Fouts DE

References (20)

Title : AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates - Chan_2020_J.Antimicrob.Chemother_75_2760
Author(s) : Chan AP , Choi Y , Clarke TH , Brinkac LM , White RC , Jacobs MR , Bonomo RA , Adams MD , Fouts DE
Ref : J Antimicrob Chemother , 75 :2760 , 2020
Abstract : OBJECTIVES: To investigate the genomic context of a novel resistance island (RI) in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates and global isolates. METHODS: Using a combination of long and short reads generated from the Oxford Nanopore and Illumina platforms, contiguous chromosomes and plasmid sequences were determined. BLAST-based analysis was used to identify the RI insertion target. RESULTS: Genomes of four multiply antibiotic-resistant A. baumannii clinical strains, from a US hospital system, belonging to prevalent MLST ST2 (Pasteur scheme) and ST281 (Oxford scheme) clade F isolates were sequenced to completion. A class 1 integron carrying aadB (tobramycin resistance) and aadA2 (streptomycin/spectinomycin resistance) was identified. The class 1 integron was 6.8kb, bounded by IS26 at both ends, and embedded in a new target location between an alpha/beta-hydrolase and a reductase. Due to its novel insertion site and unique RI composition, we suggest naming this novel RI AbGRI4. Molecular analysis of global A. baumannii isolates identified multiple AbGRI4 RI variants in non-ST2 clonal lineages, including variations in the resistance gene cassettes, integron backbone and insertion breakpoints at the hydrolase gene. CONCLUSIONS: A novel RI insertion target harbouring a class 1 integron was identified in a subgroup of ST2/ST281 clinical isolates. Variants of the RI suggested evolution and horizontal transfer of the RI across clonal lineages. Long- and short-read hybrid assembly technology completely resolved the genomic context of IS-bounded RIs, which was not possible using short reads alone.
ESTHER : Chan_2020_J.Antimicrob.Chemother_75_2760
PubMedSearch : Chan_2020_J.Antimicrob.Chemother_75_2760
PubMedID: 32681170

Title : Genome Sequences of the Listeria ivanovii subsp. ivanovii Type Strain and Two Listeria ivanovii subsp. londoniensis Strains - Hupfeld_2015_Genome.Announc_3_e01440
Author(s) : Hupfeld M , Fouts DE , Loessner MJ , Klumpp J
Ref : Genome Announc , 3 : , 2015
Abstract : We present the complete genomes of Listeria ivanovii subsp. ivanovii WSLC 3010 (ATCC 19119(T)), Listeria ivanovii subsp. londoniensis WSLC 30151 (SLCC 8854), and Listeria ivanovii subsp. londoniensis WSLC 30167 (SLCC 6032), representing the type strain of the species and two strains of the same serovar but different properties, respectively.
ESTHER : Hupfeld_2015_Genome.Announc_3_e01440
PubMedSearch : Hupfeld_2015_Genome.Announc_3_e01440
PubMedID: 25614561
Gene_locus related to this paper: lismo-LMO2452 , lisip-g2zf96 , lisiv-a0a097bbs7

Title : Genome Sequences of Three Frequently Used Listeria monocytogenes and Listeria ivanovii Strains - Klumpp_2014_Genome.Announc_2_e00404
Author(s) : Klumpp J , Staubli T , Schmitter S , Hupfeld M , Fouts DE , Loessner MJ
Ref : Genome Announc , 2 : , 2014
Abstract : We present the complete de novo assembled genome sequences of Listeria monocytogenes strains WSLC 1001 (ATCC 19112) and WSLC 1042 (ATCC 23074) and Listeria ivanovii WSLC 3009, three strains frequently used for the propagation and study of bacteriophages because they are presumed to be free of inducible prophages.
ESTHER : Klumpp_2014_Genome.Announc_2_e00404
PubMedSearch : Klumpp_2014_Genome.Announc_2_e00404
PubMedID: 24786957
Gene_locus related to this paper: lisiv-e3zgw7

Title : Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity - Ricaldi_2012_PLoS.Negl.Trop.Dis_6_e1853
Author(s) : Ricaldi JN , Fouts DE , Selengut JD , Harkins DM , Patra KP , Moreno A , Lehmann JS , Purushe J , Sanka R , Torres M , Webster NJ , Vinetz JM , Matthias MA
Ref : PLoS Negl Trop Dis , 6 :e1853 , 2012
Abstract : The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T) and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics.
ESTHER : Ricaldi_2012_PLoS.Negl.Trop.Dis_6_e1853
PubMedSearch : Ricaldi_2012_PLoS.Negl.Trop.Dis_6_e1853
PubMedID: 23145189
Gene_locus related to this paper: 9lept-i0xnk5 , 9lept-i0xm07 , 9lept-v6g5z6 , 9lept-i0xpz4 , 9lept-i0xli4

