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phylogeny

  • Global Epidemiology and Evolutionary History of <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> ST45
    Epidemiology
    Global Epidemiology and Evolutionary History of Staphylococcus aureus ST45

    Staphylococcus aureus ST45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. It is one of the most prevalent carrier lineages but also frequently causes severe invasive disease, such as bacteremia. Little is known about its evolutionary history. In this study, we used whole-genome sequencing to analyze a large collection of 451...

    N. Effelsberg, M. Stegger, L. Peitzmann, O. Altinok, G. W. Coombs, B. Pichon, A. Kearns, P. R. Randad, C. D. Heaney, S. Bletz, F. Schaumburg, A. Mellmann
  • Open Access
    Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance
    Minireview
    Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance

    Foodborne pathogen surveillance in the United States is transitioning from strain identification using restriction digest technology (pulsed-field gel electrophoresis [PFGE]) to shotgun sequencing of the entire genome (whole-genome sequencing [WGS]). WGS requires a new suite of analysis tools, some of which have long histories in academia but are new to the field of public health and regulatory decision making.

    Ruth E. Timme, Errol Strain, Joseph D. Baugher, Steven Davis, Narjol Gonzalez-Escalona, Maria Sanchez Leon, Marc W. Allard, Eric W. Brown, Sandra Tallent, Hugh Rand
  • Bacteriology
    Whole-Genome Sequencing of Aggregatibacter Species Isolated from Human Clinical Specimens and Description of Aggregatibacter kilianii sp. nov.
    May Murra, Lisbeth Lützen, Aynur Barut, Reinhard Zbinden, Marianne Lund, Palle Villesen, Niels Nørskov-Lauritsen
  • Clinical Veterinary Microbiology
    Phylogenetic Characterization of Salmonella enterica Serovar Typhimurium and Its Monophasic Variant Isolated from Food Animals in Japan Revealed Replacement of Major Epidemic Clones in the Last 4 Decades
    Nobuo Arai, Tsuyoshi Sekizuka, Yukino Tamamura, Kiyoshi Tanaka, Lisa Barco, Hidemasa Izumiya, Masahiro Kusumoto, Atsushi Hinenoya, Shinji Yamasaki, Taketoshi Iwata, Ayako Watanabe, Makoto Kuroda, Ikuo Uchida, Masato Akiba
  • Virology
    Comparative Evaluation of Subtyping Tools for Surveillance of Newly Emerging HIV-1 Strains
    Lavinia Fabeni, Giulia Berno, Joseph Fokam, Ada Bertoli, Claudia Alteri, Caterina Gori, Federica Forbici, Desiré Takou, Alessandra Vergori, Mauro Zaccarelli, Gaetano Maffongelli, Vanni Borghi, Alessandra Latini, Alfredo Pennica, Claudio Maria Mastroianni, Francesco Montella, Cristina Mussini, Massimo Andreoni, Andrea Antinori, Carlo Federico Perno, Maria Mercedes Santoro, The Resistance Study Group
  • Open Access
    Epidemiology
    Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus
    Narjol Gonzalez-Escalona, Keith A. Jolley, Elizabeth Reed, Jaime Martinez-Urtaza
  • Open Access
    Bacteriology
    Epidemiological and Molecular Characterization of an Invasive Group A Streptococcus emm32.2 Outbreak
    Jennifer E. Cornick, Anmol M. Kiran, Roberto Vivancos, Jon Van Aartsen, Jenny Clarke, Edward Bevan, Mansoor Alsahag, Maaike Alaearts, Laura Bricio Moreno, Howard F. Jenkinson, Angela H. Nobbs, James Anson, Aras Kadioglu, Neil French, Dean B. Everett
  • Open Access
    Epidemiology
    Comparative Genome Analysis and Global Phylogeny of the Toxin Variant Clostridium difficile PCR Ribotype 017 Reveals the Evolution of Two Independent Sublineages
    M. D. Cairns, M. D. Preston, C. L. Hall, D. N. Gerding, P. M. Hawkey, H. Kato, H. Kim, E. J. Kuijper, T. D. Lawley, H. Pituch, S. Reid, B. Kullin, T. V. Riley, K. Solomon, P. J. Tsai, J. S. Weese, R. A. Stabler, B. W. Wren
  • Mycology
    Multilocus Phylogeny and Antifungal Susceptibility of Aspergillus Section Circumdati from Clinical Samples and Description of A. pseudosclerotiorum sp. nov
    J. P. Z. Siqueira, D. A. Sutton, J. Gené, D. García, N. Wiederhold, S. W. Peterson, J. Guarro
  • Letter to the Editor
    The groEL Gene Is a Promising Target for Species-Level Identification of Tsukamurella
    Jade L. L. Teng, Ying Tang, Tsz Ho Chiu, Candy L. W. Cheung, Antonio H. Y. Ngan, Cheung Ngai, Samson S. Y. Wong, Tak-Lun Que, Susanna K. P. Lau, Patrick C. Y. Woo

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