129 results on '"Raoult, Didier"'
Search Results
2. No global increase in resistance to antibiotics: a snapshot of resistance from 2001 to 2016 in Marseille, France
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Le Page, Stéphanie, Dubourg, Gregory, Baron, Sophie Alexandra, Rolain, Jean-Marc, and Raoult, Didier
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- 2019
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3. Role of Sex, Age, Previous Valve Lesion, and Pregnancy in the Clinical Expression and Outcome of Q Fever after a Large Outbreak
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Tissot-Dupont, Hervé and Raoult, Didier
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- 2007
4. Serosurvey among Mediterranean Spotted Fever Patients of a New Spotted Fever Group Rickettsial Strain (Bar29)
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Cardeñosa, Neus, Segura, Ferran, and Raoult, Didier
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- 2003
5. Ticks and Tickborne Bacterial Diseases in Humans: An Emerging Infectious Threat
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Parola, Philippe and Raoult, Didier
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- 2001
6. Outbreak of Rickettsia africae Infections in Participants of an Adventure Race in South Africa
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Fournier, Pierre-Edouard, Roux, Veronique, and Raoult, Didier
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- 1998
7. A Focus of Tick-Borne Relapsing Fever in Southern Zaire
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Dupont, Hervé Tissot, La Scola, Bernard, Williams, Raymond, and Raoult, Didier
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- 1997
8. Study of the 16S-23S Ribosomal DNA Internal Spacer of Coxiella burnetii
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Stein, Andreas, Kruszewska, Danuta, Gouvernet, Joanny, and Raoult, Didier
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- 1997
9. Survey of the Seroprevalence of Bartonella quintana in Homeless People
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Brouqui, Philippe, Dupont, Herve Tissot, and Raoult, Didier
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- 1996
10. Microbe Interactions Undermine Predictions [with Response]
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RAOULT, DIDIER, TELFER, SANDRA, LAMBIN, XAVIER, BIRTLES, RICHARD, BELDOMENICO, PABLO, BURTHE, SARAH, PATERSON, STEVE, and BEGON, MIKE
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- 2011
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11. Increasing Trend of Invasive Group B Streptococcal Infections, Marseille, France
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Abat, Cedric, Chaudet, Hervé, Raoult, Didier, and Colson, Philippe
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- 2014
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12. Exposure of Cats in Southern Africa to Coxiella burnetii, the Agent of Q Fever
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Matthewman, Linda, Kelly, Patrick, Hayter, Deidre, Downie, Susan, Wray, Kylie, Bryson, Nigel, Rycroft, Andrew, and Raoult, Didier
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- 1997
13. Domestic Cats as Indicators of the Presence of Spotted Fever and Typhus Group Rickettsiae
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Matthewman, Linda, Kelly, Patrick, Hayter, Diane, Downie, Susan, Wray, Kylie, Bryson, Nigel, Rycroft, Andrew, and Raoult, Didier
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- 1997
14. Non transmissible diseases are often transmissible
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Raoult, Didier, Keil, U., Spelsberg, A., Cassini, Alessandro, Kramarz, Piotr, Colzani, Edoardo, Nicoll, Angus, and Sprenger, Marc
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- 2012
15. Q Fever, Free Amoeba, and Air Conditioning
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Raoult, Didier
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- 2010
16. Editorial Commentary: Reemergence of Q Fever after 11 September 2001
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Raoult, Didier
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- 2009
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17. Seasonal Variation in Klebsiella pneumoniae Bloodstream Infection on 4 Continents
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Anderson, Deverick J., Richet, Hervé, Chen, Luke F., Spelman, Denis W., Huang, Andrew T., Sexton, Daniel J., and Raoult, Didier
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- 2008
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18. A Pedagogical Farm as a Source of Q Fever in a French City
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Tissot-Dupont, Hervé, Amadei, Marie-Antoinette, Nezri, Meyer, and Raoult, Didier
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- 2005
19. Biocides Currently Used for Bronchoscope Decontamination Are Poorly Effective Against Free‐Living Amoebae
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Greub, Gilbert and Raoult, Didier
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- 2003
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20. A Nosocomial Outbreak of Legionella pneumophila Caused by Contaminated Transesophageal Echocardiography Probes
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Levy, Pierre‐Yves, Teysseire, Nadine, Etienne, Jérôme, and Raoult, Didier
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- 2003
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21. Can Whipple’s Disease Be Transmitted by Gastroscopes?
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Scola, Bernard La, Rolain, Jean‐Marc, Maurin, Max, and Raoult, Didier
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- 2003
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22. Serologic Response to Rickettsial Antigens in Patients with Astrakhan Fever
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Eremeeva, Marina E., Balayeva, Natalia M., Ignatovich, Valentina F., and Raoult, Didier
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- 1995
23. Q Fever
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Raoult, Didier
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- 1995
24. Prevalence of Antibodies to Coxiella burnetii, Rickettsia conorii, and Rickettsia typhi in Seven African Countries
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Dupont, Hervé Tissot, Brouqui, Philippe, and Raoult, Didier
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- 1995
25. Where Are We With Human Lice? A Review of the Current State of Knowledge
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Amanzougaghene, Nadia, Fenollar, Florence, Raoult, Didier, Mediannikov, Oleg, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)
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Insecticides ,disease-vector ,Review ,phylogeny ,Evolution, Molecular ,Insecticide Resistance ,Cellular and Infection Microbiology ,[SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,Animals ,Humans ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Genome ,Bacteria ,biology ,Pediculus humanus ,Pediculus ,Lice Infestations ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Insect Vectors ,Mitochondria ,Phylogeography ,Communicable Disease Control ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,epidemiology ,control - Abstract
International audience; Pediculus humanus is an obligate bloodsucking ectoparasite of human that includes two ecotypes, head louse and body louse, which differ slightly in morphology and biology, but have distinct ecologies. Phylogenetically, they are classified on six mitochondrial clades (A, B, C, D, E, and F), head louse encompasses the full genetic diversity of clades, while body louse belongs to clades A and D. Recent studies suggested that not only body louse, but also head louse can transmit disease, which warrants greater attention as a serious public health problem. The recent sequencing of body louse genome confirmed that P. humanus has the smallest genome of any hemimetabolous insect reported to date, and also revealed numerous interesting characteristics in the nuclear and mitochondrial genomes. The transcriptome analyses showed that body and head lice were almost genetically identical. Indeed, the phenotypic flexibility associated with the emergence of body lice, is probably a result of regulatory changes, perhaps epigenetic in origin, triggered by environmental signals. Current lice control strategies have proven unsuccessful. For instance, ivermectin represents a relatively new and very promising pediculicide. However, ivermectin resistance in the field has begun to be reported. Therefore, novel opportunities for pest control strategies are needed. Our objective here is to review the current state of knowledge on the biology, epidemiology, phylogeny, disease-vector and control of this fascinating and very intimate human parasite.