Title : Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence - Chen_2011_BMC.Genomics_12_294
Author(s) : Chen Y , Stine OC , Badger JH , Gil AI , Nair GB , Nishibuchi M , Fouts DE
Ref : BMC Genomics , 12 :294 , 2011
Abstract : BACKGROUND: Vibrio parahaemolyticus is a common cause of foodborne disease. Beginning in 1996, a more virulent strain having serotype O3:K6 caused major outbreaks in India and other parts of the world, resulting in the emergence of a pandemic. Other serovariants of this strain emerged during its dissemination and together with the original O3:K6 were termed strains of the pandemic clone. Two genomes, one of this virulent strain and one pre-pandemic strain have been sequenced. We sequenced four additional genomes of V. parahaemolyticus in this study that were isolated from different geographical regions and time points. Comparative genomic analyses of six strains of V. parahaemolyticus isolated from Asia and Peru were performed in order to advance knowledge concerning the evolution of V. parahaemolyticus; specifically, the genetic changes contributing to serotype conversion and virulence. Two pre-pandemic strains and three pandemic strains, isolated from different geographical regions, were serotype O3:K6 and either toxin profiles (tdh+, trh-) or (tdh-, trh+). The sixth pandemic strain sequenced in this study was serotype O4:K68.
RESULTS: Genomic analyses revealed that the trh+ and tdh+ strains had different types of pathogenicity islands and mobile elements as well as major structural differences between the tdh pathogenicity islands of the pre-pandemic and pandemic strains. In addition, the results of single nucleotide polymorphism (SNP) analysis showed that 94% of the SNPs between O3:K6 and O4:K68 pandemic isolates were within a 141 kb region surrounding the O- and K-antigen-encoding gene clusters. The "core" genes of V. parahaemolyticus were also compared to those of V. cholerae and V. vulnificus, in order to delineate differences between these three pathogenic species. Approximately one-half (49-59%) of each species' core genes were conserved in all three species, and 14-24% of the core genes were species-specific and in different functional categories.
CONCLUSIONS: Our data support the idea that the pandemic strains are closely related and that recent South American outbreaks of foodborne disease caused by V. parahaemolyticus are closely linked to outbreaks in India. Serotype conversion from O3:K6 to O4:K68 was likely due to a recombination event involving a region much larger than the O-antigen- and K-antigen-encoding gene clusters. Major differences between pathogenicity islands and mobile elements are also likely driving the evolution of V. parahaemolyticus. In addition, our analyses categorized genes that may be useful in differentiating pathogenic Vibrios at the species level.
ESTHER : Chen_2011_BMC.Genomics_12_294
PubMedSearch : Chen_2011_BMC.Genomics_12_294
PubMedID: 21645368
Gene_locus related to this paper: vibpa-PHAC , vibpa-VP0148 , vibpa-VP0409 , vibpa-VP0429 , vibpa-VP0693 , vibpa-VP0837 , vibpa-VP0869 , vibpa-VP1025 , vibpa-VP1181 , vibpa-VP1678 , vibpa-VP2790 , vibpa-VP2974 , vibpa-VPA0054 , vibpa-VPA0070 , vibpa-VPA0468 , vibpa-VPA1061 , vibpa-VPA1249 , vibpa-VPA1467 , vibpa-VPA1496 , vibpa-VPA1595 , vibpa-y674 , vibpa-y969

Title : Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937 - Glasner_2011_J.Bacteriol_193_2076
Author(s) : Glasner JD , Yang CH , Reverchon S , Hugouvieux-Cotte-Pattat N , Condemine G , Bohin JP , Van Gijsegem F , Yang S , Franza T , Expert D , Plunkett G, 3rd , San Francisco MJ , Charkowski AO , Py B , Bell K , Rauscher L , Rodriguez-Palenzuela P , Toussaint A , Holeva MC , He SY , Douet V , Boccara M , Blanco C , Toth I , Anderson BD , Biehl BS , Mau B , Flynn SM , Barras F , Lindeberg M , Birch PR , Tsuyumu S , Shi X , Hibbing M , Yap MN , Carpentier M , Dassa E , Umehara M , Kim JF , Rusch M , Soni P , Mayhew GF , Fouts DE , Gill SR , Blattner FR , Keen NT , Perna NT
Ref : Journal of Bacteriology , 193 :2076 , 2011
Abstract : Dickeya dadantii is a plant-pathogenic enterobacterium responsible for the soft rot disease of many plants of economic importance. We present here the sequence of strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria.
ESTHER : Glasner_2011_J.Bacteriol_193_2076
PubMedSearch : Glasner_2011_J.Bacteriol_193_2076
PubMedID: 21217001
Gene_locus related to this paper: dicd3-e0scu7 , dicd3-e0sjp0 , erwch-INDC , dicd3-e0sgk0 , dicze-c6cmc7 , 9entr-u6zcq0 , dicd3-e0sg49

