-
2025Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems, Science, 388, 6747, (2025)..
-
2025Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems., Science 2025 May; 388(6747): eads0768.
-
2025The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range., Mol Biol Evol 2025 Mar; 42(3): .
-
2024Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes., Nat Microbiol 2024 Dec; 9(12): 3345-3361.
-
2024Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids, Nature Microbiology, In press, ⟨10.1038/s41564-024-01844-1⟩.
-
2024Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species., PLoS Biol 2024 Oct; 22(10): e3002814.
-
2024Adaptation mechanisms of Clostridioides difficile to auranofin and its impact on human gut microbiota., NPJ Biofilms Microbiomes 2024 Sep; 10(1): 86.
-
2024Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans., Cell Host Microbe 2024 May; (): .
-
2024Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases., Microbiome 2024 Mar; 12(1): 50.
-
2024Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency, Nature Communications, 2024, 15 (1), pp.2032. ⟨10.1038/s41467-024-46147-5⟩.
-
2024Phage-plasmids promote recombination and emergence of phages and plasmids., Nat Commun 2024 Feb; 15(1): 1545.
-
2024Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems., Science Advances , 2024, 10 (2), pp.eadj3498. ⟨10.1126/sciadv.adj3498⟩.
-
2024Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites., Nat Microbiol 2024 Jan; 9(1): 228-240.
-
2023Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes., Mol Biol Evol 2023 Oct; 40(10): .
-
2023Latent evolution of biofilm formation depends on life-history and genetic background, npj Biofilms and Microbiomes, 2023, 9 (1), pp.53. ⟨10.1038/s41522-023-00422-3⟩.
-
2023Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies., Elife 2023 Mar; 12(): .
-
2023The Capsule Increases Susceptibility to Last-Resort Polymyxins, but Not to Other Antibiotics, in Klebsiella pneumoniae., Antimicrob Agents Chemother 2023 Mar; (): e0012723.
-
2023Identification and characterization of thousands of bacteriophage satellites across bacteria., Nucleic Acids Res 2023 Mar; (): .
-
2023Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola., Microlife 2023 ; 4(): uqad038.
-
2022Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation., Nucleic Acids Res 2022 Nov; (): .
-
2022Genomics, Transcriptomics, and Metabolomics Reveal That Minimal Modifications in the Host Are Crucial for the Compensatory Evolution of ColE1-Like Plasmids., mSphere 2022 Nov; (): e0018422.
-
2022Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling., mBio 2022 Oct; (): e0251422.
-
2022Human commensal gut Proteobacteria withstand type VI secretion attacks through immunity protein-independent mechanisms., Nat Commun 2021 Oct; 12(1): 5751.
-
2022Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion., mBio 2022 Sep; (): e0185122.
-
2022How capsules protect the cell, shape genetic exchanges and drive bacterial evolution Comment la capsule protège la cellule, façonne les échanges génétiques et influence l’évolution bactérienne, Life Sciences [q-bio]. Universite Paris Cité, 2022. English. ⟨NNT : ⟩.
-
2022Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids., Mol Biol Evol 2022 Jun; 39(6): .
-
2022Phages and their satellites encode hotspots of antiviral systems., Cell Host Microbe 2022 May; 30(5): 740-753.e5.
-
2022IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella., Microorganisms 2022 Mar; 10(4): .
-
2022To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites., Philos Trans R Soc Lond B Biol Sci 2022 Jan; 377(1842): 20200475.
-
2021Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance., PLoS Genet 2021 Nov; 17(11): e1009919.
-
2021NK-B cell cross talk induces CXCR5 expression on natural killer cells., iScience 2021 Oct; 24(10): 103109.
-
2021Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae., PLoS Biol 2021 Jul; 19(7): e3001276.
-
2021Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires., Nucleic Acids Res 2021 03; 49(5): 2655-2673.
-
2021Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection., ISME J 2021 Mar; 15(3): 702-719.
-
2021The impact of genetic diversity on gene essentiality within the Escherichia coli species., Nat Microbiol 2021 03; 6(3): 301-312.
-
2021Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa., Mol Biol Evol 2021 Feb; (): .
-
2020Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation., ISME J 2020 Dec; 14(12): 2980-2996.
-
2020Extensive antimicrobial resistance mobilization via multicopy plasmid encapsidation mediated by temperate phages., J Antimicrob Chemother 2020 Nov; 75(11): 3173-3180.
-
2020Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation, ISME J (2020). https://doi.org/10.1038/s41396-020-0726-z.
-
2020Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids., Nat Commun 2020 07; 11(1): 3602.
-
2020A synthesis of bacterial and archaeal phenotypic trait data., Sci Data 2020 06; 7(1): 170.
-
2020Phylogenetic background and habitat drive the genetic diversification of Escherichia coli., PLoS Genet. 2020 Jun; 16(6): e1008866.
-
2020The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold., J. Biol. Chem. 2020 May; 295(19): 6594-6604.
-
2020The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries., Trends Microbiol. 2020 May; 28(5): 372-386.
-
2020Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae., BMC Biol 2020 Apr; 18(1): 43.
-
2020Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells., J. Mol. Biol. 2020 02; 432(3): 745-761.
-
2020Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria., Nat Commun 2020 02; 11(1): 758.
-
2020Unlinked rRNA genes are widespread among bacteria and archaea., ISME J 2020 02; 14(2): 597-608.
-
2020Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements, Nucleic Acids Res. 2020 Jan;48(2):748-760.
-
2020Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan., Methods Mol. Biol. 2020 ; 2075(): 265-283.
-
2019Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes., Pathogens 2019 Dec; 9(1): .
-
2019Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility, PLoS Biol. 2019 Jul;17(7):e3000390.
-
2019A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria, Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2019 May;374(1772):20180088.
-
2019Ultrafast search of all deposited bacterial and viral genomic data, Nat. Biotechnol. 2019 Feb;37(2):152-159.
-
2018Genetic exchanges are more frequent in bacteria encoding capsules, PLoS Genet. 2018 12;14(12):e1007862.
-
2018HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance, Proc. Natl. Acad. Sci. U.S.A. 2018 12;115(52):13359-13364.
-
2018Cytometry meets next-generation sequencing – RNA-Seq of sorted subpopulations reveals regional replication and iron-triggered prophage induction in Corynebacterium glutamicum, Sci Rep 2018 Oct;8(1):14856.
-
2018CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins, Nucleic Acids Res. 2018 Jul;46(W1):W246-W251.
-
2018Kin discrimination and outer membrane exchange in Myxococcus xanthus: A comparative analysis among natural isolates, Mol. Ecol. 2018 Jun;.
-
2018Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements, Mol. Biol. Evol. 2018 Jun;.
-
2018Parallels between experimental and natural evolution of legume symbionts, Nat Commun 2018 06;9(1):2264.
-
2018Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics, Mol. Biol. Evol. 2018 Jun;35(6):1338-1347.
-
2018Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria, PLoS Biol. 2018 May;16(5):e2005056.
-
2018Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov., Antonie Van Leeuwenhoek 2018 Jan; 111(1): 55-72.
-
2018Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement, Microb Biotechnol 2018 01;11(1):3-17.
-
2018PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms., Front Microbiol 2018 ; 9(): 469.
