Now showing items 1-20 of 36

  • Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland 

    Reuter, Sandra; Török, Estee M; Holden, Matthew Tg; Reynolds, Rosy; Raven, Kathy E; Blane, Beth; Donker, Tjibbe; Bentley, Stephen D; Aanensen, David M; Grundmann, Hajo; Feil, Edward J; Spratt, Brian G; Parkhill, Julian; Peacock, Sharon J (2016-02) - Journal article
    The correct interpretation of microbial sequencing data applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a ...
  • Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles 

    Nandi, Tannistha; Holden, Matthew; Didelot, Xavier; Mehershahi, Kurosh; Boddey, Justin A; Beacham, Ifor; Peak, Ian; Harting, John; Baybayan, Primo; Guo, Yan; Wang, Susana; How, Lee Chee; Sim, Bernice; Essex-Lopresti, Angela; Sarkar-Tyson, Mitali; Nelson, Michelle; Smither, Sophie; Ong, Catherine; Aw, Lay Tin; Hoon, Chua Hui; Michell, Stephen; Studholme, David J; Titball, Richard; Chen, Swaine L; Parkhill, Julian; Tan, Patrick (2015-01) - Journal article
    Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed ...
  • Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission 

    Paterson, Gavin K; Harrison, Ewan M; Murray, Gemma G R; Welch, John J; Warland, James H; Holden, Matthew T G; Morgan, Fiona J E; Ba, Xiaoliang; Koop, Gerrit; Harris, Simon R; Maskell, Duncan J; Peacock, Sharon J; Herrtage, Michael E; Parkhill, Julian; Holmes, Mark A (2015-03-27) - Journal article
    Genome sequencing is revolutionizing clinical microbiology and our understanding of infectious diseases. Previous studies have largely relied on the sequencing of a single isolate from each individual. However, it is not ...
  • The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081 

    Thomson, Nicholas R.; Howard, Sarah; Wren, Brendan W.; Holden, Matthew T. G.; Crossman, Lisa; Challis, Gregory L.; Churcher, Carol; Mungall, Karen; Brooks, Karen; Chillingworth, Tracey; Feltwell, Theresa; Abdellah, Zahra; Hauser, Heidi; Jagels, Kay; Maddison, Mark; Moule, Sharon; Sanders, Mandy; Whitehead, Sally; Quail, Michael A.; Dougan, Gordon; Parkhill, Julian; Prentice, Michael B. (2006-12) - Journal article
    The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our ...
  • The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity 

    Warne, Ben; Harkins, Catriona P; Harris, Simon R; Vatsiou, Alexandra; Stanley-Wall, Nicola; Parkhill, Julian; Peacock, Sharon J; Palmer, Tracy; Holden, Matthew T G (2016-03-13) - Journal article
    BACKGROUND: Type VII protein secretion (T7SS) is a specialised system for excreting extracellular proteins across bacterial cell membranes and has been associated with virulence in Staphylococcus aureus. The genetic diversity ...
  • Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis 

    Ward, Philip N.; Holden, Matthew T. G.; Leigh, James A.; Lennard, Nicola; Bignell, Alexandra; Barron, Andy; Clark, Louise; Quail, Michael A.; Woodward, John; Barrell, Bart G.; Egan, Sharon A.; Field, Terence R.; Maskell, Duncan; Kehoe, Michael; Dowson, Christopher G.; Chanter, Neil; Whatmore, Adrian M.; Bentley, Stephen D.; Parkhill, Julian (2009-01-28) - Journal item
    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 ...
  • Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system 

    Hsu, Li-Yang; Harris, Simon R; Chlebowicz, Monika A; Lindsay, Jodi A; Koh, Tse-Hsien; Krishnan, Prabha; Tan, Thean-Yen; Hon, Pei-Yun; Grubb, Warren B; Bentley, Stephen D; Parkhill, Julian; Peacock, Sharon J; Holden, Matthew Tg (2015-04-23) - Journal article
    Background In the past decade, several countries have seen gradual replacement of endemic multi-resistant healthcare-associated methicillin-resistant Staphylococcus aureus (MRSA) with clones that are more susceptible to ...
  • Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW) 

    Holden, Matthew T. G.; Lindsay, Jodi A.; Corton, Craig; Quail, Michael A.; Cockfield, Joshua D.; Pathak, Smriti; Batra, Rahul; Parkhill, Julian; Bentley, Stephen D.; Edgeworth, Jonathan D. (2010-02) - Journal article
    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 ...
  • The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay 

