Biology subjects

Drancourt, M.

Publications and source records attributed to Drancourt, M..

At least 19 recordsLinked to original sources

bioRxiv2024

Emerging Mycobacterium bovis in Lebanon: a snapshot based on whole-genome sequencing.

BackgroundTuberculosis is a pressing public health issue in Lebanon, a country of approximately five million people, including around 1.5 million refugees from Palestine and Syria. Prior research has revealed uncontrolled animal sources of Mycobacterium bovis, emphasizing the necessity for a comprehensive approach to combat tuberculosis in the region. Methods48 clinical Mycobacterium tuberculosis complex isolates were identified through whole genome sequence. Also, 43 animal fecal samples were collected from various farms across Lebanon to investigate the presence of the M. tuberculosis complex using CRISPR-csm4 PCR. ResultsGenomic analysis revealed that 39/48 (81.25%) of isolates were M. tuberculosis and 9/48 (18.75%) were M. bovis. M. tuberculosis was distributed over four lineages, Indo-Oceanic L1 (n = 3/39)(7.6%), East-Asian L2 (n = 1/39)(2.5%), East-African Indian L3 (n = 5/39)(12.8%) and Euro-American L4 (n = 30/39)(76.9%). Sub-lineage L4.8 (Euro-American (mainly T), comprising 8/39 of the isolates (20.5%) was predominant, followed by sub-lineages L3 (East-African Indian, n = 5/39 isolates)(12.8%), L4.2.2.2 (Euro-American (Ural), n= 4/39 isolates)(10.2%) and L4.6.5 (Euro American, n=4/39 isolates)(10.2%). Nine M. bovis were classified into two clades, designated as unknown2 (n=2/9; 22.2%) and unknown3 (n=7/9; 77.8%). Interestingly, none of the clades or others were detected in the 48 faecal samples using CRISPR standard PCR and qPCR. ConclusionsThis study offers insights into human and bovine tuberculosis in Lebanon, emphasizing M. tuberculosis lineages prevalence and M. bovis distribution into two clades, aiding the fight against tuberculosis, especially bovine tuberculosis, and renewing our understanding of tuberculosis dynamics in Lebanon.

microbiology↗

bioRxiv2024

Pre-Columbian treponemes clarify worldwide spread of treponematosis

Syphilis dramatically hit Europe at the end of the fifteen century before spreading to other continents. Yet the origin of the sudden pandemic in the Old World remains debated, in particular because the leading Columbus hypothesis of a New World origin of historical syphilis in Europe lacks paleomicrobiological confirmation. Here we screened a worldwide set of >1,700 ancient humans and identified ancient Treponema pallidum strains in two pre-Columbian child sacrifices from Tlatelolco, Mexico. Over 12,000 Treponema-specific reads were recovered to define a novel Treponema pallidum ancient population: Treponema pallidum str. tlatelolcoensis. Phylogenetics show that this population displays ancestral features but also bears the genetic building blocks of disease-causing modern Treponema pallidum subspecies, hence demonstrating how pre-Colombian Americas were the source of worldwide spread of treponematosis.

microbiology↗

bioRxiv2023

Resuscitating Sleeping Beauties: reviving a six-hundred-year-old amoeba and endosymbiont.

Coprolites are sources of ancient human gut microbiota and parasites. Paleomicrobiological investigation of a 14th-century coprolite revealed amoeba cysts that when cultured were identified as Acanthamoeba castellanii strain Namur. Genomic DNA sequencing indicated a 69-Mb, 57.9% GC content genome encoding 40,545 proteins, including 266 amoeba sequences sharing the best hit with amoeba-resisting microorganisms, including 170 with giant viruses. An endosymbiont we named Coprolita marseillensis was revealed by electron microscopy that harbored a 1-Mb genome of Rickettsiales ancestry encoding 1,738 predicted genes. Most of the amoeba genomic complement was related to biological functions giving the amoeba the capacity to survive in various ecological niches, including genes associated with anaerobic respiration and dormancy that were detected in bacteria resuscitated from permafrost, but not in controls that had not been resurrected. Investigating these 600-year-old "sleeping beauties" indicated the centuries-long survival of unicellular organisms and the mixed capability of anaerobic respiration coupled with dormancy.

microbiology↗

bioRxiv2022

Dental pulp metagenomics reveals ancient human Herpesviridae.