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- 2020
26. Editorial Commentary: From Cat Scratch Disease to Bartonella henselae Infection
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Raoult, Didier
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- 2007
27. A Homeless Man with Maculopapular Rash Who Died in Marseille, France
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Parola, Philippe, Raoult, Didier, and Brouqui, Philippe
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- 2004
28. Editorial Commentary: A New Rickettsial Disease in the United States
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Raoult, Didier
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- 2004
29. Prevalence of Antibodies to Rickettsia conorii, Rickettsia africae, Rickettsia typhi and Coxiella burnetii in Mauritania
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Niang, Mohamadou, Parola, Philippe, Tissot-Dupont, Hervé, Baidi, Lô, Brouqui, Philippe, and Raoult, Didier
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- 1998
30. Leptospirosis, one neglected disease in rural Senegal.
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Roqueplo, Cédric, Kodjo, Angeli, Demoncheaux, Jean‐Paul, Scandola, Pierre, Bassene, Hubert, Diatta, Georges, Sokhna, Cheikh, Raoult, Didier, Davoust, Bernard, and Mediannikov, Oleg
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LEPTOSPIROSIS ,DONKEYS ,AGGLUTINATION tests ,LEPTOSPIRA ,BLOOD testing ,BLOOD sampling - Abstract
A serological study was carried out in two Senegalese villages located in the Sine‐Saloum region in order to estimate the presence of anti‐leptospiral antibodies in humans and animals, and to identify the predominant serogroups. Seven hundred and forty‐nine serum samples were collected from humans (n = 545), dogs (n = 33), donkeys (n = 20), goats (n = 52), sheep (n = 43) and N'Dama cattle (n = 56), all originated from Dielmo and Ndiop villages. All samples were tested for different serovars of pathogenic Leptospira species by the microscopic agglutination test. Considering titres ≥ 1:100, 7.7% [CI 95:5.5 to 9.9] on the 545 human blood samples tested and 42.2% [CI95:35.4 to 48.9] on the 204 animal blood samples tested were found to be positive to one or more serovars. The results obtained indicate that the Australis serogroup is the most prevalent serogroup in human (67.3%) and cattle (27.3%). Serogroup Icterohaemorhagiae is the most frequent serogroup in goat (55.6%) and donkey (37.5%). Canicola (23.4%), Icterohaemorhagiae (21.1%) and Australis (12.5%) serogroups are the most prevalent serogroups in dogs. This study shows that diverse Leptospira serovars occur in a wide range of wild and domestic mammal species, as well as in humans in Senegal. However, further studies are needed to better understand the complexity of Leptospira epidemiology in Africa, identify the reservoirs of different serogroups and estimate its impact on livestock. Understanding the multi‐host epidemiology of leptospirosis is essential to control and prevent the disease. [ABSTRACT FROM AUTHOR]
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- 2019
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31. High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice
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Amanzougaghene, Nadia, Mumcuoglu, Kosta Y., Fenollar, Florence, Alfi, Shir, Yesilyurt, Gonca, Raoult, Didier, Mediannikov, Oleg, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem (HUJ), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)
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Epidemiology ,lcsh:Medicine ,Artificial Gene Amplification and Extension ,Disease Vectors ,Biochemistry ,Body lice ,Abdomen ,Medicine and Health Sciences ,Israel ,lcsh:Science ,History, Ancient ,Phylogeny ,Likelihood Functions ,Ancient DNA ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,Pediculus ,Cytochromes b ,humanities ,Polymerase chain reaction ,Insects ,Nucleic acids ,Head lice ,Anatomy ,Lice ,Research Article ,Arthropoda ,Molecular Sequence Data ,Research and Analysis Methods ,Real-Time Polymerase Chain Reaction ,parasitic diseases ,Genetics ,Animals ,Humans ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Molecular Biology Techniques ,Molecular Biology ,Ovum ,Evolutionary Biology ,Population Biology ,Base Sequence ,lcsh:R ,Organisms ,Biology and Life Sciences ,Paleontology ,Genetic Variation ,DNA ,Invertebrates ,Insect Vectors ,Earth sciences ,Haplotypes ,RNA, Ribosomal ,Haplogroups ,lcsh:Q ,Paleogenetics ,Sequence Alignment ,Population Genetics - Abstract
International audience; The human head louse, Pediculus humanus capitis, is subdivided into several significantly divergent mitochondrial haplogroups, each with particular geographical distributions. Historically, they are among the oldest human parasites, representing an excellent marker for tracking older events in human evolutionary history. In this study, ancient DNA analysis using real-time polymerase chain reaction (qPCR), combined with conventional PCR, was applied to the remains of twenty-four ancient head lice and their eggs from the Roman period which were recovered from Israel. The lice and eggs were found in three combs, one of which was recovered from archaeological excavations in the Hatzeva area of the Judean desert, and two of which found in Moa, in the Arava region, close to the Dead Sea. Results show that the head lice remains dating approximately to 2,000 years old have a cytb haplogroup A, which is worldwide in distribution, and haplogroup B, which has thus far only been found in contemporary lice from America, Europe, Australia and, most recently, Africa. More specifically, this haplogroup B has a B36 haplotype, the most common among B haplogroups, and has been present in America for at least 4,000 years. The present findings confirm that clade B lice existed, at least in the Middle East, prior to contacts between Native Americans and Europeans. These results support a Middle Eastern origin for clade B followed by its introduction into the New World with the early peoples. Lastly, the presence of Acinetobacter baumannii DNA was demonstrated by qPCR and sequencing in four head lice remains belonging to clade A.
