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whole-genome sequencing

  • Open Access
    Genomic Epidemiology and Evolution of <em>Escherichia coli</em> in Wild Animals in Mexico
    Research Article | Host-Microbe Biology
    Genomic Epidemiology and Evolution of Escherichia coli in Wild Animals in Mexico

    Escherichia coli is a clinically important bacterial species implicated in human- and livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals.

    Robert Murphy, Martin Palm, Ville Mustonen, Jonas Warringer, Anne Farewell, Leopold Parts, Danesh Moradigaravand
  • 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
    Novel Effective <span class="named-content genus-species" id="named-content-1">Bacillus cereus</span> Group Species “<em>Bacillus clarus</em>” Is Represented by Antibiotic-Producing Strain ATCC 21929 Isolated from Soil
    Observation | Ecological and Evolutionary Science
    Novel Effective Bacillus cereus Group Species “Bacillus clarus” Is Represented by Antibiotic-Producing Strain ATCC 21929 Isolated from Soil

    The B. cereus group comprises numerous closely related lineages with various degrees of pathogenic potential and industrial relevance. Species-level taxonomic classification of B. cereus group strains is important for risk evaluation and communication but remains challenging. Biochemical and...

    Marysabel Méndez Acevedo, Laura M. Carroll, Manjari Mukherjee, Emma Mills, Lingzi Xiaoli, Edward G. Dudley, Jasna Kovac
  • Open Access
    Phylogenetic Characterization Reveals Prevalent <span class="named-content genus-species" id="named-content-1">Shigella flexneri</span> ST100 Clone in Beijing, China, 2005 to 2018
    Research Article | Clinical Science and Epidemiology
    Phylogenetic Characterization Reveals Prevalent Shigella flexneri ST100 Clone in Beijing, China, 2005 to 2018

    Beijing is the largest transportation hub in China, with a highly mobile population. Shigella flexneri is a major cause of bacillary dysentery in Beijing. However, little is known about the genetic features and population structure of locally circulating S. flexneri clones. Whole-genome sequencing...

    Lang Yang, Bing Lü, Quanyi Wang, Kaiying Wang, Yanfeng Lin, Chaojie Yang, Shaofu Qiu, Peng Li, Hongbin Song
  • Open Access
    Horizontal Plasmid Transfer among <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> Isolates Is the Key Factor for Dissemination of Extended-Spectrum β-Lactamases among Children in Tanzania
    Research Article | Clinical Science and Epidemiology
    Horizontal Plasmid Transfer among Klebsiella pneumoniae Isolates Is the Key Factor for Dissemination of Extended-Spectrum β-Lactamases among Children in Tanzania

    Horizontal spread of plasmids carrying multiple resistance genes is considered an important mechanism behind the global health problem caused by multidrug-resistant bacteria. Nevertheless, knowledge about spread of plasmids in a community is limited. Our detailed molecular analyses of K. pneumoniae isolated from hospitalized and healthy children in Tanzania disclosed...

    Torunn Pedersen, Marit Gjerde Tellevik, Øyvind Kommedal, Paul Christoffer Lindemann, Sabrina John Moyo, Jessin Janice, Bjørn Blomberg, Ørjan Samuelsen, Nina Langeland
  • Open Access
    IMP-38-Producing High-Risk Sequence Type 307 <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> Strains from a Neonatal Unit in China
    Research Article | Clinical Science and Epidemiology
    IMP-38-Producing High-Risk Sequence Type 307 Klebsiella pneumoniae Strains from a Neonatal Unit in China

    We described the genome and resistome characterization of a carbapenem-resistant Klebsiella pneumoniae ST307 strain carrying blaIMP-38 in China. This report highlights that the high-risk ST307 clone continues to acquire different antimicrobial resistance genes, posing significant challenges to clinical practice, and should be closely monitored....

    Siyi Wang, Juan Zhao, Ning Liu, Fang Yang, Yiming Zhong, Xiumei Gu, Zijuan Jian, Qun Yan, Qingxia Liu, Hongling Li, Yanming Li, Jing Liu, Hui Li, Liang Chen, Wenen Liu
  • Open Access
    An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (<span class="named-content genus-species" id="named-content-1">Puccinia striiformis</span> f. sp. <em>tritici</em>) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population
    Research Article | Host-Microbe Biology
    An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population

    Stripe rust is a destructive disease of wheat worldwide. Growing resistant cultivars is the most effective, easy-to-use, economical, and environmentally friendly strategy for the control of the disease. However, P. striiformis f. sp. tritici can produce new virulent races that may circumvent race-specific resistance. Therefore, understanding the genetic basis...

    Chongjing Xia, Yu Lei, Meinan Wang, Wanquan Chen, Xianming Chen
  • Open Access
    Combining Whole-Genome Sequencing and Multimodel Phenotyping To Identify Genetic Predictors of <em>Salmonella</em> Virulence
    Research Article | Host-Microbe Biology
    Combining Whole-Genome Sequencing and Multimodel Phenotyping To Identify Genetic Predictors of Salmonella Virulence

    Salmonella species are bacteria that are a major source of foodborne disease through contamination of a diversity of foods, including meat, eggs, fruits, nuts, and vegetables. More than 2,600 different Salmonella enterica serovars have been identified, and only a few of them are associated with illness in humans. Despite the fact that they are genetically...

    Alanna Crouse, Catherine Schramm, Jean-Guillaume Emond-Rheault, Adrian Herod, Maud Kerhoas, John Rohde, Samantha Gruenheid, Irena Kukavica-Ibrulj, Brian Boyle, Celia M. T. Greenwood, Lawrence D. Goodridge, Rafael Garduno, Roger C. Levesque, Danielle Malo, France Daigle
  • Open Access
    Insights on Population Structure and Within-Host Genetic Changes among Meningococcal Carriage Isolates from U.S. Universities
    Research Article | Host-Microbe Biology
    Insights on Population Structure and Within-Host Genetic Changes among Meningococcal Carriage Isolates from U.S. Universities

    U.S. university students are at a higher risk of invasive meningococcal disease than the general population. The responsible pathogen, Neisseria meningitidis, can be carried asymptomatically in the oropharynx; the dynamics of meningococcal carriage and the genetic features that distinguish carriage versus disease states are not completely understood. Through our...

    Sandeep J. Joseph, Nadav Topaz, How-Yi Chang, Melissa J. Whaley, Jeni T. Vuong, Alexander Chen, Fang Hu, Susanna E. Schmink, Laurel T. Jenkins, Lorraine D. Rodriguez-Rivera, Jennifer D. Thomas, Anna M. Acosta, Lucy McNamara, Heidi M. Soeters, Sarah Mbaeyi, Xin Wang
  • Open Access
    Natural Transmission of <span class="named-content genus-species" id="named-content-1">Helicobacter saguini</span> Causes Multigenerational Inflammatory Bowel Disease in C57/129 IL-10<sup>−/−</sup> Mice
    Observation | Host-Microbe Biology
    Natural Transmission of Helicobacter saguini Causes Multigenerational Inflammatory Bowel Disease in C57/129 IL-10−/− Mice

    While family history is a significant risk factor for developing inflammatory bowel disease (IBD), it is unclear whether the microbiome from parents is a transmissible influence on disease in their offspring. Furthermore, it is unknown whether IBD-associated microbes undergo genomic adaptations during multigenerational transmission and chronic colonization in their hosts. Herein, we show that a single bacterial species,...

    Anthony Mannion, Zeli Shen, Yan Feng, Dylan Puglisi, Sureshkumar Muthupalani, Mark T. Whary, James G. Fox

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