-
2017Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria, Nature Communications 8, 2094..
-
2017Adaptive laboratory evolution of Corynebacterium glutamicum towards higher growth rates on glucose minimal medium, Sci Rep 2017 Dec;7(1):16780.
-
2017The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems., Genes (Basel) 2017 Nov; 8(11): .
-
2017The chromosomal organization of horizontal gene transfer in bacteria, Nat Commun 2017 Oct;8(1):841.
-
2017Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter, Environ. Microbiol. 2017 Oct;.
-
2017Recruitment of a lineage-specific virulence regulatory pathway promotes intracellular infection by a plant pathogen experimentally evolved into a legume symbiont., Mol Biol Evol. 2017 May 23. doi: 10.1093/molbev/msx165.
-
2017Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies, PLoS Comput. Biol. 2017 Sep;13(9):e1005745.
-
2017Integrative and conjugative elements and their hosts: composition, distribution and organization, Nucleic Acids Res. 2017 Sep;45(15):8943-8956.
-
2017Psychrobacter pasteurii and Psychrobacter piechaudii sp. nov., two novel species within the genus Psychrobacter., Int J Syst Evol Microbiol 2017 Sep; 67(9): 3192-3197.
-
2017A widespread family of polymorphic toxins encoded by temperate phages, BMC Biol. 2017 Aug;15(1):75.
-
2017In-vivo loss of carbapenem resistance by extensively drug-resistant Klebsiella pneumoniae during treatment via porin expression modification, Sci Rep 2017 Jul;7(1):6722.
-
2017Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens, PLoS Pathog. 2017 Jul;13(7):e1006525.
-
2017Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts, BMC Genomics 2017 07;18(1):525.
-
2017Second-order cooperation: Cooperative offspring as a living public good arising from second-order selection on non-cooperative individuals, Evolution 2017 07;71(7):1802-1814.
-
2017Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain., Nat Commun 2017 05; 8(): 15483.
-
2017Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone, Microb Genom 2017 Apr;3(4):e000110.
-
2017Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer, Curr Opin Microbiol. 2017 May 17;38:66-73.
-
2017Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance., mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩.
-
2017Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae, Environ. Microbiol. 2017 May;19(5):1881-1898.
-
2017Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder, Methods Mol Biol. 2017;1615:1-21.
-
2017A Naturally Occurring Single Nucleotide Polymorphism in a Multicopy Plasmid Produces a Reversible Increase in Antibiotic Resistance., Antimicrob Agents Chemother 2017 Feb; 61(2): .
-
2017Diagnosis in France of a Non-Toxigenic tox Gene-Bearing Strain of Corynebacterium diphtheriae in a Young Male Back From Senegal., Open Forum Infect Dis 2017 ; 4(1): ofw271.
-
2017Citrobacter europaeus sp. nov., isolated from water and human faecal samples., Int J Syst Evol Microbiol 2017 Jan; 67(1): 170-173.
-
2017A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins., Front Microbiol 2017 ; 8(): 443.
-
2016Community-acquired meningitis caused by a CG86 hypervirulent Klebsiella pneumoniae strain: first case report in the Caribbean, BMC Infect. Dis. 2016 Dec;16(1):736.
-
20161926-2016: 90 Years of listeriology, Microbes Infect. 2016 Dec;18(12):711-723.
-
2016Listeria monocytogenes sequence type 1 is predominant in ruminant rhombencephalitis., Sci Rep 2016 Nov; 6(): 36419.
-
2016Dom34 Links Translation to Protein O-mannosylation, PLoS Genet. 2016 Oct;12(10):e1006395.
-
2016Molecular Epidemiology of Colonizing and Infecting Isolates of Klebsiella pneumoniae, mSphere 2016 Sep-Oct;1(5).
-
2016Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes., Nat Microbiol 2016 Oct; 2(): 16185.
-
2016Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1, Nat Microbiol 2016 10;1(11):16209.
-
2016Discovery and Function of a General Core Hormetic Stress Response in E. coli Induced by Sublethal Concentrations of Antibiotics, Cell Rep 2016 09;17(1):46-57.
-
2016Evolution by flight and fight: diverse mechanisms of adaptation by actively motile microbes, ISME J 2017 02;11(2):555-568.
-
2016Silencing of cryptic prophages in Corynebacterium glutamicum, Nucleic Acids Res. 2016 12;44(21):10117-10131.
-
2016Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis, Sci Rep 2016;6:30379.
-
2016Regulation of genetic flux between bacteria by restriction-modification systems., Proc Natl Acad Sci U S A. 2016 May 17;113(20):5658-63. doi: 10.1073/pnas.1603257113. .
-
2016Identification and analysis of integrons and cassette arrays in bacterial genomes., Nucleic Acids Res. 2016 Apr 29. pii: gkw319..
-
2016Emergence of Antimicrobial-Resistant Escherichia coli of Animal Origin Spreading in Humans., Mol Biol Evol 2016 Apr; 33(4): 898-914.
-
2016Genetic and life-history traits associated with the distribution of prophages in bacteria., ISME J. 2016 Mar 25. doi: 10.1038/ismej.2016.47. .
-
2016Using Sex to Cure the Genome, PLoS Biol 14(3): e1002417. doi:10.1371/ journal.pbio.1002417.
-
2016Identification of protein secretion systems in bacterial genomes, Scientific Reports 6, 23080 (2016).
-
2016Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity., Nat Genet 2016 Mar; 48(3): 308-313.
-
2016The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography, Mol Biol Evol (2016) doi: 10.1093/molbev/msw048 .
-
2016Liver Abscess Caused by Infection with Community-Acquired Klebsiella quasipneumoniae subsp. quasipneumoniae, Emerging Infect. Dis. 2016 Mar;22(3):529-31.
-
2016Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications., BMC Genomics 2016 Feb; 17(): 118.
-
2016Coevolution of the Organization and Structure of Prokaryotic Genomes., Cold Spring Harb Perspect Biol. 2016 Jan 4;8(1).
-
2015Clonogrouping, a Rapid Multiplex PCR Method for Identification of Major Clones of Listeria monocytogenes., J Clin Microbiol 2015 Oct; 53(10): 3355-8.
-
2015Phylogenetic lineages, clones and β-lactamases in an international collection of Klebsiella oxytoca isolates non-susceptible to expanded-spectrum cephalosporins, J. Antimicrob. Chemother. 2015 Dec;70(12):3230-7.
-
2015Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations, Mol. Microbiol. 2015 Nov;98(4):636-50.
-
2015Rapid and widespread de novo evolution of kin discrimination, Proc. Natl. Acad. Sci. U.S.A. 2015 Jul;112(29):9076-81.
-
2015Tracking Nosocomial Klebsiella pneumoniae Infections and Outbreaks by Whole-Genome Analysis: Small-Scale Italian Scenario within a Single Hospital, J. Clin. Microbiol. 2015 Sep;53(9):2861-8.
-
2015Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health, Proc. Natl. Acad. Sci. U.S.A. 2015 Jul;112(27):E3574-81.
-
2015Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes, Curr. Biol. 2015 Jun;25(13):1673-81.
-
2015Mechanisms of Competition in Biofilm Communities, Microbiol Spectr 2015 Jun;3(3).
