Publlications (FR)

Publications avec des chercheurs de GenoScreen dans les auteurs

80 publications de 2008 à 2024

2024 (1 publication)

Guyeux, C., Senelle, G., Le Meur, A., Supply, P., Gaudin, C., Phelan, J. E. Refrégier, G. (2024). Newly Identified Mycobacterium africanum Lineage 10, Central Africa. Emerging Infectious Diseases, 30(3), 560-563.

2023 (3 publications)

Yenew B., Ghodousi A., Gaudin C., Supply P. et al., A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex, Nat. Commun., Nov. 2023, 14(1):7519. doi: 10.1038/s41467-023-42755-9.

Jouet A, Gaudin C, Badalato N, Lenoir E, Ferré A, Clément M, Laurent Y, Supply P. et al. Hi-plex deep amplicon sequencing for identification, high-resolution genotyping and multidrug resistance prediction of Mycobacterium leprae directly from patient biopsies by using Deeplex Myc-Lep. EBioMedicine. 2023 Jul;93:104649. doi: 10.1016/j.ebiom.2023.104649.

Vallier M., Segurens B., Larsonneur E., Meyer V., Ferreira S., Christophe Caloustian C., Jean-François Deleuze JF., Dougados M., Chamaillard M., Characterisation of gut microbiota composition in patients with axial spondyloarthritis and its modulation by TNF inhibitor treatment. RMD Open. March 2023, 9:e002794. doi: 10.1136/rmdopen-2022-002794.

2022 (2 publications)

Merker M, Rasigade JP, Barbier M, Cox H, Feuerriegel S, A. Kohl T, Shitikov E, Klaos K, Gaudin C, Antoine R, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Crudu V, Supply P, Niemann S, Wirth T. Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis. Nature Communications. 2021-2022 Oct-Aug.

Marijke Braet S, Jouet A, Aubry A, Van Dyck-Lippens M, Lenoir E, Assoumani Y, Baco A, Mzembaba A, Cambau E, Ezidio Gonçalves Vasconcellos S, Rigouts L, Suffys PN, Hasker E, Supply P, de Jong BC. Investigating drug resistance of Mycobacterium leprae in the Comoros: an observational deep-sequencing study. Lancet. 2022 July.

Camille d'Humières C , Nadia Gaïa N., Stéphanie Ferreira et al. Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections, Front. Microbiol. 2022 Apr 21; 13:863777.

2021 (5 publications)

Sokol H, Contreras V, Maisonnasse P, Desmons A, Delache B, Sencio V, Machelart A, Brisebarre A, Humbert L, Deryuter L, Gauliard E, Heumel S, Rainteau D, Dereuddre-Bosquet N, Menu E, Ho Tsong Fang R, Lamaziere A, Brot L, Wahl C, Oeuvray C, Rolhion N, Van Der Werf S, Ferreira S, Le Grand R, Trottein F. SARS-CoV-2 infection in nonhuman primates alters the composition and functional activity of the gut microbiota. Gut Microbes. 2021 Jan-Dec, 13(1):1-19.

Hilaire P, Landemaine L, Contreras S, Blanquart-Goudezeune H, Siguier P, Cornet F, Chiapello H, Loux V, Clavaud C, Morand SC. Complete Genome Sequence of Staphylococcus epidermidis PH1-28, Isolated from the Forehead of a Hyperseborrheic Donor. Microbiol Resour Announc. 2021 March, 10(9):e00165-21.

Allen AC, Malaga W, Gaudin C, Volle A, Moreau F, Hassan A, Astarie-Dequeker C, Peixoto A, Antoine R, Pawlik A, Frigui W, Berrone C, Brosch R, Supply P, Guilhot C. Parallel in vivo experimental evolution reveals that increased stress resistance was key for the emergence of persistent tuberculosis bacilli. Nat Microbiol. 2021 Aug, 6(8):1082-1093.

Hilaire P, Contreras S, Blanquart-Goudezeune H, Verbeke J, Delépine B, Marmiesse L, Peyraud R, Morand SC. Complete Genome Sequence of Sphingobium xenophagum PH3-15, Isolated from La Roche-Posay Thermal Water Sources. Microbiol Resour Announc. 2021 Aug, 10(33):e0070021.

