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Clinical Science and Epidemiology

  • Open Access
    Development of <span class="named-content genus-species" id="named-content-1">Candida auris</span> Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates
    Editor's Pick Research Article | Clinical Science and Epidemiology
    Development of Candida auris Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates

    Candida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and causes mainly hospital-associated outbreaks. To track and trace outbreaks and to relate them to new introductions from elsewhere, whole-genome sequencing and amplified fragment length polymorphism (AFLP) have been used for molecular typing....

    Theun de Groot, Ynze Puts, Indira Berrio, Anuradha Chowdhary, Jacques F. Meis
  • Open Access
    Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens
    Research Article | Clinical Science and Epidemiology
    Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens

    Globally, there are an estimated 10.6 million cases of meningitis and 288,000 deaths every year, with the vast majority occurring in low- and middle-income countries. In addition, many survivors suffer from long-term neurological sequelae. Most laboratories assay only for common bacterial etiologies using culture and directed PCR, and the majority of meningitis cases lack microbiological diagnoses, impeding institution of evidence-based...

    Senjuti Saha, Akshaya Ramesh, Katrina Kalantar, Roly Malaker, Md Hasanuzzaman, Lillian M. Khan, Madeline Y. Mayday, M. S. I. Sajib, Lucy M. Li, Charles Langelier, Hafizur Rahman, Emily D. Crawford, Cristina M. Tato, Maksuda Islam, Yun-Fang Juan, Charles de Bourcy, Boris Dimitrov, James Wang, Jennifer Tang, Jonathan Sheu, Rebecca Egger, Tiago Rodrigues De Carvalho, Michael R. Wilson, Samir K. Saha, Joseph L. DeRisi
  • Open Access
    Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> Lineage from the Indian Subcontinent
    Research Article | Clinical Science and Epidemiology
    Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent

    The Bengal Bay clone (ST772) is a community-associated and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh and India in 2004. In this study, we showed that the Bengal Bay clone emerged from a virulent progenitor circulating on the Indian subcontinent. Its subsequent global transmission was associated with travel or family contact in...

    Eike J. Steinig, Sebastian Duchene, D. Ashley Robinson, Stefan Monecke, Maho Yokoyama, Maisem Laabei, Peter Slickers, Patiyan Andersson, Deborah Williamson, Angela Kearns, Richard V. Goering, Elizabeth Dickson, Ralf Ehricht, Margaret Ip, Matthew V. N. O’Sullivan, Geoffrey W. Coombs, Andreas Petersen, Grainne Brennan, Anna C. Shore, David C. Coleman, Annalisa Pantosti, Herminia de Lencastre, Henrik Westh, Nobumichi Kobayashi, Helen Heffernan, Birgit Strommenger, Franziska Layer, Stefan Weber, Hege Vangstein Aamot, Leila Skakni, Sharon J. Peacock, Derek Sarovich, Simon Harris, Julian Parkhill, Ruth C. Massey, Mathew T. G. Holden, Stephen D. Bentley, Steven Y. C. Tong
  • Open Access
    A Single Salt Bridge in VIM-20 Increases Protein Stability and Antibiotic Resistance under Low-Zinc Conditions
    Research Article | Clinical Science and Epidemiology
    A Single Salt Bridge in VIM-20 Increases Protein Stability and Antibiotic Resistance under Low-Zinc Conditions

    Antibiotic resistance is a growing clinical threat. One of the most serious areas of concern is the ability of some bacteria to degrade carbapenems, drugs that are often reserved as last-resort antibiotics. Resistance to carbapenems can be conferred by a large group of related enzymes called metallo-β-lactamases that rely on zinc ions for function and for overall stability. Here, we studied an extensive panel of 45 different metallo-β-...

    Zishuo Cheng, Ben A. Shurina, Christopher R. Bethel, Pei W. Thomas, Steven H. Marshall, Caitlyn A. Thomas, Kundi Yang, Robert L. Kimble, Jonathan S. Montgomery, Matthew G. Orischak, Callie M. Miller, Jordan L. Tennenbaum, Jay C. Nix, David L. Tierney, Walter Fast, Robert A. Bonomo, Richard C. Page, Michael W. Crowder
  • Open Access
    High-Risk International Clones of Carbapenem-Nonsusceptible <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Endemic to Indonesian Intensive Care Units: Impact of a Multifaceted Infection Control Intervention Analyzed at the Genomic Level
    Research Article | Clinical Science and Epidemiology
    High-Risk International Clones of Carbapenem-Nonsusceptible Pseudomonas aeruginosa Endemic to Indonesian Intensive Care Units: Impact of a Multifaceted Infection Control Intervention Analyzed at the Genomic Level

    In low-to-middle-income countries such as Indonesia, work in intensive care units (ICUs) can be hampered by lack of resources. Conducting large epidemiological studies in such settings using genomic tools is rather challenging. Still, we were able to systematically study the transmissions of carbapenem-nonsusceptible strains of P. aeruginosa (CNPA) within and between...