-
2015Advances in the Development of Biotherapeutics, Biomed Res Int 2015;2015:793876.
-
2015Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations, MBio 2015;6(3):e00552-15.
-
2015Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov., Int J Syst Evol Microbiol 2015 May; 65(Pt 5): 1486-1490.
-
2015A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria, Nucleic Acids Res. 2015 May;43(10):5002-16.
-
2015In silico analysis of usher encoding genes in Klebsiella pneumoniae and characterization of their role in adhesion and colonization, PLoS ONE 2015;10(3):e0116215.
-
2015Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations, Evolution 2015 Mar;69(3):788-802.
-
2015Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii, Genome Biol Evol 2015 Mar;7(3):856-70.
-
2015Association of tellurite resistance with hypervirulent clonal groups of Klebsiella pneumoniae, J. Clin. Microbiol. 2015 Apr;53(4):1380-2.
-
2015Acinetobacter seifertii sp. nov., a member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex isolated from human clinical specimens, Int. J. Syst. Evol. Microbiol. 2015 Mar;65(Pt 3):934-42.
-
2015New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration., Front Microbiol 2015 ; 6(): 1483.
-
2014Exploring the diversity of Listeria monocytogenes biofilm architecture by high-throughput confocal laser scanning microscopy and the predominance of the honeycomb-like morphotype, Appl. Environ. Microbiol. 2015 Mar;81(5):1813-9.
-
2014Molecular epidemiology of carbapenem non-susceptible Acinetobacter baumannii in France, PLoS ONE 2014;9(12):e115452.
-
2014Multicenter outbreak of infections by Saprochaete clavata, an unrecognized opportunistic fungal pathogen., mBio 2014 Dec; 5(6): .
-
2014Klebsiella variicola is a frequent cause of bloodstream infection in the stockholm area, and associated with higher mortality compared to K. pneumoniae, PLoS ONE 2014;9(11):e113539.
-
2014TLR9 activation is triggered by the excess of stimulatory versus inhibitory motifs present in Trypanosomatidae DNA, PLoS Negl Trop Dis 2014 Nov;8(11):e3308.
-
2014Resequencing microarray technology for genotyping human papillomavirus in cervical smears, PLoS ONE 2014;9(11):e109301.
-
2014Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups, Emerging Infect. Dis. 2014 Nov;20(11):1812-20.
-
2014Concise review: Genomic instability in human stem cells: current status and future challenges, Stem Cells 2014 Nov;32(11):2824-32.
-
2014MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems, PLoS ONE 2014;9(10):e110726.
-
2014The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences., Genome Biol Evol 2014 Oct; 6(10): 2866-82.
-
2014The chromosomal accommodation and domestication of mobile genetic elements, Curr. Opin. Microbiol. 2014 Dec;22:22-9.
-
2014Multiplex PCR for detection of seven virulence factors and K1/K2 capsular serotypes of Klebsiella pneumoniae, J. Clin. Microbiol. 2014 Dec;52(12):4377-80.
-
2014Development of a multiplex PCR assay for identification of Klebsiella pneumoniae hypervirulent clones of capsular serotype K2, J. Med. Microbiol. 2014 Dec;63(Pt 12):1608-14.
-
2014Leptospira mayottensis sp. nov., a pathogenic species of the genus Leptospira isolated from humans, Int. J. Syst. Evol. Microbiol. 2014 Dec;64(Pt 12):4061-7.
-
2014Differential contribution of AcrAB and OqxAB efflux pumps to multidrug resistance and virulence in Klebsiella pneumoniae, J. Antimicrob. Chemother. 2015 Jan;70(1):81-8.
-
2014Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer, PLoS Biol. 2014 Sep;12(9):e1001942.
-
2014Campylobacter coli cultured from the stools of a patient with immunoproliferative small intestinal disease., Clin Microbiol Infect 2014 Sep; 20(9): 908-11.
-
2014The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts, Nucleic Acids Res. 2014;42(16):10618-31.
-
2014Pervasive domestication of defective prophages by bacteria, Proc. Natl. Acad. Sci. U.S.A. 2014 Aug;111(33):12127-32.
-
2014Characterization of Listeria monocytogenes strains isolated during 2011-2013 from human infections in Switzerland, Foodborne Pathog. Dis. 2014 Oct;11(10):753-8.
-
2014Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola, Int. J. Syst. Evol. Microbiol. 2014 Sep;64(Pt 9):3146-52.
-
2014AlienTrimmer removes adapter oligonucleotides with high sensitivity in short-insert paired-end reads. Commentary on Turner (2014) Assessment of insert sizes and adapter content in FASTQ data from NexteraXT libraries, Front Genet 2014;5:130.
-
2014Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters, Appl. Microbiol. Biotechnol. 2014 Aug;98(15):6609-19.
-
2014Complete nucleotide sequence of two multidrug-resistant IncR plasmids from Klebsiella pneumoniae, Antimicrob. Agents Chemother. 2014 Jul;58(7):4207-10.
-
2014Comparison of widely used Listeria monocytogenes strains EGD, 10403S, and EGD-e highlights genomic variations underlying differences in pathogenicity., mBio 2014 Mar; 5(2): e00969-14.
-
2014Carbapenem-resistant Klebsiella pneumoniae exhibit variability in capsular polysaccharide and capsule associated virulence traits, J. Infect. Dis. 2014 Sep;210(5):803-13.
-
2014Draft Genome Sequence of Campylobacter coli Strain IPSID-1 Isolated from a Patient with Immunoproliferative Small Intestinal Disease., Genome Announc 2014 Mar; 2(2): .
-
2014Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Res. 2014 May;42(9):5715-27.
-
2014Microbial molecular markers and epidemiological surveillance in the era of high throughput sequencing: an update from the IMMEM-10 conference, Res. Microbiol. 2014 Feb-Mar;165(2):140-53.
-
2014A new biofilm-associated colicin with increased efficiency against biofilm bacteria, ISME J 2014 Jun;8(6):1275-88.
-
2014A PNPase dependent CRISPR System in Listeria, PLoS Genet. 2014 Jan;10(1):e1004065.
-
2013Multilocus sequence typing scheme for the Mycobacterium abscessus complex, Res. Microbiol. 2014 Feb-Mar;165(2):82-90.
-
2013Genetic architecture promotes the evolution and maintenance of cooperation, PLoS Comput. Biol. 2013;9(11):e1003339.
-
2013“Epidemic clones” of Listeria monocytogenes are widespread and ancient clonal groups., J Clin Microbiol 2013 Nov; 51(11): 3770-9.
-
2013wzi Gene sequencing, a rapid method for determination of capsular type for Klebsiella strains, J. Clin. Microbiol. 2013 Dec;51(12):4073-8.
-
2013Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability, PLoS Genet. 2013;9(9):e1003825.
-
2013Different factors associated with CTX-M-producing ST131 and non-ST131 Escherichia coli clinical isolates, PLoS ONE 2013;8(9):e72191.
-
2013AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads, Genomics 2013 Nov-Dec;102(5-6):500-6.
-
2013Deciphering bartonella diversity, recombination, and host specificity in a rodent community, PLoS ONE 2013;8(7):e68956.
-
2013Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity, PLoS ONE 2013;8(7):e68731.