Hellal J., Joulian C., Urien C., Ferreira S., Denonfoux J., Hermon L., Vuilleumier S., Imfeld G., Chlorinated ethene biodegradation and associated bacterial taxa in multi-polluted groundwater: Insights from biomolecular markers and stable isotope analysis, Science of The Total Environment, 2021 apr; 763:142950.

2020 (8 publications)

Jouet A, Gaudin C, Badalato N, Allix-Béguec C, Duthoy S, Ferré A, Diels M, Laurent Y, Contreras S, Feuerriegel S, Niemann S, André E, Kaswa MK, Tagliani E, Cabibbe A, Mathys V, Cirillo D, de Jong BC, Rigouts L, Supply P. Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs. Eur Respir J. 2020 Sep 17:2002338. DOI: 10.1183/13993003.02338-2020.

Vandenborght LE, Enaud R, Urien C, Coron N, Girodet PO, Ferreira S, Berger P, Delhaes L. Type 2-high asthma is associated with a specific indoor mycobiome and microbiome. J Allergy Clin Immunol. 2020 Sep 11:S0091-6749(20)31248-3.

Feuerriegel S, Kohl TA, Utpatel C, Andres S, Maurer FP, Heyckendorf J, Jouet A, Badalato N, Foray L, Kamara RF, Conteh OS, Supply P, Niemann S. Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex®-MycTB. Eur Respir J. 2020 Aug 6:2001796. DOI: 10.1183/13993003.01796-2020.

Foligné B, George F, Standaert A, Garat A, Poiret S, Peucelle V, Ferreira S, Sobry H, Muharram G, Lucau-Danila A, Daniel C. High-dose dietary supplementation with zinc prevents gut inflammation: Investigation of the role of metallothioneins and beyond by transcriptomic and metagenomic studies. FASEB J. 2020 Jul 30.

Ngabonziza JCS, Loiseau C, Marceau M, Jouet A, Menardo F, Tzfadia O, Antoine R, Niyigena EB, Mulders W, Fissette K, Diels M, Gaudin C, Duthoy S, Ssengooba W, André E, Kaswa MK, Habimana YM, Brites D, Affolabi D, Mazarati JB, de Jong BC, Rigouts L, Gagneux S, Meehan CJ, Supply P. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun. 2020 Jun 9;11(1):2917.

Sencio V, Barthelemy A, Tavares LP, Machado MG, Soulard D, Cuinat C, Queiroz-Junior CM, Noordine ML, Salomé-Desnoulez S, Deryuter L, Foligné B, Wahl C, Frisch B, Vieira AT, Paget C, Milligan G, Ulven T, Wolowczuk I, Faveeuw C, Le Goffic R, Thomas M, Ferreira S, Teixeira MM, Trottein F. Gut Dysbiosis during Influenza Contributes to Pulmonary Pneumococcal Superinfection through Altered Short-Chain Fatty Acid Production. Cell Rep. 2020 Mar 3;30(9):2934-2947.

Soret P, Vandenborght LE, Francis F, Coron N, Enaud R, Avalos M, Schaeverbeke T, Berger P, Fayon M, Thiebaut R, Delhaes L; Mucofong Investigation Group. Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis. Sci Rep. 2020 Feb 27;10(1):3589.

El Achkar S, Demanche C, Osman M, Rafei R, Ismail MB, Gaudin C, Duthoy S, De Matos F, Yaacoub H, Pinçon C, Hamze M, Supply P. Zoonotic tuberculosis in humans assessed by next-generation sequencing: an 18-month nationwide study in Lebanon. Eur Respir J. 2020 Jan 2;55(1).

2019 (4 publications)

Saint-Lu N, Burdet C, Sablier-Gallis F, Corbel T, Nevière A, Sayah-Jeanne S, Pulse M, Weiss W, Ferreira S, Andremont A, Mentré F, de Gunzburg J. DAV131A Protects Hamsters from Lethal Clostridioides difficile Infection Induced by Fluoroquinolones. Antimicrob Agents Chemother. 2019 Dec 20;64(1).

Ng KCS, Supply P, Cobelens FGJ, Gaudin C, Gonzalez-Martin J, de Jong BC, Rigouts L. How well do routine molecular diagnostics detect rifampicin heteroresistance in Mycobacterium tuberculosis? J Clin Microbiol. 2019 Aug 14.