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- 2016
32. Yersinia pestis DNA sequences in late medieval skeletal finds, Bavaria
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Tran, Thi-Nguyen-Ny, Raoult, Didier, Drancourt, Michel, Wiechmann, Ingrid, Harbeck, Michaela, and Grupe, Gisela
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Microbiology (medical) ,Letter ,Epidemiology ,Yersinia pestis ,Black Death ,lcsh:Medicine ,Bacterial genome size ,Bubonic plague ,DNA sequencing ,Article ,lcsh:Infectious and parasitic diseases ,Microbiology ,Plasmid ,homopolymeric tract ,medicine ,lcsh:RC109-216 ,Typing ,Letters to the Editor ,bacteria ,Genotyping ,biology ,lcsh:R ,medicine.disease ,biology.organism_classification ,plague ,Infectious Diseases ,genotyping ,Bacteria - Abstract
To the Editor: We read with interest the report by Wiechmann et al. that, in the investigation of late medieval plague, partial sequencing of the Yersinia pestis pPCP1 plasmid yielded the observation of a 3-T homopolymeric tract which differed from the 5-T homopolymeric tract of the Orientalis Y. pestis CO92 type strain (1). This observation was unexpected because previous data from multispacer sequence typing and glp D gene sequencing yielded only the Orientalis biotype in cases of ancient plague (2). Using suicide PCR (3), we therefore further investigated pPCP1 in 10 negative control dental pulp specimens and 60 specimens collected from 1 Justinian Orientalis plague site (2), 2 Black Death Orientalis sites, and 2 additional medieval plague sites. All negative controls remained negative; 14 (23%) of 60 plague specimens yielded a PCR product, and 7 interpretable sequences yielded a 3-T homopolymeric tract in all cases. We further tested a Y. pestis isolate collection comprising 2 Antiqua, 6 Medievalis, and 4 Orientalis strains. No amplification was obtained in DNA-free PCR mix and 5 Y. enterocolitica–negative control isolates, whereas sequencing yielded a 3-T homopolymeric tract in all 12 Y. pestis isolates. BLAST analysis (http://blast.ncbi.nlm.nih.gov/blast.cgi) indicated that the 5-T homopolymeric tract has been found only once in the Y. pestis CO92 strain (4) and in none of 22 modern and 11 ancient sequences (Table). This 5-T homopolymeric tract is therefore CO92 strain specific and not a marker for the Orientalis biotype. This pPCP1 plasmid sequence, located into a noncoding region of the 3′ extremity of the plasmid, is characterized by several homopolymeric tracts of poly (A) and poly (T), including the 1 herein investigated. Instability of the T-stretches has been reported in bacterial genomes (5) as being hot spots for mutations (5). Table Alignment of pPCP1 Yersinis pestis modern and ancient sequences Therefore, in our assessment, the data reported for the late medieval Bavaria burial (1) do not support that deaths of persons buried in this site resulted from a non-Orientalis plague. Typing modern or ancient Y. pestis strains should not rely on poly (A) and poly (T) homopolymeric tracts sequencing.
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- 2011
33. Detection of Rickettsia felis, Rickettsia typhi, Bartonella species and Yersinia pestis in fleas (Siphonaptera) from Africa
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Leulmi, Hamza, Socolovschi, Cristina, Laudisoit, Anne, Houemenou, Gualbert, Davoust, Bernard, Bitam, Idir, Raoult, Didier, Parola, Philippe, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Liverpool, Université de Liège, Laboratoire VALCORE, Université M'Hamed Bougara Boumerdes (UMBB), and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)
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DNA, Bacterial ,lcsh:Arctic medicine. Tropical medicine ,lcsh:RC955-962 ,Epidemiology ,Yersinia pestis ,Molecular Sequence Data ,Plant Science ,Disease Surveillance ,Disease Vectors ,Tanzania ,Rodents ,Vector Biology ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,Medicine and Health Sciences ,Animals ,Humans ,Clinical Epidemiology ,Disease Dynamics ,Rickettsia typhi ,Rickettsia ,lcsh:Public aspects of medicine ,Arthropod Vectors ,Biology and Life Sciences ,lcsh:RA1-1270 ,Plant Pathology ,Insect Vectors ,Plagues ,Polymerase chain reaction ,Fleas ,Infectious Disease Surveillance ,Africa ,Rickettsia felis ,Siphonaptera ,[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie ,Human medicine ,Bartonella ,Research Article - Abstract
Little is known about the presence/absence and prevalence of Rickettsia spp, Bartonella spp. and Yersinia pestis in domestic and urban flea populations in tropical and subtropical African countries. Methodology/Principal findings Fleas collected in Benin, the United Republic of Tanzania and the Democratic Republic of the Congo were investigated for the presence and identity of Rickettsia spp., Bartonella spp. and Yersinia pestis using two qPCR systems or qPCR and standard PCR. In Xenopsylla cheopis fleas collected from Cotonou (Benin), Rickettsia typhi was detected in 1% (2/199), and an uncultured Bartonella sp. was detected in 34.7% (69/199). In the Lushoto district (United Republic of Tanzania), R. typhi DNA was detected in 10% (2/20) of Xenopsylla brasiliensis, and Rickettsia felis was detected in 65% (13/20) of Ctenocephalides felis strongylus, 71.4% (5/7) of Ctenocephalides canis and 25% (5/20) of Ctenophthalmus calceatus calceatus. In the Democratic Republic of the Congo, R. felis was detected in 56.5% (13/23) of Ct. f. felis from Kinshasa, in 26.3% (10/38) of Ct. f. felis and 9% (1/11) of Leptopsylla aethiopica aethiopica from Ituri district and in 19.2% (5/26) of Ct. f. strongylus and 4.7% (1/21) of Echidnophaga gallinacea. Bartonella sp. was also detected in 36.3% (4/11) of L. a. aethiopica. Finally, in Ituri, Y. pestis DNA was detected in 3.8% (1/26) of Ct. f. strongylus and 10% (3/30) of Pulex irritans from the villages of Wanyale and Zaa. Conclusion Most flea-borne infections are neglected diseases which should be monitored systematically in domestic rural and urban human populations to assess their epidemiological and clinical relevance. Finally, the presence of Y. pestis DNA in fleas captured in households was unexpected and raises a series of questions regarding the role of free fleas in the transmission of plague in rural Africa, especially in remote areas where the flea density in houses is high., Author Summary Fleas are associated with many bacterial diseases such as rickettsioses, bartonelloses and plague. These diseases may be severe, and little is known about their prevalence. Accordingly, we believe that our data shed light on the problem of unexplained fevers in tropical and subtropical African areas. Using molecular tools, we surveyed and studied selected flea-borne agents, namely Rickettsia spp. (R. felis and R. typhi), Bartonella spp. and Y. pestis, in fleas collected in Ituri (Linga and Rethy health zone) and Kinshasa in the Democratic Republic of the Congo, the Lushoto district in the United Republic of Tanzania and in Cotonou in Benin. We found that these bacteria are present in the studied regions. R. typhi and an unidentified Bartonella sp. were detected in fleas from Cotonou (Benin). R. felis and R. typhi were also detected in the Lushoto district (United Republic of Tanzania). Finally, we detected R. felis, Bartonella sp. and Y. pestis in the Democratic Republic of the Congo. As these emerging zoonotic diseases have a global distribution and affect public health, the implementation of vector control strategies is urgent.