-
2013Marker-free plasmids for biotechnological applications – implications and perspectives, Trends Biotechnol. 2013 Sep;31(9):539-47.
-
2013Escherichia coli resistance to nonbiocidal antibiofilm polysaccharides is rare and mediated by multiple mutations leading to surface physicochemical modifications, Antimicrob. Agents Chemother. 2013 Aug;57(8):3960-8.
-
2013Optimized Multilocus variable-number tandem-repeat analysis assay and its complementarity with pulsed-field gel electrophoresis and multilocus sequence typing for Listeria monocytogenes clone identification and surveillance., J Clin Microbiol 2013 Jun; 51(6): 1868-80.
-
2013From in vitro to in vivo Models of Bacterial Biofilm-Related Infections, Pathogens 2013;2(2):288-356.
-
2013Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona, PLoS Genet. 2013 Apr;9(4):e1003471.
-
2013Characterization of an extended-spectrum class A β-lactamase from a novel enterobacterial species taxonomically related to Rahnella spp./Ewingella spp, J. Antimicrob. Chemother. 2013 Aug;68(8):1733-6.
-
2013A novel murine model of rhinoscleroma identifies Mikulicz cells, the disease signature, as IL-10 dependent derivatives of inflammatory monocytes, EMBO Mol Med 2013 Apr;5(4):516-30.
-
2013An appraisal of human mitochondrial DNA instability: new insights into the role of non-canonical DNA structures and sequence motifs, PLoS ONE 2013;8(3):e59907.
-
2013Clinical trial evaluating color change and tooth sensitivity throughout and following in-office bleaching, Int J Periodontics Restorative Dent 2013 Mar-Apr;33(2):209-15.
-
2013Evolution. With a little help from prokaryotes, Science 2013 Mar;339(6124):1154-5.
-
2013Development of variable number of tandem repeats typing schemes for Ralstonia solanacearum, the agent of bacterial wilt, banana Moko disease and potato brown rot, J. Microbiol. Methods 2013 Mar;92(3):366-74.
-
2013From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases, Euro Surveill. 2013;18(4):20386.
-
2013Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis, Nat. Genet. 2013 Feb;45(2):172-9.
-
2013Natural selection for operons depends on genome size, Genome Biol Evol 2013;5(11):2242-54.
-
2013Natural genome diversity of AI-2 quorum sensing in Escherichia coli: conserved signal production but labile signal reception, Genome Biol Evol 2013;5(1):16-30.
-
2012The adaptation of temperate bacteriophages to their host genomes, Mol. Biol. Evol. 2013 Apr;30(4):737-51.
-
2012Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria, PLoS ONE 2012;7(11):e49403.
-
2012Are diabetes management guidelines applicable in ‘real life’?, Diabetol Metab Syndr 2012;4(1):47.
-
2012Influence of platform and abutment angulation on peri-implant bone. A three-dimensional finite element stress analysis, J Oral Implantol 2013 Dec;39(6):663-9.
-
2012Complete nucleotide sequence of the first KPC-2- and SHV-12-encoding IncX plasmid, pKpS90, from Klebsiella pneumoniae, Antimicrob. Agents Chemother. 2013 Jan;57(1):618-20.
-
2012Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements, Microbiology (Reading, Engl.) 2012 Dec;158(Pt 12):2997-3004.
-
2012Population genetic structure of 4,12:a:- Salmonella enterica strains from harbor porpoises, Appl. Environ. Microbiol. 2012 Dec;78(24):8829-33.
-
2012The emergence of multidrug-resistant Klebsiella pneumoniae of international clones ST13, ST16, ST35, ST48 and ST101 in a teaching hospital in the Paris region, Epidemiol. Infect. 2013 Aug;141(8):1705-12.
-
2012The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems, PLoS Genet. 2012 Sep;8(9):e1002983.
-
2012Microbiological and clinical characteristics of bacteraemia caused by the hypermucoviscosity phenotype of Klebsiella pneumoniae in Korea, Epidemiol. Infect. 2013 Jan;141(1):188.
-
2012Evolution of conjugation and type IV secretion systems, Mol. Biol. Evol. 2013 Feb;30(2):315-31.
-
2012Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages, J. Bacteriol. 2012 Nov;194(21):5829-39.
-
2012A new zebrafish model of oro-intestinal pathogen colonization reveals a key role for adhesion in protection by probiotic bacteria, PLoS Pathog. 2012;8(7):e1002815.
-
2012Impact of hypoxia and long-term cultivation on the genomic stability and mitochondrial performance of ex vivo expanded human stem/stromal cells, Stem Cell Res 2012 Nov;9(3):225-36.
-
2012Multilocus sequence typing analysis of Staphylococcus lugdunensis implies a clonal population structure, J. Clin. Microbiol. 2012 Sep;50(9):3003-9.
-
2012A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin, J. Bacteriol. 2012 Sep;194(18):4951-8.
-
2012Phylogenetic distribution of CTX-M- and non-extended-spectrum-β-lactamase-producing Escherichia coli isolates: group B2 isolates, except clone ST131, rarely produce CTX-M enzymes, J. Clin. Microbiol. 2012 Sep;50(9):2974-81.
-
2012Primary liver abscess due to CC23-K1 virulent clone of Klebsiella pneumoniae in France, Clin. Microbiol. Infect. 2012 Sep;18(9):E338-9.
-
2012Inter-hospital outbreak of Klebsiella pneumoniae producing KPC-2 carbapenemase in Ireland, J. Antimicrob. Chemother. 2012 Oct;67(10):2367-72.
-
2012Antibiofilm polysaccharides, Environ. Microbiol. 2013 Feb;15(2):334-46.
-
2012Multilocus sequence typing as a replacement for serotyping in Salmonella enterica, PLoS Pathog. 2012;8(6):e1002776.
-
2012Azole preexposure affects the Aspergillus fumigatus population in patients., Antimicrob. Agents Chemother. 2012 Sep; 56(9): 4948-50.
-
2012CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections, PLoS ONE 2012;7(5):e36995.
-
2012Detection of OXA-48 carbapenemase in the pandemic clone Escherichia coli O25b:H4-ST131 in the course of investigation of an outbreak of OXA-48-producing Klebsiella pneumoniae, Antimicrob. Agents Chemother. 2012 Jul;56(7):4030-1.
-
2012Multi-species biofilms: how to avoid unfriendly neighbors, FEMS Microbiol. Rev. 2012 Sep;36(5):972-89.
-
2012Klebsiella pneumoniae resistant to third-generation cephalosporins in five African and two Vietnamese major towns: multiclonal population structure with two major international clonal groups, CG15 and CG258, Clin. Microbiol. Infect. 2013 Apr;19(4):349-55.
-
2012Cefoxitin as an alternative to carbapenems in a murine model of urinary tract infection due to Escherichia coli harboring CTX-M-15-type extended-spectrum β-lactamase., Antimicrob Agents Chemother 2012 Mar; 56(3): 1376-81.
-
2012After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection, Genome Res. 2012 Apr;22(4):721-34.
-
2012Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens, PLoS Pathog. 2012 Feb;8(2):e1002503.
-
2012Protein-DNA interactions define the mechanistic aspects of circle formation and insertion reactions in IS2 transposition, Mob DNA 2012;3(1):1.
