36 results on '"Gorgé, O."'
Search Results
2. L’Institut de recherche biomédicale des armées (IRBA) et l’épidémiologie des eaux usées : intérêt pour les forces armées
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Boni, M., Gorgé, O., Mullot, J.-U., Wurtzer, S., Moulin, L., Maday, Y., Obépine, GIS, Canini, F., Chantre, M., Teyssou, R., Maréchal, V., Janvier, F., and Tournier, J.-N.
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- 2022
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3. Evaluation des risques chimiques environnementaux pour les militaires déployés à l’étranger
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BUREL-EBEL, L., primary, GORGÉ, O., additional, LE GOFF, P.-A., additional, BRETON, D., additional, and MULLOT, J.-U., additional
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- 2018
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4. First cases of Omicron in France are exhibiting mild symptoms, November 2021–January 2022
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Andrieu, A., Broustal, O., Chene, S., Chent, S., Fougère, E., Gbaguidi, G., Hamidouche, M., Lamy, A., Mano, Q., Mastrovito, B., Mercier, A., Modenesi, G., Picard, G., Prudhomme, J., Rapilly, F., Riondel, A., Rivière, M., Villegas Ramirez, B., Zhu-Soubise, A., Zurbaran, M., Amzert, A., Andreoletti, L., Bal, A., Beaurepere, R., Behillil, S., Belec, L., Bernard, C., Bocket, L., Bouri, L., Bourlet, T., Bressollette-Bodin, C., Brichler, S., Brugerolles, C., Cado, S., Calvez, V., Capron, N., Castelain, S., Castro-Alvarez, J., Chaix, M.-L., Charpentier, C., Che, D., Chillou, C., Colson, P., Coudene, P., Crinquette, A., De Rougemont, A., Delagrèverie, H., Delamare, C., Denecker-Berardino, T., Descamps, D., Desroches, M., Destras, G., Dos Santos, G., Ducancelle, A., Ducreux, S., Duret, T., Enouf, V., Fafi-Kremer, S., Felici, C., Fourati, S., Fournier, P.-E., Gaudy, C., Germain, H., Giordanengo, V., Gorge, O., Haim-Boukobza, S., Henquell, C., Holstein, A., Houhamdi, L., Izopet, J., Jacomo, V., Jacques, A., Jaffar-Bandjee, M.-C., Jimenez, M., Josset, L., Kemeny, S., Lafon, M.-E., Le Bars, A., Le Corguille, G., Lepiller, Q., Levasseur, A., Leveque, N., Lina, B., Madelaine, C., Malabat, C., Marque-Juillet, S., Martin-Dunavit, T., Mavingui, P., Merens, A., Messak, I., Morand-Joubert, L., Naudot, X., Neybecker, P., Pawlotsky, J.-M., Pilorge, L., Plantier, J.-C., Poggi, C., Pretet, M., Ragot, C., Raoul, H., Rogez, S., Roque-Afonso, A.-M., Roquebert, B., Rousset, D., Rozenberg, F., Sagot, C., Sahnoune, S., Salgado, D., Sand, O., Saudemont, C., Schvoerer, E., Simon-Loriere, E., Stephan, R., Sudour, J., Thibault, V., Tuaillon, E., Vabret, A., Vallee, E., Van Der Werf, S., Van Helden, J., Verdurme, L., Vignola, A., Wilkinson, D., Yazdanpanah, Y., Maisa, A., Spaccaferri, G., Fournier, L., Schaeffer, J., Deniau, J., Rolland, P., and Coignard, B.
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- 2022
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5. Investigation of a COVID-19 Outbreak on an Aircraft Carrier: An Epidemic Model Based on Real Data
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Marbac, Gorgé O, Mrenda Bm, Santi VPd, Frédéric Janvier, Chapus C, Texier G, Lacrosse C, Dia A, Letois F, Dutasta F, Tournier J, Anthony Levasseur, Laval Fd, Marchi J, Sarilar, Cobola J, Nolent F, Hervé Chaudet, and Jean-Baptiste Meynard
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medicine.medical_specialty ,Informed consent ,Transmission (medicine) ,Medical record ,Epidemiology ,Emergency medicine ,Cohort ,Attack rate ,medicine ,Outbreak ,Herd immunity - Abstract
Background: From mid-March to mid-April 2020, the French aircraft carrier Charles de Gaulle suffered a COVID-19 outbreak. An investigation was performed to describe the outbreak, including how the virus was introduced on board. We present the clinical pictures of COVID-19 cases with risk factors for infection and severity, effectiveness of preventive measures, and we discuss the real collective protective rate. Methods: A confirmed case was any service member with a positive SARS-CoV-2 RT-PCR and/or who presented symptoms of anosmia and/or ageusia. We considered the entire crew as a cohort and questioned them about individual, epidemiological, and clinical data. We performed viral genome sequencing and searched for SARS-CoV-2 in the environment. Results: The attack rate was 65% (1085/1767). The sex ratio was 6·9, and median age was 29 years. There were four clinical profiles: asymptomatic (13·0%), non-specific symptomatic (8·1%), specific symptomatic (76·3%), and severe (i.e. requiring oxygen therapy, 2·6%). Active smoking prevented severe COVID-19; age and obesity were risk factors. The instantaneous reproduction rate Rt and viral sequencing supported the hypothesis of several introductions of the virus on board, with an acceleration of the Rt when preventive measures were lifted. Physical distancing prevented infection (ORa, 0·55, 95% CI, 0·40-0·76). In the end, transmission stopped when the proportion of infected personnel was large enough to prevent the virus from circulating (65%, 95% CI, 62-68). Discussion: Asymptomatic and non-specific clinical pictures of COVID-19, combined with a lack of knowledge at that time about the specific symptoms of COVID-19 (anosmia, ageusia), delayed detection of the outbreak. Once it was identified, the lack of an isolation ward made it difficult to manage transmission on board, and the outbreak spread until a collective protective rate was reached. However, physical distancing was effective when applied. Syndromic surveillance and point-of-care biology could enable early detection of such viral emergences or outbreaks. Funding Information: No funding to declare. Declaration of Interests: The authors declare that they have no competing interests. Ethics Approval Statement: This was not an experimental protocol, but an outbreak investigation with routine care provided to infected individuals, so no ethical approval from any named institutional and/or licensing/ethics committee was required. We obtained individual informed consent to analyze data. No administrative authorization was required to access and use medical records. We chose not to provide certain details and to aggregate certain data in order to maintain patient anonymity. All methods were carried out in accordance with relevant guidelines and regulations.
