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3. Increased fecal ethanol and enriched ethanol-producing gut bacteria Limosilactobacillus fermentum, Enterocloster bolteae, Mediterraneibacter gnavus and Streptococcus mutans in nonalcoholic steatohepatitis

Author

Mbaye, Babacar, primary, Magdy Wasfy, Reham, additional, Borentain, Patrick, additional, Tidjani Alou, Maryam, additional, Mottola, Giovanna, additional, Bossi, Vincent, additional, Caputo, Aurelia, additional, Gerolami, Rene, additional, and Million, Matthieu, additional

Published
2023
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4. Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case–Control Culturomics Study

Author

Magdy Wasfy, Reham, primary, Mbaye, Babacar, additional, Borentain, Patrick, additional, Tidjani Alou, Maryam, additional, Murillo Ruiz, Maria Leticia, additional, Caputo, Aurelia, additional, Andrieu, Claudia, additional, Armstrong, Nicholas, additional, Million, Matthieu, additional, and Gerolami, Rene, additional

Published
2023
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5. Preliminary landscape of Candidatus Saccharibacteria in the human microbiome

Author

Naud, Sabrina, primary, Valles, Camille, additional, Abdillah, Abdourahim, additional, Abou Chacra, Linda, additional, Mekhalif, Fatima Zouina, additional, Ibrahim, Ahmad, additional, Caputo, Aurelia, additional, Baudoin, Jean-Pierre, additional, Gouriet, Frédérique, additional, Bittar, Fadi, additional, Lagier, Jean-Christophe, additional, Ranque, Stéphane, additional, Fenollar, Florence, additional, Tidjani Alou, Maryam, additional, and Raoult, Didier, additional

Published
2023
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8. Limosilactobacillus fermentum, Lactococcus lactis and Thomasclavelia ramosa are enriched and Methanobrevibacter smithii is depleted in patients with non-alcoholic steatohepatitis

Author

Mbaye, Babacar, primary, Wasfy, Reham Magdy, additional, Alou, Maryam Tidjani, additional, Borentain, Patrick, additional, Andrieu, Claudia, additional, Caputo, Aurelia, additional, Raoult, Didier, additional, Gerolami, Rene, additional, and Million, Matthieu, additional

Published
2023
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12. Limosilactobacillus Fermentum, Lactococcus Lactis and Erysipelatoclostridiumramosum are Enriched and Methanobrevibactersmithii is Depleted in Patients with Non-Alcoholic Steatohepatitis

Author

Mbaye, Babacar, primary, Wasfy, Reham Magdy, additional, Alou, Maryam Tidjani, additional, Borentain, Patrick, additional, Andrieu, Claudia, additional, Caputo, Aurelia, additional, Raoult, Didier, additional, Gerolami, Rene, additional, and MILLION, Matthieu, additional

Published
2023
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16. Pangenomic analysis of Coxiella burnetii unveils new traits in genome architecture.

Author

Abdallah, Rita Abou, Million, Matthieu, Delerce, Jeremy, Anani, Hussein, Diop, Awa, Caputo, Aurelia, Zgheib, Rita, Rousset, Elodie, Boumedine, Karim Sidi, Raoult, Didier, and Fournier, Pierre-Edouard