-
2012Severity of Escherichia coli bacteraemia is independent of the intrinsic virulence of the strains assessed in a mouse model, Clin. Microbiol. Infect. 2013 Jan;19(1):85-90.
-
2011Human leptospira isolates circulating in Mayotte (Indian Ocean) have unique serological and molecular features, J. Clin. Microbiol. 2012 Feb;50(2):307-11.
-
2011Investment in rapid growth shapes the evolutionary rates of essential proteins, Proc. Natl. Acad. Sci. U.S.A. 2011 Dec;108(50):20030-5.
-
2011Complete genome sequence of the fish pathogen Flavobacterium branchiophilum, Appl. Environ. Microbiol. 2011 Nov;77(21):7656-62.
-
2011Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples., J Clin Microbiol 2011 Sep; 49(9): 3268-75.
-
2011The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation, PLoS Genet. 2011 Aug;7(8):e1002222.
-
2011Expansion of European vacA and cagA alleles to East-Asian Helicobacter pylori strains in Cambodia, Infect. Genet. Evol. 2011 Dec;11(8):1899-905.
-
2011Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia, PLoS ONE 2011;6(7):e22058.
-
2011Clinical relevance of cagA and vacA gene polymorphisms in Helicobacter pylori isolates from Senegalese patients, Clin. Microbiol. Infect. 2012 Feb;18(2):153-9.
-
2011Emerging severe and fatal infections due to Klebsiella pneumoniae in two university hospitals in France, J. Clin. Microbiol. 2011 Aug;49(8):3012-4.
-
2011Characterization of the cryptic Escherichia lineages: rapid identification and prevalence, Environ. Microbiol. 2011 Sep;13(9):2468-77.
-
2011Worldwide distribution of major clones of Listeria monocytogenes., Emerg Infect Dis 2011 Jun; 17(6): 1110-2.
-
2011PCR-based identification of Klebsiella pneumoniae subsp. rhinoscleromatis, the agent of rhinoscleroma, PLoS Negl Trop Dis 2011 May;5(5):e1052.
-
2011Characterization of the novel Listeria monocytogenes PCR serogrouping profile IVb-v1., Int J Food Microbiol 2011 May; 147(1): 74-7.
-
2011Screening of Escherichia coli species biodiversity reveals new biofilm-associated antiadhesion polysaccharides, MBio 2011;2(3):e00043-11.
-
2011Widespread carbapenem resistant Acinetobacter baumannii clones in Italian hospitals revealed by a multicenter study, Infect. Genet. Evol. 2011 Aug;11(6):1319-26.
-
2011Probable zoonotic leprosy in the southern United States, N. Engl. J. Med. 2011 Apr;364(17):1626-33.
-
2011Epidemiology of methicillin-susceptible Staphylococcus aureus lineages in five major African towns: high prevalence of Panton-Valentine leukocidin genes, Clin. Microbiol. Infect. 2011 Apr;17(4):633-9.
-
2011CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection, J. Bacteriol. 2011 May;193(10):2460-7.
-
2011Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size, Mol. Biol. Evol. 2011 Aug;28(8):2339-49.
-
2011Mutation detection in plasmid-based biopharmaceuticals, Biotechnol J 2011 Apr;6(4):378-91.
-
2011Animal and human pathogenic Escherichia coli strains share common genetic backgrounds, Infect. Genet. Evol. 2011 Apr;11(3):654-62.
-
2011Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp. nov. (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp. nov. (formerly Acinetobacter genomic species 13TU), Res. Microbiol. 2011 May;162(4):393-404.
-
2011Rapid genotyping of Achromobacter xylosoxidans, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia isolates using melting curve analysis of RAPD-generated DNA fragments (McRAPD), Res. Microbiol. 2011 May;162(4):386-92.
-
2011Multilocus VNTR analysis of Mycobacterium ulcerans strains isolated in Côte d’Ivoire, J Infect Dev Ctries 2011 Feb;5(1):59-63.
-
2011Molecular epidemiological investigation of multidrug-resistant Acinetobacter baumannii strains in four Mediterranean countries with a multilocus sequence typing scheme, Clin. Microbiol. Infect. 2011 Feb;17(2):197-201.
-
2011Epidemiology of methicillin-resistant Staphylococcus aureus lineages in five major African towns: emergence and spread of atypical clones, Clin. Microbiol. Infect. 2011 Feb;17(2):160-5.
-
2011Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes, PLoS Genet. 2011;7(1):e1001284.
-
2010Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays, PLoS ONE 2010;5(12):e15243.
-
2010High prevalence of the arginine catabolic mobile element in carriage isolates of methicillin-resistant Staphylococcus epidermidis, J. Antimicrob. Chemother. 2011 Jan;66(1):29-36.
-
2010Evolution and population structure of Salmonella enterica serovar Newport, J. Bacteriol. 2010 Dec;192(24):6465-76.
-
2010Multilocus microsatellite markers for molecular typing of Candida glabrata: application to analysis of genetic relationships between bloodstream and digestive system isolates, J. Clin. Microbiol. 2010 Nov;48(11):4028-34.
-
2010Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?, PLoS Genet. 2010 Sep;6(9):e1001104.
-
2010Mobility of plasmids, Microbiol. Mol. Biol. Rev. 2010 Sep;74(3):434-52.
-
2010The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella, PLoS ONE 2010;5(6):e11126.
-
2010Analysis of DNA repeats in bacterial plasmids reveals the potential for recurrent instability events, Appl. Microbiol. Biotechnol. 2010 Aug;87(6):2157-67.
-
2010Emergence of carbapenem-resistant Hafnia: the fall of the last soldier., Clin Infect Dis 2010 May; 50(10): 1429-31.
-
2010Population genetic structure of Anopheles gambiae and Anopheles arabiensis in Niger, J. Med. Entomol. 2010 May;47(3):355-66.
-
2010No evidence for elemental-based streamlining of prokaryotic genomes, Trends Ecol. Evol. (Amst.) 2010 Jun;25(6):319-20; author reply 320-1.
-
2010The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool, PLoS ONE 2010;5(4):e10034.
-
2010What traits are carried on mobile genetic elements, and why?, Heredity (Edinb) 2011 Jan;106(1):1-10.
-
2010Eukaryotic microbial diversity of phototrophic microbial mats in two Icelandic geothermalhot springs, Int. Microbiol. 2010 Mar;13(1):21-32.
-
2010Molecular epidemiology of multidrug-resistant Acinetobacter baumannii in a tertiary care hospital in Naples, Italy, shows the emergence of a novel epidemic clone, J. Clin. Microbiol. 2010 Apr;48(4):1223-30.
-
2010The systemic imprint of growth and its uses in ecological (meta)genomics, PLoS Genet. 2010 Jan;6(1):e1000808.
-
2010Species delineation and clonal diversity in four Bifidobacterium species as revealed by multilocus sequencing, Res. Microbiol. 2010 Mar;161(2):82-90.
-
2009Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage, Microbiology (Reading, Engl.) 2010 Apr;156(Pt 4):1084-96.
-
2009Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence, Curr. Biol. 2009 Nov;19(20):1683-91.