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- 2021
6. Taphonomy of DNA in rodents
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Geigl, E.M., Guimaraes, S., Gorgé, O., Stoetzel, Emmanuelle, Morin, D., Fernandez-Jalvo, Y., Grange, T., Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), and Millan-Brun, Anne-Lise
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[SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory ,[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory - Abstract
International audience; Micromammals, particularly rodents, are important paleoenvironmental indicators and their investigation has the potential to deliver a large amount of invaluable information for the interpretation of archeological sites and past environments. Data from paleogenetic and paleogenomic analyses of this important resource could contribute substantially to these interpretations. Most rodent remains, however, originate from accumulations through predators, such as pellets of raptors. In modern pellets, we could show that the passage of rodents through the digestive tract heavily damages DNA in their bones and teeth although the extent of DNA damage depends on the location of the remains in the stomach of the predator and the duration they are subject to the attack of the gastric juices. Thus, a minute portion of DNA can be rather well preserved. It is likely that it is this portion that is prone to long-term preservation since we could show DNA to be preserved in rodent remains from the El Harhoura2 cave in Morocco in levels dated to ca. 6,000 and 44,000 years. We also performed experiments of monitored taphonomy and analyzed DNA degradation and the transformation of the microbiome in bones of mice buried for different time intervals covering a period of 2 years. These experiments shed light on the processes through which biological specimens turn into environmental specimens.
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- 2016
7. Owl pellets: a wise DNA source for small mammal genetics
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Guimaraes, S., primary, Fernandez‐Jalvo, Y., additional, Stoetzel, E., additional, Gorgé, O., additional, Bennett, E. A., additional, Denys, C., additional, Grange, T., additional, and Geigl, E.‐M., additional
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- 2015
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8. Etude de la qualité de l’air à Kaboul: résultats d’une campagne de mesures
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CRÉHANGE, G., primary, GOLLION, A., additional, GORGÉ, O., additional, DELACOUR, H., additional, MERENS, A., additional, CAIRE-MAURISIER, F., additional, PLANTAMURA, J., additional, BOHAND, S., additional, and MULLOT, J.-U., additional
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- 2014
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9. Owl pellets: a wise DNA source for small mammal genetics.
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Guimaraes, S., Fernandez‐Jalvo, Y., Stoetzel, E., Gorgé, O., Bennett, E. A., Denys, C., Grange, T., and Geigl, E.‐M.
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BIRD droppings ,BIRDS of prey ,ANIMAL droppings ,SPECIES diversity - Abstract
Pellets of raptors are an important source for the study of the taxonomy, phylogeography and ecological diversity of small vertebrates. Since birds of prey are efficient collecting agents for both rare species and those reluctant to enter traps, they offer an important complement to traditional trapping efforts in the field. The possibility of using bones and teeth recovered from pellets as a convenient alternative DNA source for genetic studies requires a more complete understanding of the DNA preservation of these partially digested remains. It is not yet clear, for example, to which degree DNA is preserved and how heterogeneous DNA preservation is in the different skeletal remains found in pellets since systematic quantitative analyses are missing. Here, we attempt to improve this knowledge by quantifying the degradation of DNA during the digestion process of raptors using 62 individual rodent bones and teeth from different pellets. We show a very high variability in DNA preservation between bones. Interestingly, variability between bones within the same pellet is much higher than that found between pellets, which has major consequences for genetic studies as it implies that bones from the same pellet that could belong to different individuals/species should be tested individually when multiple markers are analyzed. We find that neither the identity of the skeletal part nor microscopic observation of the degree of digestion are useful proxies for DNA preservation, and we thus recommend the use of screening strategies to identify the most suitable bones to include in analyses. We conclude that pellets of owls, whether freshly collected or from natural history collections, can be a practical noninvasive source for genetic studies of small vertebrates provided the design of the study takes into account the short DNA molecule length, the low quantity of DNA preserved and the heterogeneity in DNA preservation. [ABSTRACT FROM AUTHOR]
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- 2016
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10. Analysis of the three Yersinia pestis CRISPR loci provides new tools for phylogenetic studies and possibly for the investigation of ancient DNA
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Vergnaud, G., Li, Y., Gorgé, O., Cui, Y., Song, Y., Zhou, D., Grissa, I., Dentovskaya, S. V., Platonov, M. E., Rakin, A., Balakhonov, S. V., Neubauer, H., Pourcel, C., Andrey Anisimov, Yang, R., Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
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DNA, Bacterial ,MESH: Interspersed Repetitive Sequences ,Yersinia pestis ,Molecular Sequence Data ,MESH: Yersinia pestis ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,MESH: Base Sequence ,MESH: History, Ancient ,MESH: Plague ,Disease Outbreaks ,Evolution, Molecular ,Species Specificity ,Humans ,MESH: Species Specificity ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,MESH: Disease Outbreaks ,MESH: Phylogeny ,History, Ancient ,Phylogeny ,MESH: Evolution, Molecular ,Plague ,MESH: Humans ,MESH: Molecular Sequence Data ,Base Sequence ,MESH: DNA, Bacterial ,Interspersed Repetitive Sequences ,Genes, Bacterial ,Yersinia pseudotuberculosis ,MESH: Yersinia pseudotuberculosis ,MESH: Genes, Bacterial - Abstract
The precise nature of the pathogen having caused early plague pandemics is uncertain. Although Yersinia pestis is a likely candidate for all three plague pandemics, the very rare direct evidence that can be deduced from ancient DNA (aDNA) analysis is controversial. Moreover, which of the three biovars, Antiqua, Medievalis or Orientalis, was associated with these pandemics is still debated. There is a need for phylogenetic analysis performed on Y. pestis strains isolated from countries from which plague probably arose and is still endemic. In addition there exist technical difficulties inherent to aDNA investigations and a lack of appropriate genetic targets. The recently described CRISPRs (clustered regularly interspaced short palindromic repeats) may represent such a target. CRISPR loci consist of a succession of highly conserved regions separated by specific "spacers" usually of viral origin. To be of use, data describing the mechanisms of evolution and diversity of CRISPRs in Y. pestis, its closest neighbors, and other species which might contaminate ancient DNA, are necessary. The investigation of closely related Y. pestis isolates has revealed recent mutation events in which elements constituting CRISPRs were acquired or lost, providing essential insight on their evolution. Rules deduced represent the basis for subsequent interpretation. In the present study, the CRISPR loci from representative Y. pestis and Yersinia pseudotuberculosis strains were investigated by PCR amplification and sequence analysis. The investigation of this wider panel of strains, including other subspecies or ecotypes within Y. pestis and also Y. pseudotuberculosis strains provides a database of the existing CRISPR spacers and helps predict the expected CRISPR structure of the Y. pestis ancestor. This knowledge will open the way to the development of a spoligotyping assay, in which spacers can be amplified even from highly degraded DNA samples. The data obtained show that CRISPR analysis can provide a very powerful typing tool, adapted to the systematic, large-scale genotyping of Y. pestis isolates, and the creation of international typing databases. In addition, CRISPRs do constitute a very promising new tool and genetic target to investigate ancient DNA. The corresponding genetic targets are small (