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- 2014
34. Point-of-Care Laboratory of Pathogen Diagnosis in Rural Senegal
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Sokhna, Cheikh, Mediannikov, Oleg, Fenollar, Florence, Bassene, Hubert, Diatta, Georges, Tall, Adama, Trape, Jean-François, Drancourt, Michel, Raoult, Didier, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), ANR-11-BSV3-0008,MALEMAF,Recherche de pathogènes émergents en Afrique(2011), ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)
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Bacterial Diseases ,Male ,Rural Population ,Epidemiology ,Fevers ,Bacteremia ,Dengue Fever ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,Gram Negative ,Gastrointestinal Infections ,Rickettsia ,Child ,Aged, 80 and over ,Bartonellosis ,lcsh:Public aspects of medicine ,Relapsing Fever ,Bacterial Infections ,Middle Aged ,Trench Fever ,Senegal ,Medical Microbiology ,Coxiella burnetii ,Child, Preschool ,Medicine ,Infectious diseases ,Female ,Bartonella ,Research Article ,Neglected Tropical Diseases ,Q-Fever ,Adult ,lcsh:Arctic medicine. Tropical medicine ,Adolescent ,lcsh:RC955-962 ,Point-of-Care Systems ,Microbiology ,Infectious Disease Epidemiology ,Humans ,Biology ,Aged ,Clinical Laboratory Techniques ,Infant, Newborn ,Tropical Diseases (Non-Neglected) ,Infant ,lcsh:RA1-1270 ,Borrelia Infection ,Diagnostic medicine ,Malaria ,Emerging Infectious Diseases ,Bacterial pathogens ,[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie - Abstract
Background In tropical Africa, where the spectrum of the bacterial pathogens that cause fevers is poorly understood and molecular-based diagnostic laboratories are rare, the time lag between test results and patient care is a critical point for treatment of disease. Methodology/Principal Findings We implemented POC laboratory in rural Senegal to resolve the time lag between test results and patient care. During the first year of the study (February 2011 to January 2012), 440 blood specimens from febrile patients were collected in Dielmo and Ndiop villages. All samples were screened for malaria, dengue fever, Borrelia spp., Coxiella burnetii, Tropheryma whipplei, Rickettsia conorii, R. africae, R. felis, and Bartonella spp. Conclusions/Significance We identified DNA from at least one pathogenic bacterium in 80/440 (18.2%) of the samples from febrile patients. B. crocidurae was identified in 35 cases (9.5%), and R. felis DNA was found in 30 cases (6.8%). The DNA of Bartonella spp. was identified in 23/440 cases (4.3%), and DNA of C. burnetii was identified in 2 cases (0.5%). T. whipplei (0.2%) was diagnosed in one patient. No DNA of R. africae or R. conorii was identified. Among the 7 patients co-infected by two different bacteria, we found R. felis and B. crocidurae in 4 cases, B. crocidurae and Bartonella spp. in 2 cases, and B. crocidurae and C. burnetii in 1 case. Malaria was diagnosed in 54 cases. In total, at least one pathogen (bacterium or protozoa) was identified in 127/440 (28.9%) of studied samples. Here, the authors report the proof of concept of POC in rural tropical Africa. Discovering that 18.2% of acute infections can be successfully treated with doxycycline should change the treatment strategy for acute fevers in West Africa., Author Summary In tropical Africa, clinical laboratories capable of performing complicated diagnostic studies like PCR are rare and are almost always found in large cities. Moreover, a number of infectious diseases, many of them are emerging and neglected, may be quickly and reliably diagnosed only by molecular biology. This is one of the reasons why the repertoire of bacterial infectious diseases in tropical Africa is poorly known. The laboratory based on the Point-of-Care (POC) principle has been designed in order to resolve the time lag between test results and patient care, which is the critical point for the treatment. We report here the first successful experience of the installation of POC laboratory in rural Senegal. During the first year of the study (February 2011 to January 2012) we identified DNA from at least one pathogenic bacterium in 80/440 (18.2%) of the samples from febrile patients. In most of the cases it was relapsing fever and rickettsiosis agents. Malaria was diagnosed in 54 cases. In total, at least one pathogen (bacterium or protozoa) was identified in 127/440 (28.9%) of studied samples. Discovering that at least 18.2% of acute infections can be successfully treated with doxycycline should change the treatment strategy for acute fevers in West Africa.
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- 2013
35. The correlation of Q fever and Coxiella burnetii DNA in household environments in rural Senegal
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Ratmanov, Pavel, Bassene, H., Fenollar, F., Tall, A., Sokhna, Cheikh, Raoult, Didier, and Mediannikov, Oleg
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PCR ,Coxiella burnetii ,Epidemiology ,bacteria ,bacterial infections and mycoses ,Q fever - Abstract
During 2008-2011, we tested 874 blood samples from febrile patients who had a fever >37.5 degrees C, and 207 surface samples in households for Coxiella burnetii DNA in two rural Senegalese villages (Dielmo and Ndiop). Fisher's exact test and Spearman's correlation coefficient were used for statistical analysis. We identified four blood samples as positive for Coxiella burnetii DNA. The prevalence of Q fever in all tested samples was 0.46% in the two villages. C. burnetii DNA was also found in 7.5% of the dust samples in Ndiop, and in 0.9% in Dielmo; the prevalence in households was 22.6% in Ndiop and 2.6% in Dielmo. In Ndiop we found a weak correlation between positive environmental samples and the occurrence of the disease. Our findings show an association of environmental C. burnetii with human Q fever cases in a recently identified endemic area in rural Senegal.
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- 2013
36. Bartonella spp. bacteremia and rheumatic symptoms in patients from Lyme disease–endemic region
- Author
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Ben Beard, C., Nelson, Christina A., Mead, Paul S., Petersen, Lyle R., Raoult, Didier, Maggi, Ricardo G., Mozayeni, B. Robert, Pultorak, Elizabeth L., Hegarty, Barbara C., Bradley, Julie M., Correa, Maria, and Breitschwerdt, Edward B.
- Subjects
myalgia ,Male ,Pediatrics ,Letter ,Epidemiology ,lcsh:Medicine ,Bacteremia ,Lyme disease ,hemic and lymphatic diseases ,Surveys and Questionnaires ,DNA sequencing ,bacteria ,Child ,Aged, 80 and over ,education.field_of_study ,Lyme Disease ,biology ,Middle Aged ,Infectious Diseases ,PCR ,Child, Preschool ,Population study ,Female ,medicine.symptom ,Bartonella ,Bartonella Infection ,Microbiology (medical) ,Adult ,medicine.medical_specialty ,Adolescent ,rheumatologic ,Population ,Article ,lcsh:Infectious and parasitic diseases ,Young Adult ,blood ,Internal medicine ,Bartonella Infections ,Arthropathy ,medicine ,Humans ,In patient ,lcsh:RC109-216 ,cardiovascular diseases ,Borrelia burgdorferi ,Serotyping ,Letters to the Editor ,education ,Aged ,Bartonella henselae ,business.industry ,Research ,Arthritis ,lcsh:R ,biology.organism_classification ,medicine.disease ,bacterial infections and mycoses ,Molecular Typing ,Cross-Sectional Studies ,Immunology ,rheumatic ,business - Abstract
Prevalence of Bartonella spp. was high, especially among patients with a history of Lyme disease., Bartonella spp. infection has been reported in association with an expanding spectrum of symptoms and lesions. Among 296 patients examined by a rheumatologist, prevalence of antibodies against Bartonella henselae, B. koehlerae, or B. vinsonii subsp. berkhoffii (185 [62%]) and Bartonella spp. bacteremia (122 [41.1%]) was high. Conditions diagnosed before referral included Lyme disease (46.6%), arthralgia/arthritis (20.6%), chronic fatigue (19.6%), and fibromyalgia (6.1%). B. henselae bacteremia was significantly associated with prior referral to a neurologist, most often for blurred vision, subcortical neurologic deficits, or numbness in the extremities, whereas B. koehlerae bacteremia was associated with examination by an infectious disease physician. This cross-sectional study cannot establish a causal link between Bartonella spp. infection and the high frequency of neurologic symptoms, myalgia, joint pain, or progressive arthropathy in this population; however, the contribution of Bartonella spp. infection, if any, to these symptoms should be systematically investigated.