Title : Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche - Purushe_2010_Microb.Ecol_60_721
Author(s) : Purushe J , Fouts DE , Morrison M , White BA , Mackie RI , Coutinho PM , Henrissat B , Nelson KE
Ref : Microb Ecol , 60 :721 , 2010
Abstract : The Prevotellas comprise a diverse group of bacteria that has received surprisingly limited attention at the whole genome-sequencing level. In this communication, we present the comparative analysis of the genomes of Prevotella ruminicola 23 (GenBank: CP002006) and Prevotella bryantii B(1)4 (GenBank: ADWO00000000), two gastrointestinal isolates. Both P. ruminicola and P. bryantii have acquired an extensive repertoire of glycoside hydrolases that are targeted towards non-cellulosic polysaccharides, especially GH43 bifunctional enzymes. Our analysis demonstrates the diversity of this genus. The results from these analyses highlight their role in the gastrointestinal tract, and provide a template for additional work on genetic characterization of these species.
ESTHER : Purushe_2010_Microb.Ecol_60_721
PubMedSearch : Purushe_2010_Microb.Ecol_60_721
PubMedID: 20585943
Gene_locus related to this paper: prebr-d8dt96 , prebr-d8du06 , prebr-d8dv28 , prebr-d8dwg8 , prebr-d8dy06 , prer2-d5esm6 , prebr-d8dul5 , prebr-d8dxa2 , prebr-d8dw03 , prer2-d5erq4 , prer2-d5ewz1 , prebr-d8dv01 , prer2-axea1 , prer2-axfa

Title : Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus - DeBoy_2008_J.Bacteriol_190_5455
Author(s) : DeBoy RT , Mongodin EF , Fouts DE , Tailford LE , Khouri H , Emerson JB , Mohamoud Y , Watkins K , Henrissat B , Gilbert HJ , Nelson KE
Ref : Journal of Bacteriology , 190 :5455 , 2008
Abstract : The plant cell wall, which consists of a highly complex array of interconnecting polysaccharides, is the most abundant source of organic carbon in the biosphere. Microorganisms that degrade the plant cell wall synthesize an extensive portfolio of hydrolytic enzymes that display highly complex molecular architectures. To unravel the intricate repertoire of plant cell wall-degrading enzymes synthesized by the saprophytic soil bacterium Cellvibrio japonicus, we sequenced and analyzed its genome, which predicts that the bacterium contains the complete repertoire of enzymes required to degrade plant cell wall and storage polysaccharides. Approximately one-third of these putative proteins (57) are predicted to contain carbohydrate binding modules derived from 13 of the 49 known families. Sequence analysis reveals approximately 130 predicted glycoside hydrolases that target the major structural and storage plant polysaccharides. In common with that of the colonic prokaryote Bacteroides thetaiotaomicron, the genome of C. japonicus is predicted to encode a large number of GH43 enzymes, suggesting that the extensive arabinose decorations appended to pectins and xylans may represent a major nutrient source, not just for intestinal bacteria but also for microorganisms that occupy terrestrial ecosystems. The results presented here predict that C. japonicus possesses an extensive range of glycoside hydrolases, lyases, and esterases. Most importantly, the genome of C. japonicus is remarkably similar to that of the gram-negative marine bacterium, Saccharophagus degradans 2-40(T). Approximately 50% of the predicted C. japonicus plant-degradative apparatus appears to be shared with S. degradans, consistent with the utilization of plant-derived complex carbohydrates as a major substrate by both organisms.
ESTHER : DeBoy_2008_J.Bacteriol_190_5455
PubMedSearch : DeBoy_2008_J.Bacteriol_190_5455
PubMedID: 18556790
Gene_locus related to this paper: celju-b3pei5 , celju-b3pf25 , celju-b3pfb5 , celju-b3pgh5 , celju-b3pgz5 , celju-b3ph03 , celju-b3pi00 , celju-b3pi89 , celju-b3pj26 , celju-b3pju5 , celju-b3pks4 , celju-b3pks5 , celju-b3plp7 , celju-metx , celju-b3phr4 , celju-b3pjj6 , celju-b3pcj5 , celju-b3pcu6 , celju-b3pei0