    Hjerde, Erik; Lorentzen, Marit Sjo; Holden, Matthew T. G.; Seeger, Kathy; Paulsen, Steinar; Bason, Nathalie; Churcher, Carol; Harris, David; Norbertczak, Halina; Quail, Michael A.; Sanders, Suzanne; Thurston, Scott; Parkhill, Julian; Willassen, Nils Peder; Thomson, Nicholas R. (2008-12-19) - Journal article
    Background: The fish pathogen Aliivibrio salmonicida is the causative agent of cold-water vibriosis in marine aquaculture. The Gram-negative bacterium causes tissue degradation, hemolysis and sepsis in vivo. Results: In ...
  • Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting 

    Tong, Steven Y C; Holden, Matthew T G; Nickerson, Emma K; Cooper, Ben S; Köser, Claudio U; Cori, Anne; Jombart, Thibaut; Cauchemez, Simon; Fraser, Christophe; Wuthiekanun, Vanaporn; Thaipadungpanit, Janjira; Hongsuwan, Maliwan; Day, Nicholas P; Limmathurotsakul, Direk; Parkhill, Julian; Peacock, Sharon J (2014-12-09) - Journal article
    Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infection. Whole-genome sequencing of MRSA has been used to define phylogeny and transmission in well-resourced healthcare settings, yet the ...
  • Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection 

    Harris, Simon R; Robinson, Carl; Steward, Karen F; Webb, Katy S; Paillot, Romain; Parkhill, Julian; Holden, Matthew T G; Waller, Andrew S (2015-09) - Journal article
    Strangles, the most frequently diagnosed infectious disease of horses worldwide, is caused by Streptococcus equi. Despite its prevalence, the global diversity and mechanisms underlying the evolution of S. equi as a ...
  • Genomic dissection of an Icelandic epidemic of respiratory disease in horses and associated zoonotic cases 

    Björnsdóttir, Sigríður; Harris, Simon R.; Svansson, Vilhjálmur; Gunnarsson, Eggert; Sigurðardóttir, Ólöf G.; Gammeljord, Kristina; Steward, Karen F.; Newton, J. Richard; Robinson, Carl; Charbonneau, Amelia R. L.; Parkhill, Julian; Holden, Matthew T. G.; Waller, Andrew S. (2017-08-01) - Journal article
    Iceland is free of the major infectious diseases of horses. However, in 2010 an epidemic of respiratory disease of unknown cause spread through the country's native horse population of 77,000. Microbiological investigations ...
  • Genomic evidence for the evolution of Streptococcus equi : host restriction, increased virulence, and genetic exchange with human pathogens 

    Holden, Matthew T. G.; Heather, Zoe; Paillot, Romain; Steward, Karen F.; Webb, Katy; Ainslie, Fern; Jourdan, Thibaud; Bason, Nathalie C.; Holroyd, Nancy E.; Mungall, Karen; Quail, Michael A.; Sanders, Mandy; Simmonds, Mark; Willey, David; Brooks, Karen; Aanensen, David M.; Spratt, Brian G.; Jolley, Keith A.; Maiden, Martin C. J.; Kehoe, Michael; Chanter, Neil; Bentley, Stephen D.; Robinson, Carl; Maskell, Duncan J.; Parkhill, Julian; Waller, Andrew S. (2009-03) - Journal article
    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 ...
  • A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic 

    Holden, Matthew Thomas Geoffrey; Hsu, Li-Yang; Kurt, Kevin; Weinert, Lucy A.; Mather, Alison E.; Harris, Simon R.; Strommenger, Birgit; Layer, Franziska; Witte, Wolfgang; de Lencastre, Herminia; Skov, Robert; Westh, Henrik; Zemlickova, Helena; Coombs, Geoffrey; Kearns, Angela M.; Hill, Robert L. R.; Edgeworth, Jonathan; Gould, Ian; Gant, Vanya; Cooke, Jonathan; Edwards, Giles F.; McAdam, Paul R.; Templeton, Kate E.; McCann, Angela; Zhou, Zhemin; Castillo-Ramirez, Santiago; Feil, Edward J.; Hudson, Lyndsey O.; Enright, Mark C.; Balloux, Francois; Aanensen, David M.; Spratt, Brian G.; Fitzgerald, J. Ross; Parkhill, Julian; Achtman, Mark; Bentley, Stephen D.; Nuebel, Ulrich (2013-04) - Journal article
    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 ...
  • Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis 

