Bentley SD

References (37)

Title : A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic - Holden_2013_Genome.Res_23_653
Author(s) : Holden MT , Hsu LY , Kurt K , Weinert LA , Mather AE , Harris SR , Strommenger B , Layer F , Witte W , de Lencastre H , Skov R , Westh H , Zemlickova H , Coombs G , Kearns AM , Hill RL , Edgeworth J , Gould I , Gant V , Cooke J , Edwards GF , McAdam PR , Templeton KE , McCann A , Zhou Z , Castillo-Ramirez S , Feil EJ , Hudson LO , Enright MC , Balloux F , Aanensen DM , Spratt BG , Fitzgerald JR , Parkhill J , Achtman M , Bentley SD , Nubel U
Ref : Genome Res , 23 :653 , 2013
Abstract : The widespread use of antibiotics in association with high-density clinical care has driven the emergence of drug-resistant bacteria that are adapted to thrive in hospitalized patients. Of particular concern are globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones that cause outbreaks and epidemics associated with health care. The most rapidly spreading and tenacious health-care-associated clone in Europe currently is EMRSA-15, which was first detected in the UK in the early 1990s and subsequently spread throughout Europe and beyond. Using phylogenomic methods to analyze the genome sequences for 193 S. aureus isolates, we were able to show that the current pandemic population of EMRSA-15 descends from a health-care-associated MRSA epidemic that spread throughout England in the 1980s, which had itself previously emerged from a primarily community-associated methicillin-sensitive population. The emergence of fluoroquinolone resistance in this EMRSA-15 subclone in the English Midlands during the mid-1980s appears to have played a key role in triggering pandemic spread, and occurred shortly after the first clinical trials of this drug. Genome-based coalescence analysis estimated that the population of this subclone over the last 20 yr has grown four times faster than its progenitor. Using comparative genomic analysis we identified the molecular genetic basis of 99.8% of the antimicrobial resistance phenotypes of the isolates, highlighting the potential of pathogen genome sequencing as a diagnostic tool. We document the genetic changes associated with adaptation to the hospital environment and with increasing drug resistance over time, and how MRSA evolution likely has been influenced by country-specific drug use regimens.
ESTHER : Holden_2013_Genome.Res_23_653
PubMedSearch : Holden_2013_Genome.Res_23_653
PubMedID: 23299977
Gene_locus related to this paper: staau-SA2240

Title : Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis - Supply_2013_Nat.Genet_45_172
Author(s) : Supply P , Marceau M , Mangenot S , Roche D , Rouanet C , Khanna V , Majlessi L , Criscuolo A , Tap J , Pawlik A , Fiette L , Orgeur M , Fabre M , Parmentier C , Frigui W , Simeone R , Boritsch EC , Debrie AS , Willery E , Walker D , Quail MA , Ma L , Bouchier C , Salvignol G , Sayes F , Cascioferro A , Seemann T , Barbe V , Locht C , Gutierrez MC , Leclerc C , Bentley SD , Stinear TP , Brisse S , Medigue C , Parkhill J , Cruveiller S , Brosch R
Ref : Nat Genet , 45 :172 , 2013
Abstract : Global spread and limited genetic variation are hallmarks of M. tuberculosis, the agent of human tuberculosis. In contrast, Mycobacterium canettii and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology are restricted to East Africa. Here, we sequenced and analyzed the whole genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4-5x coverage), 454/Roche (13-18x coverage) and/or Illumina DNA sequencing (45-105x coverage). We show that STB isolates are highly recombinogenic and evolutionarily early branching, with larger genome sizes, higher rates of genetic variation, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis. Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse infection experiments showed that STB strains are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral STB-like pool of mycobacteria by gain of persistence and virulence mechanisms, and we provide insights into the molecular events involved.
ESTHER : Supply_2013_Nat.Genet_45_172
PubMedSearch : Supply_2013_Nat.Genet_45_172
PubMedID: 23291586
Gene_locus related to this paper: mycmm-b2ht49 , myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-Rv1069c , myctu-RV1215C , myctu-RV1758 , myctu-Rv2045c , myctu-RV3452 , myctu-RV3724 , myctu-Rv3802c

Title : Description and nomenclature of Neisseria meningitidis capsule locus - Harrison_2013_Emerg.Infect.Dis_19_566
Author(s) : Harrison OB , Claus H , Jiang Y , Bennett JS , Bratcher HB , Jolley KA , Corton C , Care R , Poolman JT , Zollinger WD , Frasch CE , Stephens DS , Feavers I , Frosch M , Parkhill J , Vogel U , Quail MA , Bentley SD , Maiden MC
Ref : Emerg Infect Dis , 19 :566 , 2013
Abstract : Pathogenic Neisseria meningitidis isolates contain a polysaccharide capsule that is the main virulence determinant for this bacterium. Thirteen capsular polysaccharides have been described, and nuclear magnetic resonance spectroscopy has enabled determination of the structure of capsular polysaccharides responsible for serogroup specificity. Molecular mechanisms involved in N. meningitidis capsule biosynthesis have also been identified, and genes involved in this process and in cell surface translocation are clustered at a single chromosomal locus termed cps. The use of multiple names for some of the genes involved in capsule synthesis, combined with the need for rapid diagnosis of serogroups commonly associated with invasive meningococcal disease, prompted a requirement for a consistent approach to the nomenclature of capsule genes. In this report, a comprehensive description of all N. meningitidis serogroups is provided, along with a proposed nomenclature, which was presented at the 2012 XVIIIth International Pathogenic Neisseria Conference.
ESTHER : Harrison_2013_Emerg.Infect.Dis_19_566
PubMedSearch : Harrison_2013_Emerg.Infect.Dis_19_566
PubMedID: 23628376
Gene_locus related to this paper: neime-h6t5x5

Title : A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus - Crossman_2013_ISME.J_7_148
Author(s) : Crossman LC , Chen H , Cerdeno-Tarraga AM , Brooks K , Quail MA , Pineiro SA , Hobley L , Sockett RE , Bentley SD , Parkhill J , Williams HN , Stine OC
Ref : Isme J , 7 :148 , 2013
Abstract : Bacteriovorax marinus SJ is a predatory delta-proteobacterium isolated from a marine environment. The genome sequence of this strain provides an interesting contrast to that of the terrestrial predatory bacterium Bdellovibrio bacteriovorus HD100. Based on their predatory lifestyle, Bacteriovorax were originally designated as members of the genus Bdellovibrio but subsequently were re-assigned to a new genus and family based on genetic and phenotypic differences. B. marinus attaches to gram-negative bacteria, penetrates through the cell wall to form a bdelloplast, in which it replicates, as shown using microscopy. Bacteriovorax is distinct, as it shares only 30% of its gene products with its closest sequenced relatives. Remarkably, 34% of predicted genes over 500 nt in length were completely unique with no significant matches in the databases. As expected, Bacteriovorax shares several characteristic loci with the other delta-proteobacteria. A geneset shared between Bacteriovorax and Bdellovibrio that is not conserved among other delta-proteobacteria such as Myxobacteria (which destroy prey bacteria externally via lysis), or the non-predatory Desulfo-bacteria and Geobacter species was identified. These 291 gene orthologues common to both Bacteriovorax and Bdellovibrio may be the key indicators of host-interaction predatory-specific processes required for prey entry. The locus from Bdellovibrio bacteriovorus is implicated in the switch from predatory to prey/host-independent growth. Although the locus is conserved in B. marinus, the sequence has only limited similarity. The results of this study advance understanding of both the similarities and differences between Bdellovibrio and Bacteriovorax and confirm the distant relationship between the two and their separation into different families.
ESTHER : Crossman_2013_ISME.J_7_148
PubMedSearch : Crossman_2013_ISME.J_7_148
PubMedID: 22955231
Gene_locus related to this paper: bacms-e1x4r0 , bacms-e1wxp3

Title : The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex - Bentley_2012_PLoS.Negl.Trop.Dis_6_e1552
Author(s) : Bentley SD , Comas I , Bryant JM , Walker D , Smith NH , Harris SR , Thurston S , Gagneux S , Wood J , Antonio M , Quail MA , Gehre F , Adegbola RA , Parkhill J , de Jong BC
Ref : PLoS Negl Trop Dis , 6 :e1552 , 2012
Abstract : BACKGROUND: M. africanum West African 2 constitutes an ancient lineage of the M. tuberculosis complex that commonly causes human tuberculosis in West Africa and has an attenuated phenotype relative to M. tuberculosis. METHODOLOGY/PRINCIPAL FINDINGS: In search of candidate genes underlying these differences, the genome of M. africanum West African 2 was sequenced using classical capillary sequencing techniques. Our findings reveal a unique sequence, RD900, that was independently lost during the evolution of two important lineages within the complex: the "modern" M. tuberculosis group and the lineage leading to M. bovis. Closely related to M. bovis and other animal strains within the M. tuberculosis complex, M. africanum West African 2 shares an abundance of pseudogenes with M. bovis but also with M. africanum West African clade 1. Comparison with other strains of the M. tuberculosis complex revealed pseudogenes events in all the known lineages pointing toward ongoing genome erosion likely due to increased genetic drift and relaxed selection linked to serial transmission-bottlenecks and an intracellular lifestyle. CONCLUSIONS/SIGNIFICANCE: The genomic differences identified between M. africanum West African 2 and the other strains of the Mycobacterium tuberculosis complex may explain its attenuated phenotype, and pave the way for targeted experiments to elucidate the phenotypic characteristic of M. africanum. Moreover, availability of the whole genome data allows for verification of conservation of targets used for the next generation of diagnostics and vaccines, in order to ensure similar efficacy in West Africa.
ESTHER : Bentley_2012_PLoS.Negl.Trop.Dis_6_e1552
PubMedSearch : Bentley_2012_PLoS.Negl.Trop.Dis_6_e1552
PubMedID: 22389744
Gene_locus related to this paper: myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-Rv1069c , myctu-RV1215C , myctu-RV1758 , myctu-RV3452 , myctu-RV3724 , myctu-Rv3802c