Title : Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice - Fouts_2008_PLoS.Genet_4_e1000141
Author(s) : Fouts DE , Tyler HL , DeBoy RT , Daugherty S , Ren Q , Badger JH , Durkin AS , Huot H , Shrivastava S , Kothari S , Dodson RJ , Mohamoud Y , Khouri H , Roesch LF , Krogfelt KA , Struve C , Triplett EW , Methe BA
Ref : PLoS Genet , 4 :e1000141 , 2008
Abstract : We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K. pneumoniae 342 is a member of the enteric bacteria, it serves as a model for studies of endophytic, plant-bacterial associations due to its efficient colonization of plant tissues (including maize and wheat, two of the most important crops in the world), while maintaining a mutualistic relationship that encompasses supplying organic nitrogen to the host plant. Genomic analysis examined K. pneumoniae 342 for the presence of previously identified genes from other bacteria involved in colonization of, or growth in, plants. From this set, approximately one-third were identified in K. pneumoniae 342, suggesting additional factors most likely contribute to its endophytic lifestyle. Comparative genome analyses were used to provide new insights into this question. Results included the identification of metabolic pathways and other features devoted to processing plant-derived cellulosic and aromatic compounds, and a robust complement of transport genes (15.4%), one of the highest percentages in bacterial genomes sequenced. Although virulence and antibiotic resistance genes were predicted, experiments conducted using mouse models showed pathogenicity to be attenuated in this strain. Comparative genomic analyses with the presumed human pathogen K. pneumoniae MGH78578 revealed that MGH78578 apparently cannot fix nitrogen, and the distribution of genes essential to surface attachment, secretion, transport, and regulation and signaling varied between each genome, which may indicate critical divergences between the strains that influence their preferred host ranges and lifestyles (endophytic plant associations for K. pneumoniae 342 and presumably human pathogenesis for MGH78578). Little genome information is available concerning endophytic bacteria. The K. pneumoniae 342 genome will drive new research into this less-understood, but important category of bacterial-plant host relationships, which could ultimately enhance growth and nutrition of important agricultural crops and development of plant-derived products and biofuels.
ESTHER : Fouts_2008_PLoS.Genet_4_e1000141
PubMedSearch : Fouts_2008_PLoS.Genet_4_e1000141
PubMedID: 18654632
Gene_locus related to this paper: klep3-b5xp56 , klep3-b5xqp6 , klep3-b5xzn5 , klep3-b5xzy8 , klep3-bioh , klep3-menh , klep7-a6t8q2 , klep7-a6t9v6 , klep7-a6tb98 , klep7-mhpc , klep7-y243 , klep7-y1077 , klepn-c4x8q1 , klepn-w8uta0 , klep3-rutd

Title : Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1 - Rasko_2007_J.Bacteriol_189_52
Author(s) : Rasko DA , Rosovitz MJ , Okstad OA , Fouts DE , Jiang L , Cer RZ , Kolsto AB , Gill SR , Ravel J
Ref : Journal of Bacteriology , 189 :52 , 2007
Abstract : The plasmids of the members of the Bacillus cereus sensu lato group of organisms are essential in defining the phenotypic traits associated with pathogenesis and ecology. For example, Bacillus anthracis contains two plasmids, pXO1 and pXO2, encoding toxin production and encapsulation, respectively, that define this species pathogenic potential, whereas the presence of a Bt toxin-encoding plasmid defines Bacillus thuringiensis isolates. In this study the plasmids from B. cereus isolates that produce emetic toxin or are linked to periodontal disease were sequenced and analyzed. Two periodontal isolates examined contained almost identical approximately 272-kb plasmids, named pPER272. The emetic toxin-producing isolate contained one approximately 270-kb plasmid, named pCER270, encoding the cereulide biosynthesis gene cluster. Comparative sequence analyses of these B. cereus plasmids revealed a high degree of sequence similarity to the B. anthracis pXO1 plasmid, especially in a putative replication region. These plasmids form a newly defined group of pXO1-like plasmids. However, these novel plasmids do not contain the pXO1 pathogenicity island, which in each instance is replaced by plasmid specific DNA. Plasmids pCER270 and pPER272 share regions that are not found in any other pXO1-like plasmids. Evolutionary studies suggest that these plasmids are more closely related to each other than to other identified B. cereus plasmids. Screening of a population of B. cereus group isolates revealed that pXO1-like plasmids are more often found in association with clinical isolates. This study demonstrates that the pXO1-like plasmids may define pathogenic B. cereus isolates in the same way that pXO1 and pXO2 define the B. anthracis species.
ESTHER : Rasko_2007_J.Bacteriol_189_52
PubMedSearch : Rasko_2007_J.Bacteriol_189_52
PubMedID: 17041058
Gene_locus related to this paper: bacce-c2zyv1 , bacce-q20cj0 , bacce-q20cj2 , bacti-q3elq7