Burdet C, Nguyen TT, Duval X, Ferreira S, Andremont A, Guedj J, Mentré F; DAV132-CL-1002 study group. Impact of antibiotic gut exposure on the temporal changes in microbiome diversity. Antimicrob Agents Chemother. 2019 Jul 15.

Hermon L, Hellal J, Denonfoux J, Vuilleumier S, Imfeld G, Urien C, Ferreira S, Joulian C. Functional Genes and Bacterial Communities During Organohalide Respiration of Chloroethenes in Microcosms of Multi-Contaminated Groundwater. Front Microbiol. 2019 Feb 12;10:89.

2018 (4 publications)

Pedersen MK, Andersen AB, Folkvardsen DB, Rasmussen EM, Svensson E, Lillebaek T, Supply P. Set-up and validation of mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) analysis of Mycobacterium tuberculosis using BioNumerics software. PLoS. 2018 Oct 31;13(10).

Makhado NA, Matabane E, Faccin M, Pinçon C, Jouet A, Boutachkourt F, Goeminne L, Gaudin C, Maphalala G, Beckert P, Niemann S, Delvenne JC, Delmée M, Razwiedani L, Nchabeleng M, Supply P, de Jong BC, André E.Outbreak of multidrug-resistant tuberculosis in South Africa undetected by WHO-endorsed commercial tests: an observational study.Lancet Infect Dis. 2018 Dec;18(12):1350-1359.

Burdet C, Sayah-Jeanne S, Nguyen TT, Hugon P, Sablier-Gallis F, Saint-Lu N, Corbel T, Ferreira S, Pulse M, Weiss W, Andremont A, Mentré F, de Gunzburg J. Antibiotic-induced dysbiosis predicts mortality in an animal model of Clostridium difficile infection. Antimicrob Agents Chemother. 2018 Jul 30.

Hermon L, Denonfoux J, Hellal J, Joulian C, Ferreira S, Vuilleumier S, Imfeld G. Dichloromethane biodegradation in multi-contaminated groundwater: Insights from biomolecular and compound-specific isotope analyses.Water Res. 2018 Oct 1;142:217-226.

2017 (3 publications)

Contreras S, Sagory-Zalkind P, Blanquart H, Iltis A, Morand S. Complete Genome Sequence of Vitreoscilla filiformis (ATCC 15551), Used as a Cosmetic Ingredient. Genome Announc. 2017 Aug 24;5(34). DOI: 10.1128/genomeA.00913-17.

Clément Y, Sarah G, Holtz Y, Homa F, Pointet S, Contreras S, Nabholz B, Sabot F, Sauné L, Ardisson M, Bacilieri R, Besnard G, Berger A, Cardi C, De Bellis F, Fouet O, Jourda C, Khadari B, Lanaud C, Leroy T, Pot D, Sauvage C, Scarcelli N, Tregear J, Vigouroux Y, Yahiaoui N, Ruiz M, Santoni S, Labouisse JP, Pham JL, David J, Glémin S. Evolutionary forces affecting synonymous variations in plant genomes. PLoS , 2017; May.22, volume 13.

Bruffaerts N, Vluggen C, Roupie V, Duytschaever L, Van den Poel C, Denoël J, Wattiez R, Letesson JJ, Fretin D, Rigouts L, Chapeira O, Mathys V, Saegerman C, Huygen K. Virulence and immunogenicity of genetically defined human and porcine isolates of M. avium subsp. hominissuis in an experimental mouse infection. PLoS , 2017; Feb.9, volume 12.

2016 (8 publications)

Dugat-Bony E, Garnier L, Denonfoux J, Ferreira S, Sarthou AS, Bonnarme P, Irlinger F4. Highlighting the microbial diversity of 12 French cheese varieties. International Journal of Food Microbiology, Volume 238, 5 December 2016, Pages 265-273.

Bruffaerts N, Vluggen C, Duytschaever L, Mathys V, Saegerman C, Chapeira O, Huygen K. Genome Sequences of Four Strains of Mycobacterium avium subsp. hominissuis, Isolated from Swine and Humans, Differing in Virulence in a Murine Intranasal Infection Model. Genome Announc. 2016; June 16; vol 4, issue 3.

Ribière C, Beugnot R, Parisot N, Gasc C, Defois C, Denonfoux J, Boucher D, Peyretaillade E, Peyret P. Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning. Methods Mol Biol. 2016; 1399:167-82.

