particularly relevant to the interpretation of ancient skeletal assemblages related to abrupt mortality crises, and more particularly epidemics. In such a context, the mechanisms of selection within a population or part of a population differ according to the pathogen involved. They may also vary depending on the period and location in which the population lived. Here, we illustrate the specificity of plague mortality through the study of several European burial sites contemporary with the first and second plague pandemics. The paleodemographic patterns obtained for different plague outbreaks from the 6th to the 16th centuries reveal some constant features over time and space as well as some differences that suggest a possible evolution in the epidemiological characteristics of the disease.

Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics.

Ancient DNA analysis has revealed an involvement of the bacterial pathogen Yersinia pestis in several historical pandemics, including the second plague pandemic (Europe, mid-14(th) century Black Death until the mid-18(th) century AD). Here we present reconstructed Y. pestis genomes from plague victims of the Black Death and two subsequent historical outbreaks spanning Europe and its vicinity, namely Barcelona, Spain (1300-1420 cal AD), Bolgar City, Russia (1362-1400 AD), and Ellwangen, Germany (1485-1627 cal AD). Our results provide support for (1) a single entry of Y. pestis in Europe during the Black Death, (2) a wave of plague that traveled toward Asia to later become the source population for contemporary worldwide epidemics, and (3) the presence of an historical European plague focus involved in post-Black Death outbreaks that is now likely extinct.

Ancient Down syndrome: An osteological case from Saint-Jean-des-Vignes, northeastern France, from the 5-6th century AD.

The pathological skull of a 5-7 year old child from Saint-Jean-des-Vignes (Saône-et-Loire, north-eastern France) dated to the 5-6th century AD is described. Morphological and radiographic features, metrical data and Computed Tomography (CT) scans are used to study the osteological abnormalities in comparison with normal skulls of individuals of similar age and geographic origin. The combination of features is consistent with the diagnosis of Down syndrome (e.g. brachycrany, metopism, hypodontia, periodontitis, a flattened occiput, vault thinness, and an open cranial base angle), although none is pathognomonic of the disease in isolation. Cases of Down syndrome in past populations are rare, frequently poorly described or discovered out of context. This case represents the earliest and youngest example of the condition in the archaeological record. The context and funerary treatment of this child suggests that he/she was not stigmatized by other members of the community, who afforded a normal mode of burial.

Life history of the individuals buried in the St. Benedict Cemetery (Prague, 15th-18th centuries): insights from (14)C dating and stable isotope (δ(13)C, δ(15)N, δ(18)O) analysis.

Funerary practices and bioarchaeological (sex and age) data suggest that a mortality crisis linked to an epidemic episode occurred during the fifth phase of the St. Benedict cemetery in Prague (Czech Republic). To identify this mass mortality episode, we reconstructed individual life histories (dietary and mobility factors), assessed the population's biological homogeneity, and proposed a new chronology through stable isotope analysis (δ(13)C, δ(18)O and δ(15)N) and direct radiocarbon dating. Stable isotope analysis was conducted on the bone and tooth enamel (collagen and carbonate) of 19 individuals from three multiple graves (MG) and 12 individuals from individual graves (IG). The δ(15)N values of collagen and the difference between the δ(13)C values of collagen and bone carbonate could indicate that the IG individuals had a richer protein diet than the MG individuals or different food resources. The human bone and enamel carbonate and δ(18)O values suggest that the majority of individuals from MG and all individuals from IG spent most of their lives outside of the Bohemian region. Variations in δ(18)O values also indicate that all individuals experienced residential mobility during their lives. The stable isotope results, biological (age and sex) data and eight (14)C dates clearly differentiate the MG and IG groups. The present work provides evidence for the reuse of the St. Benedict cemetery to bury soldiers despite the funeral protest ban (1635 AD). The Siege of Prague (1742 AD) by French-Bavarian-Saxon armies is identified as the cause of the St. Benedict mass mortality event.

Immuno-PCR--a new tool for paleomicrobiology: the plague paradigm.

BACKGROUND: The cause of past plague pandemics was controversial but several research teams used PCR techniques and dental pulp as the primary material to reveal that they were caused by Yersinia pestis. However, the degradation of DNA limits the ability to detect ancient infections. METHODS: We used for the first time immuno-PCR to detect Yersinia pestis antigens; it can detect protein concentrations 70 times lower than the standard ELISA. After determining the cut-off value, we tested 34 teeth that were obtained from mass graves of plague, and compared previous PCR results with ELISA and immuno-PCR results. RESULTS: The immuno-PCR technique was the most sensitive (14 out of 34) followed by the PCR technique (10 out of 34) and ELISA (3 out of 34). The combination of these three methods identified 18 out of 34 (53%) teeth as presumably being from people with the plague. CONCLUSION: Immuno-PCR is specific (no false-positive samples were found) and more sensitive than the currently used method to detect antigens of ancient infections in dental pulp. The combination of three methods, ELISA, PCR and immuno-PCR, increased the capacity to identify ancient pathogens in dental pulp.

Enthesopathies as occupational stress markers: evidence from the upper limb.

Enthesopathies--that is, "musculo-skeletal stress markers"--are frequently used to reconstruct past lifestyles and activity patterns. Relatively little attention has been paid in physical anthropology to methodological gaps implicit in this approach: almost all methods previously employed neglect current medical insights into enthesopathies and the distinction between healthy and pathological aspects has been arbitrary. This study presents a new visual method of studying fibrocartilaginous enthesopathies of the upper limb (modified from Villotte: Bull Mém Soc Anthropol Paris n.s. 18 (2006) 65-85), and application of this method to 367 males who died between the 18th and 20th centuries, from four European identified skeletal collections: the Christ Church Spitalfields Collection, the identified skeletal collection of the anthropological museum of the University of Coimbra, and the Sassari and Bologna collections of the museum of Anthropology, University of Bologna. The analysis, using generalized estimating equations to model repeated binary outcome variables, has established a strong link between enthesopathies and physical activity: men with occupations involving heavy manual tasks have significantly (P-value < 0.001) more lesions of the upper limbs than nonmanual and light manual workers. Probability of the presence of an enthesopathy also increases with age and is higher for the right side compared with the left. Our study failed to distinguish significant differences between the collections when adjusted for the other effects. It appears that enthesopathies can be used to reconstruct past lifestyles of populations if physical anthropologists: 1) pay attention to the choice of entheses in their studies and 2) use appropriate methods.

Genotyping, Orientalis-like Yersinia pestis, and plague pandemics.

Three pandemics have been attributed to plague in the last 1,500 years. Yersinia pestis caused the third, and its DNA was found in human remains from the second. The Antiqua biovar of Y. pestis may have caused the first pandemic; the other two biovars, Medievalis and Orientalis, may have caused the second and third pandemics, respectively. To test this hypothesis, we designed an original genotyping system based on intergenic spacer sequencing called multiple spacer typing (MST). We found that MST differentiated every biovar in a collection of 36 Y. pestis isolates representative of the three biovars. When MST was applied to dental pulp collected from remains of eight persons who likely died in the first and second pandemics, this system identified original sequences that matched those of Y. pestis Orientalis. These data indicate that Y. pestis caused cases of Justinian plague. The two historical plague pandemics were likely caused by Orientalis-like strains.