11. Management of unexpected laboratory exposure to Burkholderia pseudomallei.
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Mostaghat I, Couzigou C, Pilmis B, Castreau N, Raymond E, Maixant AL, Le Monnier A, Depeille A, Gorgé O, and Mizrahi A
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- Humans, Burkholderia pseudomallei, Melioidosis diagnosis, Melioidosis epidemiology, Melioidosis microbiology
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Burkholderia pseudomallei is a Gram-negative saprophytic bacillus that causes melioidosis. The infection is endemic in South-East of Asia and Northern Australia. B. pseudomallei has been designated as bioterrorism agent and its manipulation should be done in a biological safety level 3 capability. Workers in laboratories may be accidentally exposed to B. pseudomallei before its identification, with a risk of laboratory-acquired melioidosis. We want to describe a case of melioidosis occurred in our hospital and its management at laboratory. The objective of this article is to provide guidance to microbiologists confronted with a suspicious case of B. pseudomallei on the management of the exposition. We report here a couple of microbiological arguments that can usually guide microbiologists towards presumptive identification of B. pseudomallei. This case report shows the importance of MALDI-TOF MS accurate databases to ensure accurate microbial identification and antibiotic prophylaxis adapted to individuals who were exposed. We also want to underline the importance of developing an effective strategy of prevention against any accidental exposure that can occur in a microbiological laboratory.
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- 2024
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12. Population dynamics of plague vector fleas in an endemic focus: implications for plague surveillance.
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Rasoamalala F, Gostic K, Parany MJ, Rahelinirina S, Rahajandraibe S, Gorgé O, Valade E, Harimalala M, Rajerison M, and Ramasindrazana B
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- Animals, Humans, Insect Vectors microbiology, Mammals, Population Dynamics, Plague microbiology, Siphonaptera microbiology, Flea Infestations epidemiology, Flea Infestations veterinary, Yersinia pestis
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Plague is a zoonotic vector-borne disease caused by the bacterium Yersinia pestis. In Madagascar, it persists in identified foci, where it is a threat to public health generally from September to April. A more complete understanding of how the disease persists could guide control strategies. Fleas are the main vector for transmission between small mammal hosts and humans, and fleas likely play a role in the maintenance of plague. This study characterized the dynamics of flea populations in plague foci alongside the occurrence of human cases. From 2018 to 2020, small mammals were trapped at sites in the central Highlands of Madagascar. A total of 2,762 small mammals were captured and 5,295 fleas were collected. The analysis examines 2 plague vector species in Madagascar (Synopsyllus fonquerniei and Xenopsylla cheopis). Generalized linear models were used to relate flea abundance to abiotic factors, with adjustments for trap location and flea species. We observed significant effects of abiotic factors on the abundance, intensity, and infestation rate by the outdoor-associated flea species, S. fonquerniei, but weak seasonality for the indoor-associated flea species, X. cheopis. A difference in the timing of peak abundance was observed between the 2 flea species during and outside the plague season. While the present study did not identify a clear link between flea population dynamics and plague maintenance, as only one collected X. cheopis was infected, the results presented herein can be used by local health authorities to improve monitoring and control strategies of plague vector fleas in Madagascar., (© The Author(s) 2023. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
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- 2024
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13. Assessment of calcium hypochlorite for Bacillus anthracis spore surface's decontamination.
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Verguet N, Mondange L, Nolent F, Depeille A, Garnier A, Neulat-Ripoll F, Gorgé O, and Tournier JN
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- Decontamination, Spores, Bacterial, Bacillus anthracis, Disinfectants pharmacology
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Contamination with microorganisms occurs in laboratories but is also of high concern in the context of bioterrorism. Decontamination is a cornerstone that promotes good laboratory practices and occupational health and safety. Among the most resistant structures formed by microorganisms are spores, produced notably by Clostridium and Bacillus species. Here, we compared six products containing four different molecules (hydrogen peroxide, peracetic acid, sodium and calcium hypochlorite) on B. anthracis Sterne spores. We first selected the most efficient product based on its activity against spore suspensions using French and European standards. Four products showed sporicidal activity, of which only two did so in a time frame consistent with good laboratory practices. Then, we tested one of these two products under laboratory conditions on fully virulent B. anthracis spores, during common use and after contamination through a spill of a highly concentrated spore suspension. We, thus, robustly validated a decontaminant based on calcium hypochlorite not only on its ability to kill spores but also on its effectiveness under laboratory conditions. At the end, we were able to assure a complete disinfection in 1 min after spillover and in 2 min for common use., Competing Interests: Declaration of competing interest There are no conflicts to declare., (Copyright © 2023 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.)
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- 2023
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14. [The emergence of the Monkeypox virus (Mpox) or the return to public health concern of a family of forgotten viruses].
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Ferraris O, Ferrier A, Mura M, Boni M, Javelle É, Gorgé O, Iseni F, and Tournier JN
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- Humans, Public Health, Monkeypox virus, Mpox (monkeypox) epidemiology
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- 2023
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15. Analysis of Ancient Microbial DNA.
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Gorgé O, Bennett EA, Massilani D, Daligault J, Geigl EM, and Grange T
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- Animals, Humans, DNA, Ancient, Body Remains, DNA genetics, Genome, Microbial, Sequence Analysis, DNA methods, Hominidae genetics, Neanderthals genetics
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The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
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- 2023
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16. Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations.
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Frenois-Veyrat G, Gallardo F, Gorgé O, Marcheteau E, Ferraris O, Baidaliuk A, Favier AL, Enfroy C, Holy X, Lourenco J, Khoury R, Nolent F, Grosenbach DW, Hruby DE, Ferrier A, Iseni F, Simon-Loriere E, and Tournier JN
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- United States, Humans, Isoindoles pharmacology, Isoindoles therapeutic use, Benzamides pharmacology, Benzamides therapeutic use, Monkeypox virus, Mpox (monkeypox) drug therapy
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The ongoing monkeypox virus (MPXV) outbreak is the largest ever recorded outside of Africa. We isolated and sequenced a virus from the first clinical MPXV case diagnosed in France (May 2022). We report that tecovirimat (ST-246), a US Food and Drug Administration approved drug, is efficacious against this isolate in vitro at nanomolar concentrations, whereas cidofovir is only effective at micromolar concentrations. Our results support the use of tecovirimat in ongoing human clinical trials., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)
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- 2022
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17. [The French Armed Forces Biomedical Research Institute (IRBA) and wastewater-based epidemiology: Applicability and relevance in armed forces].