Title : Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens - Park_2012_BMC.Genomics_13_545
Author(s) : Park J , Zhang Y , Buboltz AM , Zhang X , Schuster SC , Ahuja U , Liu M , Miller JF , Sebaihia M , Bentley SD , Parkhill J , Harvill ET
Ref : BMC Genomics , 13 :545 , 2012
Abstract : BACKGROUND: The classical Bordetella subspecies are phylogenetically closely related, yet differ in some of the most interesting and important characteristics of pathogens, such as host range, virulence and persistence. The compelling picture from previous comparisons of the three sequenced genomes was of genome degradation, with substantial loss of genome content (up to 24%) associated with adaptation to humans.
RESULTS: For a more comprehensive picture of lineage evolution, we employed comparative genomic and phylogenomic analyses using seven additional diverse, newly sequenced Bordetella isolates. Genome-wide single nucleotide polymorphism (SNP) analysis supports a reevaluation of the phylogenetic relationships between the classical Bordetella subspecies, and suggests a closer link between ovine and human B. parapertussis lineages than has been previously proposed. Comparative analyses of genome content revealed that only 50% of the pan-genome is conserved in all strains, reflecting substantial diversity of genome content in these closely related pathogens that may relate to their different host ranges, virulence and persistence characteristics. Strikingly, these analyses suggest possible horizontal gene transfer (HGT) events in multiple loci encoding virulence factors, including O-antigen and pertussis toxin (Ptx). Segments of the pertussis toxin locus (ptx) and its secretion system locus (ptl) appear to have been acquired by the classical Bordetella subspecies and are divergent in different lineages, suggesting functional divergence in the classical Bordetellae.
CONCLUSIONS: Together, these observations, especially in key virulence factors, reveal that multiple mechanisms, such as point mutations, gain or loss of genes, as well as HGTs, contribute to the substantial phenotypic diversity of these versatile subspecies in various hosts.
ESTHER : Park_2012_BMC.Genomics_13_545
PubMedSearch : Park_2012_BMC.Genomics_13_545
PubMedID: 23051057
Gene_locus related to this paper: borbr-BB0273

Title : Lineage-specific virulence determinants of Haemophilus influenzae biogroup aegyptius - Strouts_2012_Emerg.Infect.Dis_18_449
Author(s) : Strouts FR , Power P , Croucher NJ , Corton N , Van Tonder A , Quail MA , Langford PR , Hudson MJ , Parkhill J , Kroll JS , Bentley SD
Ref : Emerg Infect Dis , 18 :449 , 2012
Abstract : An emergent clone of Haemophilus influenzae biogroup aegyptius (Hae) is responsible for outbreaks of Brazilian purpuric fever (BPF). First recorded in Brazil in 1984, the so-called BPF clone of Hae caused a fulminant disease that started with conjunctivitis but developed into septicemic shock; mortality rates were as high as 70%. To identify virulence determinants, we conducted a pan-genomic analysis. Sequencing of the genomes of the BPF clone strain F3031 and a noninvasive conjunctivitis strain, F3047, and comparison of these sequences with 5 other complete H. influenzae genomes showed that >77% of the F3031 genome is shared among all H. influenzae strains. Delineation of the Hae accessory genome enabled characterization of 163 predicted protein-coding genes; identified differences in established autotransporter adhesins; and revealed a suite of novel adhesins unique to Hae, including novel trimeric autotransporter adhesins and 4 new fimbrial operons. These novel adhesins might play a critical role in host-pathogen interactions.
ESTHER : Strouts_2012_Emerg.Infect.Dis_18_449
PubMedSearch : Strouts_2012_Emerg.Infect.Dis_18_449
PubMedID: 22377449
Gene_locus related to this paper: haein-pldb , neime-ESD

Title : Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study - Garcia-Alvarez_2011_Lancet.Infect.Dis_11_595
Author(s) : Garcia-Alvarez L , Holden MT , Lindsay H , Webb CR , Brown DF , Curran MD , Walpole E , Brooks K , Pickard DJ , Teale C , Parkhill J , Bentley SD , Edwards GF , Girvan EK , Kearns AM , Pichon B , Hill RL , Larsen AR , Skov RL , Peacock SJ , Maskell DJ , Holmes MA
Ref : Lancet Infect Dis , 11 :595 , 2011
Abstract : BACKGROUND: Animals can act as a reservoir and source for the emergence of novel meticillin-resistant Staphylococcus aureus (MRSA) clones in human beings. Here, we report the discovery of a strain of S aureus (LGA251) isolated from bulk milk that was phenotypically resistant to meticillin but tested negative for the mecA gene and a preliminary investigation of the extent to which such strains are present in bovine and human populations.
METHODS: Isolates of bovine MRSA were obtained from the Veterinary Laboratories Agency in the UK, and isolates of human MRSA were obtained from diagnostic or reference laboratories (two in the UK and one in Denmark). From these collections, we searched for mecA PCR-negative bovine and human S aureus isolates showing phenotypic meticillin resistance. We used whole-genome sequencing to establish the genetic basis for the observed antibiotic resistance. FINDINGS: A divergent mecA homologue (mecA(LGA251)) was discovered in the LGA251 genome located in a novel staphylococcal cassette chromosome mec element, designated type-XI SCCmec. The mecA(LGA251) was 70% identical to S aureus mecA homologues and was initially detected in 15 S aureus isolates from dairy cattle in England. These isolates were from three different multilocus sequence type lineages (CC130, CC705, and ST425); spa type t843 (associated with CC130) was identified in 60% of bovine isolates. When human mecA-negative MRSA isolates were tested, the mecA(LGA251) homologue was identified in 12 of 16 isolates from Scotland, 15 of 26 from England, and 24 of 32 from Denmark. As in cows, t843 was the most common spa type detected in human beings. INTERPRETATION: Although routine culture and antimicrobial susceptibility testing will identify S aureus isolates with this novel mecA homologue as meticillin resistant, present confirmatory methods will not identify them as MRSA. New diagnostic guidelines for the detection of MRSA should consider the inclusion of tests for mecA(LGA251). FUNDING: Department for Environment, Food and Rural Affairs, Higher Education Funding Council for England, Isaac Newton Trust (University of Cambridge), and the Wellcome Trust.
ESTHER : Garcia-Alvarez_2011_Lancet.Infect.Dis_11_595
PubMedSearch : Garcia-Alvarez_2011_Lancet.Infect.Dis_11_595
PubMedID: 21641281
Gene_locus related to this paper: staau-SA0897 , staau-SA2240

Title : Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors - Heilbronner_2011_FEMS.Microbiol.Lett_322_60
Author(s) : Heilbronner S , Holden MT , Van Tonder A , Geoghegan JA , Foster TJ , Parkhill J , Bentley SD
Ref : FEMS Microbiology Letters , 322 :60 , 2011
Abstract : Staphylococcus lugdunensis is an opportunistic pathogen related to Staphylococcus aureus and Staphylococcus epidermidis. The genome sequence of S. lugdunensis strain N920143 has been compared with other staphylococci, and genes were identified that could promote survival of S. lugdunensis on human skin and pathogenesis of infections. Staphylococcus lugdunensis lacks virulence factors that characterize S. aureus and harbours a smaller number of genes encoding surface proteins. It is the only staphylococcal species other than S. aureus that possesses a locus encoding iron-regulated surface determinant (Isd) proteins involved in iron acquisition from haemoglobin.
ESTHER : Heilbronner_2011_FEMS.Microbiol.Lett_322_60
PubMedSearch : Heilbronner_2011_FEMS.Microbiol.Lett_322_60
PubMedID: 21682763
Gene_locus related to this paper: stalh-d3qdw5 , stalh-d3qhh5 , stalu-q0kkp0

Title : A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin - Holt_2011_Genome.Biol.Evol_3_881
Author(s) : Holt DC , Holden MT , Tong SY , Castillo-Ramirez S , Clarke L , Quail MA , Currie BJ , Parkhill J , Bentley SD , Feil EJ , Giffard PM
Ref : Genome Biol Evol , 3 :881 , 2011
Abstract : Here we discuss the evolution of the northern Australian Staphylococcus aureus isolate MSHR1132 genome. MSHR1132 belongs to the divergent clonal complex 75 lineage. The average nucleotide divergence between orthologous genes in MSHR1132 and typical S. aureus is approximately sevenfold greater than the maximum divergence observed in this species to date. MSHR1132 has a small accessory genome, which includes the well-characterized genomic islands, nuSAalpha and nuSabeta, suggesting that these elements were acquired well before the expansion of the typical S. aureus population. Other mobile elements show mosaic structure (the prophage varphiSa3) or evidence of recent acquisition from a typical S. aureus lineage (SCCmec, ICE6013 and plasmid pMSHR1132). There are two differences in gene repertoire compared with typical S. aureus that may be significant clues as to the genetic basis underlying the successful emergence of S. aureus as a pathogen. First, MSHR1132 lacks the genes for production of staphyloxanthin, the carotenoid pigment that confers upon S. aureus its characteristic golden color and protects against oxidative stress. The lack of pigment was demonstrated in 126 of 126 CC75 isolates. Second, a mobile clustered regularly interspaced short palindromic repeat (CRISPR) element is inserted into orfX of MSHR1132. Although common in other staphylococcal species, these elements are very rare within S. aureus and may impact accessory genome acquisition. The CRISPR spacer sequences reveal a history of attempted invasion by known S. aureus mobile elements. There is a case for the creation of a new taxon to accommodate this and related isolates.
ESTHER : Holt_2011_Genome.Biol.Evol_3_881
PubMedSearch : Holt_2011_Genome.Biol.Evol_3_881
PubMedID: 21813488
Gene_locus related to this paper: staau-SA0897 , staau-SA2240

