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Vartul Sangal,
Kathryn E Holt,
Jianfeng Yuan,
Derek J Brown,
Ingrid Filliol-Toutain,
François-Xavier Weill,
Dong-Wook Kim,
Wanderley Dias da Silveira, Derek Pickard,
Nicholas R Thomson,
Julian Parkhill,
Jun Yu
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Vartul Sangal,
Kathryn E Holt,
Jianfeng Yuan,
Derek J Brown,
Ingrid Filliol-Toutain,
François-Xavier Weill,
Dong-Wook Kim,
Wanderley Dias da Silveira, Derek Pickard,
Nicholas R Thomson,
Julian Parkhill,
Jun Yu
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Vartul Sangal,
Kathryn E Holt,
Jianfeng Yuan,
Derek J Brown,
Ingrid Filliol-Toutain,
François-Xavier Weill,
Dong-Wook Kim,
Wanderley Dias da Silveira, Derek Pickard,
Nicholas R Thomson,
Julian Parkhill,
Jun Yu
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Vartul Sangal,
Kathryn E Holt,
Jianfeng Yuan,
Derek J Brown,
Ingrid Filliol-Toutain,
François-Xavier Weill,
Dong-Wook Kim,
Wanderley Dias da Silveira, Derek Pickard,
Nicholas R Thomson,
Julian Parkhill,
Jun Yu
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Vartul Sangal,
Kathryn E Holt,
Jianfeng Yuan,
Derek J Brown,
Ingrid Filliol-Toutain,
François-Xavier Weill,
Dong-Wook Kim,
Wanderley Dias da Silveira, Derek Pickard,
Nicholas R Thomson,
Julian Parkhill,
Jun Yu
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ABSTRACT: A transposon-based, genome-wide mutagenesis screen exploiting the killing activity of a lytic ViII bacteriophage was used to identify Salmonella Typhi genes that contribute to Vi polysaccharide capsule expression. Genes enriched in the screen included those within the viaB locus (tviABCDE, vexABCDE) as well as oxyR, barA/sirA and yrfF, which have not previously been associated with Vi expression. The role of these genes in Vi expression was confirmed by constructing defined null mutant derivatives of S. Typhi and these were negative for Vi expression as determined by agglutination assays with Vi-specific sera or susceptibility to Vi-targeting bacteriophage. Transcriptome analysis confirmed a reduction in expression from the viaB locus in these S. Typhi mutant derivatives and defined regulatory networks associated with Vi expression.
Journal of bacteriology 01/2013; · 3.94 Impact Factor
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Vartul Sangal,
Kathryn E Holt,
Jianfeng Yuan,
Derek J Brown,
Ingrid Filliol-Toutain,
François-Xavier Weill,
Dong-Wook Kim,
Wanderley Dias da Silveira, Derek Pickard,
Nicholas R Thomson,
Julian Parkhill,
Jun Yu
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ABSTRACT: The current Shigella sonnei pandemic involves geographically associated, multidrug resistant clones. This study has demonstrated that S. sonnei phylogeny can be accurately defined with limited SNPs. By typing 6 informative SNPs using high-resolution melting (HRM) assay major S. sonnei lineages/sublineages can be identified as defined from whole-genome variation.
Journal of clinical microbiology 10/2012; · 4.16 Impact Factor
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Evelien M Adriaenssens,
Hans-Wolfgang Ackermann,
Hany Anany,
Bob Blasdel,
Ian F Connerton,
David Goulding,
Mansel W Griffiths,
Steven P Hooton,
Elizabeth M Kutter,
Andrew M Kropinski,
Ju-Hoon Lee,
Martine Maes, Derek Pickard,
Sangryeol Ryu,
Zargham Sepehrizadeh,
S Sabouri Shahrbabak,
Ana L Toribio,
Rob Lavigne
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ABSTRACT: We suggest a bacteriophage genus, "Viunalikevirus", as a new genus within the family Myoviridae. To date, this genus includes seven sequenced members: Salmonella phages ViI, SFP10 and ΦSH19; Escherichia phages CBA120 and PhaxI; Shigella phage phiSboM-AG3; and Dickeya phage LIMEstone1. Their shared myovirus morphology, with comparable head sizes and tail dimensions, and genome organization are considered distinguishing features. They appear to have conserved regulatory sequences, a horizontally acquired tRNA set and the probable substitution of an alternate base for thymine in the DNA. A close examination of the tail spike region in the DNA revealed four distinct tail spike proteins, an arrangement which might lead to the umbrella-like structures of the tails visible on electron micrographs. These properties set the suggested genus apart from the recently ratified subfamily Tevenvirinae, although a significant evolutionary relationship can be observed.