Publications qui citent GenoScreen

1635 publications de 2008 à 2024

2024 (33 publications)

Lagourgue L, Sauvage T, Zubia M, Draisma SGA, Vieira C, Engelen A, Payri CE. Taxonomic Insights into Caulerpa (Bryopsidales, Chlorophyta) Species in French Polynesia: Confirmation of 13 Species and Reinstatement of C. pickeringii Harvey & Bailey. Diversity. 2024; 16(4):243.

Pretty L., D'Agostino K., Redhead-Harper R. et al. Diagnostic Accuracy of the Abbott SD Bioline MPT64 antigen test for identification of MTB Complex in a U.S. Clinical Mycobacteriology Laboratory. Heliyon. Volume 10, ISSUE 9, e30501, May 15, 2024.

Gouesbet, G., Renault, D., Derocles, S.A.P. and Colinet, H. (2024), Strong resistance to β-cyfluthrin in a strain of the beetle Alphitobius diaperinus: a de novo transcriptome analysis. Insect Science.

Duperron S. , Halary S. , Bouly J-P. et al. Transcriptomic insights into the dominance of two phototrophs throughout the water column of a tropical hypersaline-alkaline crater lake (Dziani Dzaha, Mayotte). Frontiers in Microbiology. Volume 15, 2024.

Garcia-Lopez M, Lurier T, Bouilloud M, Pradel J, Tatard C, Sepulveda D, et al. (2024) Prevalence, genetic diversity and eco-epidemiology of pathogenic Leptospira species in small mammal communities in urban parks Lyon city, France. PLoS ONE. 19(4): e0300523.

Le Veve A., Genete M., Lepers-Blassiau C. et al. The genetic architecture of the load linked to dominant and recessive self-incompatibility alleles in Arabidopsis halleri and A. lyrata. bioRxiv. 2024 Apr.

Matoute A, Maestri S, Saout M et al. Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana. Current Issues in Molecular Biology. 2024; 46(5):3810-3821.

Bahuaud O., Genestet C., Hodille E. et al. Rapid resistance detection is reliable for prompt adaptation of isoniazid resistant tuberculosis management. Heliyon. 2024 Apr; Volume 10, ISSUE 9, e29932.

Calbry J, Goudounet G, Charlot F, Guyon-Debast A, Perroud PF, Nogué F. The SpRY Cas9 variant release the PAM sequence constraint for genome editing in the model plant Physcomitrium patens. Transgenic Res. 2024 Apr;33(1-2):67-74.

Harran E., Kuntz G., Decors A. et al. Tracking potential Leptospira sources following human cases of leptospirosis: A One Health approach applied to an ecosystem in Brittany, France. One Health, Volume 18, 2024, 100726, ISSN 2352-7714.

Elton L., Aydin A., Stoker N. et al. A pragmatic pipeline for drug resistance identification in Mycobacterium tuberculosis using whole genome sequencing. MedRxiv, 2024.04.15.24305720.

Azariel Ruiz-Valencia, Louis Cornette de Saint Cyr, et al. A native CO2-reducing bacterium: Discovery, implementation and interests, Journal of CO2 Utilization, Volume 81, 2024, 102723, ISSN 2212-9820.

Miotto P, Cirillo DM, Schön T, Köser CU. The exceptions that prove the rule-a historical view of bedaquiline susceptibility. Genome Med. 2024, Mar 13;16(1):39.

Tram TTB, Trieu LPT, Nhat LTH, Thu DDA, Quang NL, Bang ND, Chau TTH, Thwaites GE, Walker TM, Ha VTN, Thuong NTT. 2024. Targeted sequencing from cerebrospinal fluid for rapid identification of drug-resistant tuberculous meningitis. J Clin Microbiol, 62:e01287-23.

Cloutier Charrette W., Rabodoarivelo M.-S., Point F., M. Knoblauch A. et al. Concordance of targeted and whole genome sequencing for Mycobacterium tuberculosis genotypic drug susceptibility testing, Diagnostic Microbiology and Infectious Disease, Volume 109, Issue 2, 2024, 116249, ISSN 0732-8893.

Heumel S. et al. Shotgun metagenomics and systemic targeted metabolomics highlight indole-3-propionic acid as a protective gut microbial metabolite against influenza infection. Gut microbes. Vol. 16,1 (2024): 2325067.