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Boni M, Gorgé O, Mullot JU, Wurtzer S, Moulin L, Maday Y, Obépine G, Canini F, Chantre M, Teyssou R, Maréchal V, Janvier F, and Tournier JN
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The French Armed Forces Biomedical Research Institute (IRBA) deeply involved in research on SARS-COV-2, participated in the creation of the Obépine sentinel network in charge of detecting, qualifying and quantifying the virus genome in wastewater in France. During this pandemic, wastewater-based epidemiology has proven to be a first class public health tool for assessing viral dynamics in populations and environment. Obépine has also conducted research demonstrating the low infectivity of faeces and wastewater and allowed for early detection of epidemic waves linked to new variants. The IRBA has adapted this powerful tool to the monitoring of viral infections on board the aircraft carrier Charles-de-Gaulle in order to get an operational system for anticipation after the first local outbreak in 2020. The presence of this surveillance and anticipation tool has allowed a better management of SARS-CoV-2 contingent introductions on board during stopovers or crewmembers entries. The combination of a mandatory vaccination protocol and the surveillance of viral circulation in black waters has made it possible to identify and locate cases, and thus to continue the operational mission in the COVID-19 environment while limiting the spread and preserving the health of the crew. This innovative tool can easily be redirected to the search for any other pathogens in blackwater or even, in the long term, to ensure health surveillance of any military establishment, at sea or on land, in France or on overseas bases., (© 2022 l'Académie nationale de médecine. Published by Elsevier Masson SAS. All rights reserved.)
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- 2022
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18. [Management of the COVID-19 epidemic in the carrier battle group (January-April 2020) by the Armed Forces Epidemiology and Public Health Center].
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Meynard JB, de Laval F, Texier G, Gorgé O, Degui H, and Pommier de Santi V
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Objectives: Faced with the COVID-19 epidemic that occurred within the naval air group and the nuclear aircraft carrier Charles de Gaulle, the French Armed Forces Epidemiology and Public Health Center (CESPA) carried out an investigation (January - April 2020) whose objectives were: to identify the possible routes of introduction of the virus ; to describe the characteristics of the epidemic and to describe and model the dynamics of the epidemic's spread., Methods: A telephone survey was conducted. The biological diagnoses were transmitted by the medical antennas. A time/place/population analysis was carried out, as well as the description of the clinical pictures with their exposure factors. The instantaneous reproduction rate Rt of the epidemic was modeled. A spatial analysis of the epidemic on board was carried out. Forty-three viral genomes were sequenced and compared to the reference bases., Results: 0f 1767 sailors, 1568 (89%) participated in the telephone survey and 1064 (67.9%) were confirmed cases. Four patient profiles have been described: asymptomatic (13.0%); non-specific symptomatic (8.1%); specific symptomatic (76.3%); severe cases (2.6%). In univariate and multivariate analysis, age, overweight and obesity were significantly associated with the risk of having a severe form. Smoking was a protective factor. The evolution kinetics of Rt was in favor of an introduction of the virus at the end of February with a reintroduction during the stopover in Brest. Analysis of viral genomes ruled out introduction and spread of a single strain., Conclusion: Despite the control measures taken, an epidemic occurred. The often pauci-symptomatic clinical pictures resulted in a delay in identification. CESPA was able to carry out this epidemiological investigation within a highly constrained timeframe, showing all the interest of its integrated public health model., (© 2022 l'Académie nationale de médecine. Published by Elsevier Masson SAS. All rights reserved.)
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- 2022
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19. Investigation of a COVID-19 outbreak on the Charles de Gaulle aircraft carrier, March to April 2020: a retrospective cohort study.
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de Laval F, Chaudet H, Gorgé O, Marchi J, Lacrosse C, Dia A, Marbac V, Mmadi Mrenda B, Texier G, Letois F, Chapus C, Sarilar V, Tournier JN, Levasseur A, Cobola J, Nolent F, Dutasta F, Janvier F, Meynard JB, and Pommier de Santi V
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- Adult, Aircraft, Disease Outbreaks, Female, Humans, Male, Retrospective Studies, SARS-CoV-2 genetics, COVID-19 epidemiology
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BackgroundSARS-CoV-2 emergence was a threat for armed forces. A COVID-19 outbreak occurred on the French aircraft carrier Charles de Gaulle from mid-March to mid-April 2020.AimTo understand how the virus was introduced, circulated then stopped circulation, risk factors for infection and severity, and effectiveness of preventive measures.MethodsWe considered the entire crew as a cohort and collected personal, clinical, biological, and epidemiological data. We performed viral genome sequencing and searched for SARS-CoV-2 in the environment.ResultsThe attack rate was 65% (1,148/1,767); 1,568 (89%) were included. The male:female ratio was 6.9, and median age was 29 years (IQR: 24-36). We examined four clinical profiles: asymptomatic (13.0%), non-specific symptomatic (8.1%), specific symptomatic (76.3%), and severe (i.e. requiring oxygen therapy, 2.6%). Active smoking was not associated with severe COVID-19; age and obesity were risk factors. The instantaneous reproduction rate (R
t ) and viral sequencing suggested several introductions of the virus with 4 of 5 introduced strains from within France, with an acceleration of Rt when lifting preventive measures. Physical distancing prevented infection (adjusted OR: 0.55; 95% CI: 0.40-0.76). Transmission may have stopped when the proportion of infected personnel was large enough to prevent circulation (65%; 95% CI: 62-68).ConclusionNon-specific clinical pictures of COVID-19 delayed detection of the outbreak. The lack of an isolation ward made it difficult to manage transmission; the outbreak spread until a protective threshold was reached. Physical distancing was effective when applied. Early surveillance with adapted prevention measures should prevent such an outbreak.- Published
- 2022
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20. Origin and mobility of Iron Age Gaulish groups in present-day France revealed through archaeogenomics.
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Fischer CE, Pemonge MH, Ducoussau I, Arzelier A, Rivollat M, Santos F, Barrand Emam H, Bertaud A, Beylier A, Ciesielski E, Dedet B, Desenne S, Duday H, Chenal F, Gailledrat E, Goepfert S, Gorgé O, Gorgues A, Kuhnle G, Lambach F, Lefort A, Mauduit A, Maziere F, Oudry S, Paresys C, Pinard E, Plouin S, Richard I, Roth-Zehner M, Roure R, Thevenet C, Thomas Y, Rottier S, Deguilloux MF, and Pruvost M
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The Iron Age period occupies an important place in French history because the Gauls are regularly presented as the direct ancestors of the extant French population. We documented here the genomic diversity of Iron Age communities originating from six French regions. The 49 acquired genomes permitted us to highlight an absence of discontinuity between Bronze Age and Iron Age groups in France, lending support to a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. Genomic analyses revealed strong genetic homogeneity among the regional groups associated with distinct archaeological cultures. This genomic homogenization appears to be linked to individuals' mobility between regions and gene flow with neighbouring groups from England and Spain. Thus, the results globally support a common genomic legacy for the Iron Age population of modern-day France that could be linked to recurrent gene flow between culturally differentiated communities., Competing Interests: The authors declare no competing interests., (© 2022 The Author(s).)