Archives of Virology 06/2012; 157(10):2035-46. · 2.11 Impact Factor
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Helena M B Seth-Smith,
Maria C Fookes,
Chinyere K Okoro,
Stephen Baker,
Simon R Harris,
Paul Scott, Derek Pickard,
Michael A Quail,
Carol Churcher,
Mandy Sanders,
Johan Harmse,
Gordon Dougan,
Julian Parkhill,
Nicholas R Thomson
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ABSTRACT: Integrative and conjugative elements (ICEs) are self-mobile genetic elements found in the genomes of some bacteria. These elements may confer a fitness advantage upon their host bacteria through the cargo genes that they carry. Salmonella pathogenicity island 7 (SPI-7), found within some pathogenic strains of Salmonella enterica, possesses features indicative of an ICE and carries genes implicated in virulence. We aimed to identify and fully analyze ICEs related to SPI-7 within the genus Salmonella and other Enterobacteriaceae. We report the sequence of two novel SPI-7-like elements, found within strains of Salmonella bongori, which share 97% nucleotide identity over conserved regions with SPI-7 and with each other. Although SPI-7 within Salmonella enterica serovar Typhi appears to be fixed within the chromosome, we present evidence that these novel elements are capable of excision and self-mobility. Phylogenetic analyses show that these Salmonella mobile elements share an ancestor which existed approximately 3.6 to 15.8 million years ago. Additionally, we identified more distantly related ICEs, with distinct cargo regions, within other strains of Salmonella as well as within Citrobacter, Erwinia, Escherichia, Photorhabdus, and Yersinia species. In total, we report on a collection of 17 SPI-7 related ICEs within enterobacterial species, of which six are novel. Using comparative and mutational studies, we have defined a core of 27 genes essential for conjugation. We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae.
Journal of bacteriology 03/2012; 194(6):1494-504. · 3.94 Impact Factor
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ABSTRACT: The Vi capsular polysaccharide (CPS) of Salmonella enterica serovar Typhi, the cause of human typhoid, is important for infectivity and virulence. The Vi biosynthetic machinery is encoded within the viaB locus composed of 10 genes involved in regulation of expression (tviA), polymer synthesis (tviB-tviE), and cell surface localization of the CPS (vexA-vexE). We cloned the viaB locus from S. Typhi and transposon insertion mutants of individual viaB genes were characterized in Escherichia coli DH5α. Phenotype analysis of viaB mutants revealed that tviB, tviC, tviD and tviE are involved in Vi polymer synthesis. Furthermore, expression of tviB-tviE in E. coli DH5α directed the synthesis of cytoplasmic Vi antigen. Mutants of the ABC transporter genes vexBC and the polysaccharide copolymerase gene vexD accumulated the Vi polymer within the cytoplasm and productivity in these mutants was greatly reduced. In contrast, de novo synthesis of Vi polymer in the export deficient vexA mutant was comparable to wild-type cells, with drastic effects on cell stability. VexE mutant cells exported the Vi, but the CPS was not retained at the cell surface. The secreted polymer of a vexE mutant had different physical characteristics compared to the wild-type Vi.
