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Bacterial Genomics Group

Reply to Lee and Howden.
A. L. Manson, Abeel, T. , Galagan, J. , Sundaramurthi, J. Chandrabos, Shanmugam, S. Kumar, Palaniyandi, K. , Narayanan, S. , Swaminathan, S. , and Earl, A. M. , “Reply to Lee and Howden.”, Clin Infect Dis, 2017.
Identification of Highly Specific Diversity-Oriented Synthesis-Derived Inhibitors of Clostridium difficile.
J. R. Duvall, Bedard, L. , Naylor-Olsen, A. M. , Manson, A. L. , Bittker, J. A. , Sun, W. , Fitzgerald, M. E. , He, Z. , Lee, M. D. , Marie, J. - C. , Muncipinto, G. , Rush, D. , Xu, D. , Xu, H. , Zhang, M. , Earl, A. M. , Palmer, M. A. , Foley, M. A. , Vacca, J. P. , and Scherer, C. A. , “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.
H. L. Schreiber, Conover, M. S. , Chou, W. - C. , Hibbing, M. E. , Manson, A. L. , Dodson, K. W. , Hannan, T. J. , Roberts, P. L. , Stapleton, A. E. , Hooton, T. M. , Livny, J. , Earl, A. M. , and Hultgren, S. J. , “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.
A. L. Manson, Cohen, K. A. , Abeel, T. , Desjardins, C. A. , Armstrong, D. T. , Barry, C. E. , Brand, J. , Chapman, S. B. , Cho, S. - N. , Gabrielian, A. , Gomez, J. , Jodals, A. M. , Joloba, M. , Jureen, P. , Lee, J. Seok, Malinga, L. , Maiga, M. , Nordenberg, D. , Noroc, E. , Romancenco, E. , Salazar, A. , Ssengooba, W. , Velayati, A. A. , Winglee, K. , Zalutskaya, A. , Via, L. E. , Cassell, G. H. , Dorman, S. E. , Ellner, J. , Farnia, P. , Galagan, J. E. , Rosenthal, A. , Crudu, V. , Homorodean, D. , Hsueh, P. - R. , Narayanan, S. , Pym, A. S. , Skrahina, A. , Swaminathan, S. , Van der Walt, M. , Alland, D. , Bishai, W. R. , Cohen, T. , Hoffner, S. , Birren, B. W. , and Earl, A. M. , “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.
K. R. Wollenberg, Desjardins, C. A. , Zalutskaya, A. , Slodovnikova, V. , Oler, A. J. , Quiñones, M. , Abeel, T. , Chapman, S. B. , Tartakovsky, M. , Gabrielian, A. , Hoffner, S. , Skrahin, A. , Birren, B. W. , Rosenthal, A. , Skrahina, A. , and Earl, A. M. , “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.
G. C. Cerqueira, Earl, A. M. , Ernst, C. M. , Grad, Y. H. , Dekker, J. P. , Feldgarden, M. , Chapman, S. B. , Reis-Cunha, J. L. , Shea, T. P. , Young, S. , Zeng, Q. , Delaney, M. L. , Kim, D. , Peterson, E. M. , O'Brien, T. F. , Ferraro, M. Jane, Hooper, D. C. , Huang, S. S. , Kirby, J. E. , Onderdonk, A. B. , Birren, B. W. , Hung, D. T. , Cosimi, L. A. , Wortman, J. R. , Murphy, C. I. , and Hanage, W. P. , “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.
D. Zhang, Gomez, J. E. , Chien, J. - Y. , Haseley, N. , Desjardins, C. A. , Earl, A. M. , Hsueh, P. - R. , and Hung, D. T. , “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.
P. Dehoux, Marvaud, J. Christophe, Abouelleil, A. , Earl, A. M. , Lambert, T. , and Dauga, C. , “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.
J. Abed, Emgård, J. E. M. , Zamir, G. , Faroja, M. , Almogy, G. , Grenov, A. , Sol, A. , Naor, R. , Pikarsky, E. , Atlan, K. A. , Mellul, A. , Chaushu, S. , Manson, A. L. , Earl, A. M. , Ou, N. , Brennan, C. A. , Garrett, W. S. , and Bachrach, G. , “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.
S. Schmidt Grant, Wellington, S. , Kawate, T. , Desjardins, C. A. , Silvis, M. R. , Wivagg, C. , Thompson, M. , Gordon, K. , Kazyanskaya, E. , Nietupski, R. , Haseley, N. , Iwase, N. , Earl, A. M. , Fitzgerald, M. , and Hung, D. T. , “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.
C. A. Desjardins, Cohen, K. A. , Munsamy, V. , Abeel, T. , Maharaj, K. , Walker, B. J. , Shea, T. P. , Almeida, D. V. , Manson, A. L. , Salazar, A. , Padayatchi, N. , O'Donnell, M. R. , Mlisana, K. P. , Wortman, J. , Birren, B. W. , Grosset, J. , Earl, A. M. , and Pym, A. S. , “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.