Title : Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain - Gill_2005_J.Bacteriol_187_2426
Author(s) : Gill SR , Fouts DE , Archer GL , Mongodin EF , DeBoy RT , Ravel J , Paulsen IT , Kolonay JF , Brinkac L , Beanan M , Dodson RJ , Daugherty SC , Madupu R , Angiuoli SV , Durkin AS , Haft DH , Vamathevan J , Khouri H , Utterback T , Lee C , Dimitrov G , Jiang L , Qin H , Weidman J , Tran K , Kang K , Hance IR , Nelson KE , Fraser CM
Ref : Journal of Bacteriology , 187 :2426 , 2005
Abstract : Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent of infections often associated with implanted medical devices. We have sequenced the approximately 2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the approximately 2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative analysis of these and other staphylococcal genomes was used to explore the evolution of virulence and resistance between these two species. The S. aureus and S. epidermidis genomes are syntenic throughout their lengths and share a core set of 1,681 open reading frames. Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria appears to have shaped their virulence and resistance profiles. Integrated plasmids in S. epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S. epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic differences are likely the result of single nucleotide polymorphisms, which are most numerous in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis.
ESTHER : Gill_2005_J.Bacteriol_187_2426
PubMedSearch : Gill_2005_J.Bacteriol_187_2426
PubMedID: 15774886
Gene_locus related to this paper: staau-LIP , staau-lipas , staau-MW0741 , staau-MW2456 , staau-q6gfm6 , staau-SA0011 , staau-SA0569 , staau-SA0572 , staau-SA0897 , staau-SA1143 , staau-SA2240 , staau-SA2306 , staau-SA2367 , staau-SA2422 , staau-SAV0321 , staau-SAV0446 , staau-SAV0457 , staau-SAV0655 , staau-SAV1014 , staau-SAV1765 , staau-SAV1793 , staau-SAV2188 , staau-SAV2350 , staau-SAV2484 , staau-SAV2594 , staep-lipas , staep-SE0011 , staep-SE0226 , staep-SE0386 , staep-SE0389 , staep-SE0424 , staep-SE0564 , staep-SE0714 , staep-SE0745 , staep-SE0980 , staep-SE1436 , staep-SE1460 , staep-SE1510 , staep-SE1780 , staep-SE1929 , staep-SERP2035 , staep-SE2050 , staep-SE2095 , staep-SE2213 , staep-SE2328

Title : Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes - Seshadri_2005_Science_307_105
Author(s) : Seshadri R , Adrian L , Fouts DE , Eisen JA , Phillippy AM , Methe BA , Ward NL , Nelson WC , DeBoy RT , Khouri HM , Kolonay JF , Dodson RJ , Daugherty SC , Brinkac LM , Sullivan SA , Madupu R , Nelson KE , Kang KH , Impraim M , Tran K , Robinson JM , Forberger HA , Fraser CM , Zinder SH , Heidelberg JF
Ref : Science , 307 :105 , 2005
Abstract : Dehalococcoides ethenogenes is the only bacterium known to reductively dechlorinate the groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its 1,469,720-base pair chromosome contains large dynamic duplicated regions and integrated elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were adjacent to genes for transcription regulators, and five hydrogenase complexes were identified. These findings, plus a limited repertoire of other metabolic modes, indicate that D. ethenogenes is highly evolved to utilize halogenated organic compounds and H2. Diversification of reductive dehalogenase functions appears to have been mediated by recent genetic exchange and amplification. Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph.
ESTHER : Seshadri_2005_Science_307_105
PubMedSearch : Seshadri_2005_Science_307_105
PubMedID: 15637277
Gene_locus related to this paper: dehm1-q3z6q3 , dehm1-q3z6x9 , dehm1-q3z6z2 , dehm1-q3z8f3 , dehm1-q3za50