Abstract

Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis able to cause large outbreaks. The disease is polymorphic. Symptomatic primary infection is named acute Q fever and is associated with hepatitis, pneumonia, fever, and auto-immune complications while persistent focalized infections, mainly endocarditis, and vascular infections, occur in a minority of patients but are potentially lethal. In order to evaluate the genomic features, genetic diversity, evolution, as well as genetic determinants of antibiotic resistance, pathogenicity, and ability to cause outbreaks of Q fever, we performed a pangenomic analysis and genomic comparison of 75 C. burnetii strains including 63 newly sequenced genomes. Our analysis demonstrated that C. burnetii has an open pangenome, unique genes being found in many strains. In addition, pathogenicity islands were detected in all genomes. In consequence C. burnetii has a high genomic plasticity, higher than that of other intracellular bacteria. The core- and pan-genomes are made of 1,211 and 4,501 genes, respectively (ratio 0.27). The core gene-based phylogenetic analysis matched that obtained from multi-spacer typing and the distribution of plasmid types. Genomic characteristics were associated to clinical and epidemiological features. Some genotypes were associated to specific clinical forms and countries. MST1 genotype strains were associated to acute Q fever. A significant association was also found between clinical forms and plasmids. Strains harboring the QpRS plasmid were never found in acute Q fever and were only associated to persistent focalized infections. The QpDV and QpH1 plasmids were associated to acute Q fever. In addition, the Guyanese strain CB175, the most virulent strain to date, exhibited a unique MST genotype, a distinct COG profile and an important variation in gene number that may explain its unique pathogenesis. Therefore, strain-specific factors play an important role in determining the epidemiological and clinical manifestations of Q fever alongside with host-specific factors (valvular and vascular defects notably). [ABSTRACT FROM AUTHOR]

Published
2022
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17. Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal

Author

Baron, Sophie Alexandra, primary, Mediannikov, Oleg, additional, Abdallah, Rim, additional, Kuete Yimagou, Edmond, additional, Medkour, Hacène, additional, Dubourg, Gregory, additional, Elamire, Youssouf, additional, Afouda, Pamela, additional, Ngom, Issa Isaac, additional, Angelakis, Emmanouil, additional, Davoust, Bernard, additional, Diatta, Georges, additional, Barciela, Amanda, additional, Hernandez-Aguilar, R. Adriana, additional, Sokhna, Cheikh, additional, Caputo, Aurelia, additional, Levasseur, Anthony, additional, Rolain, Jean-Marc, additional, and Raoult, Didier, additional

Published
2021
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18. New human-associated species of the family Atopobiaceae and proposal to reclassify members of the genus Olsenella

Author

Zgheib, Rita, primary, Anani, Hussein, additional, Meng, Marine Makoa, additional, Mailhe, Morgane, additional, Ricaboni, Davide, additional, Morand, Aurélie, additional, Caputo, Aurelia, additional, Traore, Sory Ibrahima, additional, Fontanini, Anthony, additional, Armstrong, Nicholas, additional, Raoult, Didier, additional, and Fournier, Pierre Edouard, additional

Published
2021
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20. Passive Filtration, Rapid Scanning Electron Microscopy, and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Treponema Culture and Identification from the Oral Cavity

Author

Belkacemi, Souad, primary, Bou Khalil, Jacques, additional, Ominami, Yusuke, additional, Hisada, Akiko, additional, Fontanini, Anthony, additional, Caputo, Aurelia, additional, Levasseur, Anthony, additional, Lagier, Jean-Christophe, additional, Khelaifia, Saber, additional, and Raoult, Didier, additional

Published
2019
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21. Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics?

Author

Alou, Maryam Tidjani, Million, Matthieu, Traore, Sory I., Mouelhi, Donia, Khelaifia, Saber, Bachar, Dipankar, Caputo, Aurelia, Delerce, Jeremy, Brah, Souleymane, Alhousseini, Daouda, Sokhna, Cheikh, Robert, Catherine, Diallo, Bouli A., Diallo, Aldiouma, Parola, Philippe, Golden, Michael, Lagier, Jean-Christophe, 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), Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), 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, Université des sciences, des techniques et des technologies de Bamako (USTTB), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Assistance Publique - Hôpitaux de Marseille (APHM), Université Abdou Moumouni [Niamey], University of Aberdeen, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), 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 Université des Sciences, des Techniques et des Technologies de Bamako (USTTB)

Subjects
metagenomics, Culturomics, gut microbiota, Streptococcus gallolyticus, Probiotics, severe acute malnutrition, Gut microbiota, culturomics, Microbiology, digestive system, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, kwashiorkor, probiotics, Methanobrevibacter smithii, Severe acute malnutrition, Kwashiorkor, Metagenomics, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