-
2009First neisseria gonorrhoeae genotyping analysis in france: identification of a strain cluster with reduced susceptibility to Ceftriaxone, J. Clin. Microbiol. 2009 Nov;47(11):3540-5.
-
2009Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae strains in a university hospital in Tunis, Tunisia, 1999-2005, Clin. Microbiol. Infect. 2010 Feb;16(2):157-64.
-
2009Alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification, J. Mol. Biol. 2009 Dec;394(3):522-34.
-
2009Deletion formation mutations in plasmid expression vectors are unfavored by runaway amplification conditions and differentially selected under kanamycin stress, J. Biotechnol. 2009 Sep;143(4):231-8.
-
2009Structural instability of plasmid biopharmaceuticals: challenges and implications, Trends Biotechnol. 2009 Sep;27(9):503-11.
-
2009Genesis, effects and fates of repeats in prokaryotic genomes, FEMS Microbiol. Rev. 2009 May;33(3):539-71.
-
2009A novel heuristic for local multiple alignment of interspersed DNA repeats, IEEE/ACM Trans Comput Biol Bioinform 2009 Apr-Jun;6(2):180-9.
-
2009Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization, PLoS ONE 2009;4(3):e4982.
-
2009Aedes albopictus mosquito: the main vector of the 2007 Chikungunya outbreak in Gabon, PLoS ONE 2009;4(3):e4691.
-
2009Polyphasic characterization of xanthomonads pathogenic to members of the Anacardiaceae and their relatedness to species of Xanthomonas, Int. J. Syst. Evol. Microbiol. 2009 Feb;59(Pt 2):306-18.
-
2009Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths, PLoS Genet. 2009 Jan;5(1):e1000344.
-
2009Uneven distribution of mating types among genotypes of Candida glabrata isolates from clinical samples, Eukaryotic Cell 2009 Mar;8(3):287-95.
-
2008From local surveys to global surveillance: three high-throughput genotyping methods for epidemiological monitoring of Xanthomonas citri pv. citri pathotypes, Appl. Environ. Microbiol. 2009 Feb;75(4):1173-84.
-
2008Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing, J. Clin. Microbiol. 2009 Feb;47(2):300-10.
-
2008Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains, BMC Genomics 2008;9:560.
-
2008The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp, Mol. Biol. Evol. 2009 Feb;26(2):345-55.
-
2008The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients, J. Bacteriol. 2009 Jan;191(1):261-77.
-
2008Evolutionary patterns in prokaryotic genomes, Curr. Opin. Microbiol. 2008 Oct;11(5):454-60.
-
2008Development of 14 minisatellite markers for the citrus canker bacterium, Xanthomonas citri pv. citri, Mol Ecol Resour 2009 Jan;9(1):125-7.
-
2008Comparison of PFGE and multilocus sequence typing for analysis of Klebsiella pneumoniae isolates, J. Med. Microbiol. 2008 Oct;57(Pt 10):1308-10.
-
2008Origin, spread and demography of the Mycobacterium tuberculosis complex, PLoS Pathog. 2008;4(9):e1000160.
-
2008A new perspective on Listeria monocytogenes evolution., PLoS Pathog 2008 Sep; 4(9): e1000146.
-
2008Recombination frequency in plasmid DNA containing direct repeats–predictive correlation with repeat and intervening sequence length, Plasmid 2008 Sep;60(2):159-65.
-
2008High frequency plasmid recombination mediated by 28 bp direct repeats, Mol. Biotechnol. 2008 Nov;40(3):252-60.
-
2008An assessment of the impacts of molecular oxygen on the evolution of proteomes, Mol. Biol. Evol. 2008 Sep;25(9):1931-42.
-
2008Swelfe: a detector of internal repeats in sequences and structures, Bioinformatics 2008 Jul;24(13):1536-7.
-
2008Emergence of carbapenem resistance in Acinetobacter baumannii in the Czech Republic is associated with the spread of multidrug-resistant strains of European clone II, J. Antimicrob. Chemother. 2008 Sep;62(3):484-9.
-
2008Comparison of stress distribution between complete denture and implant-retained overdenture-2D FEA, J Oral Rehabil 2008 Oct;35(10):766-74.
-
2008MLVA-NET–a standardised web database for bacterial genotyping and surveillance, Euro Surveill. 2008 May;13(19).
-
2008The impact of the neisserial DNA uptake sequences on genome evolution and stability, Genome Biol. 2008;9(3):R60.
-
2008Persistence drives gene clustering in bacterial genomes, BMC Genomics 2008;9:4.
-
2008The organization of the bacterial genome, Annu. Rev. Genet. 2008;42:211-33.
-
2007Comparative phylogenies of Burkholderia, Ralstonia, Comamonas, Brevundimonas and related organisms derived from rpoB, gyrB and rrs gene sequences, Res. Microbiol. 2008 Apr;159(3):169-77.
-
2007Guidelines for the validation and application of typing methods for use in bacterial epidemiology, Clin. Microbiol. Infect. 2007 Oct;13 Suppl 3:1-46.
-
2007From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data, Biochimie 2008 Apr;90(4):648-59.
-
2007Causes for the intriguing presence of tRNAs in phages, Genome Res. 2007 Oct;17(10):1486-95.
-
2007Multilocus sequence typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination, Appl. Environ. Microbiol. 2007 Oct;73(20):6601-11.
-
2007Recombining population structure of Plesiomonas shigelloides (Enterobacteriaceae) revealed by multilocus sequence typing, J. Bacteriol. 2007 Nov;189(21):7808-18.
-
2007Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction., Genome Res 2007 Aug; 17(8): 1178-85.
-
2007Chikungunya outbreaks, N. Engl. J. Med. 2007 Jun;356(25):2650-2; author reply 2650-2.
-
2007[Evolutionary history of Salmonella Typhi illustrates a new pattern of epidemiologic dynamics], Med Sci (Paris) 2007 May;23(5):455-6.
-
2007Causes of insertion sequences abundance in prokaryotic genomes, Mol. Biol. Evol. 2007 Apr;24(4):969-81.
-
2007Erosion of interaction networks in reduced and degraded genomes, J. Exp. Zool. B Mol. Dev. Evol. 2007 Jan;308(1):97-103.
-
2006Evolutionary history of Salmonella typhi, Science 2006 Nov;314(5803):1301-4.
-
2006Similar compositional biases are caused by very different mutational effects, Genome Res. 2006 Dec;16(12):1537-47.
-
2006Repseek, a tool to retrieve approximate repeats from large DNA sequences, Bioinformatics 2007 Jan;23(1):119-21.
-
2006“A re-evaluation of M. prototuberculosis”: continuing the debate, PLoS Pathog. 2006 Sep;2(9):e95.
-
2006Protein evolution: causes of trends in amino-acid gain and loss, Nature 2006 Aug;442(7105):E11-2; discussion E12.
-
2006Identification of Acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry, J. Clin. Microbiol. 2006 Aug;44(8):2921-32.
-
2006Intrastrain heterogeneity of the mgpB gene in Mycoplasma genitalium is extensive in vitro and in vivo and suggests that variation is generated via recombination with repetitive chromosomal sequences, Infect. Immun. 2006 Jul;74(7):3715-26.
-
2006The quest for the universals of protein evolution, Trends Genet. 2006 Aug;22(8):412-6.