Title : Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946 - Sebaihia_2010_J.Bacteriol_192_2020
Author(s) : Sebaihia M , Bocsanczy AM , Biehl BS , Quail MA , Perna NT , Glasner JD , DeClerck GA , Cartinhour S , Schneider DJ , Bentley SD , Parkhill J , Beer SV
Ref : Journal of Bacteriology , 192 :2020 , 2010
Abstract : Erwinia amylovora causes the economically important disease fire blight that affects rosaceous plants, especially pear and apple. Here we report the complete genome sequence and annotation of strain ATCC 49946. The analysis of the sequence and its comparison with sequenced genomes of closely related enterobacteria revealed signs of pathoadaptation to rosaceous hosts.
ESTHER : Sebaihia_2010_J.Bacteriol_192_2020
PubMedSearch : Sebaihia_2010_J.Bacteriol_192_2020
PubMedID: 20118253
Gene_locus related to this paper: erwac-d4hwt0 , erwac-d4hxs4 , erwac-d4i2q5 , erwac-d4i3s4 , erwac-d4i259 , erwae-d4idw0 , erwpe-d0fwy1 , erwse-e3dex4

Title : Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species - Donati_2010_Genome.Biol_11_R107
Author(s) : Donati C , Hiller NL , Tettelin H , Muzzi A , Croucher NJ , Angiuoli SV , Oggioni M , Dunning Hotopp JC , Hu FZ , Riley DR , Covacci A , Mitchell TJ , Bentley SD , Kilian M , Ehrlich GD , Rappuoli R , Moxon ER , Masignani V
Ref : Genome Biol , 11 :R107 , 2010
Abstract : BACKGROUND: Streptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptococci of the Mitis group.
RESULTS: Despite evidence of extensive recombination, the S. pneumoniae phylogenetic tree revealed six major lineages. With the exception of serotype 1, the tree correlated poorly with capsular serotype, geographical site of isolation and disease outcome. The distribution of dispensable genes--genes present in more than one strain but not in all strains--was consistent with phylogeny, although horizontal gene transfer events attenuated this correlation in the case of ancient lineages. Homologous recombination, involving short stretches of DNA, was the dominant evolutionary process of the core genome of S. pneumoniae. Genetic exchange occurred both within and across the borders of the species, and S. mitis was the main reservoir of genetic diversity of S. pneumoniae. The pan-genome size of S. pneumoniae increased logarithmically with the number of strains and linearly with the number of polymorphic sites of the sampled genomes, suggesting that acquired genes accumulate proportionately to the age of clones. Most genes associated with pathogenicity were shared by all S. pneumoniae strains, but were also present in S. mitis, S. oralis and S. infantis, indicating that these genes are not sufficient to determine virulence.
CONCLUSIONS: Genetic exchange with related species sharing the same ecological niche is the main mechanism of evolution of S. pneumoniae. The open pan-genome guarantees the species a quick and economical response to diverse environments.
ESTHER : Donati_2010_Genome.Biol_11_R107
PubMedSearch : Donati_2010_Genome.Biol_11_R107
PubMedID: 21034474

Title : The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions - Letek_2010_PLoS.Genet_6_e1001145
Author(s) : Letek M , Gonzalez P , Macarthur I , Rodriguez H , Freeman TC , Valero-Rello A , Blanco M , Buckley T , Cherevach I , Fahey R , Hapeshi A , Holdstock J , Leadon D , Navas J , Ocampo A , Quail MA , Sanders M , Scortti MM , Prescott JF , Fogarty U , Meijer WG , Parkhill J , Bentley SD , Vazquez-Boland JA
Ref : PLoS Genet , 6 :e1001145 , 2010
Abstract : We report the genome of the facultative intracellular parasite Rhodococcus equi, the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci. This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S genome lacks the extensive catabolic and secondary metabolic complement of environmental rhodococci, and it displays unique adaptations for host colonization and competition in the short-chain fatty acid-rich intestine and manure of herbivores--two main R. equi reservoirs. Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for intramacrophage survival, most of the potential virulence-associated genes identified in R. equi are conserved in environmental rhodococci or have homologs in nonpathogenic Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of existing core actinobacterial traits, triggered by key host niche-adaptive HGT events. We tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by global transcription profiling and expression network analysis. Two chromosomal genes conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory integration of chromosomal metabolic genes under the control of the HGT-acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi.
ESTHER : Letek_2010_PLoS.Genet_6_e1001145
PubMedSearch : Letek_2010_PLoS.Genet_6_e1001145
PubMedID: 20941392
Gene_locus related to this paper: coreq-e9sxw6 , coreq-e9t5k8 , coreq-e9t5k9 , coreq-e9t7v9 , rhoha-e9t397 , rhoe1-e4w8b9 , rhoe1-e4w8k3 , rhoe1-e4w8s0 , rhoe1-e4w9r2 , rhoe1-e4wah6 , rhoe1-e4wb26 , rhoe1-e4wb75 , rhoe1-e4wdz9 , rhoe1-e4wg39 , rhoe1-e4wg83 , rhoe1-e4whm4 , rhoe1-e4wih4 , rhoe1-e4wja5 , rhoe1-e4wjd9 , rhoe1-e4wjy2 , rhoe1-e4wat8 , coreq-e9t814 , rhoe1-e4wbp9 , coreq-e9t0s6 , coreq-e9swc5 , rhoe1-e4wix8 , rhoe1-e4wjy1

Title : Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen - O'Toole_2010_BMC.Genomics_11_164
Author(s) : O'Toole PW , Snelling WJ , Canchaya C , Forde BM , Hardie KR , Josenhans C , Graham R , McMullan G , Parkhill J , Belda E , Bentley SD
Ref : BMC Genomics , 11 :164 , 2010
Abstract : BACKGROUND: Helicobacter mustelae causes gastritis, ulcers and gastric cancer in ferrets and other mustelids. H. mustelae remains the only helicobacter other than H. pylori that causes gastric ulceration and cancer in its natural host. To improve understanding of H. mustelae pathogenesis, and the ulcerogenic and carcinogenic potential of helicobacters in general, we sequenced the H. mustelae genome, and identified 425 expressed proteins in the envelope and cytosolic proteome. RESULTS: The H. mustelae genome lacks orthologs of major H. pylori virulence factors including CagA, VacA, BabA, SabA and OipA. However, it encodes ten autotransporter surface proteins, seven of which were detected in the expressed proteome, and which, except for the Hsr protein, are of unknown function. There are 26 putative outer membrane proteins in H. mustelae, some of which are most similar to the Hof proteins of H. pylori. Although homologs of putative virulence determinants of H. pylori (NapA, plasminogen adhesin, collagenase) and Campylobacter jejuni (CiaB, Peb4a) are present in the H. mustelae genome, it also includes a distinct complement of virulence-related genes including a haemagglutinin/haemolysin protein, and a glycosyl transferase for producing blood group A/B on its lipopolysaccharide. The most highly expressed 264 proteins in the cytosolic proteome included many corresponding proteins from H. pylori, but the rank profile in H. mustelae was distinctive. Of 27 genes shown to be essential for H. pylori colonization of the gerbil, all but three had orthologs in H. mustelae, identifying a shared set of core proteins for gastric persistence. CONCLUSIONS: The determination of the genome sequence and expressed proteome of the ulcerogenic species H mustelae provides a comparative model for H. pylori to investigate bacterial gastric carcinogenesis in mammals, and to suggest ways whereby cag minus H. pylori strains might cause ulceration and cancer. The genome sequence was deposited in EMBL/GenBank/DDBJ under accession number FN555004.
ESTHER : O'Toole_2010_BMC.Genomics_11_164
PubMedSearch : O'Toole_2010_BMC.Genomics_11_164
PubMedID: 20219135
Gene_locus related to this paper: helm1-d3uha6 , helm1-d3uix4

Title : Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06 - Bennett_2010_BMC.Genomics_11_652
Author(s) : Bennett JS , Bentley SD , Vernikos GS , Quail MA , Cherevach I , White B , Parkhill J , Maiden MC
Ref : BMC Genomics , 11 :652 , 2010
Abstract : BACKGROUND: The genus Neisseria contains two important yet very different pathogens, N. meningitidis and N. gonorrhoeae, in addition to non-pathogenic species, of which N. lactamica is the best characterized. Genomic comparisons of these three bacteria will provide insights into the mechanisms and evolution of pathogenesis in this group of organisms, which are applicable to understanding these processes more generally.
RESULTS: Non-pathogenic N. lactamica exhibits very similar population structure and levels of diversity to the meningococcus, whilst gonococci are essentially recent descendents of a single clone. All three species share a common core gene set estimated to comprise around 1190 CDSs, corresponding to about 60% of the genome. However, some of the nucleotide sequence diversity within this core genome is particular to each group, indicating that cross-species recombination is rare in this shared core gene set. Other than the meningococcal cps region, which encodes the polysaccharide capsule, relatively few members of the large accessory gene pool are exclusive to one species group, and cross-species recombination within this accessory genome is frequent. CONCLUSION: The three Neisseria species groups represent coherent biological and genetic groupings which appear to be maintained by low rates of inter-species horizontal genetic exchange within the core genome. There is extensive evidence for exchange among positively selected genes and the accessory genome and some evidence of hitch-hiking of housekeeping genes with other loci. It is not possible to define a 'pathogenome' for this group of organisms and the disease causing phenotypes are therefore likely to be complex, polygenic, and different among the various disease-associated phenotypes observed.
ESTHER : Bennett_2010_BMC.Genomics_11_652
PubMedSearch : Bennett_2010_BMC.Genomics_11_652
PubMedID: 21092259
Gene_locus related to this paper: neigo-pip , neil0-e4zan3 , neima-metx , neime-NMB0276 , neime-NMB1877