Title : Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species - Fouts_2005_PLoS.Biol_3_e15
Author(s) : Fouts DE , Mongodin EF , Mandrell RE , Miller WG , Rasko DA , Ravel J , Brinkac LM , DeBoy RT , Parker CT , Daugherty SC , Dodson RJ , Durkin AS , Madupu R , Sullivan SA , Shetty JU , Ayodeji MA , Shvartsbeyn A , Schatz MC , Badger JH , Fraser CM , Nelson KE
Ref : PLoS Biol , 3 :e15 , 2005
Abstract : Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability in C. upsaliensis than in the other species. Many genes involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are conserved across the species, but variations that appear to be species specific are evident for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic profiles, as well as their resistance profiles to a range of antibiotics. It is evident that the newly identified hypothetical and conserved hypothetical proteins, as well as uncharacterized two-component regulatory systems and membrane proteins, may hold additional significant information on the major differences in virulence among the species, as well as the specificity of the strains for particular hosts.
ESTHER : Fouts_2005_PLoS.Biol_3_e15
PubMedSearch : Fouts_2005_PLoS.Biol_3_e15
PubMedID: 15660156
Gene_locus related to this paper: camje-CJ0796C , camjr-q5ht69 , camjr-q5ht95 , camjr-q5huc7 , camjr-q5hwg6 , camju-a3yll6

Title : The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1 - Rasko_2004_Nucleic.Acids.Res_32_977
Author(s) : Rasko DA , Ravel J , Okstad OA , Helgason E , Cer RZ , Jiang L , Shores KA , Fouts DE , Tourasse NJ , Angiuoli SV , Kolonay J , Nelson WC , Kolsto AB , Fraser CM , Read TD
Ref : Nucleic Acids Research , 32 :977 , 2004
Abstract : We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated that B.cereus ATCC 10987 was more similar to B.anthracis Ames than B.cereus ATCC 14579, while containing a number of unique metabolic capabilities such as urease and xylose utilization and lacking the ability to utilize nitrate and nitrite. Additionally, genetic mechanisms for variation of capsule carbohydrate and flagella surface structures were identified. Bacillus cereus ATCC 10987 contains a single large plasmid (pBc10987), of approximately 208 kb, that is similar in gene content and organization to B.anthracis pXO1 but is lacking the pathogenicity-associated island containing the anthrax lethal and edema toxin complex genes. The chromosomal similarity of B.cereus ATCC 10987 to B.anthracis Ames, as well as the fact that it contains a large pXO1-like plasmid, may make it a possible model for studying B.anthracis plasmid biology and regulatory cross-talk.
ESTHER : Rasko_2004_Nucleic.Acids.Res_32_977
PubMedSearch : Rasko_2004_Nucleic.Acids.Res_32_977
PubMedID: 14960714
Gene_locus related to this paper: bacan-BA1727 , bacan-BA2392 , bacan-BA2687 , bacan-BA3165 , bacan-BA3178 , bacan-BA3343 , bacan-BA4324 , bacan-BA5009 , bacan-BA5110 , bacc1-q72z64 , bacc1-q73a27 , bacc1-q73ab2 , bacc1-q73br9 , bacc1-q73bx8 , bacc1-q73c56 , bacc1-q73c93 , bacc1-q73cm7 , bacc1-q730c7 , bacc1-q731i0 , bacc1-q732y1 , bacc1-q732z3 , bacc1-q734r1 , bacc1-q735c5 , bacc1-q737t7 , bacc1-q738j2 , bacc1-q739p5 , bacce-BC0192 , bacce-BC0968 , bacce-BC1027 , bacce-BC1788 , bacce-BC1954 , bacce-BC2141 , bacce-BC2171 , bacce-BC3642 , bacce-BC4345 , bacce-BC4730 , bacce-BC4862 , bacce-BC4904 , bacce-BC5130 , bacce-BCE3188 , bacce-lipP , bacce-PHAC , bacce-q72yu1 , bacce-q73af5 , bacce-q735f1 , bacce-q736x9 , bacce-q738e6 , baccr-pepx