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- 2022
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21. Rodent control to fight plague: field assessment of methods based on rat density reduction.
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Rahelinirina S, Scobie K, Ramasindrazana B, Andrianaivoarimanana V, Rasoamalala F, Randriantseheno LN, Rakotoniaina JS, Gorgé O, Lambin X, Valade E, Telfer S, and Rajerison M
- Subjects
- Animals, Bacterial Zoonoses prevention & control, Insect Vectors, Madagascar, Plague epidemiology, Population Density, Rats, Plague prevention & control, Rodent Control methods, Siphonaptera microbiology
- Abstract
Rodents represent a serious threat to food security and public health. The extent to which rodent control can mitigate the risk from rodent-borne disease depends on both the effectiveness of control in reducing rodent abundance and the impact on disease epidemiology. Focusing on a plague-endemic region of Madagascar, this study compared the effectiveness of 3 methods: live-traps, snap-traps, and rodenticides. Control interventions were implemented inside houses between May and October 2019. Tracking tiles monitored rodent abundance. Rodent fleas, the vector involved in plague transmission, were collected. Rodent populations consisted of Rattus rattus and Mus musculus. In terms of trap success, we found that our live-trap regime was more effective than snap-traps. While all 3 control strategies appeared to reduce in-house rodent activity in the short term, we found no evidence of a longer-term effect, with in-house rodent abundance in treated sites comparable to non-treatment sites by the following month. Endemic flea, Synopsyllus fonquerniei, is a key plague vector usually found on rats living outdoors. Although we found no evidence that its abundance inside houses increased following control, this may have been due to a lack of power caused by significant variation in S. fonquerniei abundance. The presence of S. fonquerniei in houses was more likely when S. fonquerniei abundance on outdoor rats was higher, which in turn correlated with high rat abundance. Our results emphasize that control strategies need to consider this connectivity between in-house rat-flea populations and the outdoor populations, and any potential consequences for plague transmission., (© 2021 The Authors. Integrative Zoology published by International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.)
- Published
- 2021
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22. Differential serological and neutralizing antibody dynamics after an infection by a single SARS-CoV-2 strain.
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Billon-Denis E, Ferrier-Rembert A, Garnier A, Cheutin L, Vigne C, Tessier E, Denis J, Badaut C, Rougeaux C, Depeille Wuille A, Timera H, Boutin LI, Drouet I, Verguet N, Nolent F, Gorgé O, Ferraris O, and Tournier JN
- Subjects
- Adult, Antibodies, Neutralizing biosynthesis, COVID-19 transmission, Cross Infection immunology, Enzyme-Linked Immunosorbent Assay, Female, Humans, Immunoglobulin G biosynthesis, Male, Middle Aged, Nasopharynx virology, SARS-CoV-2 classification, SARS-CoV-2 genetics, Antibodies, Neutralizing blood, Antibodies, Viral blood, COVID-19 immunology, Immunoglobulin G blood, Infectious Disease Transmission, Patient-to-Professional, SARS-CoV-2 immunology
- Abstract
Background: We report here the case of two coworkers infected by the same SARS-CoV-2 strain, presenting two different immunological outcomes., Case: One patient presented a strong IgG anti-receptor-binding domain immune response correlated with a low and rapidly decreasing titer of neutralizing antibodies. The other patient had a similar strong IgG anti-receptor-binding domain immune response but high neutralizing antibody titers., Discussion and Conclusion: Thus, host individual factors may be the main drivers of the immune response varying with age and clinical severity., (© 2021. Springer-Verlag GmbH Germany, part of Springer Nature.)
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- 2021
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23. Tolerance engineering in Deinococcus geothermalis by heterologous efflux pumps.
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Boulant E, Cambon E, Vergalli J, Bernard R, Neulat-Ripoll F, Nolent F, Gorgé O, Girleanu M, Favier AL, Leonetti JP, and Bolla JM
- Subjects
- Cloning, Molecular, Fermentation, Gene Expression, Genome, Bacterial, Deinococcus genetics, Deinococcus metabolism, Genetic Engineering, Industrial Microbiology, Membrane Transport Proteins genetics, Membrane Transport Proteins metabolism
- Abstract
Producing industrially significant compounds with more environmentally friendly represents a challenging task. The large-scale production of an exogenous molecule in a host microfactory can quickly cause toxic effects, forcing the cell to inhibit production to survive. The key point to counter these toxic effects is to promote a gain of tolerance in the host, for instance, by inducing a constant flux of the neo-synthetized compound out of the producing cells. Efflux pumps are membrane proteins that constitute the most powerful mechanism to release molecules out of cells. We propose here a new biological model, Deinococcus geothermalis, organism known for its ability to survive hostile environment; with the aim of coupling the promising industrial potential of this species with that of heterologous efflux pumps to promote engineering tolerance. In this study, clones of D. geothermalis containing various genes encoding chromosomal heterologous efflux pumps were generated. Resistant recombinants were selected using antibiotic susceptibility tests to screen promising candidates. We then developed a method to determine the efflux efficiency of the best candidate, which contains the gene encoding the MdfA of Salmonella enterica serovar Choleraesuis. We observe 1.6 times more compound in the external medium of the hit recombinant than that of the WT at early incubation time. The data presented here will contribute to better understanding of the parameters required for efficient production in D. geothermalis.
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- 2021
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24. Genomic and RT-qPCR analysis of trimethoprim-sulfamethoxazole and meropenem resistance in Burkholderia pseudomallei clinical isolates.