Title : Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW) - Holden_2010_J.Bacteriol_192_888
Author(s) : Holden MT , Lindsay JA , Corton C , Quail MA , Cockfield JD , Pathak S , Batra R , Parkhill J , Bentley SD , Edgeworth JD
Ref : Journal of Bacteriology , 192 :888 , 2010
Abstract : The 3.1-Mb genome of an outbreak methicillin-resistant Staphylococcus aureus (MRSA) strain (TW20) contains evidence of recently acquired DNA, including two large regions (635 kb and 127 kb). The strain is resistant to a wide range of antibiotics, antiseptics, and heavy metals due to resistance genes encoded on mobile genetic elements and also mutations in housekeeping genes.
ESTHER : Holden_2010_J.Bacteriol_192_888
PubMedSearch : Holden_2010_J.Bacteriol_192_888
PubMedID: 19948800
Gene_locus related to this paper: staau-LIP , staau-MW0741 , staau-MW2456 , staau-q6gfm6 , staau-SA0569 , staau-SA0572 , staau-SA0897 , staau-SA1143 , staau-SA2240 , staau-SA2306 , staau-SA2422 , staau-SAV0321 , staau-SAV0446 , staau-SAV0457 , staau-SAV0655 , staau-SAV1014 , staau-SAV1765 , staau-SAV1793 , staau-SAV2188 , staau-SAV2350 , staau-SAV2594

Title : Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis - Ward_2009_BMC.Genomics_10_54
Author(s) : Ward PN , Holden MT , Leigh JA , Lennard N , Bignell A , Barron A , Clark L , Quail MA , Woodward J , Barrell BG , Egan SA , Field TR , Maskell D , Kehoe M , Dowson CG , Chanter N , Whatmore AM , Bentley SD , Parkhill J
Ref : BMC Genomics , 10 :54 , 2009
Abstract : BACKGROUND: Streptococcus uberis, a Gram positive bacterial pathogen responsible for a significant proportion of bovine mastitis in commercial dairy herds, colonises multiple body sites of the cow including the gut, genital tract and mammary gland. Comparative analysis of the complete genome sequence of S. uberis strain 0140J was undertaken to help elucidate the biology of this effective bovine pathogen. RESULTS: The genome revealed 1,825 predicted coding sequences (CDSs) of which 62 were identified as pseudogenes or gene fragments. Comparisons with related pyogenic streptococci identified a conserved core (40%) of orthologous CDSs. Intriguingly, S. uberis 0140J displayed a lower number of mobile genetic elements when compared with other pyogenic streptococci, however bacteriophage-derived islands and a putative genomic island were identified. Comparative genomics analysis revealed most similarity to the genomes of Streptococcus agalactiae and Streptococcus equi subsp. zooepidemicus. In contrast, streptococcal orthologs were not identified for 11% of the CDSs, indicating either unique retention of ancestral sequence, or acquisition of sequence from alternative sources. Functions including transport, catabolism, regulation and CDSs encoding cell envelope proteins were over-represented in this unique gene set; a limited array of putative virulence CDSs were identified. CONCLUSION: S. uberis utilises nutritional flexibility derived from a diversity of metabolic options to successfully occupy a discrete ecological niche. The features observed in S. uberis are strongly suggestive of an opportunistic pathogen adapted to challenging and changing environmental parameters.
ESTHER : Ward_2009_BMC.Genomics_10_54
PubMedSearch : Ward_2009_BMC.Genomics_10_54
PubMedID: 19175920
Gene_locus related to this paper: stru0-b9drp1 , stru0-b9dsd7 , stru0-b9dum0 , stru0-b9dvu1 , stru0-pepx

Title : The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients - Holden_2009_J.Bacteriol_191_261
Author(s) : Holden MT , Seth-Smith HM , Crossman LC , Sebaihia M , Bentley SD , Cerdeno-Tarraga AM , Thomson NR , Bason N , Quail MA , Sharp S , Cherevach I , Churcher C , Goodhead I , Hauser H , Holroyd N , Mungall K , Scott P , Walker D , White B , Rose H , Iversen P , Mil-Homens D , Rocha EP , Fialho AM , Baldwin A , Dowson C , Barrell BG , Govan JR , Vandamme P , Hart CA , Mahenthiralingam E , Parkhill J
Ref : Journal of Bacteriology , 191 :261 , 2009
Abstract : Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications in the treatment of this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since this organism has high levels of antibiotic resistance, making it difficult to eradicate; the resulting chronic infections are associated with severe declines in lung function and increased mortality rates. B. cenocepacia strain J2315 was isolated from a CF patient and is a member of the epidemic ET12 lineage that originated in Canada or the United Kingdom and spread to Europe. The 8.06-Mb genome of this highly transmissible pathogen comprises three circular chromosomes and a plasmid and encodes a broad array of functions typical of this metabolically versatile genus, as well as numerous virulence and drug resistance functions. Although B. cenocepacia strains can be isolated from soil and can be pathogenic to both plants and man, J2315 is representative of a lineage of B. cenocepacia rarely isolated from the environment and which spreads between CF patients. Comparative analysis revealed that ca. 21% of the genome is unique in comparison to other strains of B. cenocepacia, highlighting the genomic plasticity of this species. Pseudogenes in virulence determinants suggest that the pathogenic response of J2315 may have been recently selected to promote persistence in the CF lung. The J2315 genome contains evidence that its unique and highly adapted genetic content has played a significant role in its success as an epidemic CF pathogen.
ESTHER : Holden_2009_J.Bacteriol_191_261
PubMedSearch : Holden_2009_J.Bacteriol_191_261
PubMedID: 18931103
Gene_locus related to this paper: burcj-b4e794 , 9burk-a0u8m3 , burcj-b4ek59 , burcj-b4ehl7 , burca-q1bk56 , burce-a0a088tsj6 , burcj-b4ecv6

Title : Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81 - Croucher_2009_J.Bacteriol_191_1480
Author(s) : Croucher NJ , Walker D , Romero P , Lennard N , Paterson GK , Bason NC , Mitchell AM , Quail MA , Andrew PW , Parkhill J , Bentley SD , Mitchell TJ
Ref : Journal of Bacteriology , 191 :1480 , 2009
Abstract : Streptococcus pneumoniae is a human commensal and pathogen able to cause a variety of diseases that annually result in over a million deaths worldwide. The S. pneumoniae(Spain23F) sequence type 81 lineage was among the first recognized pandemic clones and was responsible for almost 40% of penicillin-resistant pneumococcal infections in the United States in the late 1990s. Analysis of the chromosome sequence of a representative strain, and comparison with other available genomes, indicates roles for integrative and conjugative elements in the evolution of pneumococci and, more particularly, the emergence of the multidrug-resistant Spain 23F ST81 lineage. A number of recently acquired loci within the chromosome appear to encode proteins involved in the production of, or immunity to, antimicrobial compounds, which may contribute to the proficiency of this strain at nasopharyngeal colonization. However, further sequencing of other pandemic clones will be required to establish whether there are any general attributes shared by these strains that are responsible for their international success.
ESTHER : Croucher_2009_J.Bacteriol_191_1480
PubMedSearch : Croucher_2009_J.Bacteriol_191_1480
PubMedID: 19114491
Gene_locus related to this paper: strpi-pepx , strpj-b8zns7 , strpn-AXE1 , strpn-b2dz20 , strpn-SP0614 , strpn-SP1343

Title : Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens - Holden_2009_PLoS.Pathog_5_e1000346
Author(s) : Holden MT , Heather Z , Paillot R , Steward KF , Webb K , Ainslie F , Jourdan T , Bason NC , Holroyd NE , Mungall K , Quail MA , Sanders M , Simmonds M , Willey D , Brooks K , Aanensen DM , Spratt BG , Jolley KA , Maiden MC , Kehoe M , Chanter N , Bentley SD , Robinson C , Maskell DJ , Parkhill J , Waller AS
Ref : PLoS Pathog , 5 :e1000346 , 2009
Abstract : The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered. Streptococcus equi subspecies equi (S. equi) is a host-restricted pathogen of horses that has evolved from the zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). These pathogens share approximately 80% genome sequence identity with the important human pathogen Streptococcus pyogenes. We sequenced and compared the genomes of S. equi 4047 and S. zooepidemicus H70 and screened S. equi and S. zooepidemicus strains from around the world to uncover evidence of the genetic events that have shaped the evolution of the S. equi genome and led to its emergence as a host-restricted pathogen. Our analysis provides evidence of functional loss due to mutation and deletion, coupled with pathogenic specialization through the acquisition of bacteriophage encoding a phospholipase A(2) toxin, and four superantigens, and an integrative conjugative element carrying a novel iron acquisition system with similarity to the high pathogenicity island of Yersinia pestis. We also highlight that S. equi, S. zooepidemicus, and S. pyogenes share a common phage pool that enhances cross-species pathogen evolution. We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchange between S. equi, S. zooepidemicus, and S. pyogenes continues to influence the evolution of these important streptococci.
ESTHER : Holden_2009_PLoS.Pathog_5_e1000346
PubMedSearch : Holden_2009_PLoS.Pathog_5_e1000346
PubMedID: 19325880
Gene_locus related to this paper: stre4-c0mbg3 , stre4-pepx , strem-b4u0u4 , strem-b4u3j8 , strs7-pepx

