Dougherty BA

References (8)

Title : Genetic organization of transposase regions surrounding blaKPC carbapenemase genes on plasmids from Klebsiella strains isolated in a New York City hospital - Gootz_2009_Antimicrob.Agents.Chemother_53_1998
Author(s) : Gootz TD , Lescoe MK , Dib-Hajj F , Dougherty BA , He W , Della-Latta P , Huard RC
Ref : Antimicrobial Agents & Chemotherapy , 53 :1998 , 2009
Abstract : Carbapenem-resistant Klebsiella strains carrying Klebsiella pneumoniae carbapenemases (KPC) are endemic to New York City and are spreading across the United States and internationally. Recent studies have indicated that the KPC structural gene is located on a 10-kb plasmid-borne element designated Tn4401. Fourteen Klebsiella pneumoniae strains and one Klebsiella oxytoca strain isolated at a New York City hospital in 2005 carrying either bla(KPC-2) or bla(KPC-3) were examined for isoforms of Tn4401. Ten of the Klebsiella strains contained a 100-bp deletion in Tn4401, corresponding to the Tn4401a isoform. The presence of this deletion adjacent to the upstream promoter region of bla(KPC) in Tn4401a resulted in a different -35 promoter sequence of TGGAGA than that of CTGATT present in isoform Tn4401b. Complete sequencing of one plasmid carrying bla(KPC) from each of three nonclonal isolates indicated the presence of genes encoding other types of antibiotic resistance determinants. The 70.6-kb plasmid from K. pneumoniae strain S9 carrying bla(KPC-2) revealed two identical copies of Tn4401b inserted in an inverse fashion, but in this case, one of the elements disrupted a group II self-splicing intron. In K. pneumoniae strain S15, the Tn4401a element carrying bla(KPC-2) was found on both a large 120-kb plasmid and a smaller 24-kb plasmid. Pulsed-field gel electrophoresis results indicate that the isolates studied represent a heterogeneous group composed of unrelated as well as closely related Klebsiella strains. Our results suggest that endemic KPC-positive Klebsiella strains constitute a generally nonclonal population comprised of various alleles of bla(KPC) on several distinct plasmid genetic backgrounds. This study increases our understanding of the genetic composition of the evolving and expanding role of KPC-producing, healthcare-associated, gram-negative pathogens.
ESTHER : Gootz_2009_Antimicrob.Agents.Chemother_53_1998
PubMedSearch : Gootz_2009_Antimicrob.Agents.Chemother_53_1998
PubMedID: 19258268
Gene_locus related to this paper: klepn-b6uyy9

Title : Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis - Paulsen_2003_Science_299_2071
Author(s) : Paulsen IT , Banerjei L , Myers GS , Nelson KE , Seshadri R , Read TD , Fouts DE , Eisen JA , Gill SR , Heidelberg JF , Tettelin H , Dodson RJ , Umayam L , Brinkac L , Beanan M , Daugherty S , DeBoy RT , Durkin S , Kolonay J , Madupu R , Nelson W , Vamathevan J , Tran B , Upton J , Hansen T , Shetty J , Khouri H , Utterback T , Radune D , Ketchum KA , Dougherty BA , Fraser CM
Ref : Science , 299 :2071 , 2003
Abstract : The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.
ESTHER : Paulsen_2003_Science_299_2071
PubMedSearch : Paulsen_2003_Science_299_2071
PubMedID: 12663927
Gene_locus related to this paper: entfa-EF0101 , entfa-EF0274 , entfa-EF0381 , entfa-EF0449 , entfa-EF0667 , entfa-EF0786 , entfa-EF1028 , entfa-EF1236 , entfa-EF1505 , entfa-EF1536 , entfa-EF1670 , entfa-EF2618 , entfa-EF2728 , entfa-EF2792 , entfa-EF2963 , entfa-EF3191

Title : Complete genome sequence of a virulent isolate of Streptococcus pneumoniae - Tettelin_2001_Science_293_498
Author(s) : Tettelin H , Nelson KE , Paulsen IT , Eisen JA , Read TD , Peterson S , Heidelberg J , DeBoy RT , Haft DH , Dodson RJ , Durkin AS , Gwinn M , Kolonay JF , Nelson WC , Peterson JD , Umayam LA , White O , Salzberg SL , Lewis MR , Radune D , Holtzapple E , Khouri H , Wolf AM , Utterback TR , Hansen CL , McDonald LA , Feldblyum TV , Angiuoli S , Dickinson T , Hickey EK , Holt IE , Loftus BJ , Yang F , Smith HO , Venter JC , Dougherty BA , Morrison DA , Hollingshead SK , Fraser CM
Ref : Science , 293 :498 , 2001
Abstract : The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.
ESTHER : Tettelin_2001_Science_293_498
PubMedSearch : Tettelin_2001_Science_293_498
PubMedID: 11463916
Gene_locus related to this paper: strp2-q04l35 , strpj-b8zns7 , strpn-AXE1 , strpn-b2dz20 , strpn-pepx , strpn-SP0614 , strpn-SP0666 , strpn-SP0777 , strpn-SP0902 , strpn-SP1343

