Search

International audience; While recent advances in genetics make it possible to follow the genetic exchanges between populations and their phenotypic consequences, the impact of the genetic exchanges on the sensory perception of populations has yet to be explored. From this perspective, the present study investi- gated the consequences of African gene flow on odor perception in a Malagasy population with a predominantly East Asian genetic background. To this end, we combined psychophysical tests with genotype data of 235 individuals who were asked to smell the odorant molecule beta-ionone (βI). Results showed that in this population the ancestry of the OR5A1 gene significantly influences the ability to detect βI. At the individual level, African ancestry significantly protects against specific anosmia/hyposmia due to the higher frequency of the functional gene (OR ratios = 14, CI: 1.8–110, p-value = 0.012). At the population level, African introgression decreased the prevalence of specific anosmia/hyposmia to this odorous compound. Taken together, these findings validate the conjecture that in addition to cultural exchanges, genetic transfer may also influence the sensory perception of the population in contact.

International audience

SUMMARY The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.

Objectives Depicting past epidemics currently relies on DNA-based detection of pathogens, an approach limited to pathogens with well-preserved DNA sequences. We used paleoserology as a complementary approach detecting specific antibodies under a mini line-blot format including positive and negative control antigens. Methods Mini line blot assay incorporated skim milk as negative control, Staphylococcus aureus as positive control, and antigens prepared from lice-borne pathogens Rickettsia prowazekii, Borrelia recurrentis, Bartonella quintana, and Yersinia pestis. Paleoserums were extracted from rehydrated dental pulp recovered from buried individuals. Mini line blots observed with the naked eye, were quantified using a scanner and appropriate software. Paleoserology was applied to the indirect detection of lice-borne pathogens in seven skeletons exhumed from a 16th-17th century suspected military burial site (Auxi-le-Château); and 14 civils exhumed from a 5th-13th century burial site (Saint-Mont). Direct detection of pathogens was performed using quantitative real-time PCR. Results In Auxi-le-Château, paleoserology yielded 7/7 interpretable paleoserums including 7/7 positives for B. recurrentis including one also positive for B. quintana. In Saint-Mont, paleoserology yielded 8/14 interpretable paleoserums and none reacted against any of the four pathogens. Antibodies against R. prowazekii and Y. pestis were not detected. The seroprevalence was significantly higher in the military burial site of Auxi-le-Château than in the civil burial site of Saint-Mont. Real-time PCR detection of B. quintana yielded 5/21 positive (3 at Saint-Mont and 2 at Auxi-le-Château) whereas B. recurrentis was not detected. Conclusions Paleoserology unmasked an outbreak of relapsing B. recurrentis fever in one 16th - 17th century military garrison, missed by real-time PCR. Paleoserology offers a new tool for investigating past epidemics, in complement to DNA sequence-based approaches.

International audience; The 17th century plague epidemic had a particularly strong demographic toll in Southern Europe, especially Italy, where it caused long-lasting economical damage. Whether this resulted from ineffective sanitation measures or more pathogenic Yersinia pestis strains remains unknown. DNA screening of 26 skeletons from the 1629-1630 plague cemetery of Lariey (French Alps) identified two teeth rich in plague genetic material. Further sequencing revealed two Y. pestis genomes phylogenetically closest to those from the 1636 outbreak of San Procolo a Naturno, Italy. They both belonged to a cluster extending from the Alps to Northern Germany that probably propagated during the Thirty Years war. Sequence variation did not support faster evolutionary rates in the Italian genomes and revealed only rare private non-synonymous mutations not affecting virulence genes. This, and the more heterogeneous spatial diffusion of the epidemic outside Italy, suggests environmental or social rather than biological causes for the severe Italian epidemic trajectory.

OBJECTIVES The evaluation of developmental stability (DS) by measuring fluctuating asymmetry (FA), a bioindicator of general cumulative stress, is an approach that has often been used to characterize health status in past populations. New techniques of geometric morphometrics now enable a better appreciation of FA than before, with a more refined quantification of variation. The aim of our study is to determine the effectiveness of geometric morphometrics analyses of asymmetry in the human femur for the study of individual DS and inferring health status of human populations. MATERIALS AND METHODS We conducted a comparative analysis between two diachronic populations of distinct and known health status. Two samples of 70 pairs of adult femurs from individuals of comparable age range and sex were selected and CT-scanned. For each 3D reconstruction, two sets of 27 landmarks were digitized to quantify and minimize the effect of measurement error on the evaluation of FA. RESULTS While the measurement of FA in femoral centroid size seemed comparable between the samples, the amount of FA in femoral shape differed. Individuals who experienced high levels of environmental stress presented higher intra-individual variation. In parallel, results did not reveal any significant differences in DS between sexes or age groups. DISCUSSION The geometric morphometrics analysis of femoral asymmetry was effective for distinguishing two populations. After considering various factors of influence, genetics and biomechanics seem to have a limited impact on the results. Expressing FA appears to be normal but dependent on the disturbances of DS produced by environmental stress.