Title : Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens - Silby_2009_Genome.Biol_10_R51
Author(s) : Silby MW , Cerdeno-Tarraga AM , Vernikos GS , Giddens SR , Jackson RW , Preston GM , Zhang XX , Moon CD , Gehrig SM , Godfrey SA , Knight CG , Malone JG , Robinson Z , Spiers AJ , Harris S , Challis GL , Yaxley AM , Harris D , Seeger K , Murphy L , Rutter S , Squares R , Quail MA , Saunders E , Mavromatis K , Brettin TS , Bentley SD , Hothersall J , Stephens E , Thomas CM , Parkhill J , Levy SB , Rainey PB , Thomson NR
Ref : Genome Biol , 10 :R51 , 2009
Abstract : BACKGROUND: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. RESULTS: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. CONCLUSIONS: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.
ESTHER : Silby_2009_Genome.Biol_10_R51
PubMedSearch : Silby_2009_Genome.Biol_10_R51
PubMedID: 19432983
Gene_locus related to this paper: psef5-metx , psefl-este , psefs-c3jz63 , psefs-c3jzq8 , psefs-c3k1v7 , psefs-c3k3d6 , psefs-c3k3m8 , psefs-c3k3s9 , psefs-c3k5q5 , psefs-c3k6c6 , psefs-c3k7v4 , psefs-c3k8m7 , psefs-c3k8y7 , psefs-c3k9z2 , psefs-c3k032 , psefs-c3k320 , psefs-c3k362 , psefs-c3k632 , psefs-c3k927 , psefs-c3kan9 , psefs-c3kbe5 , psefs-c3kdh9 , psefs-c3ke34 , psefs-laaa , psepf-q3k5t9 , psepf-q3k6f3 , psepf-q3k524 , psepf-q3kcu9 , psepf-q3kd07 , psepf-q3kf33 , psepf-q3kh87 , psefs-c3jxp6 , psepf-q3kf85 , psefs-c3k813 , psefs-c3keb8 , psefl-e2xkc8 , psefs-c3k9x6

Title : The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants - Crossman_2008_Genome.Biol_9_R74
Author(s) : Crossman LC , Gould VC , Dow JM , Vernikos GS , Okazaki A , Sebaihia M , Saunders D , Arrowsmith C , Carver T , Peters N , Adlem E , Kerhornou A , Lord A , Murphy L , Seeger K , Squares R , Rutter S , Quail MA , Rajandream MA , Harris D , Churcher C , Bentley SD , Parkhill J , Thomson NR , Avison MB
Ref : Genome Biol , 9 :R74 , 2008
Abstract : BACKGROUND: Stenotrophomonas maltophilia is a nosocomial opportunistic pathogen of the Xanthomonadaceae. The organism has been isolated from both clinical and soil environments in addition to the sputum of cystic fibrosis patients and the immunocompromised. Whilst relatively distant phylogenetically, the closest sequenced relatives of S. maltophilia are the plant pathogenic xanthomonads. RESULTS: The genome of the bacteremia-associated isolate S. maltophilia K279a is 4,851,126 bp and of high G+C content. The sequence reveals an organism with a remarkable capacity for drug and heavy metal resistance. In addition to a number of genes conferring resistance to antimicrobial drugs of different classes via alternative mechanisms, nine resistance-nodulation-division (RND)-type putative antimicrobial efflux systems are present. Functional genomic analysis confirms a role in drug resistance for several of the novel RND efflux pumps. S. maltophilia possesses potentially mobile regions of DNA and encodes a number of pili and fimbriae likely to be involved in adhesion and biofilm formation that may also contribute to increased antimicrobial drug resistance. CONCLUSION: The panoply of antimicrobial drug resistance genes and mobile genetic elements found suggests that the organism can act as a reservoir of antimicrobial drug resistance determinants in a clinical environment, which is an issue of considerable concern.
ESTHER : Crossman_2008_Genome.Biol_9_R74
PubMedSearch : Crossman_2008_Genome.Biol_9_R74
PubMedID: 18419807
Gene_locus related to this paper: strm5-b4sjf3 , strm5-b4sly1 , strm5-b4smq6 , strm5-b4st20 , strm5-bioh , strmk-b2fhb1 , strmk-b2fju9 , strmk-b2fkx8 , strmk-b2fl50 , strmk-b2fl54 , strmk-b2flj0 , strmk-b2fnc5 , strmk-b2fre3 , strmk-b2frm1 , strmk-b2frs0 , strmk-b2fsp0 , strmk-b2ftw9 , strmk-b2fuf3 , strmk-metx , xanma-P95782 , strmk-b2fmj5 , strmk-b2fpy9 , strmk-b2ftk7 , strmk-b2frv5

Title : Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation - Bentley_2008_J.Bacteriol_190_2150
Author(s) : Bentley SD , Corton C , Brown SE , Barron A , Clark L , Doggett J , Harris B , Ormond D , Quail MA , May G , Francis D , Knudson D , Parkhill J , Ishimaru CA
Ref : Journal of Bacteriology , 190 :2150 , 2008
Abstract : Clavibacter michiganensis subsp. sepedonicus is a plant-pathogenic bacterium and the causative agent of bacterial ring rot, a devastating agricultural disease under strict quarantine control and zero tolerance in the seed potato industry. This organism appears to be largely restricted to an endophytic lifestyle, proliferating within plant tissues and unable to persist in the absence of plant material. Analysis of the genome sequence of C. michiganensis subsp. sepedonicus and comparison with the genome sequences of related plant pathogens revealed a dramatic recent evolutionary history. The genome contains 106 insertion sequence elements, which appear to have been active in extensive rearrangement of the chromosome compared to that of Clavibacter michiganensis subsp. michiganensis. There are 110 pseudogenes with overrepresentation in functions associated with carbohydrate metabolism, transcriptional regulation, and pathogenicity. Genome comparisons also indicated that there is substantial gene content diversity within the species, probably due to differential gene acquisition and loss. These genomic features and evolutionary dating suggest that there was recent adaptation for life in a restricted niche where nutrient diversity and perhaps competition are low, correlated with a reduced ability to exploit previously occupied complex niches outside the plant. Toleration of factors such as multiplication and integration of insertion sequence elements, genome rearrangements, and functional disruption of many genes and operons seems to indicate that there has been general relaxation of selective pressure on a large proportion of the genome.
ESTHER : Bentley_2008_J.Bacteriol_190_2150
PubMedSearch : Bentley_2008_J.Bacteriol_190_2150
PubMedID: 18192393
Gene_locus related to this paper: clam3-a5cqb1 , clam3-a5crq6 , clam3-a5csc5 , clam3-a5css8 , clams-b0rcr0 , clams-b0rdd6 , clams-b0rdd7 , clams-b0rde2 , clams-b0rde3 , clams-b0rer7 , clams-b0rga8 , clams-b0riv5 , clam3-a5cp43 , clam3-a5cp56

Title : Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome - Hiller_2007_J.Bacteriol_189_8186
Author(s) : Hiller NL , Janto B , Hogg JS , Boissy R , Yu S , Powell E , Keefe R , Ehrlich NE , Shen K , Hayes J , Barbadora K , Klimke W , Dernovoy D , Tatusova T , Parkhill J , Bentley SD , Post JC , Ehrlich GD , Hu FZ
Ref : Journal of Bacteriology , 189 :8186 , 2007
Abstract : The distributed-genome hypothesis (DGH) states that pathogenic bacteria possess a supragenome that is much larger than the genome of any single bacterium and that these pathogens utilize genetic recombination and a large, noncore set of genes as a means of diversity generation. We sequenced the genomes of eight nasopharyngeal strains of Streptococcus pneumoniae isolated from pediatric patients with upper respiratory symptoms and performed quantitative genomic analyses among these and nine publicly available pneumococcal strains. Coding sequences from all strains were grouped into 3,170 orthologous gene clusters, of which 1,454 (46%) were conserved among all 17 strains. The majority of the gene clusters, 1,716 (54%), were not found in all strains. Genic differences per strain pair ranged from 35 to 629 orthologous clusters, with each strain's genome containing between 21 and 32% noncore genes. The distribution of the orthologous clusters per genome for the 17 strains was entered into the finite-supragenome model, which predicted that (i) the S. pneumoniae supragenome contains more than 5,000 orthologous clusters and (ii) 99% of the orthologous clusters ( approximately 3,000) that are represented in the S. pneumoniae population at frequencies of >or=0.1 can be identified if 33 representative genomes are sequenced. These extensive genic diversity data support the DGH and provide a basis for understanding the great differences in clinical phenotype associated with various pneumococcal strains. When these findings are taken together with previous studies that demonstrated the presence of a supragenome for Streptococcus agalactiae and Haemophilus influenzae, it appears that the possession of a distributed genome is a common host interaction strategy.
ESTHER : Hiller_2007_J.Bacteriol_189_8186
PubMedSearch : Hiller_2007_J.Bacteriol_189_8186
PubMedID: 17675389
Gene_locus related to this paper: strpn-AXE1 , strpn-pepx , strpn-SP1343

Title : Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18 - Bentley_2007_PLoS.Genet_3_e23
Author(s) : Bentley SD , Vernikos GS , Snyder LA , Churcher C , Arrowsmith C , Chillingworth T , Cronin A , Davis PH , Holroyd NE , Jagels K , Maddison M , Moule S , Rabbinowitsch E , Sharp S , Unwin L , Whitehead S , Quail MA , Achtman M , Barrell B , Saunders NJ , Parkhill J
Ref : PLoS Genet , 3 :e23 , 2007
Abstract : The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements) provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an impact on the interaction with the host tissues, and understanding these mechanisms is important to aid our understanding of the intimate and complex relationship between the human nasopharynx and the meningococcus.
ESTHER : Bentley_2007_PLoS.Genet_3_e23
PubMedSearch : Bentley_2007_PLoS.Genet_3_e23
PubMedID: 17305430
Gene_locus related to this paper: neigo-pip , neima-metx , neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1828 , neime-NMB1877 , neimf-a1kta9