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Schnetterle M, Gorgé O, Nolent F, Boughammoura A, Sarilar V, Vigier C, Guillier S, Koch L, Degand N, Ramisse V, Tichadou X, Girleanu M, Favier AL, Valade E, Biot F, and Neulat-Ripoll F
- Subjects
- Aged, 80 and over, Anti-Bacterial Agents, Humans, Malaysia, Male, Membrane Transport Proteins genetics, Meropenem, Microbial Sensitivity Tests, Real-Time Polymerase Chain Reaction, Trimethoprim, Sulfamethoxazole Drug Combination, Whole Genome Sequencing, Burkholderia pseudomallei drug effects, Burkholderia pseudomallei genetics, Drug Resistance, Multiple, Bacterial genetics, Melioidosis microbiology
- Abstract
Background: Melioidosis is an endemic disease in southeast Asia and northern Australia caused by the saprophytic bacteria Burkholderia pseudomallei, with a high mortality rate. The clinical presentation is multifaceted, with symptoms ranging from acute septicemia to multiple chronic abscesses. Here, we report a chronic case of melioidosis in a patient who lived in Malaysia in the 70s and was suspected of contracting tuberculosis. Approximately 40 years later, in 2014, he was diagnosed with pauci-symptomatic melioidosis during a routine examination. Four strains were isolated from a single sample. They showed divergent morphotypes and divergent antibiotic susceptibility, with some strains showing resistance to trimethoprim-sulfamethoxazole and fluoroquinolones. In 2016, clinical samples were still positive for B. pseudomallei, and only one type of strain, showing atypical resistance to meropenem, was isolated., Principal Findings: We performed whole genome sequencing and RT-qPCR analysis on the strains isolated during this study to gain further insights into their differences. We thus identified two types of resistance mechanisms in these clinical strains. The first one was an adaptive and transient mechanism that disappeared during the course of laboratory sub-cultures; the second was a mutation in the efflux pump regulator amrR, associated with the overexpression of the related transporter., Conclusion: The development of such mechanisms may have a clinical impact on antibiotic treatment. Indeed, their transient nature could lead to an undiagnosed resistance. Efflux overexpression due to mutation leads to an important multiple resistance, reducing the effectiveness of antibiotics during treatment., Competing Interests: The authors have declared that no competing interests exist.
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- 2021
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25. Case Report of an Injectional Anthrax in France, 2012.
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Thouret JM, Rogeaux O, Beaudouin E, Levast M, Ramisse V, Biot FV, Valade E, Thibault F, Gorgé O, and Tournier JN
- Abstract
(1) Background: Bacillus anthracis is a spore-forming, Gram-positive bacterium causing anthrax, a zoonosis affecting mainly livestock. When occasionally infecting humans, B. anthracis provokes three different clinical forms: cutaneous, digestive and inhalational anthrax. More recently, an injectional anthrax form has been described in intravenous drug users. (2) Case presentation: We report here the clinical and microbiological features, as well as the strain phylogenetic analysis, of the only injectional anthrax case observed in France so far. A 27-year-old patient presented a massive dermohypodermatitis with an extensive edema of the right arm, and the development of drug-resistant shocks. After three weeks in an intensive care unit, the patient recovered, but the microbiological identification of B. anthracis was achieved after a long delay. (3) Conclusions: Anthrax diagnostic may be difficult clinically and microbiologically. The phylogenetic analysis of the Bacillus anthracis strain PF1 confirmed its relatedness to the injectional anthrax European outbreak group-II.
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- 2020
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26. Three New Cases of Melioidosis, Guadeloupe, French West Indies.
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Melot B, Bastian S, Dournon N, Valade E, Gorgé O, Le Fleche A, Idier C, Vernier M, Fernandes E, Hoen B, Breurec S, and Carles M
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- Aged, Anti-Bacterial Agents therapeutic use, Diagnosis, Differential, Fatal Outcome, Female, Humans, Male, Melioidosis diagnostic imaging, Melioidosis drug therapy, Middle Aged, Tomography, X-Ray Computed, Burkholderia pseudomallei isolation & purification, Melioidosis diagnosis
- Abstract
Melioidosis has been detected in the Caribbean, and an increasing number of cases has been reported in the past few decades, but only 2 cases were reported in Guadeloupe during the past 20 years. We describe 3 more cases that occurred during 2016-2017 and examine arguments for increasing endemicity.
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- 2020
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27. Polyamino-Isoprenyl Derivatives as Antibiotic Adjuvants and Motility Inhibitors for Bordetella bronchiseptica Porcine Pulmonary Infection Treatment.
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Borselli D, Brunel JM, Gorgé O, and Bolla JM
- Abstract
The spreading of multidrug-resistant bacteria and the lack of novel antibiotic molecules leave clinicians and veterinarians with very limited options to treat bacterial infections, especially those caused by Gram-negative pathogens. To reduce the selection of antibiotic resistance mechanisms and their transfer to human pathogens, veterinary pharmaceutical companies have dramatically decreased the number of antibiotics used. Among all the investigated alternate solutions, chemosensitizers, which decrease the amount of the used drugs, appear to be one of the most promising strategies. In this study, we reported that polyamino-isoprenyl derivatives can potentiate florfenicol activity against veterinary sensitive reference strains as well as clinical isolates. These molecules induce inner membrane depolarization and subsequently inhibit efflux pumps by collapsing the proton-motive force (PMF). Considering that Bordetella bronchiseptica rotor flagellum is highly PMF dependent and that flagellar motility represents an important factor involved in colonization, we monitored the swimming and swarming motilities of bacteria and showed a strong inhibition in the presence of the lead selected compound. Taken together, our results suggest that this class of molecules are able to increase treatment efficacy and decrease drug consumption.
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- 2019
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28. Transcriptomic studies and assessment of Yersinia pestis reference genes in various conditions.
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Koch L, Poyot T, Schnetterle M, Guillier S, Soulé E, Nolent F, Gorgé O, Neulat-Ripoll F, Valade E, Sebbane F, and Biot F
- Subjects
- Computational Biology, Gene Expression Regulation, Bacterial, Reference Standards, Temperature, Workflow, Yersinia pestis genetics, Bacterial Proteins genetics, Gene Expression Profiling standards, Yersinia pestis growth & development
- Abstract
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a very sensitive widespread technique considered as the gold standard to explore transcriptional variations. While a particular methodology has to be followed to provide accurate results many published studies are likely to misinterpret results due to lack of minimal quality requirements. Yersinia pestis is a highly pathogenic bacterium responsible for plague. It has been used to propose a ready-to-use and complete approach to mitigate the risk of technical biases in transcriptomic studies. The selection of suitable reference genes (RGs) among 29 candidates was performed using four different methods (GeNorm, NormFinder, BestKeeper and the Delta-Ct method). An overall comprehensive ranking revealed that 12 following candidate RGs are suitable for accurate normalization: gmk, proC, fabD, rpoD, nadB, rho, thrA, ribD, mutL, rpoB, adk and tmk. Some frequently used genes like 16S RNA had even been found as unsuitable to study Y. pestis. This methodology allowed us to demonstrate, under different temperatures and states of growth, significant transcriptional changes of six efflux pumps genes involved in physiological aspects as antimicrobial resistance or virulence. Previous transcriptomic studies done under comparable conditions had not been able to highlight these transcriptional modifications. These results highlight the importance of validating RGs prior to the normalization of transcriptional expression levels of targeted genes. This accurate methodology can be extended to any gene of interest in Y. pestis. More generally, the same workflow can be applied to identify and validate appropriate RGs in other bacteria to study transcriptional variations.