International audience; Chemical decomposition and fragmentation may limit the detection of ancient host and microbial DNA while some proteins can be detected for extended periods of time. We applied paleoproteomics on 300-year-old dental pulp specimens recovered from 16 individuals in two archeological funeral sites in France, comprising one documented plague site and one documented plague-negative site. The dental pulp paleoproteome of the 16 teeth comprised 439 peptides representative of 30 proteins of human origin and 211 peptides representative of 27 proteins of non-human origin. Human proteins consisted of conjunctive tissue and blood proteins including IgA immunoglobulins. Four peptides were indicative of three presumable Yersinia pestis proteins detected in 3/8 dental pulp specimens from the plague-positive site but not in the eight dental pulp specimens collected in the plague-negative site. Paleoproteomics applied to the dental pulp is a new and innovative approach to screen ancient individuals for the detection of blood-borne pathogens and host inflammatory response.

International audience; A rapid diagnostic test (RDT) that detects Yersinia pestis F1 antigen was applied to 28 putative plague victims exhumed from seven burial sites in southeastern France dating to the 16th–18th centuries.Yersinia pestis F1 antigen was detected in 19 of the 28(67.9%) samples. The 27 samples used as negative controlsyielded negative results. Soil samples taken fromarcheological sites related to both positive and negativesamples tested negative for F1 antigen. The detectionthreshold of the RDT for plague (0.5 ng/ml) is sufficientfor a preliminary retrospective diagnosis of Y. pestisinfection in human remains. The high specificity andsensitivity of the assay were confirmed. For two sitespositive to F1 antigen (Lambesc and Marseille), Y. pestis specific DNA (pla gene) had been identified previouslyby PCR-sequence based analyses. Specifically, the positive results for two samples, from the Lambesc cemetery and the Marseille pit burial, matched those previously reported using PCR. Independent analyses in Italy and France of different samples taken from the same burial sites (Draguignan and Martigues) led to the identification of both Y. pestis F1 antigen and Y. pestis pla and gplD genes. These data are clear evidence of the presence of Y. pestis in the ancient human remains examined in this study.

A rapid diagnostic dipstick test (RDT) that detects Yersinia pestis F1 antigen has been recently applied on 18 putative plague victims exhumed from four archaeological burial sites in southeastern France dating back to the 16(th), 17(th) and 18(th) centuries. The Y. pestis antigen F1 was detected in 12 ancient samples out of 18 (67%). Negative controls confirmed their negativity (100%). Our results emphasize that the detection threshold of the RDT for plague (0.5 ng/ml) is sufficient for a first retrospective diagnosis of Y. pestis infection in ancient remains, and confirm the high specificity and sensitivity of the assay. Double-blind analyses performed by using two different techniques (RDT and 'suicide PCR') led us to the identification of the Y. pestis F1 antigen and the Y. pestis pla and gplD genes. These data provide clear evidence of the presence of Y. pestis in the examined specimens.

Background. Many soldiers in Napoleon's Grand Army died of infectious diseases during its retreat from Russia. Because soldiers were commonly infested with body lice, it has been speculated that louse-borne infectious diseases, such as epidemic typhus (caused by Rickettsia prowazekii), were common. Methods. We investigated this possibility during recent excavations of a mass grave of Napoleon's soldiers in Vilnius, Lithuania. Segments of 5 body lice, identified morphologically and by polymerase chain reaction (PCR) amplification and sequencing, were found in earth from the grave that also contained fragments of soldiers' uniforms. Results. DNA of Bartonella quintana (the agent of trench fever) was identified by PCR and sequencing in 3 of the lice. Similarly, PCR and sequencing of dental pulp from the remains of 35 soldiers revealed DNA of B. quintana in 7 soldiers and DNA of R. prowazekii in 3 other soldiers. Conclusions. Our results show that louse-borne infectious diseases affected nearly one-third of Napoleon's soldiers buried in Vilnius and indicate that these diseases might have been a major factor in the French retreat from Russia.

