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Clinical Science and Epidemiology

  • Open Access
    <span class="named-content genus-species" id="named-content-1">Streptococcus pyogenes</span> Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island
    Research Article | Clinical Science and Epidemiology
    Streptococcus pyogenes Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island

    Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-thirds of CU are caused by Treponema pallidum subspecies pertenue and Haemophilus ducreyi, the cause(s) of the remaining one-third is unknown.

    Brad Griesenauer, Camila González-Beiras, Katherine R. Fortney, Huaiying Lin, Xiang Gao, Charmie Godornes, David E. Nelson, Barry P. Katz, Sheila A. Lukehart, Oriol Mitjà, Qunfeng Dong, Stanley M. Spinola
  • Open Access
    Emergence of the Novel Aminoglycoside Acetyltransferase Variant <em>aac(6′)-Ib-D179Y</em> and Acquisition of Colistin Heteroresistance in Carbapenem-Resistant <em>Klebsiella pneumoniae</em> Due to a Disrupting Mutation in the DNA Repair Enzyme MutS
    Research Article | Clinical Science and Epidemiology
    Emergence of the Novel Aminoglycoside Acetyltransferase Variant aac(6′)-Ib-D179Y and Acquisition of Colistin Heteroresistance in Carbapenem-Resistant Klebsiella pneumoniae Due to a Disrupting Mutation in the DNA Repair Enzyme MutS

    The emergence of multidrug resistance in pathogens such as Klebsiella pneumoniae is of great clinical concern. Antimicrobial resistance sometimes arises during the course of an infection.

    Toyotaka Sato, Takayuki Wada, Suguru Nishijima, Yukari Fukushima, Chie Nakajima, Yasuhiko Suzuki, Satoshi Takahashi, Shin-ichi Yokota
  • Open Access
    On the Origin of <span class="named-content genus-species" id="named-content-1">Candida auris</span>: Ancestor, Environmental Stresses, and Antiseptics
    Opinion/Hypothesis | Clinical Science and Epidemiology
    On the Origin of Candida auris: Ancestor, Environmental Stresses, and Antiseptics

    Candida auris has emerged as a serious threat to the health care settings. Advancements in molecular biology have provided several insights into the evolution of C. auris since it was first described in 2009.

    Megha Sharma, Arunaloke Chakrabarti
  • 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
    Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients
    Research Article | Clinical Science and Epidemiology
    Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients

    SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to...

    Heba H. Mostafa, John A. Fissel, Brian Fanelli, Yehudit Bergman, Victoria Gniazdowski, Manoj Dadlani, Karen C. Carroll, Rita R. Colwell, Patricia J. Simner
  • Open Access
    Na<sup>+</sup>-NQR Confers Aminoglycoside Resistance via the Regulation of <span class="sc">l-</span>Alanine Metabolism
    Research Article | Clinical Science and Epidemiology
    Na+-NQR Confers Aminoglycoside Resistance via the Regulation of l-Alanine Metabolism

    The Na+-NQR complex functions as a unique redox-driven sodium pump, generating membrane potential directly. However, whether it mediates generation of membrane potential indirectly is unknown. The present study shows that the Na+-NQR complex impacts membrane potential through other antiporter families Atp and Mnh. It proceeds by ATP and then cAMP/CRP regulon, which inhibits l-alanine...

    Ming Jiang, Su-fang Kuang, Shi-shi Lai, Song Zhang, Jun Yang, Bo Peng, Xuan-xian Peng, Zhuang-gui Chen, Hui Li
  • 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
    Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area
    Research Article | Clinical Science and Epidemiology
    Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area

    There is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, TX, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture and evolution and the relationship between virus genotypes and patient...

    S. Wesley Long, Randall J. Olsen, Paul A. Christensen, David W. Bernard, James J. Davis, Maulik Shukla, Marcus Nguyen, Matthew Ojeda Saavedra, Prasanti Yerramilli, Layne Pruitt, Sishir Subedi, Hung-Che Kuo, Heather Hendrickson, Ghazaleh Eskandari, Hoang A. T. Nguyen, J. Hunter Long, Muthiah Kumaraswami, Jule Goike, Daniel Boutz, Jimmy Gollihar, Jason S. McLellan, Chia-Wei Chou, Kamyab Javanmardi, Ilya J. Finkelstein, James M. Musser
  • Open Access
    The Interaction of Natural and Vaccine-Induced Immunity with Social Distancing Predicts the Evolution of the COVID-19 Pandemic
    Research Article | Clinical Science and Epidemiology
    The Interaction of Natural and Vaccine-Induced Immunity with Social Distancing Predicts the Evolution of the COVID-19 Pandemic

    The ability of our society to function effectively moving forward will depend on how the spread of the SARS-CoV-2 virus is contained. Immunity to the virus will be critical to this equation.

    Michael F. Good, Michael T. Hawkes
  • Open Access
    Immune Response and Microbiota Profiles during Coinfection with <span class="named-content genus-species" id="named-content-1">Plasmodium vivax</span> and Soil-Transmitted Helminths
    Research Article | Clinical Science and Epidemiology
    Immune Response and Microbiota Profiles during Coinfection with Plasmodium vivax and Soil-Transmitted Helminths

    Plasmodium (malaria) and helminth parasite coinfections are frequent, and both infections can be affected by the host gut microbiota. However, the relationship between coinfection and the gut microbiota is unclear. By performing comprehensive analyses on blood/stool samples from 130 individuals in Colombia, we found that the gut microbiota may have a stronger relationship with the number of...

    Alice V. Easton, Mayra Raciny-Aleman, Victor Liu, Erica Ruan, Christian Marier, Adriana Heguy, Maria Fernanda Yasnot, Ana Rodriguez, P’ng Loke

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