Title : Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes - Sebaihia_2007_Genome.Res_17_1082
Author(s) : Sebaihia M , Peck MW , Minton NP , Thomson NR , Holden MT , Mitchell WJ , Carter AT , Bentley SD , Mason DR , Crossman L , Paul CJ , Ivens A , Wells-Bennik MH , Davis IJ , Cerdeno-Tarraga AM , Churcher C , Quail MA , Chillingworth T , Feltwell T , Fraser A , Goodhead I , Hance Z , Jagels K , Larke N , Maddison M , Moule S , Mungall K , Norbertczak H , Rabbinowitsch E , Sanders M , Simmonds M , White B , Whithead S , Parkhill J
Ref : Genome Res , 17 :1082 , 2007
Abstract : Clostridium botulinum is a heterogeneous Gram-positive species that comprises four genetically and physiologically distinct groups of bacteria that share the ability to produce botulinum neurotoxin, the most poisonous toxin known to man, and the causative agent of botulism, a severe disease of humans and animals. We report here the complete genome sequence of a representative of Group I (proteolytic) C. botulinum (strain Hall A, ATCC 3502). The genome consists of a chromosome (3,886,916 bp) and a plasmid (16,344 bp), which carry 3650 and 19 predicted genes, respectively. Consistent with the proteolytic phenotype of this strain, the genome harbors a large number of genes encoding secreted proteases and enzymes involved in uptake and metabolism of amino acids. The genome also reveals a hitherto unknown ability of C. botulinum to degrade chitin. There is a significant lack of recently acquired DNA, indicating a stable genomic content, in strong contrast to the fluid genome of Clostridium difficile, which can form longer-term relationships with its host. Overall, the genome indicates that C. botulinum is adapted to a saprophytic lifestyle both in soil and aquatic environments. This pathogen relies on its toxin to rapidly kill a wide range of prey species, and to gain access to nutrient sources, it releases a large number of extracellular enzymes to soften and destroy rotting or decayed tissues.
ESTHER : Sebaihia_2007_Genome.Res_17_1082
PubMedSearch : Sebaihia_2007_Genome.Res_17_1082
PubMedID: 17519437
Gene_locus related to this paper: clobh-A5I3I2 , clobh-A51055 , clob1-a7fqm2 , clob1-a7fv94 , clobl-a7gbn0 , clobh-pip , clobh-a5i3m0

Title : The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation - Thomson_2005_Genome.Res_15_629
Author(s) : Thomson NR , Yeats C , Bell K , Holden MT , Bentley SD , Livingstone M , Cerdeno-Tarraga AM , Harris B , Doggett J , Ormond D , Mungall K , Clarke K , Feltwell T , Hance Z , Sanders M , Quail MA , Price C , Barrell BG , Parkhill J , Longbottom D
Ref : Genome Res , 15 :629 , 2005
Abstract : The obligate intracellular bacterial pathogen Chlamydophila abortus strain S26/3 (formerly the abortion subtype of Chlamydia psittaci) is an important cause of late gestation abortions in ruminants and pigs. Furthermore, although relatively rare, zoonotic infection can result in acute illness and miscarriage in pregnant women. The complete genome sequence was determined and shows a high level of conservation in both sequence and overall gene content in comparison to other Chlamydiaceae. The 1,144,377-bp genome contains 961 predicted coding sequences, 842 of which are conserved with those of Chlamydophila caviae and Chlamydophila pneumoniae. Within this conserved Cp. abortus core genome we have identified the major regions of variation and have focused our analysis on these loci, several of which were found to encode highly variable protein families, such as TMH/Inc and Pmp families, which are strong candidates for the source of diversity in host tropism and disease causation in this group of organisms. Significantly, Cp. abortus lacks any toxin genes, and also lacks genes involved in tryptophan metabolism and nucleotide salvaging (guaB is present as a pseudogene), suggesting that the genetic basis of niche adaptation of this species is distinct from those previously proposed for other chlamydial species.
ESTHER : Thomson_2005_Genome.Res_15_629
PubMedSearch : Thomson_2005_Genome.Res_15_629
PubMedID: 15837807
Gene_locus related to this paper: chlab-q5l5y2 , chlab-q5l6t6

Title : Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors - Bell_2004_Proc.Natl.Acad.Sci.U.S.A_101_11105
Author(s) : Bell KS , Sebaihia M , Pritchard L , Holden MT , Hyman LJ , Holeva MC , Thomson NR , Bentley SD , Churcher LJ , Mungall K , Atkin R , Bason N , Brooks K , Chillingworth T , Clark K , Doggett J , Fraser A , Hance Z , Hauser H , Jagels K , Moule S , Norbertczak H , Ormond D , Price C , Quail MA , Sanders M , Walker D , Whitehead S , Salmond GP , Birch PR , Parkhill J , Toth IK
Ref : Proc Natl Acad Sci U S A , 101 :11105 , 2004
Abstract : The bacterial family Enterobacteriaceae is notable for its well studied human pathogens, including Salmonella, Yersinia, Shigella, and Escherichia spp. However, it also contains several plant pathogens. We report the genome sequence of a plant pathogenic enterobacterium, Erwinia carotovora subsp. atroseptica (Eca) strain SCRI1043, the causative agent of soft rot and blackleg potato diseases. Approximately 33% of Eca genes are not shared with sequenced enterobacterial human pathogens, including some predicted to facilitate unexpected metabolic traits, such as nitrogen fixation and opine catabolism. This proportion of genes also contains an overrepresentation of pathogenicity determinants, including possible horizontally acquired gene clusters for putative type IV secretion and polyketide phytotoxin synthesis. To investigate whether these gene clusters play a role in the disease process, an arrayed set of insertional mutants was generated, and mutations were identified. Plant bioassays showed that these mutants were significantly reduced in virulence, demonstrating both the presence of novel pathogenicity determinants in Eca, and the impact of functional genomics in expanding our understanding of phytopathogenicity in the Enterobacteriaceae.
ESTHER : Bell_2004_Proc.Natl.Acad.Sci.U.S.A_101_11105
PubMedSearch : Bell_2004_Proc.Natl.Acad.Sci.U.S.A_101_11105
PubMedID: 15263089
Gene_locus related to this paper: erwct-q6czi2 , erwct-q6czl9 , erwct-q6czu1 , erwct-q6d0l3 , erwct-q6d1e3 , erwct-q6d1l9 , erwct-q6d2k4 , erwct-q6d2x2 , erwct-q6d3m9 , erwct-q6d4b7 , erwct-q6d6t8 , erwct-q6d7j1 , erwct-q6d7p5 , erwct-q6d7w3 , erwct-q6d8k2 , erwct-q6d8q7 , erwct-q6d9l2 , erwct-q6d041 , erwct-q6d134 , erwct-q6d207 , erwct-q6d508 , erwct-q6d615 , erwct-q6d673 , erwct-q6d739.1 , erwct-q6d739.2 , erwct-q6d884 , erwct-q6da42 , erwct-q6da66 , erwct-q6dac1 , erwct-q6dar9 , erwct-Y3465

Title : Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei - Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240
Author(s) : Holden MT , Titball RW , Peacock SJ , Cerdeno-Tarraga AM , Atkins T , Crossman LC , Pitt T , Churcher C , Mungall K , Bentley SD , Sebaihia M , Thomson NR , Bason N , Beacham IR , Brooks K , Brown KA , Brown NF , Challis GL , Cherevach I , Chillingworth T , Cronin A , Crossett B , Davis P , DeShazer D , Feltwell T , Fraser A , Hance Z , Hauser H , Holroyd S , Jagels K , Keith KE , Maddison M , Moule S , Price C , Quail MA , Rabbinowitsch E , Rutherford K , Sanders M , Simmonds M , Songsivilai S , Stevens K , Tumapa S , Vesaratchavest M , Whitehead S , Yeats C , Barrell BG , Oyston PC , Parkhill J
Ref : Proc Natl Acad Sci U S A , 101 :14240 , 2004
Abstract : Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of melioidosis. This Gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic areas of the world and accounts for 20% of community-acquired septicaemias in northeastern Thailand where half of those affected die. Here we report the complete genome of B. pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase pairs, showing significant functional partitioning of genes between them. The large chromosome encodes many of the core functions associated with central metabolism and cell growth, whereas the small chromosome carries more accessory functions associated with adaptation and survival in different niches. Genomic comparisons with closely and more distantly related bacteria revealed a greater level of gene order conservation and a greater number of orthologous genes on the large chromosome, suggesting that the two replicons have distinct evolutionary origins. A striking feature of the genome was the presence of 16 genomic islands (GIs) that together made up 6.1% of the genome. Further analysis revealed these islands to be variably present in a collection of invasive and soil isolates but entirely absent from the clonally related organism B. mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is an important feature of recent genetic evolution and that this has resulted in a genetically diverse pathogenic species.
ESTHER : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240
PubMedSearch : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240
PubMedID: 15377794
Gene_locus related to this paper: burma-a5j5w8 , burma-a5tj72 , burma-a5tq93 , burma-metx , burma-q62a61 , burma-q62ar2.1 , burma-q62ar2.2 , burma-q62ax8 , burma-q62b60 , burma-q62b79 , burma-q62bh9 , burma-q62bl4 , burma-q62bl7 , burma-q62c00 , burma-q62cg5 , burma-q62d41 , burma-q62d56 , burma-q62d83 , burma-q62dg2 , burma-q62du7 , burma-q62e67 , burma-q62eb8 , burma-q62ed8 , burma-q62f28 , burma-q62fx7 , burma-q62g26 , burma-q62gx9 , burma-q62gy2 , burma-q62hq2 , burma-q62i62 , burma-q62ib8 , burma-q62ie8 , burma-q62j07 , burma-q62j15 , burma-q62jn5 , burma-q62jy7 , burma-q62kb7 , burma-q62kg0 , burma-q62kh9 , burma-q62lp7 , burma-q62m40 , burma-q62mc3 , burma-q62mf4 , burma-q62mq7 , burma-q629m1 , burma-q629p4 , burma-q629u0 , burp1-q3jvq2 , burps-a4lm41 , burps-q3v7s4 , burps-q63hx2 , burps-q63i95 , burps-q63im5 , burps-q63is4 , burps-q63ja6 , burps-q63ja9 , burps-q63jh5 , burps-q63l17 , burps-q63l41 , burps-q63l44 , burps-q63lt9 , burps-q63me1 , burps-q63mj7 , burps-q63mj8 , burps-q63mn8 , burps-q63mr2 , burps-q63n52 , burps-q63p18 , burps-q63p99 , burps-q63ug2 , burps-q63ug5 , burps-q63xf9 , burps-q63y36 , burps-q63y45 , burps-q63y52 , burps-q63y59 , burta-q2t474 , burps-hboh