-
2006Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak, PLoS Med. 2006 Jul;3(7):e263.
-
2006An integrative method for accurate comparative genome mapping, PLoS Comput. Biol. 2006 Aug;2(8):e75.
-
2006Identification of erythrobactin, a hydroxamate-type siderophore produced by Saccharopolyspora erythraea, Lett. Appl. Microbiol. 2006 Apr;42(4):375-80.
-
2006Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages, PLoS Genet. 2006 Mar;2(3):e32.
-
2006Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes, Mol. Microbiol. 2006 Mar;59(5):1506-18.
-
2005Variants of the Klebsiella pneumoniae OKP chromosomal beta-lactamase are divided into two main groups, OKP-A and OKP-B, Antimicrob. Agents Chemother. 2005 Dec;49(12):5149-52.
-
2005Inference and analysis of the relative stability of bacterial chromosomes, Mol. Biol. Evol. 2006 Mar;23(3):513-22.
-
2005Laryngeal scleroma associated with Klebsiella pneumoniae subsp. ozaenae, J. Clin. Microbiol. 2005 Nov;43(11):5811-3.
-
2005Comparisons of dN/dS are time dependent for closely related bacterial genomes, J. Theor. Biol. 2006 Mar;239(2):226-35.
-
2005Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125, Genome Res. 2005 Oct;15(10):1325-35.
-
2005Regional occurrence of plasmid-mediated carbapenem-hydrolyzing oxacillinase OXA-58 in Acinetobacter spp. in Europe, J. Clin. Microbiol. 2005 Sep;43(9):4885-8.
-
2005Repetitive-DNA-element PCR fingerprinting and antibiotic resistance of pan-European multi-resistant Acinetobacter baumannii clone III strains, J. Med. Microbiol. 2005 Sep;54(Pt 9):851-6.
-
2005Comparative and evolutionary analysis of the bacterial homologous recombination systems, PLoS Genet. 2005 Aug;1(2):e15.
-
2005Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis, PLoS Pathog. 2005 Sep;1(1):e5.
-
2005Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates, J. Clin. Microbiol. 2005 Aug;43(8):4178-82.
-
2005Six groups of the OXY beta-Lactamase evolved over millions of years in Klebsiella oxytoca, Antimicrob. Agents Chemother. 2005 Aug;49(8):3453-62.
-
2005How essential are nonessential genes?, Mol. Biol. Evol. 2005 Nov;22(11):2147-56.
-
2005Identification of coagulase-negative staphylococci other than Staphylococcus epidermidis by automated ribotyping, Clin. Microbiol. Infect. 2005 Mar;11(3):177-84.
-
2005Identification and antimicrobial susceptibility of 100 Klebsiella animal clinical isolates, Vet. Microbiol. 2005 Feb;105(3-4):307-12.
-
2005The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus., Nucleic Acids Res 2005 ; 33(3): 1111-22.
-
2004Diversity of aminoglycoside-resistance genes and their association with class 1 integrons among strains of pan-European Acinetobacter baumannii clones, J. Med. Microbiol. 2004 Dec;53(Pt 12):1233-40.
-
2004Codon usage bias from tRNA’s point of view: redundancy, specialization, and efficient decoding for translation optimization, Genome Res. 2004 Nov;14(11):2279-86.
-
2004Order and disorder in bacterial genomes, Curr. Opin. Microbiol. 2004 Oct;7(5):519-27.
-
2004Species distribution and ribotype diversity of Burkholderia cepacia complex isolates from French patients with cystic fibrosis, J. Clin. Microbiol. 2004 Oct;42(10):4824-7.
-
2004Development of a rapid identification method for Klebsiella pneumoniae phylogenetic groups and analysis of 420 clinical isolates, Clin. Microbiol. Infect. 2004 Oct;10(10):942-5.
-
2004Molecular serotyping of Klebsiella species isolates by restriction of the amplified capsular antigen gene cluster, J. Clin. Microbiol. 2004 Aug;42(8):3388-98.
-
2004Diversity and evolution of the class A chromosomal beta-lactamase gene in Klebsiella pneumoniae, Antimicrob. Agents Chemother. 2004 Jul;48(7):2400-8.
-
2004Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes, J. Mol. Evol. 2004 Jun;58(6):692-700.
-
2004The replication-related organization of bacterial genomes, Microbiology (Reading, Engl.) 2004 Jun;150(Pt 6):1609-27.
-
2004Identification of a new geographically widespread multiresistant Acinetobacter baumannii clone from European hospitals, Res. Microbiol. 2004 Mar;155(2):105-12.
-
2004Discrimination of Klebsiella pneumoniae and Klebsiella oxytoca phylogenetic groups and other Klebsiella species by use of amplified fragment length polymorphism, Res. Microbiol. 2004 Jan-Feb;155(1):17-23.
-
2003Gene essentiality determines chromosome organisation in bacteria, Nucleic Acids Res. 2003 Nov;31(22):6570-7.
-
2003DNA repeats lead to the accelerated loss of gene order in bacteria, Trends Genet. 2003 Nov;19(11):600-3.
-
2003Evaluation of the polymorphisms associated with tandem repeats for Pseudomonas aeruginosa strain typing, J. Clin. Microbiol. 2003 Nov;41(11):4991-7.
-
2003An analysis of determinants of amino acids substitution rates in bacterial proteins, Mol. Biol. Evol. 2004 Jan;21(1):108-16.
-
2003Identification of Klebsiella oxytoca using a specific PCR assay targeting the polygalacturonase pehX gene, Res. Microbiol. 2003 Oct;154(8):587-92.
-
2003Occurrence and spread of SHV extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates in Curacao, J. Antimicrob. Chemother. 2003 Sep;52(3):530-2.
-
2003Associations between inverted repeats and the structural evolution of bacterial genomes, Genetics 2003 Aug;164(4):1279-89.
-
2003A strand-specific model for chromosome segregation in bacteria, Mol. Microbiol. 2003 Aug;49(4):895-903.
-
2003Essentiality, not expressiveness, drives gene-strand bias in bacteria, Nat. Genet. 2003 Aug;34(4):377-8.
-
2003An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction, Genome Res. 2003 Jun;13(6A):1123-32.
-
2003Phylogenetic diversity of bat trypanosomes of subgenus Schizotrypanum based on multilocus enzyme electrophoresis, random amplified polymorphic DNA, and cytochrome b nucleotide sequence analyses, Infect. Genet. Evol. 2003 Feb;2(3):201-8.
-
2003Evidence for genetic exchange and hybridization in Trypanosoma cruzi based on nucleotide sequences and molecular karyotype, Infect. Genet. Evol. 2003 Feb;2(3):173-83.
-
2002mecA gene is widely disseminated in Staphylococcus aureus population, J. Clin. Microbiol. 2002 Nov;40(11):3970-5.
-
2002A new family of highly variable proteins in the Chlamydophila pneumoniae genome, Nucleic Acids Res. 2002 Oct;30(20):4351-60.
-
2002Evaluation of the Etest ESBL and the BD Phoenix, VITEK 1, and VITEK 2 automated instruments for detection of extended-spectrum beta-lactamases in multiresistant Escherichia coli and Klebsiella spp, J. Clin. Microbiol. 2002 Oct;40(10):3703-11.