    Andreu Coello Pelegrin, Yulia Rosa Saharman, Aurélien Griffon, Mattia Palmieri, Caroline Mirande, Anis Karuniawati, Rudyanto Sedono, Dita Aditianingsih, Wil H. F. Goessens, Alex van Belkum, Henri A. Verbrugh, Corné H. W. Klaassen, Juliëtte A. Severin
  • Open Access
    Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure
    Research Article | Clinical Science and Epidemiology
    Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure

    Antibiotic resistance hinders the treatment of bacterial infection. To guide effective therapy, clinical microbiology laboratories routinely perform susceptibility testing to determine the antibiotic sensitivity of an infecting pathogen. This approach relies on the assumption that it can reliably distinguish bacteria capable of expressing antibiotic resistance in patients, an idea challenged by the present study. We report that the...

    Louise Kime, Christopher P. Randall, Frank I. Banda, Francesc Coll, John Wright, Joseph Richardson, Joanna Empel, Julian Parkhill, Alex J. O’Neill
  • Open Access
    Vaginal Biomarkers That Predict Cervical Length and Dominant Bacteria in the Vaginal Microbiomes of Pregnant Women
    Research Article | Clinical Science and Epidemiology
    Vaginal Biomarkers That Predict Cervical Length and Dominant Bacteria in the Vaginal Microbiomes of Pregnant Women

    Premature birth and its complications are the largest contributors to infant death in the United States and globally. A short cervical length and the depletion of Lactobacillus species are known risk factors for preterm birth. However, in many resource-poor areas of the world, the technology to test for their occurrence is unavailable, and pregnant women with these risk factors are neither identified nor treated. In this study...

    Steven S. Witkin, Antonio F. Moron, Benjamin J. Ridenhour, Evelyn Minis, Alan Hatanaka, Stephanno G. P. Sarmento, Marcelo S. Franca, Francisco H. C. Carvalho, Tatiana K. Hamamoto, Rosiane Mattar, Ester Sabino, Iara M. Linhares, Marilza V. C. Rudge, Larry J. Forney
  • Open Access
    Plasmid Dissemination and Selection of a Multidrug-Resistant <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> Strain during Transplant-Associated Antibiotic Therapy
    Research Article | Clinical Science and Epidemiology
    Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy

    Antibiotic-resistant bacteria are a serious threat to medically fragile patient populations. The spread of antibiotic resistance through plasmid-mediated mechanisms is of grave concern as it can lead to the conversion of endogenous patient-associated strains to difficult-to-treat pathogens.

    Sean Conlan, Anna F. Lau, Clay Deming, Christine D. Spalding, ShihQueen Lee-Lin, Pamela J. Thomas, Morgan Park, John P. Dekker, Karen M. Frank, Tara N. Palmore, Julia A. Segre
  • Open Access
    Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly
    Research Article | Clinical Science and Epidemiology
    Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly

    Dietary flavonoids, which have been implicated in lowering chronic disease risk and improving blood pressure, represent a diverse group of polyphenolic compounds found in many commonly consumed foods such as tea, red wine, apples, and berries. The bioactivity and bioavailability of more dietary flavonoids can be influenced by gastrointestinal microbiome metabolism. With demonstrated prebiotic and antimicrobial effects in in vitro...

    Kerry L. Ivey, Andrew T. Chan, Jacques Izard, Aedin Cassidy, Geraint B. Rogers, Eric B. Rimm
  • Open Access
    Polymicrobial Nature of Tick-Borne Diseases
    Editor's Pick Research Article | Clinical Science and Epidemiology
    Polymicrobial Nature of Tick-Borne Diseases

    Tick-borne diseases have increased in prevalence in the United States and abroad. The reasons for these increases are multifactorial, but climate change is likely to be a major factor. One of the main features of the increase is the geographic expansion of tick vectors, notably Amblyomma americanum, which has brought new pathogens to new areas. The clinical spectrum of tick-borne diseases can range from asymptomatic to fatal...

    Santiago Sanchez-Vicente, Teresa Tagliafierro, James L. Coleman, Jorge L. Benach, Rafal Tokarz

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