Title : Whole genome comparisons of serotype 4b and 1\/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species - Nelson_2004_Nucleic.Acids.Res_32_2386
Author(s) : Nelson KE , Fouts DE , Mongodin EF , Ravel J , DeBoy RT , Kolonay JF , Rasko DA , Angiuoli SV , Gill SR , Paulsen IT , Peterson J , White O , Nelson WC , Nierman W , Beanan MJ , Brinkac LM , Daugherty SC , Dodson RJ , Durkin AS , Madupu R , Haft DH , Selengut J , Van Aken S , Khouri H , Fedorova N , Forberger H , Tran B , Kathariou S , Wonderling LD , Uhlich GA , Bayles DO , Luchansky JB , Fraser CM
Ref : Nucleic Acids Research , 32 :2386 , 2004
Abstract : The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69 strain-specific genes were identified in L.monocytogenes strains F2365 (serotype 4b, cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858 (serotype 4b, meat isolate), respectively. Eighty-three genes were restricted to serotype 1/2a and 51 to serotype 4b strains. These strain- and serotype-specific genes probably contribute to observed differences in pathogenicity, and the ability of the organisms to survive and grow in their respective environmental niches. The serotype 1/2a-specific genes include an operon that encodes the rhamnose biosynthetic pathway that is associated with teichoic acid biosynthesis, as well as operons for five glycosyl transferases and an adenine-specific DNA methyltransferase. A total of 8603 and 105 050 high quality single nucleotide polymorphisms (SNPs) were found on the draft genome sequences of strain H7858 and strain F6854, respectively, when compared with strain F2365. Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs.
ESTHER : Nelson_2004_Nucleic.Acids.Res_32_2386
PubMedSearch : Nelson_2004_Nucleic.Acids.Res_32_2386
PubMedID: 15115801
Gene_locus related to this paper: lismc-c1l0d9 , lismf-q71xq4 , lismo-LMO0110 , lismo-LMO0493 , lismo-LMO0580 , lismo-LMO0752 , lismo-LMO0760 , lismo-LMO0857 , lismo-LMO0950 , lismo-LMO0951 , lismo-LMO0977 , lismo-LMO1128 , lismo-LMO1258 , lismo-LMO1674 , lismo-LMO2089 , lismo-LMO2109 , lismo-LMO2433 , lismo-LMO2450 , lismo-LMO2452 , lismo-LMO2453 , lismo-LMO2578 , lismo-LMO2677 , lismo-LMO2755 , lismo-metx

Title : Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes - Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646
Author(s) : Seshadri R , Myers GS , Tettelin H , Eisen JA , Heidelberg JF , Dodson RJ , Davidsen TM , DeBoy RT , Fouts DE , Haft DH , Selengut J , Ren Q , Brinkac LM , Madupu R , Kolonay J , Durkin SA , Daugherty SC , Shetty J , Shvartsbeyn A , Gebregeorgis E , Geer K , Tsegaye G , Malek J , Ayodeji B , Shatsman S , McLeod MP , Smajs D , Howell JK , Pal S , Amin A , Vashisth P , McNeill TZ , Xiang Q , Sodergren E , Baca E , Weinstock GM , Norris SJ , Fraser CM , Paulsen IT
Ref : Proc Natl Acad Sci U S A , 101 :5646 , 2004
Abstract : We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function.
ESTHER : Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646
PubMedSearch : Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646
PubMedID: 15064399
Gene_locus related to this paper: trede-q73j01 , trede-q73kf5 , trede-q73kp3 , trede-q73ks1 , trede-q73nf8 , trede-q73qt5 , trede-q73qv0 , trede-q73ra4 , trede-q73ri8 , trede-Q93EK3 , trede-TDE0521

Title : The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria - Read_2003_Nature_423_81
Author(s) : Read TD , Peterson SN , Tourasse N , Baillie LW , Paulsen IT , Nelson KE , Tettelin H , Fouts DE , Eisen JA , Gill SR , Holtzapple EK , Okstad OA , Helgason E , Rilstone J , Wu M , Kolonay JF , Beanan MJ , Dodson RJ , Brinkac LM , Gwinn M , DeBoy RT , Madpu R , Daugherty SC , Durkin AS , Haft DH , Nelson WC , Peterson JD , Pop M , Khouri HM , Radune D , Benton JL , Mahamoud Y , Jiang L , Hance IR , Weidman JF , Berry KJ , Plaut RD , Wolf AM , Watkins KL , Nierman WC , Hazen A , Cline R , Redmond C , Thwaite JE , White O , Salzberg SL , Thomason B , Friedlander AM , Koehler TM , Hanna PC , Kolsto AB , Fraser CM
Ref : Nature , 423 :81 , 2003
Abstract : Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity--including haemolysins, phospholipases and iron acquisition functions--and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis.
ESTHER : Read_2003_Nature_423_81
PubMedSearch : Read_2003_Nature_423_81
PubMedID: 12721629
Gene_locus related to this paper: bacan-BA0160 , bacan-BA0950 , bacan-BA0954 , bacan-BA1019 , bacan-BA1242 , bacan-BA1727 , bacan-BA1747 , bacan-BA1866 , bacan-BA1914 , bacan-BA2015 , bacan-BA2392 , bacan-BA2417 , bacan-BA2557 , bacan-BA2607 , bacan-BA2687 , bacan-BA2694 , bacan-BA2738 , bacan-BA2865 , bacan-BA3068 , bacan-BA3165 , bacan-BA3178 , bacan-BA3187 , bacan-BA3343 , bacan-BA3372 , bacan-BA3703 , bacan-BA3805 , bacan-BA3863 , bacan-BA3877 , bacan-BA3887 , bacan-BA4324 , bacan-BA4328 , bacan-BA4338 , bacan-BA4577 , bacan-BA4983 , bacan-BA5009 , bacan-BA5110 , bacan-BA5136 , bacan-DHBF , bacan-q81tt2 , bacce-BC0192 , bacce-BC1788 , bacce-BC1954 , bacce-BC2141 , bacce-BC2171 , bacce-BC4730 , bacce-BC4862 , bacce-BC5130 , bacce-PHAC , bacce-q72yu1 , baccr-pepx