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- 2012
37. Comparison of Real-Time Quantitative PCR and Culture for the Diagnosis of Emerging Rickettsioses
- Author
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Angelakis, Emmanouil, Richet, Hervé, Rolain, Jean-Marc, La Scola, Bernard, Raoult, Didier, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Bacterial Diseases ,Drugs and Devices ,lcsh:Arctic medicine. Tropical medicine ,Time Factors ,Non-Clinical Medicine ,lcsh:RC955-962 ,Clinical Research Design ,Epidemiology ,Biopsy ,Cell Culture Techniques ,Dermatology ,Real-Time Polymerase Chain Reaction ,Sensitivity and Specificity ,Microbiology ,Antibiotics ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,Animals ,Humans ,Serologic Tests ,Rickettsia ,Biology ,Cells, Cultured ,Dermacentor ,Skin ,Bacteriological Techniques ,Health Care Policy ,lcsh:Public aspects of medicine ,lcsh:RA1-1270 ,Rickettsia Infections ,Vectors and Hosts ,Fibroblasts ,bacterial infections and mycoses ,Specimen preparation and treatment ,Diagnostic medicine ,Polymerase chain reaction ,Infectious Diseases ,Serology ,Skin infections ,Medicine ,Research Article - Abstract
Background Isolation of Rickettsia species from skin biopsies may be replaced by PCR. We evaluated culture sensitivity compared to PCR based on sampling delay and previous antibiotic treatment. Methodology/Principal Findings Skin biopsies and ticks from patients with suspected Rickettsia infection were screened for Rickettsia spp. using qPCR, and positive results were amplified and sequenced for the gltA and ompA genes. Immunofluorescence for spotted fever group rickettsial antigens was done for 79 patients. All skin biopsies and only ticks that tested positive using qPCR were cultured in human embryonic lung (HEL) fibroblasts using the centrifugation-shell vial technique. Patients and ticks were classified as definitely having rickettsioses if there was direct evidence of infection with a Rickettsia sp. using culture or molecular assays or in patients if serology was positive. Data on previous antibiotic treatments were obtained for patients with rickettsiosis. Rickettsia spp. infection was diagnosed in 47 out of 145 patients (32%), 41 by PCR and 12 by culture, whereas 3 isolates were obtained from PCR negative biopsies. For 3 of the patients serology was positive although PCR and culture were negative. Rickettsia africae was the most common detected species (n = 25, [17.2%]) and isolated bacterium (n = 5, [3.4%]). The probability of isolating Rickettsia spp. was 12 times higher in untreated patients and 5.4 times higher in patients from our hometown. Rickettsia spp. was amplified in 24 out of 95 ticks (25%) and we isolated 7 R. slovaca and 1 R. raoultii from Dermacentor marginatus. Conclusions/Significance We found a positive correlation between the bacteria copies and the isolation success in skin biopsies and ticks. Culture remains critical for strain analysis but is less sensitive than serology and PCR for the diagnosis of a Rickettsia infection., Author Summary Diagnosis of Rickettsia infection would benefit by use of the more rapid and sensitive method of quantitative real-time PCR than the time-intensive and less sensitive method of culturing Rickettsia species from skin biopsies. We evaluated culture sensitivity compared to PCR according to sampling delay and previous antibiotic treatment. We found that skin biopsies can be positive even when molecular tests were negative, and a negative result using molecular assays did not exclude the diagnosis of Rickettsia spp. infection. Rickettsia africae was the most common species in skin biopsies and R. slovaca was most common in ticks. We found a positive correlation between the number of bacteria copies and the isolation success in skin biopsies and ticks. The probability of isolating Rickettsia spp. was higher in untreated patients and in patients from our hometown. To increase the sensitivity of culture, skin biopsies should be sampled before treatment early in the course of the disease and should be inoculated as soon as possible.
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- 2012
38. Evidence of circulation of an epidemic strain of in France by multispacer typing
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Li, W., Raoult, Didier, Rolain, Jean-Marc, Scola, B., Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Department of Molecular Genetics and Microbiology, Duke University Medical Center, and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Genotyping ,Epidemiology ,France - Abstract
International audience; Multispacer typing (MST) was used to type ten strains detected in French patients. Incorporating 79 Swedish strains, phylogenetic analysis demonstrated that although tularemia appears as a sporadic disease in France, it is caused by an epidemic cluster of strains.
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- 2011
39. Implementation of Syndromic Surveillance Systems in Two Rural Villages in Senegal.
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Abat, Cédric, Colson, Philippe, Chaudet, Hervé, Rolain, Jean-Marc, Bassene, Hubert, Diallo, Aldiouma, Mediannikov, Oleg, Fenollar, Florence, Raoult, Didier, and Sokhna, Cheikh
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COMMUNICABLE disease diagnosis ,COMMUNICABLE disease treatment ,RURAL health ,MEDICAL microbiology ,SURVEILLANCE detection ,PUBLIC health - Abstract
Infectious diseases still represent a major challenge for humanity. In this context, their surveillance is critical. From 2010 to 2016, two Point-Of-Care (POC) laboratories have been successfully implemented in the rural Saloum region of Senegal. In parallel, a homemade syndromic surveillance system called EPIMIC was implemented to monitor infectious diseases using data produced by the POC laboratory of the Timone hospital in Marseille, France. The aim of this study is to describe the steps necessary for implementing EPIMIC using data routinely produced by two POC laboratories (POC-L) established in rural Senegal villages. After improving EPIMIC, we started to monitor the 15 pathogens routinely diagnosed in the two POC-L using the same methodology we used in France. In 5 years, 2,577 deduplicated patients-samples couples from 775 different patients have been tested in the Dielmo and Ndiop POC-L. 739 deduplicated patients-samples couples were found to be positive to at least one of the tested pathogens. The retrospective analysis of the Dielmo and Ndiop POC data with EPIMIC allowed to generate 443 alarms. Since January 2016, 316 deduplicated patients-samples couples collected from 298 different patients were processed in the Niakhar POC laboratory. 56 deduplicated patients-samples couples were found to be positive to at least one of the tested pathogens. The retrospective analysis of the data of the Niakhar POC laboratory with EPIMIC allowed to generate 14 alarms. Although some improvements are still needed, EPIMIC has been successfully spread using data routinely produced by two rural POC-L in Senegal, West Africa. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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40. Head Lice of Pygmies Reveal the Presence of Relapsing Fever Borreliae in the Republic of Congo.