Title : Complete genome sequence of Neisseria meningitidis serogroup B strain MC58 - Tettelin_2000_Science_287_1809
Author(s) : Tettelin H , Saunders NJ , Heidelberg J , Jeffries AC , Nelson KE , Eisen JA , Ketchum KA , Hood DW , Peden JF , Dodson RJ , Nelson WC , Gwinn ML , Deboy R , Peterson JD , Hickey EK , Haft DH , Salzberg SL , White O , Fleischmann RD , Dougherty BA , Mason T , Ciecko A , Parksey DS , Blair E , Cittone H , Clark EB , Cotton MD , Utterback TR , Khouri H , Qin H , Vamathevan J , Gill J , Scarlato V , Masignani V , Pizza M , Grandi G , Sun L , Smith HO , Fraser CM , Moxon ER , Rappuoli R , Venter JC
Ref : Science , 287 :1809 , 2000
Abstract : The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.
ESTHER : Tettelin_2000_Science_287_1809
PubMedSearch : Tettelin_2000_Science_287_1809
PubMedID: 10710307
Gene_locus related to this paper: neigo-pip , neima-metx , neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB0868 , neime-NMB1828 , neime-NMB1877

Title : The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus - Klenk_1997_Nature_390_364
Author(s) : Klenk HP , Clayton RA , Tomb JF , White O , Nelson KE , Ketchum KA , Dodson RJ , Gwinn M , Hickey EK , Peterson JD , Richardson DL , Kerlavage AR , Graham DE , Kyrpides NC , Fleischmann RD , Quackenbush J , Lee NH , Sutton GG , Gill S , Kirkness EF , Dougherty BA , McKenney K , Adams MD , Loftus B , Peterson S , Reich CI , McNeil LK , Badger JH , Glodek A , Zhou L , Overbeek R , Gocayne JD , Weidman JF , McDonald L , Utterback T , Cotton MD , Spriggs T , Artiach P , Kaine BP , Sykes SM , Sadow PW , D'Andrea KP , Bowman C , Fujii C , Garland SA , Mason TM , Olsen GJ , Fraser CM , Smith HO , Woese CR , Venter JC
Ref : Nature , 390 :364 , 1997
Abstract : Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction-modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.
ESTHER : Klenk_1997_Nature_390_364
PubMedSearch : Klenk_1997_Nature_390_364
PubMedID: 9389475
Gene_locus related to this paper: arcfu-AF0514 , arcfu-AF0675 , arcfu-AF1134 , arcfu-AF1563 , arcfu-AF1753 , arcfu-AF1763 , arcfu-est1 , arcfu-est2 , arcfu-est3 , arcfu-estea , arcfu-o28594 , arcfu-o29442 , arcfu-pcbd

Title : The complete genome sequence of the gastric pathogen Helicobacter pylori. - Tomb_1997_Nature_388_539
Author(s) : Tomb J-F , White O , Kerlavage AR , Clayton RA , Sutton GG , Fleischmann RD , Ketchum KA , Klenk H-P , Gill S , Dougherty BA , Nelson K , Quackenbush J , Zhou L , Kirkness EF , Peterson S , Loftus B , Richardson D , Dodson R , Khalak HG , Glodek A , McKenney K , FitzGerald LM , Lee N , Adams MD , Hickey EK , Berg DE , Gocayne JD , Utterback TR , Peterson JD , Kelley JM , Cotton MD , Weidman JM , Fujii C , Bowman C , Watthey L , Wallin E , Hayes WS , Borodovsky M , Karp PD , Smith HO , Fraser CM , Venter JC
Ref : Nature , 388 :539 , 1997
Abstract : Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.
ESTHER : Tomb_1997_Nature_388_539
PubMedSearch : Tomb_1997_Nature_388_539
PubMedID: 9252185
Gene_locus related to this paper: helpy-HP0739 , helpy-o25061

Title : The minimal gene complement of Mycoplasma genitalium - Fraser_1995_Science_270_397
Author(s) : Fraser CM , Gocayne JD , White O , Adams MD , Clayton RA , Fleischmann RD , Bult CJ , Kerlavage AR , Sutton G , Kelley JM , Fritchman RD , Weidman JF , Small KV , Sandusky M , Fuhrmann J , Nguyen D , Utterback TR , Saudek DM , Phillips CA , Merrick JM , Tomb JF , Dougherty BA , Bott KF , Hu PC , Lucier TS , Peterson SN , Smith HO , Hutchison CA, 3rd , Venter JC
Ref : Science , 270 :397 , 1995
Abstract : The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the smallest known genome of any free-living organism, has been determined by whole-genome random sequencing and assembly. A total of only 470 predicted coding regions were identified that include genes required for DNA replication, transcription and translation, DNA repair, cellular transport, and energy metabolism. Comparison of this genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.
ESTHER : Fraser_1995_Science_270_397
PubMedSearch : Fraser_1995_Science_270_397
PubMedID: 7569993
Gene_locus related to this paper: mycge-esl1 , mycge-esl2 , mycge-esl3 , mycge-pip

Title : Whole-genome random sequencing and assembly of Haemophilus influenzae Rd - Fleischmann_1995_Science_269_496
Author(s) : Fleischmann RD , Adams MD , White O , Clayton RA , Kirkness EF , Kerlavage AR , Bult CJ , Tomb JF , Dougherty BA , Merrick JM , McKenney K , Sutton G , FitzHugh W , Fields C , Gocayne JD , Scott J , Shirley R , Liu LI , Glodek A , Kelley JM , Weidman JF , Phillips CA , Spriggs T , Hedblom E , Cotton MD , Utterback TR , Hanna MC , Nguyen DT , Saudek DM , Brandon RC , FineLD , Fritchman JL , Fuhrmann JL , Geoghagen NS , Gnehm CL , McDonald LA , Keith V , Small KV , Fraser CM , Smith HO , Venter JC
Ref : Science , 269 :496 , 1995
Abstract : An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.
ESTHER : Fleischmann_1995_Science_269_496
PubMedSearch : Fleischmann_1995_Science_269_496
PubMedID: 7542800
Gene_locus related to this paper: haein-HI0193 , haein-metx , haein-pldb , haein-sfgh , haein-y1552 , haein-yfbb