Title : Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance - Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_9786
Author(s) : Holden MT , Feil EJ , Lindsay JA , Peacock SJ , Day NP , Enright MC , Foster TJ , Moore CE , Hurst L , Atkin R , Barron A , Bason N , Bentley SD , Chillingworth C , Chillingworth T , Churcher C , Clark L , Corton C , Cronin A , Doggett J , Dowd L , Feltwell T , Hance Z , Harris B , Hauser H , Holroyd S , Jagels K , James KD , Lennard N , Line A , Mayes R , Moule S , Mungall K , Ormond D , Quail MA , Rabbinowitsch E , Rutherford K , Sanders M , Sharp S , Simmonds M , Stevens K , Whitehead S , Barrell BG , Spratt BG , Parkhill J
Ref : Proc Natl Acad Sci U S A , 101 :9786 , 2004
Abstract : Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic plasticity has facilitated the evolution of many virulent and drug-resistant strains, presenting a major and constantly changing clinical challenge. We sequenced the approximately 2.8-Mbp genomes of two disease-causing S. aureus strains isolated from distinct clinical settings: a recent hospital-acquired representative of the epidemic methicillin-resistant S. aureus EMRSA-16 clone (MRSA252), a clinically important and globally prevalent lineage; and a representative of an invasive community-acquired methicillin-susceptible S. aureus clone (MSSA476). A comparative-genomics approach was used to explore the mechanisms of evolution of clinically important S. aureus genomes and to identify regions affecting virulence and drug resistance. The genome sequences of MRSA252 and MSSA476 have a well conserved core region but differ markedly in their accessory genetic elements. MRSA252 is the most genetically diverse S. aureus strain sequenced to date: approximately 6% of the genome is novel compared with other published genomes, and it contains several unique genetic elements. MSSA476 is methicillin-susceptible, but it contains a novel Staphylococcal chromosomal cassette (SCC) mec-like element (designated SCC(476)), which is integrated at the same site on the chromosome as SCCmec elements in MRSA strains but encodes a putative fusidic acid resistance protein. The crucial role that accessory elements play in the rapid evolution of S. aureus is clearly illustrated by comparing the MSSA476 genome with that of an extremely closely related MRSA community-acquired strain; the differential distribution of large mobile elements carrying virulence and drug-resistance determinants may be responsible for the clinically important phenotypic differences in these strains.
ESTHER : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_9786
PubMedSearch : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_9786
PubMedID: 15213324
Gene_locus related to this paper: staau-d2feb3 , staau-d2uin3 , 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-SAV2594

Title : Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei - Bentley_2003_Lancet_361_637
Author(s) : Bentley SD , Maiwald M , Murphy LD , Pallen MJ , Yeats CA , Dover LG , Norbertczak HT , Besra GS , Quail MA , Harris DE , von Herbay A , Goble A , Rutter S , Squares R , Squares S , Barrell BG , Parkhill J , Relman DA
Ref : Lancet , 361 :637 , 2003
Abstract : BACKGROUND: Whipple's disease is a rare multisystem chronic infection, involving the intestinal tract as well as various other organs. The causative agent, Tropheryma whipplei, is a Gram-positive bacterium about which little is known. Our aim was to investigate the biology of this organism by generating and analysing the complete DNA sequence of its genome. METHODS: We isolated and propagated T whipplei strain TW08/27 from the cerebrospinal fluid of a patient diagnosed with Whipple's disease. We generated the complete sequence of the genome by the whole genome shotgun method, and analysed it with a combination of automatic and manual bioinformatic techniques. FINDINGS: Sequencing revealed a condensed 925938 bp genome with a lack of key biosynthetic pathways and a reduced capacity for energy metabolism. A family of large surface proteins was identified, some associated with large amounts of non-coding repetitive DNA, and an unexpected degree of sequence variation. INTERPRETATION: The genome reduction and lack of metabolic capabilities point to a host-restricted lifestyle for the organism. The sequence variation indicates both known and novel mechanisms for the elaboration and variation of surface structures, and suggests that immune evasion and host interaction play an important part in the lifestyle of this persistent bacterial pathogen.
ESTHER : Bentley_2003_Lancet_361_637
PubMedSearch : Bentley_2003_Lancet_361_637
PubMedID: 12606174
Gene_locus related to this paper: trowh-TW083.1 , trowh-TW083.2 , trowh-TWT693

Title : The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129 - Cerdeno-Tarraga_2003_Nucleic.Acids.Res_31_6516
Author(s) : Cerdeno-Tarraga AM , Efstratiou A , Dover LG , Holden MT , Pallen M , Bentley SD , Besra GS , Churcher C , James KD , De Zoysa A , Chillingworth T , Cronin A , Dowd L , Feltwell T , Hamlin N , Holroyd S , Jagels K , Moule S , Quail MA , Rabbinowitsch E , Rutherford KM , Thomson NR , Unwin L , Whitehead S , Barrell BG , Parkhill J
Ref : Nucleic Acids Research , 31 :6516 , 2003
Abstract : Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This potentially fatal infectious disease is controlled in many developed countries by an effective immunisation programme. However, the disease has made a dramatic return in recent years, in particular within the Eastern European region. The largest, and still on-going, outbreak since the advent of mass immunisation started within Russia and the newly independent states of the former Soviet Union in the 1990s. We have sequenced the genome of a UK clinical isolate (biotype gravis strain NCTC13129), representative of the clone responsible for this outbreak. The genome consists of a single circular chromosome of 2 488 635 bp, with no plasmids. It provides evidence that recent acquisition of pathogenicity factors goes beyond the toxin itself, and includes iron-uptake systems, adhesins and fimbrial proteins. This is in contrast to Corynebacterium's nearest sequenced pathogenic relative, Mycobacterium tuberculosis, where there is little evidence of recent horizontal DNA acquisition. The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus.
ESTHER : Cerdeno-Tarraga_2003_Nucleic.Acids.Res_31_6516
PubMedSearch : Cerdeno-Tarraga_2003_Nucleic.Acids.Res_31_6516
PubMedID: 14602910
Gene_locus related to this paper: cordi-DIP1007 , cordi-DIP1729 , cordi-q6ned6 , cordi-q6nes3 , cordi-q6nes4 , cordi-q6nes6 , cordi-q6nes8 , cordi-q6nev5 , cordi-q6nex0 , cordi-q6nez6 , cordi-q6nf79 , cordi-q6nfa8 , cordi-q6nfg5 , cordi-q6nfz1 , cordi-q6ng42 , cordi-q6ngl8 , cordi-q6nhd8 , cordi-q6niz3 , cordi-q6nj46 , cordi-q6njn3 , cordi-q6njn4 , cordi-q6njt5 , cordi-q6nkb6 , cordk-h2hkn5