Following a recent report on ancient human Herpesviridae (HHV), we adapted a standard protocol used for the high-throughput sequencing of modern DNA to recover ancient DNA (aDNA) from dental pulp specimens collected at two historical burial sites. Investigation of 36 soldiers buried in Sevastopol, Crimea, during the 1853-1856 Crimean War yielded genomic sequences covering 8.5% of the herpes simplex virus (HSV)-1 genome, 15.7% of the HSV-2 genome, 1.9% of the Epstein-Barr virus (EBV) genome and 3.9% of the cytomegalovirus genome. Further investigation of 16 civilians buried in the 17th century in Amiens, France, yielded genomic sequences covering 9.8% of the HHV-1 genome and 2.2% of the HHV-6A genome; all data obtained with parallel negative controls was appropriately negative. Specific qPCRs confirmed the presence of four HSV-1, two HSV-2 and one EBV sequences in Sevastopol and two HSV-1 and one HHV-6 sequences in Amiens. HHV-6 was further detected by fluorescent in situ hybridization. These results demonstrated the usefulness of modern metagenomic protocols for high-throughput sequencing of aDNA in dental pulp.

microbiology↗

bioRxiv2021

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry identification of methanogens of clinical interest.

Methanogens, the archaea uniquely detoxifying fermentative hydrogen into methane in the digestive tract, are increasingly detected in pathology situations, rendering their rapid identification mandatory. We improved the experimental protocol to identify broth-cultured methanogens by matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI- TOF-MS). A database incorporating 34 reference spectra derived from 16 methanogen reference strains representative of eight species, supported further identification of 21 Methanobrevibacter smithii and 14 Methanobrevibacter oralis isolates broth-cultured from human stool and oral fluid, respectively, with scores > 2. In addition, MALDI-TOF-MS differentiated five Methanobrevibacter smithii genotypes incorporated in the study. Data here reported found MALDI-TOF-MS as a first line identification method for methanogens recovered from microbiota and clinical samples.

microbiology↗

bioRxiv2021

Dairy products as sources of methanogens for humans

Methanogens are detected in human gut from the first moments of life and there is a diversification of methanogens during infancy. However, the sources of acquisition of methanogens are not well elucidated. We therefore investigated 56 dairy products as potential sources of methanogens by applying molecular biology. In the presence of negative controls, we obtained an overall prevalence of methanogens in 85.7% (48/56) of samples by real-time PCR. Further PCR-sequencing identified 73.2% (41/56) of Methanobrevibacter smithii. We also found for the first time in dairy products 1.8% (1/56) of Methanobrevibacter oralis, 7.1% (4/56) of Methanobrevibacter millerae, 1.8% (1/56) of Methanobrevibacter ruminantium, 1.8% (1/56) of Methanocorpusculum sp. We observed a significant presence (p-value=0.001) of methanogens in fermented dairy products compared to unfermented dairy products. This study gives credit to the fact that dairy products could be considered as a source of methanogens for humans, especially for children.

microbiology↗

bioRxiv2021

Unbiased lexicometry analyses illuminate plague dynamics during the second pandemic

Knowledge of the second plague pandemic that swept over Europe during the 14th-19th centuries, mainly relies on the exegesis of contemporary texts, prone to interpretive bias. Leveraging bioinformatic tools routinely used in biology, we here developed a quantitative lexicography of 32 texts describing two major plague outbreaks using contemporary plague-unrelated texts as negative controls. Nested, network and category analyses of a 207-word pan-lexicome over-represented in plague-related texts, indicated that "buboes" and "carbuncles" words were significantly associated with plague, signaling ectoparasite- borne plague. Moreover, plague-related words were associated with the words "merchandise", "movable", "tatters", "bed" and "clothes", while no association was found with rats and fleas. These results support the hypothesis that during the second plague pandemic, human ectoparasites were the major drivers of plague. Analyzing ancient texts using here reported method would certify plague-related historical records and indicate particularities of each plague outbreak, including sources of the causative Yersinia pestis.

bioinformatics↗

bioRxiv2021

Speciation of the Mycobacterium tuberculosis complex using mass spectrometry: a proof-of-concept.