PLoS ONE 01/2012; 7(9):e45609. · 4.09 Impact Factor
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Elizabeth M Kutter,
Kyobi Skutt-Kakaria,
Bob Blasdel,
Ayman El-Shibiny,
Anna Castano,
Daniel Bryan,
Andrew M Kropinski,
Andre Villegas,
Hans-Wolfgang Ackermann,
Ana L Toribio, Derek Pickard,
Hany Anany,
Todd Callaway,
Andrew D Brabban
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ABSTRACT: Phage vB_EcoM_CBA120 (CBA120), isolated against Escherichia coli O157:H7 from a cattle feedlot, is morphologically very similar to the classic phage ViI of Salmonella enterica serovar Typhi. Until recently, little was known genetically or physiologically about the ViI-like phages, and none targeting E. coli have been described in the literature. The genome of CBA120 has been fully sequenced and is highly similar to those of both ViI and the Shigella phage AG3. The core set of structural and replication-related proteins of CBA120 are homologous to those from T-even phages, but generally are more closely related to those from T4-like phages of Vibrio, Aeromonas and cyanobacteria than those of the Enterobacteriaceae. The baseplate and method of adhesion to the host are, however, very different from those of either T4 or the cyanophages. None of the outer baseplate proteins are conserved. Instead of T4's long and short tail fibers, CBA120, like ViI, encodes tail spikes related to those normally seen on podoviruses. The 158 kb genome, like that of T4, is circularly permuted and terminally redundant, but unlike T4 CBA120 does not substitute hmdCyt for cytosine in its DNA. However, in contrast to other coliphages, CBA120 and related coliphages we have isolated cannot incorporate 3H-thymidine (3H-dThd) into their DNA. Protein sequence comparisons cluster the putative "thymidylate synthase" of CBA120, ViI and AG3 much more closely with those of Delftia phage φW-14, Bacillus subtilis phage SPO1, and Pseudomonas phage YuA, all known to produce and incorporate hydroxymethyluracil (hmdUra).
Virology Journal 09/2011; 8:430. · 2.34 Impact Factor
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Nicola K Petty,
Theresa Feltwell, Derek Pickard,
Simon Clare,
Ana L Toribio,
Maria Fookes,
Kevin Roberts,
Rita Monson,
Satheesh Nair,
Robert A Kingsley, [......],
Richard Rance,
Lu Yu,
Jyoti S Choudhary,
Carol Churcher,
Michael A Quail,
Julian Parkhill,
Gad Frankel,
Gordon Dougan,
George P C Salmond,
Nicholas R Thomson
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ABSTRACT: Citrobacter rodentium is a natural mouse pathogen that causes attaching and effacing (A/E) lesions. It shares a common virulence strategy with the clinically significant human A/E pathogens enteropathogenic E. coli (EPEC) and enterohaemorrhagic E. coli (EHEC) and is widely used to model this route of pathogenesis. We previously reported the complete genome sequence of C. rodentium ICC168, where we found that the genome displayed many characteristics of a newly evolved pathogen. In this study, through PFGE, sequencing of isolates showing variation, whole genome transcriptome analysis and examination of the mobile genetic elements, we found that, consistent with our previous hypothesis, the genome of C. rodentium is unstable as a result of repeat-mediated, large-scale genome recombination and because of active transposition of mobile genetic elements such as the prophages. We sequenced an additional C. rodentium strain, EX-33, to reveal that the reference strain ICC168 is representative of the species and that most of the inactivating mutations were common to both isolates and likely to have occurred early on in the evolution of this pathogen. We draw parallels with the evolution of other bacterial pathogens and conclude that C. rodentium is a recently evolved pathogen that may have emerged alongside the development of inbred mice as a model for human disease.
PLoS Pathogens 04/2011; 7(4):e1002018. · 9.13 Impact Factor
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Michail H Karavolos,
David M Bulmer,
Hannah Spencer,
Giordano Rampioni,
Ira Schmalen,
Stephen Baker, Derek Pickard,
Joe Gray,
Maria Fookes,
Klaus Winzer,
Alasdair Ivens,
Gordon Dougan,
Paul Williams,
C M Anjam Khan
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ABSTRACT: Salmonella enterica serovar Typhi (S. typhi) causes typhoid fever. We show that exposure of S. typhi to neuroendocrine stress hormones results in haemolysis, which is associated with the release of haemolysin E in membrane vesicles. This effect is attributed to increased expression of the small RNA micA and RNA chaperone Hfq, with concomitant downregulation of outer membrane protein A. Deletion of micA or the two-component signal-transduction system, CpxAR, abolishes the phenotype. The hormone response is inhibited by the β-blocker propranolol. We provide mechanistic insights into the basis of neuroendocrine hormone-mediated haemolysis by S. typhi, increasing our understanding of inter-kingdom signalling.