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Amanzougaghene, Nadia, Akiana, Jean, Mongo Ndombe, Géor, Davoust, Bernard, Nsana, Nardiouf Sjelin, Parra, Henri-Joseph, Fenollar, Florence, Raoult, Didier, and Mediannikov, Oleg
- Subjects
PEDICULOSIS ,PYGMIES ,EPIDEMIOLOGY ,IMMUNOREGULATION ,FEVER - Abstract
Background: Head lice, Pediculus humanus capitis, occur in four divergent mitochondrial clades (A, B, C and D), each having particular geographical distributions. Recent studies suggest that head lice, as is the case of body lice, can act as a vector for louse-borne diseases. Therefore, understanding the genetic diversity of lice worldwide is of critical importance to our understanding of the risk of louse-borne diseases. Methodology/Principal Findings: Here, we report the results of the first molecular screening of pygmies’ head lice in the Republic of Congo for seven pathogens and an analysis of lice mitochondrial clades. We developed two duplex clade-specific real-time PCRs and identified three major mitochondrial clades: A, C, and D indicating high diversity among the head lice studied. We identified the presence of a dangerous human pathogen, Borrelia recurrentis, the causative agent of relapsing fever, in ten clade A head lice, which was not reported in the Republic of Congo, and B. theileri in one head louse. The results also show widespread infection among head lice with several species of Acinetobacter. A. junii was the most prevalent, followed by A. ursingii, A. baumannii, A. johnsonii, A. schindleri, A. lwoffii, A. nosocomialis and A. towneri. Conclusions/Significance: Our study is the first to show the presence of B. recurrentis in African pygmies’ head lice in the Republic of Congo. This study is also the first to report the presence of DNAs of B. theileri and several species of Acinetobacter in human head lice. Further studies are needed to determine whether the head lice can transmit these pathogenic bacteria from person to another. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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41. Understanding the cholera epidemic, Haiti
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Pun, Sher Bahadur, Piarroux, Renaud, Barrais, Robert, Faucher, Benoît, Haus, Rachel, Piarroux, Martine, Gaudart, Jean, Magloire, Roc, and Raoult, Didier
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medicine.medical_specialty ,Letter ,Sanitation ,lcsh:Medicine ,cholera ,medicine.disease_cause ,Article ,epidemic ,lcsh:Infectious and parasitic diseases ,Rivers ,Risk Factors ,Epidemiology ,Epidemic spread ,medicine ,Odds Ratio ,Cluster Analysis ,Humans ,lcsh:RC109-216 ,Socioeconomics ,Letters to the Editor ,bacteria ,Epidemics ,Vibrio cholerae ,outbreak ,business.industry ,Rapid expansion ,lcsh:R ,virus diseases ,Outbreak ,medicine.disease ,Cholera ,Haiti ,Survival Rate ,Geography ,Infectious disease (medical specialty) ,Population Surveillance ,Synopsis ,epidemiology ,Watery diarrhea ,business ,Developed country ,Peacekeeping - Abstract
Cholera strains isolated in Haiti were genetically most similar to strains detected in Bangladesh in 2002 and 2008; thus, cholera was most likely introduced into Haiti from southern Asia (2). Despite the genetic similarity in the strains, no attempt was made by the researchers to ascertain and rule out the source of the outbreak in Bangladeshi policemen stationed at Mirebalais between September and October 2010. Another, although less likely, source for the introduction of cholera into Haiti could have been travelers or relief workers who may have recently been to southern Asia. Most relief workers probably come from countries without endemic cholera, but they cannot definitely be ruled out as a source of cholera in Haiti. For example, in industrialized countries, cholera has been detected among travelers, albeit in smaller numbers, returning home from cholera-endemic areas (3,4). However, Piarroux et al. offered no information about travelers or relief workers or whether they had been screened for V. cholerae infection before coming to Haiti (1). Of note, the United Nations reported that none of the Nepalese peacekeepers was found to be positive for the strain in Haiti (5); hence, other possible explanations for the origin of the outbreak simply cannot be overlooked. Figure Patients with confirmed and suspected cases of cholera admitted to Sukraraj Tropical and Infectious Disease Hospital, by week, Katmandu, Nepal, July–November 2010. Case definitions: suspected cholera, acute watery diarrhea, with or without vomiting, ...
- Published
- 2011
42. Enterococcus faecalis urinary-tract infections: Do they have a zoonotic origin?
- Author
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Abat, Cédric, Huart, Michael, Garcia, Vincent, Dubourg, Grégory, and Raoult, Didier
- Subjects
ANIMALS ,ANTIBIOTICS ,ENTEROCOCCUS ,EPIDEMICS ,EPIDEMIOLOGY ,MICROBIAL sensitivity tests ,POULTRY ,URINARY tract infections ,ZOONOSES ,GRAM-positive bacterial infections ,COMMUNITY-acquired infections ,PHARMACODYNAMICS ,INFECTIOUS disease transmission - Abstract
Major human pathogens are frequently isolated from meat-producing animals, particularly poultry. Among them is Enterococcus faecalis, which is known to be one of the main cause of human urinary-tract infections worldwide. Early in 2015, we detected several, consecutive abnormal increases in the weekly number of human E. faecalis infections in various medical settings in the Provence-Alpes-Côte d'Azur region of France, especially including community-acquired urinary-tract infections. Speculating that this region-wide epidemiological event may have originated from animal-based food, we initiated this work to provide an overview of the epidemiology of E. faecalis, with a particular focus on the possible link between E. faecalis clones isolated from food-producing animals and those responsible for human urinary-tract infections. At that time, only one study had clearly identified strong epidemiological links between E. faecalis clones isolated from food-producing animals and human E. faecalis urinary-tract infections. This observation, coupled with our region-wide epidemiological experience, leads us to strongly believe that E. faecalis is a real zoonotic pathogen with potentially highly significant impact on human health. This is of particular concern because of its ability to acquire antibiotic-resistance genes and to infect animals and humans. Various strategies must be urgently implemented to address this public health threat, in particular through the development and implementation of large integrated automated surveillance systems based on animal and human health data to enable us to detect E. faecalis epidemiological events. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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43. Louse-Borne Relapsing Fever (Borrelia recurrentis) in a Somali Refugee Arriving in Italy: A Re-emerging Infection in Europe?