Mycobacteria that form the Mycobacterium tuberculosis complex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing, and currently relies on DNA analysis, including whole genome sequencing (WGS), which takes a whole day. In this study, we report on the unprecedented identification of the M. tuberculosis complex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative gold standard. In a first step, an optimised peptide extraction applied to 24 isolates otherwise identified in three of the 11 M. tuberculosis complex species by WGS, yielded 94 MALDI-TOF spectra which clustered according to WGS identification. In a second step, 70/74 (95%) other isolates were correctly identified at the species level by this clustering method. This study is the first to report a MALDI-TOF-MS method of identification of M. tuberculosis complex mycobacteria at the species level and is easily implantable in clinical microbiology laboratories.

microbiology↗

bioRxiv2020

Geographic microevolution of Mycobacterium ulcerans sustains Buruli ulcer extension, Australia

The reason why severe cases of Buruli ulcers caused by Mycobacterium ulcerans are emerging in some South Australia counties has not been determined. In this study, we measured the diversity of M. ulcerans complex whole genome sequences (WGS) and reported a marker of this diversity. Using this marker as a probe, we compared WGS diversity in Buruli ulcer-epidemic South Australia counties versus non-epidemic Australian counties and further refined comparisons at the level of counties where severe Buruli ulcer cases have been reported. Analyzing 218 WGS (35 complete and 183 reconstructed WGS, including 174 Australian WGS) yielded 15 M. ulcerans complex genotypes, including three genotypes specific to Australia and one genotype specific to South Australia. A 1,068-bp PPE family protein gene exhibiting genotype-specific sequence variations was employed to further probe 13 minority clones hidden in sequence reads. The repartition of these clones significantly differed between South Australia and the rest of Australia. In addition, a significantly higher prevalence of 3/13 clones was observed in South Australia counties of the Mornington Peninsula, Melbourne and Bellarine Peninsula than in other South Australia counties. The data presented in this report suggest that the microevolution of three M. ulcerans complex clones drove the emergence of severe Buruli ulcer cases in some South Australia counties. Sequencing one specific PPE gene served to efficiently probe M. ulcerans complex clones. Further functional studies may balance the environmental adaptation and virulence of these clones.

evolutionary biology↗

bioRxiv2020

Experimental pieces of evidence for Mycobacterium ulcerans dormancy.

BackgroundWhether Mycobacterium ulcerans, the etiological agent of the neglected Buruli ulcer in numerous tropical countries, would exist in a dormant state as reported for closely related Mycobacterium species, is not established. MethodologySix M. ulcerans strains were exposed to a progressive depletion in oxygen for two months, using a previously described Wayne model of dormancy; and further examined by microscopy using DDD staining, microcalorimetry and subculture in the presence of dead and replicative M. ulcerans as controls. Principal Findings/ConclusionsM. ulcerans CU001 strain died during the progressive oxygen depletion and four of five remaining strains exhibited Nile Red-stained intracellular lipid droplets after DDD staining and a 14-20-day regrowth when exposed to ambient air, diagnosing dormancy. A fifth M. ulcerans 19423 strain stained negative in DDD and slowly regrew in 27 days. Three tested M. ulcerans strains yielded microcalorimetric pattern similar to that of the negative (dead) homologous controls, differing from that of the homologous positive (replicative) controls. The relevance of these experimental observations, suggesting a previously unreported dormancy state of M. ulcerans, needs to be investigated in the natural ecological niches where M. ulcerans thrive and in Buruli ulcer lesions. Author summaryMycobacterium ulcerans is an environmental opportunistic pathogen of mammals and humans, causing a subcutaneous necrotizing infection named Buruli ulcer. Molecular detection of M. ulcerans DNA revealed different ecological niches where M. ulcerans may thrive, but the molecular biology approach does not catch the physiological state of M. ulcerans in these different ecological niches. Thus, the reservoir and the mode of transmission of M. ulcerans remain elusive. Here, we investigated experimental dormancy of M. ulcerans by using a previously described Wayne model of dormancy coupled with microscopy using DDD staining, microcalorimetry and subculture. Our findings demonstrate for the first time that some M. ulcerans strains exhibit a physiological state of dormancy; potentially limiting isolation and culture of M. ulcerans from environmental niches.