EMBO Reports 02/2011; 12(3):252-8. · 7.36 Impact Factor
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Derek Pickard,
Ana Luisa Toribio,
Nicola K Petty,
Andries van Tonder,
Lu Yu,
David Goulding,
Bart Barrell,
Richard Rance,
David Harris,
Michael Wetter,
John Wain,
Jyoti Choudhary,
Nicholas Thomson,
Gordon Dougan
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ABSTRACT: A number of bacteriophages have been identified that target the Vi capsular antigen of Salmonella enterica serovar Typhi. Here we show that these Vi phages represent a remarkably diverse set of phages belonging to three phage families, including Podoviridae and Myoviridae. Genome analysis facilitated the further classification of these phages and highlighted aspects of their independent evolution. Significantly, a conserved protein domain carrying an acetyl esterase was found to be associated with at least one tail fiber gene for all Vi phages, and the presence of this domain was confirmed in representative phage particles by mass spectrometric analysis. Thus, we provide a simple explanation and paradigm of how a diverse group of phages target a single key virulence antigen associated with this important human-restricted pathogen.
Journal of bacteriology 11/2010; 192(21):5746-54. · 3.94 Impact Factor
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Pieter-Jan Ceyssens,
Andrew Brabban,
Larissa Rogge,
Matthew Spooner Lewis, Derek Pickard,
David Goulding,
Gordon Dougan,
Jean-Paul Noben,
Andrew Kropinski,
Elizabeth Kutter,
Rob Lavigne
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ABSTRACT: We present a detailed analysis of the genome architecture, structural proteome and infection-related properties of three Pseudomonas phages, designated LUZ7, LIT1 and PEV2. These podoviruses encapsulate 72.5 to 74.9 kb genomes and lyse their host after 25 min aerobic infection. PEV2 can successfully infect under anaerobic conditions, but its latent period is tripled, the lysis proceeds far slower and the burst size decreases significantly. While the overall genome structure of these phages resembles the well-studied coliphage N4, these Pseudomonas phages encode a cluster of tail genes which displays significant similarity to a Pseudomonasaeruginosa (cryptic) prophage region. Using ESI-MS/MS, these tail proteins were shown to be part of the phage particle, as well as ten other proteins including a giant 370 kDa virion RNA polymerase. These phages are the first described representatives of a novel kind of obligatory lytic P. aeruginosa-infecting phages, belonging to the widespread "N4-like viruses" genus.
Virology 09/2010; 405(1):26-30. · 3.35 Impact Factor
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Lindsay J Hall,
Simon Clare, Derek Pickard,
Simon O Clark,
Dominic L F Kelly,
Moataz Abd El Ghany,
Christine Hale,
Jes Dietrich,
Peter Andersen,
Philip D Marsh,
Gordon Dougan
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ABSTRACT: A recombinant Salmonella enterica serovar Typhimurium (S. Typhimurium) vaccine strain was constructed that stably expressed the Mycobacterium tuberculosis fusion antigen Ag85B-ESAT6 from the chromosome. Live oral vaccination of mice with the Salmonella/Ag85B-ESAT6 strain generated a potent anti-Ag85B-ESAT6 T(H)1 response with high antibody titres with a IgG2a-bias and significant IFN-gamma production lasting over a 120-day period. When mice primed with the Salmonella/Ag85B-ESAT6 vaccine were mucosally boosted with the Ag85B-ESAT6 antigen and adjuvant the IFN-gamma responses increased markedly. To determine the protective efficacy of this vaccine strain, guinea pigs were immunised and followed for a 30-week period after aerosol challenge with M. tuberculosis. The heterologous prime-boost strategy of live Salmonella vaccine followed by a systemic boost of antigen and adjuvant reduced the levels of M. tuberculosis bacteria in the lungs and spleen to the same extent as BCG. Additionally, this vaccination regimen was observed to be statistically equivalent in terms of protection to immunisation with BCG. Thus, live oral priming with the recombinant Salmonella/Ag85B-ESAT6 and boosting with Ag85B-ESAT6 plus the adjuvant LTK63 represents an effective mucosal vaccination regimen.
