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genomics

  • Open Access
    Evolutionary Dynamics Based on Comparative Genomics of Pathogenic <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Lineages Harboring Polyketide Synthase (<em>pks</em>) Island
    Editor's Pick Research Article | Clinical Science and Epidemiology
    Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island

    Extraintestinal pathologies caused by highly virulent strains of E. coli amount to clinical implications with high morbidity and mortality rates. Pathogenic E. coli strains are evolving with the horizontal acquisition of mobile genetic elements, including pathogenicity islands such as the pks...

    Arya Suresh, Sabiha Shaik, Ramani Baddam, Amit Ranjan, Shamsul Qumar, Savita Jadhav, Torsten Semmler, Irfan A. Ghazi, Lothar H. Wieler, Niyaz Ahmed
  • Open Access
    Genomic Drivers of Multidrug-Resistant <em>Shigella</em> Affecting Vulnerable Patient Populations in the United States and Abroad
    Research Article | Clinical Science and Epidemiology
    Genomic Drivers of Multidrug-Resistant Shigella Affecting Vulnerable Patient Populations in the United States and Abroad

    Multidrug-resistant Shigella isolates with resistance to macrolides are an emerging public health threat. We define a plasmid/pathogen complex behind infections seen in the United States and globally in vulnerable patient populations and identify multiple outbreaks in the United States and evidence of intercontinental transmission.

    Jay Noboru Worley, Kiran Javkar, Maria Hoffmann, Kristen Hysell, Amanda Garcia-Williams, Kaitlin Tagg, Sanjat Kanjilal, Errol Strain, Mihai Pop, Marc Allard, Louise Francois Watkins, Lynn Bry
  • Open Access
    Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
    Research Article | Clinical Science and Epidemiology
    Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

    Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread.

    Alexander Crits-Christoph, Rose S. Kantor, Matthew R. Olm, Oscar N. Whitney, Basem Al-Shayeb, Yue Clare Lou, Avi Flamholz, Lauren C. Kennedy, Hannah Greenwald, Adrian Hinkle, Jonathan Hetzel, Sara Spitzer, Jeffery Koble, Asako Tan, Fred Hyde, Gary Schroth, Scott Kuersten, Jillian F. Banfield, Kara L. Nelson
  • Open Access
    Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span>
    Research Article | Clinical Science and Epidemiology
    Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in Staphylococcus aureus

    The majority of Staphylococcus aureus strains causing human disease are methicillin-susceptible (MSSA) and can be treated with antistaphylococcal penicillins (such as oxacillin). While acquisition of the mec gene represents the main resistance mechanism to oxacillin, S. aureus can acquire...

    Stefano G. Giulieri, Romain Guérillot, Jason C. Kwong, Ian R. Monk, Ashleigh S. Hayes, Diane Daniel, Sarah Baines, Norelle L. Sherry, Natasha E. Holmes, Peter Ward, Wei Gao, Torsten Seemann, Timothy P. Stinear, Benjamin P. Howden
  • Open Access
    Whole-Genome Analysis of Clinical <span class="named-content genus-species" id="named-content-1">Vibrio cholerae</span> O1 in Kolkata, India, and Dhaka, Bangladesh, Reveals Two Lineages of Circulating Strains, Indicating Variation in Genomic Attributes
    Research Article | Clinical Science and Epidemiology
    Whole-Genome Analysis of Clinical Vibrio cholerae O1 in Kolkata, India, and Dhaka, Bangladesh, Reveals Two Lineages of Circulating Strains, Indicating Variation in Genomic Attributes

    Cholera continues to be a global concern, as large epidemics have occurred recently in Haiti, Yemen, and countries of sub-Saharan Africa. A single lineage of Vibrio cholerae O1 has been considered to be introduced into these regions from South Asia and to cause the spread of cholera. Using genomic epidemiology, we showed that two distinct lineages exist in Bengal, one...

    Daichi Morita, Masatomo Morita, Munirul Alam, Asish K. Mukhopadhyay, Fatema-tuz Johura, Marzia Sultana, Shirajum Monira, Niyaz Ahmed, Goutam Chowdhury, Shanta Dutta, Thandavarayan Ramamurthy, Prosenjit Samanta, Eizo Takahashi, Keinosuke Okamoto, Hidemasa Izumiya, Makoto Ohnishi
  • Open Access
    Gene Loss and Acquisition in Lineages of <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Evolving in Cystic Fibrosis Patient Airways
    Research Article | Host-Microbe Biology
    Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways

    Bacterial airway infections, predominantly caused by P. aeruginosa, are a major cause of mortality and morbidity of CF patients. While short insertions and deletions as well as point mutations occurring during infection are well studied, there is a lack of understanding of how gene loss and acquisition play roles in bacterial adaptation to the human airways. Here, we...

    Migle Gabrielaite, Helle K. Johansen, Søren Molin, Finn C. Nielsen, Rasmus L. Marvig
  • Open Access
    Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance
    Minireview | Molecular Biology and Physiology
    Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance

    The landscape of infectious fungal agents includes previously unidentified or rare pathogens with the potential to cause unprecedented casualties in biodiversity, food security, and human health. The influences of human activity, including the crisis of climate change, along with globalized transport, are underlying factors shaping fungal adaptation to increased temperature and expanded geographical regions. Furthermore, the emergence...

    B. Ball, M. Langille, J. Geddes-McAlister
  • Open Access
    Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth
    Research Article | Applied and Environmental Science
    Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth

    Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole...

    John I. Miller, Stephen Techtmann, Dominique Joyner, Nagissa Mahmoudi, Julian Fortney, James A. Fordyce, Nargiz GaraJayeva, Faig S. Askerov, Claudio Cravid, Maarten Kuijper, Oliver Pelz, Terry C. Hazen
  • Open Access
    Phenotypic Parallelism during Experimental Adaptation of a Free-Living Bacterium to the Zebrafish Gut
    Research Article | Host-Microbe Biology
    Phenotypic Parallelism during Experimental Adaptation of a Free-Living Bacterium to the Zebrafish Gut

    Although animals encounter many bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. We used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of ...

    Jarrett F. Lebov, Brandon H. Schlomann, Catherine D. Robinson, Brendan J. M. Bohannan
  • Open Access
    The Hypercomplex Genome of an Insect Reproductive Parasite Highlights the Importance of Lateral Gene Transfer in Symbiont Biology
    Observation | Ecological and Evolutionary Science
    The Hypercomplex Genome of an Insect Reproductive Parasite Highlights the Importance of Lateral Gene Transfer in Symbiont Biology

    The biology of many bacteria is critically dependent on genes carried on plasmid and phage mobile elements. These elements shuttle between microbial species, thus providing an important source of biological innovation across taxa. It has recently been recognized that mobile elements are also important in symbiotic bacteria, which form long-lasting interactions with their host. In this study, we report a bacterial symbiont genome that...

    Crystal L. Frost, Stefanos Siozios, Pol Nadal-Jimenez, Michael A. Brockhurst, Kayla C. King, Alistair C. Darby, Gregory D. D. Hurst

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