-
2002Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?, Trends Microbiol. 2002 Sep;10(9):393-5.
-
2002Origin and fate of repeats in bacteria, Nucleic Acids Res. 2002 Jul;30(13):2987-94.
-
2002Base composition bias might result from competition for metabolic resources, Trends Genet. 2002 Jun;18(6):291-4.
-
2002Outbreak of a susceptible strain of Acinetobacter species 13 (sensu Tjernberg and Ursing) in an adult neurosurgical intensive care unit, J. Hosp. Infect. 2002 Jun;51(2):89-95.
-
2002Automated ribotyping of vancomycin-resistant Enterococcus faecium isolates, J. Clin. Microbiol. 2002 Jun;40(6):1977-84.
-
2002Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution, Nucleic Acids Res. 2002 May;30(9):2031-42.
-
2002Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?, Nucleic Acids Res. 2002 May;30(9):1886-94.
-
2002Comparative evaluation of the BD Phoenix and VITEK 2 automated instruments for identification of isolates of the Burkholderia cepacia complex, J. Clin. Microbiol. 2002 May;40(5):1743-8.
-
2002Chromosomal size variation in Trypanosoma cruzi is mainly progressive and is evolutionarily informative, Parasitology 2002 Mar;124(Pt 3):277-86.
-
2001Ongoing evolution of strand composition in bacterial genomes, Mol. Biol. Evol. 2001 Sep;18(9):1789-99.
-
2001Characterisation of large and small subunit rRNA and mini-exon genes further supports the distinction of six Trypanosoma cruzi lineages, Int. J. Parasitol. 2001 Sep;31(11):1218-26.
-
2001Infectious diseases and the golden age of phylogenetics: an E-debate, Infect. Genet. Evol. 2001 Jul;1(1):69-74.
-
2001Evolutionary role of restriction/modification systems as revealed by comparative genome analysis, Genome Res. 2001 Jun;11(6):946-58.
-
2001In-vivo transfer of mecA DNA to Staphylococcus aureus [corrected], Lancet 2001 May;357(9269):1674-5.
-
2001The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis, Nucleic Acids Res. 2001 May;29(10):2145-53.
-
2001Phylogenetic diversity of Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates revealed by randomly amplified polymorphic DNA, gyrA and parC genes sequencing and automated ribotyping, Int. J. Syst. Evol. Microbiol. 2001 May;51(Pt 3):915-24.
-
2000Identification of six Trypanosoma cruzi lineages by sequence-characterised amplified region markers, Mol. Biochem. Parasitol. 2000 Nov;111(1):95-105.
-
2000Molecular epidemiology of penicillin-resistant Streptococcus pneumoniae colonizing children with community-acquired pneumonia and children attending day-care centres in Fortaleza, Brazil, J. Antimicrob. Chemother. 2000 Nov;46(5):757-65.
-
2000Molecular surveillance of European quinolone-resistant clinical isolates of Pseudomonas aeruginosa and Acinetobacter spp. using automated ribotyping, J. Clin. Microbiol. 2000 Oct;38(10):3636-45.
-
2000The DB case: pattern matching evidence is not significant, Mol. Microbiol. 2000 Jul;37(1):216-8.
-
2000Genomic rearrangements in trypanosomatids: an alternative to the “one gene” evolutionary hypotheses?, Mem. Inst. Oswaldo Cruz 2000 Jul-Aug;95(4):527-34.
-
2000In vitro potency of moxifloxacin, clinafloxacin and sitafloxacin against 248 genetically defined clinical isolates of Staphylococcus aureus, J. Antimicrob. Chemother. 2000 Jul;46(1):109-13.
-
2000Sulphur islands in the Escherichia coli genome: markers of the cell’s architecture?, FEBS Lett. 2000 Jun;476(1-2):8-11.
-
2000Population structure and genetic typing of Trypanosoma cruzi, the agent of Chagas disease: a multilocus enzyme electrophoresis approach, Parasitology 2000 May;120 ( Pt 5):513-26.
-
2000Distinguishing species of the Burkholderia cepacia complex and Burkholderia gladioli by automated ribotyping, J. Clin. Microbiol. 2000 May;38(5):1876-84.
-
2000In vitro activities of sitafloxacin (DU-6859a) and six other fluoroquinolones against 8,796 clinical bacterial isolates, Antimicrob. Agents Chemother. 2000 Apr;44(4):1102-7.
-
2000Implication of gene distribution in the bacterial chromosome for the bacterial cell factory, J. Biotechnol. 2000 Mar;78(3):209-19.
-
2000Epidemiology of quinolone resistance of Klebsiella pneumoniae and Klebsiella oxytoca in Europe, Eur. J. Clin. Microbiol. Infect. Dis. 2000 Jan;19(1):64-8.
-
2000Identification of six Trypanosoma cruzi phylogenetic lineages by random amplified polymorphic DNA and multilocus enzyme electrophoresis, Int. J. Parasitol. 2000 Jan;30(1):35-44.
-
1999Molecular epidemiology of quinolone resistance and comparative in vitro activities of new quinolones against European Staphylococcus aureus isolates, FEMS Immunol. Med. Microbiol. 1999 Dec;26(3-4):281-7.
-
1999Functional and evolutionary roles of long repeats in prokaryotes, Res. Microbiol. 1999 Nov-Dec;150(9-10):725-33.
-
1999Codon usage and lateral gene transfer in Bacillus subtilis, Curr. Opin. Microbiol. 1999 Oct;2(5):524-8.
-
1999Association of alterations in ParC and GyrA proteins with resistance of clinical isolates of Enterococcus faecium to nine different fluoroquinolones, Antimicrob. Agents Chemother. 1999 Oct;43(10):2513-6.
-
1999Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes, Mol. Biol. Evol. 1999 Sep;16(9):1219-30.
-
1999Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis, Nucleic Acids Res. 1999 Sep;27(17):3567-76.
-
1999Bacterial DNA strand compositional asymmetry: response, Trends Microbiol. 1999 Aug;7(8):308.
-
1999Comparative in vitro activities of ciprofloxacin, clinafloxacin, gatifloxacin, levofloxacin, moxifloxacin, and trovafloxacin against Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, and Enterobacter aerogenes clinical isolates with alterations in GyrA and ParC proteins, Antimicrob. Agents Chemother. 1999 Aug;43(8):2051-5.
-
1999Universal replication biases in bacteria, Mol. Microbiol. 1999 Apr;32(1):11-6.
-
1999A phylogenetic analysis by multilocus enzyme electrophoresis and multiprimer random amplified polymorphic DNA fingerprinting of the Leishmania genome project Friedlin reference strain, Folia Parasitol. 1999;46(1):10-4.
-
1998Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons, Nucleic Acids Res. 1998 Jun;26(12):2971-80.
-
1998Trypanosoma cruzi: How Many Relevant Phylogenetic Subdivisions are There?, Parasitol. Today (Regul. Ed.) 1998 May;14(5):178-9.
-
1998A phylogenetic analysis of the Trypanosoma cruzi genome project CL Brener reference strain by multilocus enzyme electrophoresis and multiprimer random amplified polymorphic DNA fingerprinting, Mol. Biochem. Parasitol. 1998 May;92(2):253-63.