International audience; Severe acute malnutrition is the world-leading cause of children under-five's death. Recent metagenomics studies have established a link between gut microbiota and severe acute malnutrition, describing an immaturity with a striking depletion in oxygen sensitive prokaryotes. Amoxicillin and therapeutic diet cure most of the children with severe acute malnutrition but an irreversible disruption of the gut microbiota is suspected in the refractory and most severe cases. In these cases, therapeutic diet may be unable to reverse the microbiota alteration leading to persistent impaired development or death. In addition, as enteric sepsis is a major cause of death in this context, identification of missing gut microbes to be tested as probiotics (live bacteria that confer a benefit to the host) to restore rapidly the healthy gut microbiota and prevent the gut pathogenic invasion is of foremost importance. In this study, stool samples of malnourished patients with kwashiorkor and healthy children were collected from Niger and Senegal and analyzed by culturomics and metagenomics. We found a globally decreased diversity, a decrease in the hitherto unknown diversity (new species isolation), a depletion in oxygen sensitive prokaryotes including Methanobrevibacter smithii and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria and Streptococcus gallolyticus. A complex of 12 species identified only in healthy children using culturomics and metagenomics were identified as probiotics candidates, providing a possible, defined, reproducible, safe, and convenient alternative to fecal transplantation to restore a healthy gut microbiota in malnourished children. Microbiotherapy based on selected strains has the potential to improve the current treatment of severe acute malnutrition and prevent relapse and death by reestablishing a healthy gut microbiota.

Published
2017

22. Microvirga massiliensis sp nov., the human commensal with the largest genome

Author

Caputo, Aurelia, Lagier, Jean-Christophe, Azza, Said, Robert, Catherine, Mouelhi, Donia, Fournier, Pierre-Edouard, Raoult, Didier, Assistance Publique - Hôpitaux de Marseille (APHM), 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), Unité des Rickettsies et pathogènes émergents (URPE), 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, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-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)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48

Subjects
Male, Microvirga massiliensis, Culturomics, Adolescent, Computational Biology, large genome, Molecular Sequence Annotation, Genomics, Sequence Analysis, DNA, taxonogenomics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Bacterial Typing Techniques, Gastrointestinal Microbiome, Phenotype, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, Metagenome, France, Metagenomics, Genome, Bacterial, Phylogeny, Original Research, Alphaproteobacteria
Abstract

International audience; Microvirga massiliensis sp. nov. strain JC119(T) is a bacteria isolated in Marseille from a stool sample collected in Senegal. The 16S rRNA (JF824802) of M.massiliensis JC119(T) revealed 95% sequence identity with Microvirga lotononidis WSM3557(T) (HM362432). This bacterium is aerobic, gram negative, catalase positive, and oxidase negative. The draft genome of M.massiliensis JC119(T) comprises a 9,207,211-bp-long genome that is the largest bacterial genome of an isolate in humans. The genome exhibits a G+C content of 63.28% and contains 8685 protein-coding genes and 77 RNA genes, including 21 rRNA genes. Here, we describe the features of M.massiliensis JC119(T), together with the genome sequence information and its annotation.

Published
2016

23. Identification of Algerian Field-Caught Phlebotomine Sand Fly Vectors by MALDI-TOF MS

Author

Lafri, Ismail, Almeras, Lionel, Bitam, Idir, Caputo, Aurelia, Yssouf, Amina, Forestier, Claire-Lise, Izri, Arezki, 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), Ecole Nationale Supérieure Vétérinaire d’Alger, Université Saâd Dahlab Blida 1 (UB1), Université de Bab Ezzouar, Assistance Publique - Hôpitaux de Marseille (APHM), Programme Nationale de Lutte Contre le Paludisme, Ministry of Public Health, Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Université de Saâd Dahlab [Blida] (USDB ), COMBE, Isabelle, and INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID

Subjects
Male, lcsh:Arctic medicine. Tropical medicine, Arthropoda, lcsh:RC955-962, Sand flies, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Species Specificity, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Animals, Leishmaniasis, Phylogeny, [SDV.IB] Life Sciences [q-bio]/Bioengineering, Leishmania, lcsh:Public aspects of medicine, fungi, lcsh:RA1-1270, Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Algeria, Phlebotomus, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Sequence databases, Research Article
Abstract