K. Cochrane, McGuire, A. Manson, Priest, M. E. , Abouelleil, A. , Cerqueira, G. C. , Lo, R. , Earl, A. M. , and Allen-Vercoe, E. , “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.
L. A. Malinga, Abeel, T. , Desjardins, C. A. , Dlamini, T. C. , Cassell, G. , Chapman, S. B. , Birren, B. W. , Earl, A. M. , and Van der Walt, M. , “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.
A. Akbar Velayati, Abeel, T. , Shea, T. , Zhavnerko, G. Konstantin, Birren, B. , Cassell, G. H. , Earl, A. M. , Hoffner, S. , and Farnia, P. , “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.
K. Winglee, McGuire, A. Manson, Maiga, M. , Abeel, T. , Shea, T. , Desjardins, C. A. , Diarra, B. , Baya, B. , Sanogo, M. , Diallo, S. , Earl, A. M. , and Bishai, W. R. , “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.
K. A. Cohen, Abeel, T. , McGuire, A. Manson, Desjardins, C. A. , Munsamy, V. , Shea, T. P. , Walker, B. J. , Bantubani, N. , Almeida, D. V. , Alvarado, L. , Chapman, S. B. , Mvelase, N. R. , Duffy, E. Y. , FitzGerald, M. G. , Govender, P. , Gujja, S. , Hamilton, S. , Howarth, C. , Larimer, J. D. , Maharaj, K. , Pearson, M. D. , Priest, M. E. , Zeng, Q. , Padayatchi, N. , Grosset, J. , Young, S. K. , Wortman, J. , Mlisana, K. P. , O'Donnell, M. R. , Birren, B. W. , Bishai, W. R. , Pym, A. S. , and Earl, A. M. , “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.
E. Sefik, Geva-Zatorsky, N. , Oh, S. , Konnikova, L. , Zemmour, D. , McGuire, A. Manson, Burzyn, D. , Ortiz-Lopez, A. , Lobera, M. , Yang, J. , Ghosh, S. , Earl, A. , Snapper, S. B. , Jupp, R. , Kasper, D. , Mathis, D. , and Benoist, C. , “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.
M. O Williams, Abeel, T. , Casali, N. , Cohen, K. , Pym, A. S. , Mungall, S. B. , Desjardins, C. A. , Banerjee, A. , Drobniewski, F. , Earl, A. M. , and Cooke, G. S. , “Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing.”, Emerg Infect Dis, vol. 21, no. 6, pp. 1082-4, 2015.
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae.
M. V. Sizova, Chilaka, A. , Earl, A. M. , Doerfert, S. N. , Muller, P. A. , Torralba, M. , McCorrison, J. M. , A Durkin, S. , Nelson, K. E. , and Epstein, S. S. , “High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae.”, Stand Genomic Sci, vol. 10, p. 37, 2015.
Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster.
M. D. Valentino, McGuire, A. Manson, Rosch, J. W. , Bispo, P. J. M. , Burnham, C. , Sanfilippo, C. M. , Carter, R. A. , Zegans, M. E. , Beall, B. , Earl, A. M. , Tuomanen, E. I. , Morris, T. W. , Haas, W. , and Gilmore, M. S. , “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.
A. Manson McGuire, Cochrane, K. , Griggs, A. D. , Haas, B. J. , Abeel, T. , Zeng, Q. , Nice, J. B. , MacDonald, H. , Birren, B. W. , Berger, B. W. , Allen-Vercoe, E. , and Earl, A. M. , “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.
Z. Shen, Sheh, A. , Young, S. K. , Abouelliel, A. , Ward, D. V. , Earl, A. M. , and Fox, J. G. , “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.
M. V. Sizova, Muller, P. A. , Stancyk, D. , Panikov, N. S. , Mandalakis, M. , Hazen, A. , Hohmann, T. , Doerfert, S. N. , Fowle, W. , Earl, A. M. , Nelson, K. E. , and Epstein, S. S. , “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.
M. J. Coyne, Zitomersky, N. Levy, McGuire, A. Manson, Earl, A. M. , and Comstock, L. E. , “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.
E. A. Franzosa, Morgan, X. C. , Segata, N. , Waldron, L. , Reyes, J. , Earl, A. M. , Giannoukos, G. , Boylan, M. R. , Ciulla, D. , Gevers, D. , Izard, J. , Garrett, W. S. , Chan, A. T. , and Huttenhower, C. , “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.
B. J. Walker, Abeel, T. , Shea, T. , Priest, M. , Abouelliel, A. , Sakthikumar, S. , Cuomo, C. A. , Zeng, Q. , Wortman, J. , Young, S. K. , and Earl, A. M. , “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.
F. Lebreton, Valentino, M. D. , Duncan, L. B. , Zeng, Q. , McGuire, A. Manson, Earl, A. M. , and Gilmore, M. S. , “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.