Title : Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica - Parkhill_2003_Nat.Genet_35_32
Author(s) : Parkhill J , Sebaihia M , Preston A , Murphy LD , Thomson N , Harris DE , Holden MT , Churcher CM , Bentley SD , Mungall KL , Cerdeno-Tarraga AM , Temple L , James K , Harris B , Quail MA , Achtman M , Atkin R , Baker S , Basham D , Bason N , Cherevach I , Chillingworth T , Collins M , Cronin A , Davis P , Doggett J , Feltwell T , Goble A , Hamlin N , Hauser H , Holroyd S , Jagels K , Leather S , Moule S , Norberczak H , O'Neil S , Ormond D , Price C , Rabbinowitsch E , Rutter S , Sanders M , Saunders D , Seeger K , Sharp S , Simmonds M , Skelton J , Squares R , Squares S , Stevens K , Unwin L , Whitehead S , Barrell BG , Maskell DJ
Ref : Nat Genet , 35 :32 , 2003
Abstract : Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica are closely related Gram-negative beta-proteobacteria that colonize the respiratory tracts of mammals. B. pertussis is a strict human pathogen of recent evolutionary origin and is the primary etiologic agent of whooping cough. B. parapertussis can also cause whooping cough, and B. bronchiseptica causes chronic respiratory infections in a wide range of animals. We sequenced the genomes of B. bronchiseptica RB50 (5,338,400 bp; 5,007 predicted genes), B. parapertussis 12822 (4,773,551 bp; 4,404 genes) and B. pertussis Tohama I (4,086,186 bp; 3,816 genes). Our analysis indicates that B. parapertussis and B. pertussis are independent derivatives of B. bronchiseptica-like ancestors. During the evolution of these two host-restricted species there was large-scale gene loss and inactivation; host adaptation seems to be a consequence of loss, not gain, of function, and differences in virulence may be related to loss of regulatory or control functions.
ESTHER : Parkhill_2003_Nat.Genet_35_32
PubMedSearch : Parkhill_2003_Nat.Genet_35_32
PubMedID: 12910271
Gene_locus related to this paper: borbr-BB0273 , borbr-BB0570 , borbr-BB0670 , borbr-BB1064 , borbr-BB1079 , borbr-BB1247 , borbr-BB1498 , borbr-BB2718 , borbr-BB4129 , borbr-BB4247 , borbr-MHPC , borbr-q7wdw1 , borbr-q7wiz8 , borbr-q7wk25 , borbr-q7wmc2 , borbr-q7wpd9 , borpa-q7w3f3 , borpa-q7w9v8 , borpe-BIOH , borpe-BP0300 , borpe-BP2114 , borpe-BP2146 , borpe-BP2511 , borpe-BP3096 , borpe-BP3623 , borpe-BP3691 , borpe-CATD2 , borpe-METX , borpe-O30449 , borpe-PHBC , borpe-q7vsl4 , borpe-q7vt07 , borpe-q7vtg0 , borpe-q7vtv2 , borpe-q7vus4 , borpe-q7vuv4 , borpe-q7vv11 , borpe-q7vv48 , borpe-q7vvf6 , borpe-q7vwu4 , borpe-q7vyn0 , borpe-q7vyq4 , borpe-q7vz26 , borpe-q7vzb4 , borpe-q7vzj6 , borpe-q7w073

Title : Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) - Bentley_2002_Nature_417_141
Author(s) : Bentley SD , Chater KF , Cerdeno-Tarraga AM , Challis GL , Thomson NR , James KD , Harris DE , Quail MA , Kieser H , Harper D , Bateman A , Brown S , Chandra G , Chen CW , Collins M , Cronin A , Fraser A , Goble A , Hidalgo J , Hornsby T , Howarth S , Huang CH , Kieser T , Larke L , Murphy L , Oliver K , O'Neil S , Rabbinowitsch E , Rajandream MA , Rutherford K , Rutter S , Seeger K , Saunders D , Sharp S , Squares R , Squares S , Taylor K , Warren T , Wietzorrek A , Woodward J , Barrell BG , Parkhill J , Hopwood DA
Ref : Nature , 417 :141 , 2002
Abstract : Streptomyces coelicolor is a representative of the group of soil-dwelling, filamentous bacteria responsible for producing most natural antibiotics used in human and veterinary medicine. Here we report the 8,667,507 base pair linear chromosome of this organism, containing the largest number of genes so far discovered in a bacterium. The 7,825 predicted genes include more than 20 clusters coding for known or predicted secondary metabolites. The genome contains an unprecedented proportion of regulatory genes, predominantly those likely to be involved in responses to external stimuli and stresses, and many duplicated gene sets that may represent 'tissue-specific' isoforms operating in different phases of colonial development, a unique situation for a bacterium. An ancient synteny was revealed between the central 'core' of the chromosome and the whole chromosome of pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering.
ESTHER : Bentley_2002_Nature_417_141
PubMedSearch : Bentley_2002_Nature_417_141
PubMedID: 12000953
Gene_locus related to this paper: strco-cxest , strco-cxest2 , strco-ester , strco-estli , strco-MMYT , strco-ORF3 , strco-q9f2m1 , strco-q9rdq9 , strco-q9x8r0 , strco-SC1A6.21 , strco-SC3F7.14 , strco-SC4C2.18 , strco-SC10F4.23 , strco-SCBAC20F6.10 , strco-SCD95A , strco-SCE8.12C , strco-SCE63.01 , strco-SCF43.16C , strco-SCJ9A.33C , strco-SCO0047 , strco-SCO0135 , strco-SCO0490 , strco-SCO0503 , strco-SCO0556.1 , strco-SCO0556.2 , strco-SCO1265 , strco-SCO2123 , strco-SCO2516 , strco-SCO2723 , strco-SCO2761 , strco-SCO3396 , strco-SCO3772 , strco-SCO4160 , strco-SCO4900 , strco-SCO5215 , strco-SCO5986 , strco-SCO6351 , strco-SCO6488 , strco-SCO7057 , strco-SCO7121 , strco-SCO7396 , strco-SCO7609 , strco-SCOT , strco-SLPD , strco-TAP

Title : Genome sequence of Yersinia pestis, the causative agent of plague. - Parkhill_2001_Nature_413_523
Author(s) : Parkhill J , Wren BW , Thomson NR , Titball RW , Holden MTG , Prentice MB , Sebaihia M , James KD , Churcher C , Mungall KL , Baker S , Basham D , Bentley SD , Brooks K , Cerdeno-Tarraga AM , Chillingworth T , Cronin A , Davies RM , Davis P , Dougan G , Feltwell T , Hamlin N , Holroyd S , Jagels K , Karlyshev AV , Leather S , Moule S , Oyston PCF , Quail M , Rutherford K , Simmonds M , Skelton J , Stevens K , Whitehead S , Barrell BG
Ref : Nature , 413 :523 , 2001
Abstract : The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve.
ESTHER : Parkhill_2001_Nature_413_523
PubMedSearch : Parkhill_2001_Nature_413_523
PubMedID: 11586360
Gene_locus related to this paper: yerpe-BIOH , yerpe-dlhh , yerpe-IRP1 , yerpe-PIP , yerpe-PLDB , yerpe-PTRB , yerpe-q8zey9 , yerpe-y1616 , yerpe-y3224 , yerpe-YBTT , yerpe-YPLA , yerpe-YPO0180 , yerpe-YPO0667 , yerpe-YPO0773 , yerpe-YPO0776 , yerpe-YPO0986 , yerpe-YPO1501 , yerpe-YPO1997 , yerpe-YPO2002 , yerpe-YPO2336 , yerpe-YPO2526 , yerpe-YPO2638 , yerpe-YPO2814 , yerpe-YPO4014

Title : Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 - Parkhill_2001_Nature_413_848
Author(s) : Parkhill J , Dougan G , James KD , Thomson NR , Pickard D , Wain J , Churcher C , Mungall KL , Bentley SD , Holden MT , Sebaihia M , Baker S , Basham D , Brooks K , Chillingworth T , Connerton P , Cronin A , Davis P , Davies RM , Dowd L , White N , Farrar J , Feltwell T , Hamlin N , Haque A , Hien TT , Holroyd S , Jagels K , Krogh A , Larsen TS , Leather S , Moule S , O'Gaora P , Parry C , Quail M , Rutherford K , Simmonds M , Skelton J , Stevens K , Whitehead S , Barrell BG
Ref : Nature , 413 :848 , 2001
Abstract : Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global burden of approximately 16 million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the mucosal surface of the intestine but are normally contained in healthy individuals by the local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the 4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs, revealing the presence of hundreds of insertions and deletions compared with the Escherichia coli genome, ranging in size from single genes to large islands. Notably, the genome sequence identifies over two hundred pseudogenes, several corresponding to genes that are known to contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis.
ESTHER : Parkhill_2001_Nature_413_848
PubMedSearch : Parkhill_2001_Nature_413_848
PubMedID: 11677608
Gene_locus related to this paper: salen-OPDB , salti-q8z717 , salty-AES , salty-BIOH , salty-ENTF , salty-FES , salty-IROD , salty-IROE , salty-PLDB , salty-STM2547 , salty-STM4506 , salty-STY1441 , salty-STY2428 , salty-STY3846 , salty-yafa , salty-YBFF , salty-ycfp , salty-YFBB , salty-YJFP , salty-YQIA

Title : Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491 - Parkhill_2000_Nature_404_502
Author(s) : Parkhill J , Achtman M , James KD , Bentley SD , Churcher C , Klee SR , Morelli G , Basham D , Brown D , Chillingworth T , Davies RM , Davis P , Devlin K , Feltwell T , Hamlin N , Holroyd S , Jagels K , Leather S , Moule S , Mungall K , Quail MA , Rajandream MA , Rutherford KM , Simmonds M , Skelton J , Whitehead S , Spratt BG , Barrell BG
Ref : Nature , 404 :502 , 2000
Abstract : Neisseria meningitidis causes bacterial meningitis and is therefore responsible for considerable morbidity and mortality in both the developed and the developing world. Meningococci are opportunistic pathogens that colonize the nasopharynges and oropharynges of asymptomatic carriers. For reasons that are still mostly unknown, they occasionally gain access to the blood, and subsequently to the cerebrospinal fluid, to cause septicaemia and meningitis. N. meningitidis strains are divided into a number of serogroups on the basis of the immunochemistry of their capsular polysaccharides; serogroup A strains are responsible for major epidemics and pandemics of meningococcal disease, and therefore most of the morbidity and mortality associated with this disease. Here we have determined the complete genome sequence of a serogroup A strain of Neisseria meningitidis, Z2491. The sequence is 2,184,406 base pairs in length, with an overall G+C content of 51.8%, and contains 2,121 predicted coding sequences. The most notable feature of the genome is the presence of many hundreds of repetitive elements, ranging from short repeats, positioned either singly or in large multiple arrays, to insertion sequences and gene duplications of one kilobase or more. Many of these repeats appear to be involved in genome fluidity and antigenic variation in this important human pathogen.
ESTHER : Parkhill_2000_Nature_404_502
PubMedSearch : Parkhill_2000_Nature_404_502
PubMedID: 10761919
Gene_locus related to this paper: neima-metx , neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1877 , neimf-a1kta9 , neime-r0tza2