microbiology↗

bioRxiv2020

Stool methanogens in intestine mammal species.

Methanogens are being members of anaerobe microbiota of the digestive tract of both human and mammals. However, the sources, modes of acquisition and dynamics of digestive tract methanogens remain poorly investigated. In this study, we aimed to expand the spectrum of animals which could be sources of methanogens for human, by exploring methanogen carriage in animals in contact with the general population or with some restricted populations; comparing the repertoire of animal methanogens with the one of human methanogens in order to question methanogens as zoonotic microorganisms. We used RT-PCR, PCR-sequencing and multispacer sequence typing to investigate the presence of methanogens in 407 fecal specimens collected from nine different mammalian species. We detected by RT-PCR, the presence of methanogen DNA in all mammals here investigated and none of the negative controls. We obtained by sequencing, seven different species of methanogens, of which three (Methanobrevibacter smithii, Methanobrevibacter millerae and Methanomassiliicoccus luminyensis) are known to be part of the methanogens present in the human digestive tract. We obtained 24 M. smithii by PCR-sequencing including 12/24 (50%) in pigs, 6/24 (25%) in dogs, 4/24 (16.66%) in cats, and 1/24 (4.16%) in both sheep and horses. Genotyping these 24 M. smithii revealed five different genotypes, all know in humans. Our results are fairly representative of the methanogen community present in the digestive tract of certain animals domesticated by humans and other future studies must be done to try to cultivate methanogens here detected by molecular biology to better understand the dynamics of methanogens in animals and also the likely acquisition of methanogens in humans through direct contact with these animals or through consumption of the meat and/or milk of certain animals, in particular cows.

microbiology↗

bioRxiv2020

Human dental pulp stem cells: a sanctuary for relapsing Bartonella quintana.

Bartonella quintana is a facultative intracellular bacterium responsible for relapsing fever, an example of non-sterilizing immunity. The cellular sanctuary of B. quintana in-between febrile relapses remains unknown but repeated detection of B. quintana in dental pulp specimens suggested long-term half-life dental pulp stem cells (DPSCs) as candidates. As the capacity of DPSCs to internalize microscopic particles was unknown, we confirmed that DPSCs internalized B. quintana bacteria: Gimenez staining and fluorescence microscopy localized B. quintana bacteria inside DPSCs and this internalization did not affect the cellular multiplication of DPSCs during a one-month follow-up despite the increase in the bacterial load. B. quintana-infected DPSCs did not produce Tumor Necrosis Factor- whereas an important production of Monocytes Chemoattractant Protein-1 was observed. These unprecedented observations suggested the possibility that DPSCs were shelters for the long-term persistence of B. quintana in the host, warranting further experimental and clinical investigations.

microbiology↗

bioRxiv2020

Screening anti-infectious molecules against Mycobacterium ulcerans: a step towards decontaminating environmental specimens.