F. Lebreton, van Schaik, W. , McGuire, A. Manson, Godfrey, P. , Griggs, A. , Mazumdar, V. , Corander, J. , Cheng, L. , Saif, S. , Young, S. , Zeng, Q. , Wortman, J. , Birren, B. , Willems, R. J. L. , Earl, A. M. , and Gilmore, M. S. , “Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains.”, MBio, vol. 4, no. 4, 2013.
The "most wanted" taxa from the human microbiome for whole genome sequencing.
A. A. Fodor, DeSantis, T. Z. , Wylie, K. M. , Badger, J. H. , Ye, Y. , Hepburn, T. , Hu, P. , Sodergren, E. , Liolios, K. , Huot-Creasy, H. , Birren, B. W. , and Earl, A. M. , “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.
A. Y. Peleg, de Breij, A. , Adams, M. D. , Cerqueira, G. M. , Mocali, S. , Galardini, M. , Nibbering, P. H. , Earl, A. M. , Ward, D. V. , Paterson, D. L. , Seifert, H. , and Dijkshoorn, L. , “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.
A. Y. Peleg, Miyakis, S. , Ward, D. V. , Earl, A. M. , Rubio, A. , Cameron, D. R. , Pillai, S. , Moellering, R. C. , and Eliopoulos, G. M. , “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 vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States.
V. N. Kos, Desjardins, C. A. , Griggs, A. , Cerqueira, G. , Van Tonder, A. , Holden, M. T. G. , Godfrey, P. , Palmer, K. L. , Bodi, K. , Mongodin, E. F. , Wortman, J. , Feldgarden, M. , Lawley, T. , Gill, S. R. , Haas, B. J. , Birren, B. , and Gilmore, M. S. , “Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States.”, MBio, vol. 3, no. 3, 2012.
Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus.
K. L. Palmer, Godfrey, P. , Griggs, A. , Kos, V. N. , Zucker, J. , Desjardins, C. , Cerqueira, G. , Gevers, D. , Walker, S. , Wortman, J. , Feldgarden, M. , Haas, B. , Birren, B. , and Gilmore, M. S. , “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.
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.
G. Giannoukos, Ciulla, D. M. , Huang, K. , Haas, B. J. , Izard, J. , Levin, J. Z. , Livny, J. , Earl, A. M. , Gevers, D. , Ward, D. V. , Nusbaum, C. , Birren, B. W. , and Gnirke, A. , “Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.”, Genome Biol, vol. 13, no. 3, p. R23, 2012.
High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).
A. M. Earl, Desjardins, C. A. , FitzGerald, M. G. , Arachchi, H. M. , Zeng, Q. , Mehta, T. , Griggs, A. , Birren, B. W. , Toney, N. C. , Carr, J. , Posey, J. , and W Butler, R. , “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.
K. E. Nelson, Weinstock, G. M. , Highlander, S. K. , Worley, K. C. , Creasy, H. Huot, Wortman, J. Russo, Rusch, D. B. , Mitreva, M. , Sodergren, E. , Chinwalla, A. T. , Feldgarden, M. , Gevers, D. , Haas, B. J. , Madupu, R. , Ward, D. V. , Birren, B. W. , Gibbs, R. A. , Methé, B. , Petrosino, J. F. , Strausberg, R. L. , Sutton, G. G. , White, O. R. , Wilson, R. K. , Durkin, S. , Giglio, M. Gwinn, Gujja, S. , Howarth, C. , Kodira, C. D. , Kyrpides, N. , Mehta, T. , Muzny, D. M. , Pearson, M. , Pepin, K. , Pati, A. , Qin, X. , Yandava, C. , Zeng, Q. , Zhang, L. , Berlin, A. M. , Chen, L. , Hepburn, T. A. , Johnson, J. , McCorrison, J. , Miller, J. , Minx, P. , Nusbaum, C. , Russ, C. , Sykes, S. M. , Tomlinson, C. M. , Young, S. , Warren, W. C. , Badger, J. , Crabtree, J. , Markowitz, V. M. , Orvis, J. , Cree, A. , Ferriera, S. , Fulton, L. L. , Fulton, R. S. , Gillis, M. , Hemphill, L. D. , Joshi, V. , Kovar, C. , Torralba, M. , Wetterstrand, K. A. , Abouellleil, A. , Wollam, A. M. , Buhay, C. J. , Ding, Y. , Dugan, S. , FitzGerald, M. G. , Holder, M. , Hostetler, J. , Clifton, S. W. , Allen-Vercoe, E. , Earl, A. M. , Farmer, C. N. , Liolios, K. , Surette, M. G. , Xu, Q. , Pohl, C. , Wilczek-Boney, K. , and Zhu, D. , “A catalog of reference genomes from the human microbiome.”, Science, vol. 328, no. 5981, pp. 994-9, 2010.