Vaccine 09/2009; 27(49):6894-904. · 3.77 Impact Factor
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ABSTRACT: Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) has caused significant morbidity and mortality in humans and animals for almost three decades. We completed the full DNA sequence of one DT104 strain, NCTC13348, and showed that significant differences between the genome of this isolate and the genome of the previously sequenced strain Salmonella serovar Typhimurium LT2 are due to integrated prophage elements and Salmonella genomic island 1 encoding antibiotic resistance genes. Thirteen isolates of Salmonella serovar Typhimurium DT104 with different pulsed-field gel electrophoresis (PFGE) profiles were analyzed by using multilocus sequence typing (MLST), plasmid profiling, hybridization to a pan-Salmonella DNA microarray, and prophage-based multiplex PCR. All the isolates belonged to a single MLST type, sequence type ST19. Microarray data demonstrated that the gene contents of the 13 DT104 isolates were remarkably conserved. The PFGE DNA fragment size differences in these isolates could be explained to a great extent by differences in the prophage and plasmid contents. Thus, here the nature of variation in different Salmonella serovar Typhimurium DT104 isolates is further defined at the gene and whole-genome levels, illustrating how this phage type evolves over time.
Journal of bacteriology 11/2008; 190(24):8155-62. · 3.94 Impact Factor
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ABSTRACT: Salmonella pathogenicity island 7 (SPI-7) in Salmonella enterica serovar Typhi appears to be related to other genomic islands. Evidence suggests that SPI-7 is susceptible to spontaneous circularization, loss, and transposition. Here, we demonstrate that a region within SPI-7 has the ability to mobilize the small incQ plasmid R300B.
Journal of bacteriology 07/2008; 190(11):4084-7. · 3.94 Impact Factor
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Nicholas R Thomson,
Debra J Clayton,
Daniel Windhorst,
Georgios Vernikos,
Susanne Davidson,
Carol Churcher,
Michael A Quail,
Mark Stevens,
Michael A Jones,
Michael Watson, [......],
Karen Mungall,
Mandy Sanders,
Sally Whitehead,
Jose A Chabalgoity,
Duncan Maskell,
Tom Humphrey,
Mark Roberts,
Paul A Barrow,
Gordon Dougan,
Julian Parkhill
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ABSTRACT: We have determined the complete genome sequences of a host-promiscuous Salmonella enterica serovar Enteritidis PT4 isolate P125109 and a chicken-restricted Salmonella enterica serovar Gallinarum isolate 287/91. Genome comparisons between these and other Salmonella isolates indicate that S. Gallinarum 287/91 is a recently evolved descendent of S. Enteritidis. Significantly, the genome of S. Gallinarum has undergone extensive degradation through deletion and pseudogene formation. Comparison of the pseudogenes in S. Gallinarum with those identified previously in other host-adapted bacteria reveals the loss of many common functional traits and provides insights into possible mechanisms of host and tissue adaptation. We propose that experimental analysis in chickens and mice of S. Enteritidis-harboring mutations in functional homologs of the pseudogenes present in S. Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis of host adaptation in S. enterica.
Genome Research 07/2008; 18(10):1624-37. · 13.61 Impact Factor
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ABSTRACT: Some bacteriophages target potentially pathogenic bacteria by exploiting surface-associated virulence factors as receptors. For example, phage have been identified that exhibit specificity for Vi capsule producing Salmonella enterica serovar Typhi. Here we have characterized the Vi-associated E1-typing bacteriophage using a number of molecular approaches. The absolute requirement for Vi capsule expression for infectivity was demonstrated using different Vi-negative S. enterica derivatives. The phage particles were shown to have an icosahedral head and a long noncontractile tail structure. The genome is 45,362 bp in length with defined capsid and tail regions that exhibit significant homology to the S. enterica transducing phage ES18. Mass spectrometry was used to confirm the presence of a number of hypothetical proteins in the Vi phage E1 particle and demonstrate that a number of phage proteins are modified posttranslationally. The genome of the Vi phage E1 is significantly related to other bacteriophages belonging to the same serovar Typhi phage-typing set, and we demonstrate a role for phage DNA modification in determining host specificity.
Journal of bacteriology 05/2008; 190(7):2580-7. · 3.94 Impact Factor