Mycobacterium ulcerans, a non-tuberculous mycobacterium responsible for Buruli ulcer, is residing in poorly defined environmental niches in the vicinity of stagnant water points where very few isolates have been confirmed. In the perspective of culturing M. ulcerans from such contaminated environmental specimens, we tested the in vitro susceptibility of M. ulcerans CU001 strain co-cultivated with XTC cells to anti-infectious molecules registered in the French pharmacopoeia, using a standardised concentration, to find-out molecules inactive against M. ulcerans which could be incorporated in decontaminating solution. Of 116 tested molecules, 64 (55.1%] molecules including 34 (29.3%] antibiotics, 14 (12%] antivirals, 8 (6.8%] antiparasitic and 8 (6.8%] antifungals were ineffective against M. ulcerans CU001; leaving 52 molecules active against M. ulcerans CU001. Three such inactive antimicrobial molecules (oxytetracycline, polymyxin E and voriconazole] were then selected to make a decontamination solution shown to respect M. ulcerans CU001 viability. These three antimicrobials could be incorporated into a decontamination solution for the tentative isolation and culture of M. ulcerans from environmental samples.

microbiology↗

bioRxiv2020

A 2,000-year-old specimen with intraerythrocytic Bartonella quintana

Photogrammetry and cascading microscopy investigations of dental pulp specimens collected from 2,000-year-old individuals buried in a Roman necropolis in Besancon, France, revealed unprecedented preserved tissular and cellular morphology. Photogrammetry yielded 3-D images of the smallest archaeological human remain ever recovered. Optical microscopy examinations after standard hematoxylin-phloxine-saffron staining and anti-glycophorin A immunohistochemistry exposed dental pulp cells, in addition erythrocytes were visualized by electron microscopy, which indicated that the ancient dental pulp trapped a blood drop. Fluorescence in situ hybridization applied on red blood cells revealed the louse-borne pathogen Bartonella quintana, a finding confirmed by polymerase chain reaction assays. Through paleohistology and paleocytology, we demonstrate that ancient dental pulp preserved intact blood cells at the time of the individuals death, offering an unprecedented opportunity to engage in direct and indirect tests to diagnose pathogens in ancient buried individuals.

microbiology↗

bioRxiv2020

Five millennia of Bartonella quintana bacteremia.

Bartonella quintana caused trench fever in the framework of two World Wars and is now recognized as an agent of re-emerging infection. Many reports indicated the popularity of B. quintana exposure since the 90s. For evaluating 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 archeological sites with the presence of negative controls. Fishers exact test was used to compare the prevalence of B. quintana detection 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 bacteremia, respectively. This study collected 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 citizens, with 20% and 18.8%, respectively, in the 18th - 19th centuries, but the difference in frequency was not significant. These results confirmed the role of dental pulp in diagnosing B. quintana bacteremia in ancient populations and showed the incidence of B. quintana in both citizens and soldiers. Many recent findings contributed to understanding the coevolution of the relationship between B. quintana and humans.

microbiology↗

bioRxiv2020

Translocating Mycobacterium ulcerans: an experimental model.

Mycobacterium ulcerans is a non-tuberculous environmental mycobacterium responsible for extensive cutaneous and subcutaneous ulcers in mammals, named Buruli ulcer in patients. M. ulcerans has been seldom detected in the feces of mammals but not in patients, nevertheless the detection and isolation of M. ulcerans in animal feces does not feet with the current epidemiological schemes for the disease. Here using an experimental model in which rats were fed with 109 colony-forming units of M. ulcerans, we detected M. ulcerans in feces of challenged rats for two weeks and along their digestive tract for 10 days. M. ulcerans was further detected in the lymphatic system including cervical and axillary lymph nodes and the spleen, but not in any other tissue including the healthy and breached skin, 10 days post-challenge. These observations indicate that in some herbivorous mammals, M. ulcerans contamination by the digestive route may precede translocation and limited infection of the lymphatic tissues without systemic infection. These herbivorous mammals may be sources of M. ulcerans for exposed populations but are unlikely reservoirs for the pathogen.

microbiology↗

bioRxiv2019

Investigation of skin microbiota reveals Mycobacterium ulcerans-Aspergillus sp. trans-kingdom communication