Background Phlebotomine sand flies are known to transmit Leishmania parasites, bacteria and viruses that affect humans and animals in many countries worldwide. Precise sand fly identification is essential to prevent phlebotomine-borne diseases. Over the past two decades, progress in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as an accurate tool for arthropod identification. The objective of the present study was to investigate the usefulness of MALDI-TOF MS as a tool for identifying field-caught phlebotomine. Methodology/Principal Findings Sand flies were captured in four sites in north Algeria. A subset was morphologically and genetically identified. Six species were found in these areas and a total of 28 stored frozen specimens were used for the creation of the reference spectrum database. The relevance of this original method for sand fly identification was validated by two successive blind tests including the morphological identification of 80 new specimens which were stored at -80°C, and 292 unknown specimens, including engorged specimens, which were preserved under different conditions. Intra-species reproducibility and inter-species specificity of the protein profiles were obtained, allowing us to distinguish specimens at the gender level. Querying of the sand fly database using the MS spectra from the blind test groups revealed concordant results between morphological and MALDI-TOF MS identification. However, MS identification results were less efficient for specimens which were engorged or stored in alcohol. Identification of 362 phlebotomine sand flies, captured at four Algerian sites, by MALDI-TOF MS, revealed that the subgenus Larroussius was predominant at all the study sites, except for in M’sila where P. (Phlebotomus) papatasi was the only sand fly species detected. Conclusion The present study highlights the application of MALDI-TOF MS for monitoring sand fly fauna captured in the field. The low cost, reliability and rapidity of MALDI-TOF MS analyses opens up new ways in the management of phlebotomine sand fly-borne diseases., Author Summary Phlebotomine sand flies are known to transmit Leishmania parasites, bacteria and viruses that affect humans and animals in many countries worldwide. Algeria is among the top ten countries with the highest number of cutaneous leishmaniasis cases. To prevent the emergence of leishmaniasis and to establish vector control and monitoring, precise identification of sand fly specimens at the species level is essential. Current morphological and molecular methods are long, expensive and laborious, limiting large-scale surveys. The recent application of MALDI-TOF MS for the identification of arthropods, including sand flies, opens up new opportunities in this field. Here, for the first time, this proteomic tool was assessed for the identification of sand flies collected in the field from leishmaniasis-endemic Algerian areas. Six distinct sand fly species were found and a reference spectrum database was created. Correct identification was obtained for all non-engorged blind-tested specimens stored by freezing. As a result, this proteomic tool could be applied for the classification of phlebotomine sand fly specimens caught in the field, enabling entomological surveys to be conducted.

Published
2016

24. Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics?

Author

Tidjani Alou, Maryam, primary, Million, Matthieu, additional, Traore, Sory I., additional, Mouelhi, Donia, additional, Khelaifia, Saber, additional, Bachar, Dipankar, additional, Caputo, Aurelia, additional, Delerce, Jeremy, additional, Brah, Souleymane, additional, Alhousseini, Daouda, additional, Sokhna, Cheikh, additional, Robert, Catherine, additional, Diallo, Bouli A., additional, Diallo, Aldiouma, additional, Parola, Philippe, additional, Golden, Michael, additional, Lagier, Jean-Christophe, additional, and Raoult, Didier, additional

Published
2017
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25. Culture of previously uncultured members of the human gut microbiota by culturomics