Background: Historical records suggest that multiple burial sites from the 14th-16(th) centuries in Venice, Italy, were used during the Black Death and subsequent plague epidemics. Methodology/Principal Findings: High throughput, multiplexed real-time PCR detected DNA of seven highly transmissible pathogens in 173 dental pulp specimens collected from 46 graves. Bartonella quintana DNA was identified in five (2.9%) samples, including three from the 16th century and two from the 15th century, and Yersinia pestis DNA was detected in three (1.7%) samples, including two from the 14th century and one from the 16th century. Partial glpD gene sequencing indicated that the detected Y. pestis was the Orientalis biotype. Conclusions: These data document for the first time successive plague epidemics in the medieval European city where quarantine was first instituted in the 14th century.

From AD 1347 to AD 1353, the Black Death killed tens of millions of people in Europe, leaving misery and devastation in its wake, with successive epidemics ravaging the continent until the 18th century. The etiology of this disease has remained highly controversial, ranging from claims based on genetics and the historical descriptions of symptoms that it was caused by Yersinia pestis to conclusions that it must have been caused by other pathogens. It has also been disputed whether plague had the same etiology in northern and southern Europe. Here we identified DNA and protein signatures specific for Y. pestis in human skeletons from mass graves in northern, central and southern Europe that were associated archaeologically with the Black Death and subsequent resurgences. We confirm that Y. pestis caused the Black Death and later epidemics on the entire European continent over the course of four centuries. Furthermore, on the basis of 17 single nucleotide polymorphisms plus the absence of a deletion in glpD gene, our aDNA results identified two previously unknown but related clades of Y. pestis associated with distinct medieval mass graves. These findings suggest that plague was imported to Europe on two or more occasions, each following a distinct route. These two clades are ancestral to modern isolates of Y. pestis biovars Orientalis and Medievalis. Our results clarify the etiology of the Black Death and provide a paradigm for a detailed historical reconstruction of the infection routes followed by this disease., Author Summary Several historical epidemic waves of plague have been attributed to Yersinia pestis, the etiologic agent of modern plague. The most famous of these was the second pandemic which was active in Europe from AD 1347 until 1750, and began with the ‘Black Death’. The most informative method to establish the etiological nature of these ancient infections should be the analysis of ancient DNA, but the results of this method have been controversial. Here, by combining ancient DNA analyses and protein-specific detection, we demonstrate unambiguously that Y. pestis caused the Black Death. Furthermore, we show that at least two variants of Y. pestis spread over Europe during the second pandemic. The analysis of up to 20 diagnostic markers reveals that the two variants evolved near the time that phylogenetic branches 1 and 2 separated and may no longer exist. Our results thus resolve a long-standing debate about the etiology of the Black Death and provide key information about the evolution of the plague bacillus and the spread of the disease during the Middle Ages.

BACKGROUND: The new field of paleomicrobiology allows past outbreaks to be identified by testing dental pulp of human remains with PCR. METHODS: We identified a mass grave in Douai, France dating from the early XVIII(th) century. This city was besieged during the European war of Spanish succession. We tested dental pulp from 1192 teeth (including 40 from Douai) by quantitative PCR (qPCR) for R. prowazekii and B. quintana. We also used ultra-sensitive suicide PCR to detect R. prowazekii and genotyped positive samples. RESULTS AND DISCUSSION: In the Douai remains, we identified one case of B. quintana infection (by qPCR) and R. prowazekii (by suicide PCR) in 6/21 individuals (29%). The R. prowazekii was genotype B, a genotype previously found in a Spanish isolate obtained in the first part of the XX(th) century. CONCLUSION: Louse-borne outbreaks were raging during the XVIII(th) century; our results support the hypothesis that typhus was imported into Europe by Spanish soldiers from America.

International audience; The skeletons of four Benedictine nuns and two priests were exhumed from two burial sites in centralFrance. The corpses were dated to the 16th- 18th centuries (archaeological dating). Thick layers of lime were associated with their burials. During the Second Plague Pandemic, lime was associated with plague burials. We hypothesize that Yersinia pestis infection might have been the cause of death of these religious. A rapid diagnostic test for plague (RDT), that detects Y. pestis F1 antigen, was applied to all six putative plague victims. Y. pestis F1 antigen was detected in all six skeletons (100%). The F1 antigen concentrations ranged from 2.5 to 0.625 ng/ml. The eight samples used as negative controls yielded negative results. Soils samples taken from archaeological sites related to both positive and negative samples tested negative for F1 antigen. In earlier reports we provided suggestive evidence that the RDT for plague might be diagnostic for thedetection of Yersinia pestis in ancient human remains. This putative evidence was based on four French and one German reputed plague sites in which RDT for plague and PCR sequenced-based analyses were performed. Both tests gave results consistent with our interpretation that RDT is effective in identifying plague in skeletal remains.Several different European putative plague burial sites are currently under investigation. We hope toobtain additional material to allow statistical validation of our results obtained thus far.We now confirm that the detection threshold of the RDT for plague (0.5 ng/ml) is sufficient for a retrospective diagnosis of plague in ancient skeletal remains. This method supplements the historical record with independent biologic evidence. Thus, our hypothesis that the six religious were infected by Y. pestis during the plague outbreaks which occurred in the two sites, Poitiers and La Chaize-le-Vicomte, between 1587 and 1632, has independent biologic support.