BackgroundMycobacterium ulcerans secrete a series of non-ribosomal-encoded toxins known as mycolactones that are responsible for causing a disabling ulceration of the skin and subcutaneous tissues named Buruli ulcer. The disease is the sole non-contagion among the three most common mycobacterial diseases in humans. Direct contact with contaminated wetlands is a risk factor for Buruli ulcer, responsible for M. ulcerans skin carriage before transcutaneous inoculation with this opportunistic pathogen. Methodology and principal findingsIn this study, we analysed the bacterial and fungal skin microbiota in individuals exposed to M. ulcerans in Burkina Faso. We showed that M. ulcerans-specific DNA sequences were detected on the unbreached skin of 6/52 (11.5%) asymptomatic farmers living in Sindou versus 0/52 (0%) of those living in the non-endemic region of Tenkodogo. Then, we cultured the skin microbiota of asymptomatic M. ulcerans carriers and negative control individuals, all living in the region of Sindou. A total of 84 different bacterial and fungal species were isolated, 21 from M. ulcerans-negative skin samples, 31 from M. ulcerans-positive samples and 32 from both. More specifically, Actinobacteria, Aspergillus niger and Aspergillus flavus were significantly associated with M. ulcerans skin carriage. We further observed that in vitro, mycolactones induced spore germination of A. flavus, attracting the fungal network. ConclusionThese unprecedented observations suggest that interactions with fungi may modulate the outcome of M. ulcerans skin carriage, opening new venues to the understanding of Buruli ulcer pathology, prophylaxis and treatment of this still neglected tropical infection. Author summaryBuruli ulcer is a chronic infectious disease caused by the environmental opportunistic pathogen Mycobacterium ulcerans which secretes an exotoxin responsible for its pathogenicity. The reservoir and sources of M. ulcerans in the environment remain elusive and its mode of transmission is unclear. To acquire M. ulcerans infection, at least two conditions must be met, viable bacteria and a skin lesion as demonstrated by experimental animal models. In this study, we showed that M. ulcerans specific DNA sequences could be detected on the healthy skin of asymptomatic farmers living in one region of Burkina Faso where Buruli ulcer cases had already been reported, but not in Buruli ulcer-free regions, suggesting skin carriage after contacts with environmental sources. We also investigated the skin microbiota of M. ulcerans carriers and found significant associations of some bacteria and fungi with skin carriage of M. ulcerans. These associations may due to the effect of mycolactones on some fungi species. As we showed previously with Mucor circinelloides and here with Aspergillus flavus.

microbiology↗

bioRxiv2019

Mycolactone-independent pathogenicity of Mycobacterium ulcerans: an experimental study in plants.

Mycobacterium ulcerans, the etiologic agent of Buruli ulcer in humans and animals, secretes macrolide exotoxins mycolactones which damage tissues after a cascade of cellular effects. M. ulcerans, an environmental organism with still elusive reservoirs and sources has been detected in soil and water in endemic areas where it could be in contact with plants. Symptom observations, microscopy and molecular biology were used to investigate M. ulcerans contact with plants in an experimental model mimicking the known pathology of Buruli ulcer in humans. Solanum lycopereum (tomato) plants with scarified or intact roots were transplanted into pots containing contaminated soil with M. ulcerans or a mixture of mycolactones A/B and C in the presence of negative control groups. Whereas plants with intact roots remained asymptomatic, M. ulcerans-infected plants with scarified roots had significantly more diseased leaves than controls (p = 0.004). Optic microscopy examination showed significantly more mycobacteria in the secondary and main roots than in controls (p=0.0008). Real-time PCRs detected M. ulcerans DNA in 7/12 (58%) of infected root samples versus none in the control plants (p = 0.04). Further study of plants with mycolactones A/B and C yielded no significant difference with negative controls. These results suggest that in this model, M. ulcerans exhibits a mycolactone-independent pathogenicity whose mechanism remains to be elucidated.

microbiology↗