- Published
- 2019
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29. A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites.
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Côté NM, Daligault J, Pruvost M, Bennett EA, Gorgé O, Guimaraes S, Capelli N, Le Bailly M, Geigl EM, and Grange T
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- Animals, Archaeology, DNA genetics, Genetic Variation, Genotype, Helminths genetics, History, Ancient, Humans, Ovum cytology, Gastrointestinal Tract parasitology, Genotyping Techniques methods, High-Throughput Nucleotide Sequencing methods, Parasites genetics
- Abstract
Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies.
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- 2016
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30. Analysis of Ancient DNA in Microbial Ecology.
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Gorgé O, Bennett EA, Massilani D, Daligault J, Pruvost M, Geigl EM, and Grange T
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- Animals, DNA, Bacterial isolation & purification, Fossils, Genomics methods, Humans, Soil Microbiology, DNA, Bacterial genetics, Genome, Microbial genetics, High-Throughput Nucleotide Sequencing methods, Paleontology methods
- Abstract
The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.
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- 2016
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31. Generation of a CRISPR database for Yersinia pseudotuberculosis complex and role of CRISPR-based immunity in conjugation.
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Koskela KA, Mattinen L, Kalin-Mänttäri L, Vergnaud G, Gorgé O, Nikkari S, and Skurnik M
- Subjects
- Bacteriophages immunology, Base Sequence, Clustered Regularly Interspaced Short Palindromic Repeats genetics, Genomics, Molecular Sequence Data, Plasmids genetics, Yersinia pestis genetics, Yersinia pseudotuberculosis classification, Clustered Regularly Interspaced Short Palindromic Repeats immunology, Conjugation, Genetic immunology, Databases, Nucleic Acid, Plasmids immunology, Yersinia pseudotuberculosis genetics
- Abstract
The clustered regularly interspaced short palindromic repeat - CRISPR-associated genes (CRISPR-Cas) system is used by bacteria and archaea against invading conjugative plasmids or bacteriophages. Central to this immunity system are genomic CRISPR loci that contain fragments of invading DNA. These are maintained as spacers in the CRISPR loci between direct repeats and the spacer composition in any bacterium reflects its evolutionary history. We analysed the CRISPR locus sequences of 335 Yersinia pseudotuberculosis complex strains. Altogether 1902 different spacer sequences were identified and these were used to generate a database for the spacer sequences. Only ∼10% of the spacer sequences found matching sequences. In addition, surprisingly few spacers were shared by Yersinia pestis and Y. pseudotuberculosis strains. Interestingly, 32 different protospacers were present in the conjugative plasmid pYptb32953. The corresponding spacers were identified from 35 different Y. pseudotuberculosis strains indicating that these strains had encountered pYptb32953 earlier. In conjugation experiments, pYptb32953-specific spacers generally prevented conjugation with spacer-positive and spacer-free strains. However, some strains with one to four spacers were invaded by pYptb32953 and some spacer-free strains were fully resistant. Also some spacer-positive strains were intermediate resistant to conjugation. This suggests that one or more other defence systems are determining conjugation efficiency independent of the CRISPR-Cas system., (© 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2015
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32. Clostridium botulinum group I strain genotyping by 15-locus multilocus variable-number tandem-repeat analysis.
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Fillo S, Giordani F, Anniballi F, Gorgé O, Ramisse V, Vergnaud G, Riehm JM, Scholz HC, Splettstoesser WD, Kieboom J, Olsen JS, Fenicia L, and Lista F
- Subjects
- Botulism microbiology, Clostridium botulinum isolation & purification, Cluster Analysis, Food Microbiology, Genotype, Humans, Molecular Epidemiology methods, Pathology, Molecular methods, Phylogeny, Clostridium botulinum classification, Clostridium botulinum genetics, Minisatellite Repeats, Molecular Typing methods, Polymorphism, Genetic
- Abstract
Clostridium botulinum is a taxonomic designation that encompasses a broad variety of spore-forming, Gram-positive bacteria producing the botulinum neurotoxin (BoNT). C. botulinum is the etiologic agent of botulism, a rare but severe neuroparalytic disease. Fine-resolution genetic characterization of C. botulinum isolates of any BoNT type is relevant for both epidemiological studies and forensic microbiology. A 10-locus multiple-locus variable-number tandem-repeat analysis (MLVA) was previously applied to isolates of C. botulinum type A. The present study includes five additional loci designed to better address proteolytic B and F serotypes. We investigated 79 C. botulinum group I strains isolated from human and food samples in several European countries, including types A (28), B (36), AB (4), and F (11) strains, and 5 nontoxic Clostridium sporogenes. Additional data were deduced from in silico analysis of 10 available fully sequenced genomes. This 15-locus MLVA (MLVA-15) scheme identified 86 distinct genotypes that clustered consistently with the results of amplified fragment length polymorphism (AFLP) and MLVA genotyping in previous reports. An MLVA-7 scheme, a subset of the MLVA-15, performed on a lab-on-a-chip device using a nonfluorescent subset of primers, is also proposed as a first-line assay. The phylogenetic grouping obtained with the MLVA-7 does not differ significantly from that generated by the MLVA-15. To our knowledge, this report is the first to analyze genetic variability among all of the C. botulinum group I serotypes by MLVA. Our data provide new insights into the genetic variability of group I C. botulinum isolates worldwide and demonstrate that this group is genetically highly diverse.
- Published
- 2011
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33. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats.
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Cui Y, Li Y, Gorgé O, Platonov ME, Yan Y, Guo Z, Pourcel C, Dentovskaya SV, Balakhonov SV, Wang X, Song Y, Anisimov AP, Vergnaud G, and Yang R
- Subjects
- Genetic Variation, Genome, Bacterial, Genotype, Humans, Polymorphism, Genetic, Yersinia pestis classification, Evolution, Molecular, Interspersed Repetitive Sequences, Yersinia pestis genetics
- Abstract
Background: Yersinia pestis, the pathogen of plague, has greatly influenced human history on a global scale. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), an element participating in immunity against phages' invasion, is composed of short repeated sequences separated by unique spacers and provides the basis of the spoligotyping technology. In the present research, three CRISPR loci were analyzed in 125 strains of Y. pestis from 26 natural plague foci of China, the former Soviet Union and Mongolia were analyzed, for validating CRISPR-based genotyping method and better understanding adaptive microevolution of Y. pestis., Methodology/principal Findings: Using PCR amplification, sequencing and online data processing, a high degree of genetic diversity was revealed in all three CRISPR elements. The distribution of spacers and their arrays in Y. pestis strains is strongly region and focus-specific, allowing the construction of a hypothetic evolutionary model of Y. pestis. This model suggests transmission route of microtus strains that encircled Takla Makan Desert and ZhunGer Basin. Starting from Tadjikistan, one branch passed through the Kunlun Mountains, and moved to the Qinghai-Tibet Plateau. Another branch went north via the Pamirs Plateau, the Tianshan Mountains, the Altai Mountains and the Inner Mongolian Plateau. Other Y. pestis lineages might be originated from certain areas along those routes., Conclusions/significance: CRISPR can provide important information for genotyping and evolutionary research of bacteria, which will help to trace the source of outbreaks. The resulting data will make possible the development of very low cost and high-resolution assays for the systematic typing of any new isolate.