Author

Lagier, Jean-Christophe, primary, Khelaifia, Saber, additional, Alou, Maryam Tidjani, additional, Ndongo, Sokhna, additional, Dione, Niokhor, additional, Hugon, Perrine, additional, Caputo, Aurelia, additional, Cadoret, Frédéric, additional, Traore, Sory Ibrahima, additional, Seck, El Hadji, additional, Dubourg, Gregory, additional, Durand, Guillaume, additional, Mourembou, Gaël, additional, Guilhot, Elodie, additional, Togo, Amadou, additional, Bellali, Sara, additional, Bachar, Dipankar, additional, Cassir, Nadim, additional, Bittar, Fadi, additional, Delerce, Jérémy, additional, Mailhe, Morgane, additional, Ricaboni, Davide, additional, Bilen, Melhem, additional, Dangui Nieko, Nicole Prisca Makaya, additional, Dia Badiane, Ndeye Mery, additional, Valles, Camille, additional, Mouelhi, Donia, additional, Diop, Khoudia, additional, Million, Matthieu, additional, Musso, Didier, additional, Abrahão, Jônatas, additional, Azhar, Esam Ibraheem, additional, Bibi, Fehmida, additional, Yasir, Muhammad, additional, Diallo, Aldiouma, additional, Sokhna, Cheikh, additional, Djossou, Felix, additional, Vitton, Véronique, additional, Robert, Catherine, additional, Rolain, Jean Marc, additional, La Scola, Bernard, additional, Fournier, Pierre-Edouard, additional, Levasseur, Anthony, additional, and Raoult, Didier, additional

Published
2016
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27. Genome sequence and description of <italic>Haloferax massiliense</italic> sp. nov., a new halophilic archaeon isolated from the human gut.

Author

Khelaifia, Saber, Caputo, Aurelia, Andrieu, Claudia, Cadoret, Frederique, Armstrong, Nicholas, Michelle, Caroline, Lagier, Jean-Christophe, Djossou, Felix, Fournier, Pierre-Edouard, and Raoult, Didier

Subjects
GUT microbiome, HALOBACTERIUM genetics, ARCHAEBACTERIA, BACTERIAL cultures, PHENOTYPES, CATALASE
Abstract

By applying the culturomics concept and using culture conditions containing a high salt concentration, we herein isolated the first known halophilic archaeon colonizing the human gut. Here we described its phenotypic and biochemical characterization as well as its genome annotation. Strain Arc-HrT (= CSUR P0974 = CECT 9307) was mesophile and grew optimally at 37 °C and pH 7. Strain Arc-HrT was also extremely halophilic with an optimal growth observed at 15% NaCl. It showed gram-negative cocci, was strictly aerobic, non-motile and non-spore-forming, and exhibited catalase and oxidase activities. The 4,015,175 bp long genome exhibits a G + C% content of 65.36% and contains 3911 protein-coding and 64 predicted RNA genes. PCR-amplified 16S rRNA gene of strain Arc-HrT yielded a 99.2% sequence similarity with Haloferax prahovense, the phylogenetically closest validly published species in the Haloferax genus. The DDH was of 50.70 ± 5.2% with H. prahovense, 53.70 ± 2.69% with H. volcanii, 50.90 ± 2.64% with H. alexandrinus, 52.90 ± 2.67% with H. gibbonsii and 54.30 ± 2.70% with H. lucentense. The data herein represented confirm strain Arc-HrT as a unique species and consequently we propose its classification as representative of a novel species belonging to the genus Haloferax, as Haloferax massiliense sp. nov. [ABSTRACT FROM AUTHOR]

Published
2018
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28. Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov

Author

Angelakis, Emmanouil, primary, Bibi, Fehmida, additional, Ramasamy, Dhamodharan, additional, Azhar, Esam I, additional, Jiman-Fatani, Asif A, additional, Aboushoushah, Sally M, additional, Lagier, Jean-Christophe, additional, Robert, Catherine, additional, Caputo, Aurelia, additional, Yasir, Muhammad, additional, Fournier, Pierre-Edouard, additional, and Raoult, Didier, additional

Published
2014
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30. Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov.

