Bacterial Genomics Group
“Influence of agricultural antibiotic use on chicken meat-associated enterococci and their connection to the clinic.”, Appl Environ Microbiol, 2019. ,
“Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges.”, Genome Med, vol. 11, no. 1, p. 45, 2019. ,
“Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream.”, Sci Transl Med, vol. 11, no. 487, 2019. ,
“Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Strains.”, Front Immunol, vol. 10, p. 195, 2019. ,
“ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database.”, PLoS One, vol. 14, no. 10, p. e0223364, 2019. ,
“SynerClust: a highly scalable, synteny-aware orthologue clustering tool.”, Microb Genom, vol. 4, no. 11, 2018. ,
“Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium.”, J Antimicrob Chemother, vol. 73, no. 6, pp. 1479-1486, 2018. ,
“Gut microbiota utilize immunoglobulin A for mucosal colonization.”, Science, vol. 360, no. 6390, pp. 795-800, 2018. ,
“Identification of Novel Coumestan Derivatives as Polyketide Synthase 13 Inhibitors against Mycobacterium tuberculosis.”, J Med Chem, vol. 61, no. 3, pp. 791-803, 2018. ,
“Reply to Lee and Howden.”, Clin Infect Dis, vol. 66, no. 1, pp. 160-161, 2018. ,
“Whole-Transcriptome and -Genome Analysis of Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolates Identifies Downregulation of as a Mechanism of Ethionamide Resistance.”, Antimicrob Agents Chemother, vol. 61, no. 12, 2017. ,
“Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics.”, Clin Infect Dis, vol. 64, no. 11, pp. 1494-1501, 2017. ,
“Tracing the Enterococci from Paleozoic Origins to the Hospital.”, Cell, vol. 169, no. 5, pp. 849-861.e13, 2017. ,
“Identification of Highly Specific Diversity-Oriented Synthesis-Derived Inhibitors of Clostridium difficile.”, ACS Infect Dis, vol. 3, no. 5, pp. 349-359, 2017. ,
“Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections.”, Sci Transl Med, vol. 9, no. 382, 2017. ,
“Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance.”, Nat Genet, vol. 49, no. 3, pp. 395-402, 2017. ,
“Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus.”, J Clin Microbiol, vol. 55, no. 2, pp. 457-469, 2017. ,
“Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks.”, Proc Natl Acad Sci U S A, vol. 114, no. 5, pp. 1135-1140, 2017. ,
“Genomic Analysis of the Evolution of Fluoroquinolone Resistance in Mycobacterium tuberculosis Prior to Tuberculosis Diagnosis.”, Antimicrob Agents Chemother, vol. 60, no. 11, pp. 6600-6608, 2016. ,
“Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants.”, BMC Genomics, vol. 17, no. 1, p. 819, 2016. ,
“Fap2 Mediates Fusobacterium nucleatum Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed Gal-GalNAc.”, Cell Host Microbe, vol. 20, no. 2, pp. 215-25, 2016. ,
“Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors.”, Cell Chem Biol, vol. 23, no. 6, pp. 666-77, 2016. ,
“Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance.”, Nat Genet, vol. 48, no. 5, pp. 544-51, 2016. ,
“Complete genome sequences and analysis of the Fusobacterium nucleatum subspecies animalis 7-1 bacteriophage ɸFunu1 and ɸFunu2.”, Anaerobe, vol. 38, pp. 125-9, 2016. ,
“Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage.”, Genome Announc, vol. 4, no. 2, 2016. ,
“Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization.”, Int J Mycobacteriol, vol. 5, no. 1, pp. 66-73, 2016. ,
“Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction.”, PLoS Negl Trop Dis, vol. 10, no. 1, p. e0004332, 2016. ,
“Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.”, PLoS Med, vol. 12, no. 9, p. e1001880, 2015. ,
“MUCOSAL IMMUNOLOGY. Individual intestinal symbionts induce a distinct population of RORγ⁺ regulatory T cells.”, Science, vol. 349, no. 6251, pp. 993-7, 2015. ,
“Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing.”, Emerg Infect Dis, vol. 21, no. 6, pp. 1082-4, 2015. ,
“Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster.”, Nat Commun, vol. 5, p. 5411, 2014. ,
“Evolution of invasion in a diverse set of Fusobacterium species.”, MBio, vol. 5, no. 6, p. e01864, 2014. ,
“Draft genome sequences of six enterohepatic helicobacter species isolated from humans and one from rhesus macaques.”, Genome Announc, vol. 2, no. 5, 2014. ,
“Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium.”, Int J Syst Evol Microbiol, vol. 64, no. Pt 8, pp. 2642-9, 2014. ,
“Evidence of extensive DNA transfer between bacteroidales species within the human gut.”, MBio, vol. 5, no. 3, pp. e01305-14, 2014. ,
“Relating the metatranscriptome and metagenome of the human gut.”, Proc Natl Acad Sci U S A, vol. 111, no. 22, pp. E2329-38, 2014. ,
“Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.”, PLoS One, vol. 9, no. 11, p. e112963, 2014. ,
“High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides.”, Genome Announc, vol. 1, no. 6, 2013. ,
“Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains.”, MBio, vol. 4, no. 4, 2013. ,
“Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.”, Genome Biol, vol. 13, no. 3, p. R23, 2012. ,
“The "most wanted" taxa from the human microbiome for whole genome sequencing.”, PLoS One, vol. 7, no. 7, p. e41294, 2012. ,
“The success of acinetobacter species; genetic, metabolic and virulence attributes.”, PLoS One, vol. 7, no. 10, p. e46984, 2012. ,
“Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of Staphylococcus aureus.”, PLoS One, vol. 7, no. 1, p. e28316, 2012. ,
“Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus.”, MBio, vol. 3, no. 1, pp. e00318-11, 2012. ,
“High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).”, Stand Genomic Sci, vol. 5, no. 3, pp. 389-97, 2011. ,
“A catalog of reference genomes from the human microbiome.”, Science, vol. 328, no. 5981, pp. 994-9, 2010. ,