Clinical Science and Epidemiology
Research Article | Clinical Science and EpidemiologyEnd-to-End Protocol for the Detection of SARS-CoV-2 from Built EnvironmentsThe ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (the virus responsible for coronavirus disease 2019 [COVID-19]) pandemic has led to a global slowdown with far-reaching financial and social impacts. The SARS-CoV-2 respiratory virus is primarily transmitted from person to person through inhalation of infected droplets or aerosols. However, some studies have shown that virions can remain infectious on surfaces for...
Sponsored Content Minireview | Clinical Science and EpidemiologyThe Gut Microbiome and Individual-Specific Responses to DietNutritional content and timing are increasingly appreciated to constitute important human variables collectively impacting all aspects of human physiology and disease. However, person-specific mechanisms driving nutritional impacts on the human host remain incompletely understood, while current dietary recommendations remain empirical and nonpersonalized. Precision nutrition aims to harness individualized bodies of data, including the...
Research Article | Clinical Science and EpidemiologyBeneficial Chromosomal Integration of the Genes for CTX-M Extended-Spectrum β-Lactamase in Klebsiella pneumoniae for Stable PropagationDominant F-type plasmids harboring the gene have been pointed out to be responsible for the dissemination of the CTX-M extended-spectrum-β-lactamase (ESBL)-producing K. pneumoniae. Recently, the emergence of K. pneumoniae isolates with the blaCTX-M gene in their chromosomes has...
Research Article | Clinical Science and EpidemiologyOscillatory Dynamics in Infectivity and Death Rates of COVID-19The infectivity and death rates for COVID-19 have been observed in many countries around the world as well as in the collective data of the whole world. These oscillations show distinct circaseptan periodicity, which could be associated with numerous biological reasons as well as with improper reporting of the data collected. Since very different results are observed in different countries and even continents, such as Sweden (very...
Research Article | Clinical Science and EpidemiologyOscillations in U.S. COVID-19 Incidence and Mortality Data Reflect Diagnostic and Reporting FactorsThe incidence and mortality data for the COVID-19 data in the United States show periodic oscillations, giving the curve a distinctive serrated pattern. In this study, we show that these periodic highs and lows in incidence and mortality data are due to daily differences in testing for the virus and death reporting, respectively. These findings are important because they provide an explanation based on public health practices and...
Research Article | Clinical Science and EpidemiologyComparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic StudiesWe compared four different oral collection methods for studying the human oral microbiome: an OMNIgene ORAL kit, Scope mouthwash, nonethanol mouthwash, and Saccomanno’s fixative. Our study shows that the type of the collection method can have a large impact on the results of an oral microbiome analysis. We recommend that one consistent oral collection method should be used for all oral microbiome comparisons. While Scope and nonethanol...
Research Article | Clinical Science and EpidemiologySubspecies Niche Specialization in the Oral Microbiome Is Associated with Nasopharyngeal Carcinoma RiskThe relationship between oral health and the risk of nasopharyngeal carcinoma (NPC) was previously established. However, the role of oral microbiome has not been evaluated in the disease in a large epidemiological study. This paper clearly establishes a difference in the oral microbiomes between NPC patients and healthy controls which cannot be explained by other confounding factors. It furthermore identifies a pair of closely related...
Research Article | Clinical Science and EpidemiologyParallel Analysis of Cystic Fibrosis Sputum and Saliva Reveals Overlapping Communities and an Opportunity for Sample DecontaminationCystic fibrosis is an inherited disease characterized by chronic respiratory tract infection and progressive lung disease. Studies of cystic fibrosis lung microbiology often rely on expectorated sputum to reflect the microbiota present in the lower airways. Passage of sputum through the oropharynx during collection, however, contributes microbes present in saliva to the sample, which could confound interpretation of results. Using...
Research Article | Clinical Science and EpidemiologyStool Samples of Acute Diarrhea Inpatients as a Reservoir of ST11 Hypervirulent KPC-2-Producing Klebsiella pneumoniaeChina has been experiencing a rapid increase in the number of nosocomial infections caused by carbapenem-resistant Klebsiella pneumoniae ST11 (ST11-CRKP) for decades. The emergence of hypervirulent ST11-CRKP (ST11-CR-HvKP) strains is expected to become a serious public health issue in China, considering that carbapenem resistance and virulence have converged in an...
Research Article | Clinical Science and EpidemiologyHigh-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic TherapySubjects with cystic fibrosis battle polymicrobial lung infections throughout their lifetime. Although antibiotic therapy is a principal treatment for CF lung disease, we have little understanding of how antibiotics affect the CF lung microbiome and metabolome and how much the community changes on daily timescales. By analyzing 594 longitudinal CF sputum samples from six adult subjects, we show that the sputum microbiome and metabolome...