    Weinert, Lucy A; Chaudhuri, Roy R; Wang, Jinhong; Peters, Sarah E; Corander, Jukka; Jombart, Thibaut; Baig, Abiyad; Howell, Kate J; Vehkala, Minna; Välimäki, Niko; Harris, David; Chieu, Tran Thi Bich; Van Vinh Chau, Nguyen; Campbell, James; Schultsz, Constance; Parkhill, Julian; Bentley, Stephen D; Langford, Paul R; Rycroft, Andrew N; Wren, Brendan W; Farrar, Jeremy; Baker, Stephen; Hoa, Ngo Thi; Holden, Matthew T G; Tucker, Alexander W; Maskell, Duncan J; BRaDP1T Consortium (2015-05) - Journal article
    Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic basis of disease in S. suis, we study the genomes of 375 isolates ...
  • Global and regional dissemination and evolution of Burkholderia pseudomallei 

    Chewapreecha, Claire; Holden, Matthew T. G.; Vehkala, Minna; Välimäki, Niko; Yang, Zhirong; Harris, Simon R.; Mather, Alison E.; Tuanyok, Apichai; De Smet, Birgit; Le Hello, Simon; Bizet, Chantal; Mayo, Mark; Wuthiekanun, Vanaporn; Limmathurotsakul, Direk; Phetsouvanh, Rattanaphone; Spratt, Brian G.; Corander, Jukka; Keim, Paul; Dougan, Gordon; Dance, David A. B.; Currie, Bart J.; Parkhill, Julian; Peacock, Sharon J. (2017-01-23) - Journal article
    The environmental bacterium Burkholderia pseudomallei causes an estimated 165,000 cases of human melioidosis per year worldwide and is also classified as a biothreat agent. We used whole genome sequences of 469 B. pseudomallei ...
  • The impact of recombination on dN/dS within recently emerged bacterial clones 

    Castillo-Ramirez, Santiago; Harris, Simon R.; Holden, Matthew T. G.; He, Miao; Parkhill, Julian; Bentley, Stephen D.; Feil, Edward J. (2011-07) - Journal article
    The development of next-generation sequencing platforms is set to reveal an unprecedented level of detail on short-term molecular evolutionary processes in bacteria. Here we re-analyse genome-wide single nucleotide ...
  • Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice 

    Harkins, Catriona P.; Pichon, Bruno; Doumith, Michel; Parkhill, Julian; Westh, Henrik; Tomasz, Alexander; de Lencastre, Herminia; Bentley, Stephen D.; Kearns, Angela M.; Holden, Matthew T. G. (2017-07-20) - Journal article
    Background: The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the ...
  • The microevolution and epidemiology of Staphylococcus aureus colonization during atopic eczema disease flare 

    Harkins, Catriona P.; Pettigrew, Kerry A.; Oravcová, Katarina; Gardner, June; Hearn, R. M. Ross; Rice, Debbie; Mather, Alison E.; Parkhill, Julian; Brown, Sara J.; Proby, Charlotte M.; Holden, Matthew T. G. (2018-02) - Journal article
    Staphylococcus aureus is an opportunistic pathogen and variable component of the human microbiota. In atopic eczema (AE) a characteristic of the disease is colonization by S. aureus, with exacerbations associated with an ...
  • MRSA transmission dynamics among interconnected acute, intermediate-term, and long-term healthcare facilities in Singapore 

    Chow, Angela; Lim, Vanessa W.; Khan, Ateeb; Pettigrew, Kerry; Lye, David C. B.; Kanagasabai, Kala; Phua, Kelvin; Krishnan, Prabha; Ang, Brenda; Marimuthu, Kalisvar; Hon, Pei-Yun; Koh, Jocelyn; Leong, Ian; Parkhill, Julian; Hsu, Li-Yang; Holden, Matthew T G (2017-05-15) - Journal article
    Background: Methicillin-resistant Staphylococcus aureus (MRSA) is the most common healthcare-associated multidrug-resistant organism. Despite the interconnectedness between acute care hospitals (ACHs) and intermediate- and ...