Blondeaux A, Valibouze C, Speca S, Rousseaux C, Dubuquoy C, Blanquart H, Zerbib P, Desreumaux P, Foligné B, Titécat M. Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management. Int J Mol Sci. 2024 Feb 10;25(4):2164.

Certad G, Gantois N, Merlin S, Martel S, Even G, Viscogliosi E, Audebert C, Chabé M. Frequency and Molecular Identification of Cryptosporidium in Adult Prim’Holstein Dairy Cattle Farms in the North of France. Microorganisms. 2024; 12(2):335.

Le Loarer A., Dufossé L., Bignon J., Frédérich M., Ledoux A., et al. OSMAC Method to Assess Impact of Culture Parameters on Metabolomic Diversity and Biological Activity of Marine-Derived Actinobacteria. 2023.

Günther, G., Mhuulu, L., Diergaardt, A., Dreyer, V., Moses, M., Anyolo, K. Nepolo, E. (2024). Bedaquiline Resistance after Effective Treatment of Multidrug-Resistant Tuberculosis, Namibia. Emerging Infectious Diseases, 30(3), 568-571.

Günther, G., Mhuulu, L., Diergaardt, A., Dreyer, V., Moses, M., Anyolo, K. Nepolo, E. et al (2024). Bedaquiline Resistance after Effective Treatment of Multidrug-Resistant Tuberculosis, Namibia. Emerging Infectious Diseases, 30(3), 568-571.

Rupasinghe P, Reenaers R, Vereecken J, Mulders W, Cogneau S, Merker M, Niemann S, Vally Omar S, Rigouts L, Köser CU, Decroo T, de Jong BC. 2024. Refined understanding of the impact of the Mycobacterium tuberculosis complex diversity on the intrinsic susceptibility to pretomanid. Microbiol Spectr, 12:e00070-24.

Vuarin P., Bouchard A., Lesobre L., Levêque G., Chalah T., et al. No evidence for prezygotic postcopulatory avoidance of kin despite high inbreeding depression. Molecular Ecology, 2018, 27 (24), pp.5252-5262.

Bourgeois, Y., Warren, B. H., & Augiron, S. (2024). The burden of anthropogenic changes and mutation load in a critically endangered harrier from the Reunion biodiversity hotspot, Circus maillardi. Molecular Ecology, 33, e17300.

S. Cesbron, M. Briand, J. Dittmer, L. Bousset-Vaslin, M.-A. Jacques, A. Sarniguet. First Report of Xanthomonas campestris pv. campestris Causing Black Rot on Oilseed Rape (Brassica napus) in France. A Plant Disease, 2024 108:3, 784.

Dubé, C.E., Ziegler, M., Mercière, A. et al. Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition. Nat Commun, 12, 6402 (2021).

Valbi V., Leplat J., François A., Perez A., Trichereau B., et al. Bacterial diversity on stained glass windows. International Biodeterioration & Biodegradation, 2023, 177, pp.105529.

Schwarz J.M. et al., Diverse pollen nutrition can improve the development of solitary bees but does not mitigate negative pesticide impacts, Science of The Total Environment, Volume 912, 20 February 2024, 169494.

Vautrin et al., The short-term response of soil microbial communities to digestate application depends on the characteristics of the digestate and soil type, Applied Soil Ecology, Volume 193, January 2024, 105105.

Priyanka Guha, Siddhartha Dutta, Krishna Murti, Jay Karan Charan, Krishna Pandey, V. Ravichandiran, Sameer Dhingra. The Integration of Omics: A Promising Approach to Personalized Tuberculosis Treatment. Medicine in Omics. 2024, 100033.

Laura Niebling, Ramona Nitzsche, Thorben Sieksmeyer, Vera Haskamp, Jonas Kissenkötter, Ahmed Abd El Wahed, Thomas Teufel, Herbert Hermann, Nils Paust and Ana R. Homann. Fast and on-site animal species identification in processed meat via centrifugal microfluidics and isothermal amplification. Lab Chip. 2024. DOI: 10.1039/D3LC01103.

Rodrigues, C., Singhal, T. What is New in the Diagnosis of Childhood Tuberculosis?. Indian J Pediatr (2024).

Gupta, R.K., Anthwal, D., Bhalla, M. et al. Direct Detection of Fluoroquinolone Resistance in Sputum Samples from Tuberculosis Patients by High Resolution Melt Curve Analysis. Curr Microbiol. 81, 27 (2024).

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