Author

Edouard, Sophie, primary, Bibi, Fehmida, additional, Dhamodharan, Ramasamy, additional, Lagier, Jean-Christophe, additional, Azhar, Esam Ibraheen, additional, Robert, Catherine, additional, Caputo, Aurelia, additional, Yasir, Muhammad, additional, Jiman-Fatani, Asif Ahmad, additional, Alawi, Maha, additional, Fournier, Pierre-Edouard, additional, and Raoult, Didier, additional

Published
2014
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36. Multidrug-Resistant Klebsiella pneumoniaeClones from Wild Chimpanzees and Termites in Senegal

Author

Baron, Sophie Alexandra, Mediannikov, Oleg, Abdallah, Rim, Kuete Yimagou, Edmond, Medkour, Hacène, Dubourg, Gregory, Elamire, Youssouf, Afouda, Pamela, Ngom, Issa Isaac, Angelakis, Emmanouil, Davoust, Bernard, Diatta, Georges, Barciela, Amanda, Hernandez-Aguilar, R. Adriana, Sokhna, Cheikh, Caputo, Aurelia, Levasseur, Anthony, Rolain, Jean-Marc, and Raoult, Didier

Abstract

Antibiotic resistance genes exist naturally in various environments far from human usage. Here, we investigated multidrug-resistant Klebsiella pneumoniae, a common pathogen of chimpanzees and humans. We screened antibiotic-resistant K. pneumoniaefrom 48 chimpanzee stools and 38 termite mounds (n= 415 samples) collected in protected areas in Senegal.

Published
2021
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37. Passive Filtration, Rapid Scanning Electron Microscopy, and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for TreponemaCulture and Identification from the Oral Cavity

Author

Belkacemi, Souad, Bou Khalil, Jacques, Ominami, Yusuke, Hisada, Akiko, Fontanini, Anthony, Caputo, Aurelia, Levasseur, Anthony, Lagier, Jean-Christophe, Khelaifia, Saber, and Raoult, Didier

Abstract

We present here a new passive-filtration-based culture device combined with rapid identification with a new electron microscope (Hitachi TM4000) for the detection and culture of Treponemaspecies from the human oral cavity. Of the 44 oral samples cultivated, 15 (34%) were found to be positive for Treponemausing electron microscopy and were also culture positive. All were subcultured on agar plates; based on genome sequencing and analyses, 10 were strains of Treponema pectinovorumand 5 were strains of Treponema denticola.

Published
2019
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38. Identification of Algerian Field-Caught Phlebotomine Sand Fly Vectors by MALDI-TOF MS.

Author

Lafri I, Almeras L, Bitam I, Caputo A, Yssouf A, Forestier CL, Izri A, Raoult D, and Parola P

Subjects
Animals, Female, Male, Phlebotomus genetics, Phylogeny, Species Specificity, Phlebotomus chemistry, Phlebotomus classification, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization methods
Abstract

Background: Phlebotomine sand flies are known to transmit Leishmania parasites, bacteria and viruses that affect humans and animals in many countries worldwide. Precise sand fly identification is essential to prevent phlebotomine-borne diseases. Over the past two decades, progress in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as an accurate tool for arthropod identification. The objective of the present study was to investigate the usefulness of MALDI-TOF MS as a tool for identifying field-caught phlebotomine., Methodology/principal Findings: Sand flies were captured in four sites in north Algeria. A subset was morphologically and genetically identified. Six species were found in these areas and a total of 28 stored frozen specimens were used for the creation of the reference spectrum database. The relevance of this original method for sand fly identification was validated by two successive blind tests including the morphological identification of 80 new specimens which were stored at -80°C, and 292 unknown specimens, including engorged specimens, which were preserved under different conditions. Intra-species reproducibility and inter-species specificity of the protein profiles were obtained, allowing us to distinguish specimens at the gender level. Querying of the sand fly database using the MS spectra from the blind test groups revealed concordant results between morphological and MALDI-TOF MS identification. However, MS identification results were less efficient for specimens which were engorged or stored in alcohol. Identification of 362 phlebotomine sand flies, captured at four Algerian sites, by MALDI-TOF MS, revealed that the subgenus Larroussius was predominant at all the study sites, except for in M'sila where P. (Phlebotomus) papatasi was the only sand fly species detected., Conclusion: The present study highlights the application of MALDI-TOF MS for monitoring sand fly fauna captured in the field. The low cost, reliability and rapidity of MALDI-TOF MS analyses opens up new ways in the management of phlebotomine sand fly-borne diseases.

Published
2016
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