Title : Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83 - Nelson_2003_J.Bacteriol_185_5591
Author(s) : Nelson KE , Fleischmann RD , DeBoy RT , Paulsen IT , Fouts DE , Eisen JA , Daugherty SC , Dodson RJ , Durkin AS , Gwinn M , Haft DH , Kolonay JF , Nelson WC , Mason T , Tallon L , Gray J , Granger D , Tettelin H , Dong H , Galvin JL , Duncan MJ , Dewhirst FE , Fraser CM
Ref : Journal of Bacteriology , 185 :5591 , 2003
Abstract : The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium Porphyromonas gingivalis strain W83, a major contributor to periodontal disease, was determined. Whole-genome comparative analysis with other available complete genome sequences confirms the close relationship between the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum and the green-sulfur bacteria. Within the CFB phyla, the genomes most similar to that of P. gingivalis are those of Bacteroides thetaiotaomicron and B. fragilis. Outside of the CFB phyla the most similar genome to P. gingivalis is that of Chlorobium tepidum, supporting the previous phylogenetic studies that indicated that the Chlorobia and CFB phyla are related, albeit distantly. Genome analysis of strain W83 reveals a range of pathways and virulence determinants that relate to the novel biology of this oral pathogen. Among these determinants are at least six putative hemagglutinin-like genes and 36 previously unidentified peptidases. Genome analysis also reveals that P. gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease.
ESTHER : Nelson_2003_J.Bacteriol_185_5591
PubMedSearch : Nelson_2003_J.Bacteriol_185_5591
PubMedID: 12949112
Gene_locus related to this paper: 9gamm-q4a538 , porgi-DPP , porgi-q7mtk3 , porgi-q7mu18 , porgi-q7mub3 , porgi-q7muw6 , porgi-q7mvp4 , porgi-q7mwa7 , porgi-q7mx03

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 and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 - Nelson_2002_Environ.Microbiol_4_799
Author(s) : Nelson KE , Weinel C , Paulsen IT , Dodson RJ , Hilbert H , Martins dos Santos VA , Fouts DE , Gill SR , Pop M , Holmes M , Brinkac L , Beanan M , DeBoy RT , Daugherty S , Kolonay J , Madupu R , Nelson W , White O , Peterson J , Khouri H , Hance I , Chris Lee P , Holtzapple E , Scanlan D , Tran K , Moazzez A , Utterback T , Rizzo M , Lee K , Kosack D , Moestl D , Wedler H , Lauber J , Stjepandic D , Hoheisel J , Straetz M , Heim S , Kiewitz C , Eisen JA , Timmis KN , Dusterhoft A , Tummler B , Fraser CM
Ref : Environ Microbiol , 4 :799 , 2002
Abstract : Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.
ESTHER : Nelson_2002_Environ.Microbiol_4_799
PubMedSearch : Nelson_2002_Environ.Microbiol_4_799
PubMedID: 12534463
Gene_locus related to this paper: psep1-a5wa77 , psep1-a5wax1 , psepk-q88nk6 , psepk-q88qt0 , psepu-acoc , psepu-BIOH , psepu-bpest , psepu-ESTB , psepu-LIP , psepu-METX , psepu-PHAC1 , psepu-PHAC2 , psepu-PHAG , psepu-PHAZ , psepu-PIP , psepu-PP0375 , psepu-PP0498 , psepu-PP0532 , psepu-PP1064 , psepu-PP1184 , psepu-PP1310 , psepu-PP1500 , psepu-PP1617 , psepu-PP1829 , psepu-PP1979 , psepu-PP2083 , psepu-PP2201 , psepu-PP2236 , psepu-PP2567 , psepu-PP2804 , psepu-PP2934 , psepu-PP3195 , psepu-PP3367 , psepu-PP3404 , psepu-PP3645 , psepu-PP3807 , psepu-PP3812 , psepu-PP3943 , psepu-PP4164 , psepu-PP4165 , psepu-PP4178 , psepu-PP4249 , psepu-PP4540 , psepu-PP4551 , psepu-PP4583 , psepu-PP4624 , psepu-PP4634 , psepu-PP4916 , psepu-PP5117 , psepu-PP5161 , psepu-PP5167 , psepu-PPSD , psepu-Q8KQK1 , psepu-q9wwz4