http://www3.interscience.wiley.com/cgi-bin/fulltext/112092580/PDFSTART; International audience; Palaeodemographical studies are founded on the assumption that the sex and age distribution of the skeletal sample reflects the constitution of the original population. It is becoming increasingly clear, however, that the type and amount of information that may be derived from osteoarchaeological collections are related to the state of preservation of remains. This work proposes a new method to evaluate bone preservation, to identify age and sex biases in the preservation of human skeletal remains, and to assess whether differences in preservation patterns are more dependent on factors intrinsic or extrinsic to anatomical features of human bones. Three osteological collections and over 600 skeletonswere observed. The state of preservation of humanbones was assessed using three preservation indexes:the anatomical preservation index (API), the bone representation index (BRI), and the qualitative bone index (QBI). The results suggest that subadult skeletons are generally more poorly preserved and with bones less well-represented than adult skeletons. Among subadults, female and male skeletons have different patterns of preservation according to their age. This pattern of preservation depends on intrinsic anatomical properties of bones themselves, while external factors can only increase these differences in the state of preservation and representation of osseous remains. It is concluded from this that failure to recognize these differences may lead to misleading interpretations of paleodemography of past human populations.

Recent studies have shown that the most dimorphic tooth is the mandibular canine. We have carried out a study on a random sample of 146 skeletons dating from the plague outbreak in Marseilles (1722). We studied 1284 maxillary and 1432 mandibular permanent teeth. Sexual dimorphism was tested on 89 individuals. We selected a set of four dental indices and calculated the dimorphism percentage by ratio expression male/female. Dimorphic ranking was made, by allotting the first rank to the tooth presenting the highest dimorphism and the last rank to the one presenting the lowest ratio. Comparisons of means were made on both sexes (sex determined by post-cranial data) through a Student's test (t-test). We noted that lower canines and lateral incisor are the most interesting teeth in the dimorphic dental determination. The lower index presented the highest relative risk with RR = 1.56 [1.04-2.32]. In 58% of the cases, the lower dental index enabled a correct sex determination (determined on the basis of the post-cranial skeleton). These results showed the existence of a relative dental dimorphism (malefemale mesiodistal diameters) with humans. In conclusion, this method, using dental measurements, may be used as an additional technique to determine sex on fragmentary adult skeletons, immature material, missing pieces or ambiguities on post-cranial remains.

Yersinia pestis DNA was recently detected in human remains from 2 ancient plague pandemics in France and Germany. We have now sequenced Y. pestis glpD gene in such remains, showing a 93-bp deletion specific for biotype Orientalis. These data show that only Orientalis type caused the 3 plague pandemics.

Ancient septicemic plague epidemics were reported to have killed millions of people for 2 millenniums. However, confident diagnosis of ancient septicemia solely on the basis of historical clinical observations is not possible. The lack of suitable infected material has prevented direct demonstration of ancient septicemia; thus, the history of most infections such as plague remains hypothetical. The durability of dental pulp, together with its natural sterility, makes it a suitable material on which to base such research. We hypothesized that it would be a lasting refuge for Yersinia pestis , the plague agent. DNA extracts were made from the dental pulp of 12 unerupted teeth extracted from skeletons excavated from 16th and 18th century French graves of persons thought to have died of plague (“plague teeth”) and from 7 ancient negative control teeth. PCRs incorporating ancient DNA extracts and primers specific for the human β-globin gene demonstrated the absence of inhibitors in these preparations. The incorporation of primers specific for Y. pestis rpoB (the RNA polymerase β-subunit-encoding gene) and the recognized virulence-associated pla (the plasminogen activator-encoding gene) repeatedly yielded products that had a nucleotide sequence indistinguishable from that of modern day isolates of the bacterium. The specific pla sequence was obtained from 6 of 12 plague skeleton teeth but 0 of 7 negative controls ( P < 0.034, Fisher exact test). A nucleic acid-based confirmation of ancient plague was achieved for historically identified victims, and we have confirmed the presence of the disease at the end of 16th century in France. Dental pulp is an attractive target in the quest to determine the etiology of septicemic illnesses detected in ancient corpses. Molecular techniques could be applied to this material to resolve historical outbreaks.