- Author
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Antinori, Spinello, Mediannikov, Oleg, Corbellino, Mario, Grande, Romualdo, Parravicini, Carlo, Bestetti, Giovanna, Longhi, Erika, Ricaboni, Davide, Ehounoud, Cyrille Bilé, Fenollar, Florence, Raoult, Didier, and Rimoldi, Sara Giordana
- Subjects
RELAPSING fever ,BORRELIA recurrentis ,ANTIBIOTICS ,COMMUNICABLE disease treatment ,HEALTH of refugees - Abstract
The article presents a case study of a 22 year old refugee from Somalia who was taken to the Emergency Department (ED) of Luigi Sacco Hospital in Milano, Italy and diagnosed with louse-borne relapsing fever (LBRF) caused by Borrelia recurrentis. He was admitted to the infectious diseases ward. He was treated with antibiotic therapy and made full recovery.
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- 2016
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44. Arsenophonus nasoniae and Rickettsiae Infection of Ixodes ricinus Due to Parasitic Wasp Ixodiphagus hookeri.
- Author
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Bohacsova, Monika, Mediannikov, Oleg, Kazimirova, Maria, Raoult, Didier, and Sekeyova, Zuzana
- Subjects
RICKETTSIAS ,BACTERIAL diseases ,CASTOR bean tick ,PARASITIC wasps ,ENTEROBACTERIACEAE ,BACTERIAL DNA - Abstract
Arsenophonus nasoniae, a male-killing endosymbiont of chalcid wasps, was recently detected in several hard tick species. Following the hypothesis that its presence in ticks may not be linked to the direct occurrence of bacteria in tick's organs, we identified A. nasoniae in wasps emerging from parasitised nymphs. We confirmed that 28.1% of Ixodiphagus hookeri wasps parasitizing Ixodes ricinus ticks were infected by A. nasoniae. Moreover, in examined I. ricinus nymphs, A. nasoniae was detected only in those, which were parasitized by the wasp. However, in part of the adult wasps as well as in some ticks that contained wasp's DNA, we did not confirm A. nasoniae. We also found, that in spite of reported male-killing, some newly emerged adult wasp males were also infected by A. nasoniae. Additionally, we amplified the DNA of Rickettsia helvetica and Rickettsia monacensis (known to be Ixodes ricinus-associated bacteria) in adult parasitoid wasps. This may be related either with the digested bacterial DNA in wasp body lumen or with a role of wasps in circulation of rickettsiae among tick vectors. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
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45. Identification of blood meal sources in the main African malaria mosquito vector by MALDI-TOF MS.
- Author
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Niare, Sirama, Berenger, Jean-Michel, Dieme, Constentin, Doumbo, Ogobara, Raoult, Didier, Parola, Philippe, and Almeras, Lionel
- Subjects
BLOOD meal as feed ,MOSQUITO vectors ,MALARIA ,ANOPHELES gambiae ,EPIDEMIOLOGICAL research - Abstract
Background: The identification of blood meal sources in malaria vectors is critical to better understanding host/vector interactions and malaria epidemiology and control. Currently, the identification of mosquito blood meal origins is based on time-consuming and costly techniques such as precipitin tests, ELISA and molecular tools. Although these tools have been validated to identify the blood meal and trophic preferences of female Anopheles mosquitoes, they present several limitations. Recently, matrix-assisted, laser desorption/ionization time-of-light mass spectrometry (MALDI-TOF MS) was successfully used as a quick and accurate tool for arthropod identification, including mosquitoes. The aim of the present work was to test whether MALDI-TOF MS could also be applied to identification of blood meal sources from engorged mosquitoes. Methods: Abdomen proteins extracted from Anopheles gambiae (stricto sensu, S molecular form) that were either unengorged or artificially engorged on seven distinct types of vertebrate blood (human, horse, sheep, rabbit, mouse, rat, dog) were submitted for MALDI-TOF MS. Results: The comparison of mass spectrometry (MS) spectra from mosquito abdomens collected 1 h post-feeding, were able to discriminate blood meal origins. Moreover, using Aedes albopictus specimens, abdominal protein MS spectra from engorged mosquitoes were found specific to host blood source and independent of the mosquito species. A sequential analysis revealed stability of mosquito abdominal protein spectra up to 24 h post-feeding. Conclusions: These results indicate that MALDI-TOF MS could determine feeding patterns of freshly engorged mosquitoes up to 24 h post-blood meal. The MALDI-TOF MS technique appears to be an efficient tool for large epidemio-logical surveillance of vector-borne diseases and outbreak source identification. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
46. Origin and Evolution of Rickettsial Plasmids.
- Author
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El Karkouri, Khalid, Pontarotti, Pierre, Raoult, Didier, and Fournier, Pierre-Edouard
- Subjects
RICKETTSIAL diseases ,BIOLOGICAL evolution ,COENZYMES ,METABOLITES ,COMPARATIVE genetics - Abstract
Background: Rickettsia species are strictly intracellular bacteria that have undergone a reductive genomic evolution. Despite their allopatric lifestyle, almost half of the 26 currently validated Rickettsia species have plasmids. In order to study the origin, evolutionary history and putative roles of rickettsial plasmids, we investigated the evolutionary processes that have shaped 20 plasmids belonging to 11 species, using comparative genomics and phylogenetic analysis between rickettsial, microbial and non-microbial genomes. Results: Plasmids were differentially present among Rickettsia species. The 11 species had 1 to 4 plasmid (s) with a size ranging from 12 kb to 83 kb. We reconstructed pRICO, the last common ancestor of the current rickettsial plasmids. pRICO was vertically inherited mainly from Rickettsia/Orientia chromosomes and diverged vertically into a single or multiple plasmid(s) in each species. These plasmids also underwent a reductive evolution by progressive gene loss, similar to that observed in rickettsial chromosomes, possibly leading to cryptic plasmids or complete plasmid loss. Moreover, rickettsial plasmids exhibited ORFans, recent gene duplications and evidence of horizontal gene transfer events with rickettsial and non-rickettsial genomes mainly from the α/γ-proteobacteria lineages. Genes related to maintenance and plasticity of plasmids, and to adaptation and resistance to stress mostly evolved under vertical and/or horizontal processes. Those involved in nucleotide/carbohydrate transport and metabolism were under the influence of vertical evolution only, whereas genes involved in cell wall/membrane/envelope biogenesis, cycle control, amino acid/lipid/coenzyme and secondary metabolites biosynthesis, transport and metabolism underwent mainly horizontal transfer events. Conclusion: Rickettsial plasmids had a complex evolution, starting with a vertical inheritance followed by a reductive evolution associated with increased complexity via horizontal gene transfer as well as gene duplication and genesis. The plasmids are plastic and mosaic structures that may play biological roles similar to or distinct from their co-residing chromosomes in an obligate intracellular lifestyle. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
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47. EPIMIC: A Simple Homemade Computer Program for Real-Time EPIdemiological Surveillance and Alert Based on MICrobiological Data.
