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genome analysis

  • Open Access
    Analysis of Serial Multidrug-Resistant Tuberculosis Strains Causing Treatment Failure and Within-Host Evolution by Whole-Genome Sequencing
    Research Article | Molecular Biology and Physiology
    Analysis of Serial Multidrug-Resistant Tuberculosis Strains Causing Treatment Failure and Within-Host Evolution by Whole-Genome Sequencing

    Few studies have focused on the reasons for the low cure rate of multidrug-resistant tuberculosis in China and within-host evolution during treatment, which is of great significance for improving clinical treatment regimens. Acquired resistance events were common during the ineffective treatment, among which resistance to amikacin and high-level moxifloxacin were the most common.

    Xinchang Chen, Guiqing He, Siran Lin, Shiyong Wang, Feng Sun, Jiazhen Chen, Wenhong Zhang
  • Open Access
    Origin of OXA-23 Variant OXA-239 from a Recently Emerged Lineage of <span class="named-content genus-species" id="named-content-1">Acinetobacter baumannii</span> International Clone V
    Research Article | Clinical Science and Epidemiology
    Origin of OXA-23 Variant OXA-239 from a Recently Emerged Lineage of Acinetobacter baumannii International Clone V

    A. baumannii is a major cause of nosocomial infections all over the world. Although many isolates from developed countries have been studied in terms of their genome sequence, isolates from Latin America have been much less studied. In this study, using a population genomics approach considering the whole genomes of 148 isolates, we describe the recent emergence of...

    Lucia Graña-Miraglia, Benjamin A. Evans, Luis E. López-Jácome, Melissa Hernández-Durán, Claudia Adriana Colín-Castro, Patricia Volkow-Fernández, Miguel A. Cevallos, Rafael Franco-Cendejas, Santiago Castillo-Ramírez
  • Open Access
    IMP-68, a Novel IMP-Type Metallo-β-Lactamase in Imipenem-Susceptible <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span>
    Observation | Clinical Science and Epidemiology
    IMP-68, a Novel IMP-Type Metallo-β-Lactamase in Imipenem-Susceptible Klebsiella pneumoniae

    IMP-type metallo-β-lactamases comprise one group of the “Big 5” carbapenemases. Here, a novel blaIMP-68 gene encoding IMP-68 (harboring a Ser262Gly point mutant of IMP-11) was discovered from meropenem-resistant but imipenem-susceptible Klebsiella pneumoniae TA6363. The Ser262Gly substitution was previously identified as important for substrate...

    Hiroaki Kubota, Yasunori Suzuki, Rumi Okuno, Yumi Uchitani, Tsukasa Ariyoshi, Nobuyuki Takemura, Fuminori Mihara, Kazuhisa Mezaki, Norio Ohmagari, Mari Matsui, Satowa Suzuki, Tsuyoshi Sekizuka, Makoto Kuroda, Keiko Yokoyama, Kenji Sadamasu
  • Open Access
    Multiple β-Lactam Resistance Gene-Carrying Plasmid Harbored by <span class="named-content genus-species" id="named-content-1">Klebsiella quasipneumoniae</span> Isolated from Urban Sewage in Japan
    Research Article | Clinical Science and Epidemiology
    Multiple β-Lactam Resistance Gene-Carrying Plasmid Harbored by Klebsiella quasipneumoniae Isolated from Urban Sewage in Japan

    In our investigation of urban wastewater in Japan, carbapenem-resistant Klebsiella quasipneumoniae subsp. quasipneumoniae was isolated that carried the pTMSNI47-1 plasmid, which carries four β-lactamase genes and has transferability among Enterobacteriaceae. pTMSNI47-1 was found to encode a rarely reported carbapenemase, KHM-1. Cooperative effects of...

    Yasunori Suzuki, Miki Ida, Hiroaki Kubota, Tsukasa Ariyoshi, Ko Murakami, Makiko Kobayashi, Rei Kato, Akihiko Hirai, Jun Suzuki, Kenji Sadamasu
  • Open Access
    Discovery of <em>mcr-1</em>-Mediated Colistin Resistance in a Highly Virulent <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Lineage
    Research Article | Clinical Science and Epidemiology
    Discovery of mcr-1-Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage

    Escherichia coli ST95 is a globally disseminated clone frequently associated with bloodstream infections and neonatal meningitis. However, the ST95 lineage is defined by low levels of drug resistance amongst clinical isolates, which normally provides for uncomplicated treatment options. Here, we provide the first detailed genomic analysis of an...

    Brian M. Forde, Hosam M. Zowawi, Patrick N. A. Harris, Leah Roberts, Emad Ibrahim, Nissar Shaikh, Anand Deshmukh, Mazen A. Sid Ahmed, Muna Al Maslamani, Kyra Cottrell, Ella Trembizki, Lana Sundac, Heidi H. Yu, Jian Li, Mark A. Schembri, David M. Whiley, David L. Paterson, Scott A. Beatson
  • Open Access
    Highly Reduced Genome of the New Species <em>Mycobacterium uberis</em>, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli
    Research Article | Host-Microbe Biology
    Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli

    M. uberis is an emerging skin pathogen in dairy animals. Its genome underwent massive reduction and gene decay, leading to a minimal set of genes required for an obligatory intracellular lifestyle, which highly resembles the evolution of the leprosy agents M. leprae and...

    Andrej Benjak, Charlotte Avanzi, Yvonne Benito, Franck Breysse, Christophe Chartier, Maria-Laura Boschiroli, Christine Fourichon, Lorraine Michelet, Didier Pin, Jean-Pierre Flandrois, Pierre Bruyere, Oana Dumitrescu, Stewart T. Cole, Gerard Lina
  • Open Access
    The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span>
    Research Article | Therapeutics and Prevention
    The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli

    The emergence of pathogens resistant against most or all of the antibiotics currently used in human therapy is a global threat, and therefore the search for antimicrobials with novel targets and modes of action is of utmost importance. The myxobacterial secondary metabolite carolacton had previously been shown to inhibit biofilm formation and growth of streptococci. Here, we investigated if carolacton could act against Gram-negative...

    Jannik Donner, Michael Reck, Boyke Bunk, Michael Jarek, Constantin Benjamin App, Jan P. Meier-Kolthoff, Jörg Overmann, Rolf Müller, Andreas Kirschning, Irene Wagner-Döbler
  • Open Access
    Genomewide Mutational Diversity in <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Population Evolving in Prolonged Stationary Phase
    Research Article | Ecological and Evolutionary Science
    Genomewide Mutational Diversity in Escherichia coli Population Evolving in Prolonged Stationary Phase

    Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few...

    Savita Chib, Farhan Ali, Aswin Sai Narain Seshasayee
  • Open Access
    Genome Diversity, Recombination, and Virulence across the Major Lineages of <em>Paracoccidioides</em>
    Research Article | Ecological and Evolutionary Science
    Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides

    Characterization of genetic differences between lineages of the dimorphic human-pathogenic fungus Paracoccidioides can identify changes linked to important phenotypes and guide the development of new diagnostics and treatments. In this article, we compared genomes of 31 diverse isolates representing the major lineages of Paracoccidioides spp. and completed the first annotated genome sequences for the PS3 and PS4...

    José F. Muñoz, Rhys A. Farrer, Christopher A. Desjardins, Juan E. Gallo, Sean Sykes, Sharadha Sakthikumar, Elizabeth Misas, Emily A. Whiston, Eduardo Bagagli, Celia M. A. Soares, Marcus de M. Teixeira, John W. Taylor, Oliver K. Clay, Juan G. McEwen, Christina A. Cuomo
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