- Published
- 2008
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34. Selection and validation of a multilocus variable-number tandem-repeat analysis panel for typing Shigella spp.
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Gorgé O, Lopez S, Hilaire V, Lisanti O, Ramisse V, and Vergnaud G
- Subjects
- DNA, Bacterial analysis, Dysentery, Bacillary microbiology, Genome, Bacterial, Humans, Sequence Analysis, DNA, Bacterial Typing Techniques, Minisatellite Repeats genetics, Shigella classification, Shigella genetics
- Abstract
The Shigella genus has historically been separated into four species, based on biochemical assays. The classification within each species relies on serotyping. Recently, genome sequencing and DNA assays, in particular the multilocus sequence typing (MLST) approach, greatly improved the current knowledge of the origin and phylogenetic evolution of Shigella spp. The Shigella and Escherichia genera are now considered to belong to a unique genomospecies. Multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) provides valuable polymorphic markers for genotyping and performing phylogenetic analyses of highly homogeneous bacterial pathogens. Here, we assess the capability of MLVA for Shigella typing. Thirty-two potentially polymorphic VNTRs were selected by analyzing in silico five Shigella genomic sequences and subsequently evaluated. Eventually, a panel of 15 VNTRs was selected (i.e., MLVA15 analysis). MLVA15 analysis of 78 strains or genome sequences of Shigella spp. and 11 strains or genome sequences of Escherichia coli distinguished 83 genotypes. Shigella population cluster analysis gave consistent results compared to MLST. MLVA15 analysis showed capabilities for E. coli typing, providing classification among pathogenic and nonpathogenic E. coli strains included in the study. The resulting data can be queried on our genotyping webpage (http://mlva.u-psud.fr). The MLVA15 assay is rapid, highly discriminatory, and reproducible for Shigella and Escherichia strains, suggesting that it could significantly contribute to epidemiological trace-back analysis of Shigella infections and pathogenic Escherichia outbreaks. Typing was performed on strains obtained mostly from collections. Further studies should include strains of much more diverse origins, including all pathogenic E. coli types.
- Published
- 2008
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35. Analysis of the three Yersinia pestis CRISPR loci provides new tools for phylogenetic studies and possibly for the investigation of ancient DNA.
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Vergnaud G, Li Y, Gorgé O, Cui Y, Song Y, Zhou D, Grissa I, Dentovskaya SV, Platonov ME, Rakin A, Balakhonov SV, Neubauer H, Pourcel C, Anisimov AP, and Yang R
- Subjects
- Base Sequence, Disease Outbreaks history, Evolution, Molecular, Genes, Bacterial, History, Ancient, Humans, Interspersed Repetitive Sequences, Molecular Sequence Data, Phylogeny, Plague epidemiology, Plague microbiology, Species Specificity, Yersinia pestis classification, Yersinia pestis pathogenicity, Yersinia pseudotuberculosis classification, Yersinia pseudotuberculosis genetics, DNA, Bacterial genetics, DNA, Bacterial history, Plague history, Yersinia pestis genetics
- Abstract
The precise nature of the pathogen having caused early plague pandemics is uncertain. Although Yersinia pestis is a likely candidate for all three plague pandemics, the very rare direct evidence that can be deduced from ancient DNA (aDNA) analysis is controversial. Moreover, which of the three biovars, Antiqua, Medievalis or Orientalis, was associated with these pandemics is still debated. There is a need for phylogenetic analysis performed on Y. pestis strains isolated from countries from which plague probably arose and is still endemic. In addition there exist technical difficulties inherent to aDNA investigations and a lack of appropriate genetic targets. The recently described CRISPRs (clustered regularly interspaced short palindromic repeats) may represent such a target. CRISPR loci consist of a succession of highly conserved regions separated by specific "spacers" usually of viral origin. To be of use, data describing the mechanisms of evolution and diversity of CRISPRs in Y. pestis, its closest neighbors, and other species which might contaminate ancient DNA, are necessary. The investigation of closely related Y. pestis isolates has revealed recent mutation events in which elements constituting CRISPRs were acquired or lost, providing essential insight on their evolution. Rules deduced represent the basis for subsequent interpretation. In the present study, the CRISPR loci from representative Y. pestis and Yersinia pseudotuberculosis strains were investigated by PCR amplification and sequence analysis. The investigation of this wider panel of strains, including other subspecies or ecotypes within Y. pestis and also Y. pseudotuberculosis strains provides a database of the existing CRISPR spacers and helps predict the expected CRISPR structure of the Y. pestis ancestor. This knowledge will open the way to the development of a spoligotyping assay, in which spacers can be amplified even from highly degraded DNA samples. The data obtained show that CRISPR analysis can provide a very powerful typing tool, adapted to the systematic, large-scale genotyping of Y. pestis isolates, and the creation of international typing databases. In addition, CRISPRs do constitute a very promising new tool and genetic target to investigate ancient DNA. The corresponding genetic targets are small (<70bp), present in multiple copies (usually more than 10), highly conserved and specific. In addition, the assay can be run in any laboratory. Interpretation of the data is not dependent on accurate sequence data.
- Published
- 2007
- Full Text
- View/download PDF
36. Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis.
- Author
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Lista F, Faggioni G, Valjevac S, Ciammaruconi A, Vaissaire J, le Doujet C, Gorgé O, De Santis R, Carattoli A, Ciervo A, Fasanella A, Orsini F, D'Amelio R, Pourcel C, Cassone A, and Vergnaud G
- Subjects
- Automation, DNA, Bacterial genetics, Genetic Markers, Genotype, Phylogeny, Bacillus anthracis classification, Bacillus anthracis genetics, Electrophoresis, Capillary methods, Tandem Repeat Sequences genetics
- Abstract
Background: The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR) Analysis (MLVA) assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary., Results: Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats., Conclusion: In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the B branch was described, and two new branches, D and E, are proposed. Owing to the upgrading achieved here, precise genotyping can now be produced either by automated capillary electrophoresis, or by the more accessible but slower and for some markers slightly less accurate agarose gel methodology.
- Published
- 2006
- Full Text
- View/download PDF
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