- Author
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Colson, Philippe, Rolain, Jean-Marc, Abat, Cédric, Charrel, Rémi, Fournier, Pierre-Edouard, and Raoult, Didier
- Subjects
COMMUNICABLE diseases ,MORTALITY ,EPIDEMIOLOGY ,MICROBIOLOGY ,COMPUTER software ,STANDARD deviations ,UNIVERSITY hospitals - Abstract
Background and Aims: Infectious diseases (IDs) are major causes of morbidity and mortality and their surveillance is critical. In 2002, we implemented a simple and versatile homemade tool, named EPIMIC, for the real-time systematic automated surveillance of IDs at Marseille university hospitals, based on the data from our clinical microbiology laboratory, including clinical samples, tests and diagnoses. Methods: This tool was specifically designed to detect abnormal events as IDs are rarely predicted and modeled. EPIMIC operates using Microsoft Excel software and requires no particular computer skills or resources. An abnormal event corresponds to an increase above, or a decrease below threshold values calculated based on the mean of historical data plus or minus 2 standard deviations, respectively. Results: Between November 2002 and October 2013 (11 years), 293 items were surveyed weekly, including 38 clinical samples, 86 pathogens, 79 diagnosis tests, and 39 antibacterial resistance patterns. The mean duration of surveillance was 7.6 years (range, 1 month-10.9 years). A total of 108,427 Microsoft Excel file cells were filled with counts of clinical samples, and 110,017 cells were filled with counts of diagnoses. A total of 1,390,689 samples were analyzed. Among them, 172,180 were found to be positive for a pathogen. EPIMIC generated a mean number of 0.5 alert/week on abnormal events. Conclusions: EPIMIC proved to be efficient for real-time automated laboratory-based surveillance and alerting at our university hospital clinical microbiology laboratory-scale. It is freely downloadable from the following URL: (last accessed: 20/11/2015). [ABSTRACT FROM AUTHOR]
- Published
- 2015
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48. Real-Time Microbiology Laboratory Surveillance System to Detect Abnormal Events and Emerging Infections, Marseille, France.
- Author
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Abat, Cédric, Chaudet, Hervé, Colson, Philippe, Rolain, Jean-Marc, and Raoult, Didier
- Abstract
Infectious diseases are a major threat to humanity, and accurate surveillance is essential. We describe how to implement a laboratory data-based surveillance system in a clinical microbiology laboratory. Two historical Microsoft Excel databases were implemented. The data were then sorted and used to execute the following 2 surveillance systems in Excel: the Bacterial real-time Laboratory-based Surveillance System (BALYSES) for monitoring the number of patients infected with bacterial species isolated at least once in our laboratory during the study periodl and the Marseille Antibiotic Resistance Surveillance System (MARSS), which surveys the primary β-lactam resistance phenotypes for 15 selected bacterial species. The first historical database contained 174,853 identifications of bacteria, and the second contained 12,062 results of antibiotic susceptibility testing. From May 21, 2013, through June 4, 2014, BALYSES and MARSS enabled the detection of 52 abnormal events for 24 bacterial species, leading to 19 official reports. This system is currently being refined and improved. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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49. MALDI-TOF Identification of the Human Gut Microbiome in People with and without Diarrhea in Senegal.
- Author
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Samb-Ba, Bissoume, Mazenot, Catherine, Gassama-Sow, Amy, Dubourg, Grégory, Richet, Hervé, Hugon, Perrine, Lagier, Jean-Christophe, Raoult, Didier, and Fenollar, Florence
- Subjects
DIARRHEA ,MATRIX-assisted laser desorption-ionization ,ENTEROTYPES ,GASTROENTEROLOGY ,PUBLIC health ,GASTROINTESTINAL diseases ,PATIENTS - Abstract
Background: In Africa, there are several problems with the specific identification of bacteria. Recently, MALDI-TOF mass spectrometry has become a powerful tool for the routine microbial identification in many clinical laboratories. Methodology/Principal Findings: This study was conducted using feces from 347 individuals (162 with diarrhea and 185 without diarrhea) sampled in health centers in Dakar, Senegal. Feces were transported from Dakar to Marseille, France, where they were cultured using different culture conditions. The isolated colonies were identified using MALDI-TOF. If a colony was unidentified, 16S rRNA sequencing was performed. Overall, 2,753 isolates were tested, allowing for the identification of 189 bacteria from 5 phyla, including 2 previously unknown species, 11 species not previously reported in the human gut, 10 species not previously reported in humans, and 3 fungi. 2,718 bacterial isolates (98.8%) out of 2,750 yielded an accurate identification using mass spectrometry, as did the 3 Candida albicans isolates. Thirty-two bacterial isolates not identified by MALDI-TOF (1.2%) were identified by sequencing, allowing for the identification of 2 new species. The number of bacterial species per fecal sample was significantly higher among patients without diarrhea (8.6±3) than in those with diarrhea (7.3±3.4; P = 0.0003). A modification of the gut microbiota was observed between the two groups. In individuals with diarrhea, major commensal bacterial species such as E. coli were significantly decreased (85% versus 64%), as were several Enterococcus spp. (E. faecium and E. casseliflavus) and anaerobes, such as Bacteroides spp. (B. uniformis and B. vulgatus) and Clostridium spp. (C. bifermentans, C. orbiscindens, C. perfringens, and C. symbosium). Conversely, several Bacillus spp. (B. licheniformis, B. mojavensis, and B. pumilus) were significantly more frequent among patients with diarrhea. Conclusions/Significance: MALDI-TOF is a potentially powerful tool for routine bacterial identification in Africa, allowing for a quick identification of bacterial species. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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50. Describing the Silent Human Virome with an Emphasis on Giant Viruses.
- Author
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Popgeorgiev, Nikolay, Temmam, Sarah, Raoult, Didier, and Desnues, Christelle
- Subjects
VIRUS diseases ,MICROBIAL diversity ,ETIOLOGY of diseases ,EPIDEMIOLOGY ,PAPILLOMAVIRUSES - Abstract
Viruses are the most abundant obligate intracellular entities in our body. Until recently, they were only considered to be pathogens that caused a broad array of pathologies, ranging from mild disease to deaths in the most severe cases. However, recent advances in unbiased mass sequencing techniques as well as increasing epidemiological evidence have indicated that the human body is home to diverse viral species under non-pathological conditions. Despite these studies, the description of the presumably healthy viral flora, i.e. the normal human virome, is still in its infancy regarding viral composition and dynamics. This review summarizes our current knowledge of the human virome under non-pathological conditions. © 2013 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
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