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Research Publications (Food Safety)

This page tracks research articles published in national and international peer-reviewed journals. Recent articles are available ahead of print and searchable by Journal, Article Title, and Category. Research publications are tracked across six categories: Bacterial Pathogens, Chemical Contaminants, Natural Toxins, Parasites, Produce Safety, and Viruses. Articles produced by USDA Grant Funding Agencies (requires login) and FDA Grant Funding Agencies (requires login) are also tracked in Scopus.

Displaying 51 - 75 of 286

  1. Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection

    • Journal of Clinical Microbiology
    • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in December 2019 and has quickly become a worldwide pandemic. In response, many diagnostic manufacturers have developed molecular assays for SARS-CoV-2 under the Food and Drug Administration (FDA) Emergency Use Authorization (EUA) pathway.

      • COVID-19
      • Viruses
  2. Optimizing a Screening Protocol for Potential Extended-Spectrum {beta}-Lactamase Escherichia coli on MacConkey Agar for Use in a Global Surveillance Program

    • Journal of Clinical Microbiology
    • The increasing prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is worrisome. Coordinated efforts to better understand global prevalence and risk factors are needed. Developing lower- and middle-income countries need reliable, readily available, and cost-effective solutions for detecting ESBL E. coli to contribute to global surveillance.

      • Bacterial pathogens
  3. Comparability of Titers of Antibodies against Seasonal Influenza Virus Strains as Determined by Hemagglutination Inhibition and Microneutralization Assays

    • Journal of Clinical Microbiology
    • We compared titers of antibodies against A/H1N1, A/H3N2, and B influenza virus strains collected pre- and postvaccination using hemagglutination inhibition (HI) and microneutralization (MN) assays and data from two vaccine trials: study 1, performed with a cell-grown trivalent influenza vaccine (TIVc) using cell-grown target virus in both assays, and study 2, performed with an egg-grown adjuvanted quadrivalent influenza vaccine (aQIVe) using egg-grown target virus.

      • Viruses
  4. Gold Standard Cholera Diagnostics Are Tarnished by Lytic Bacteriophage and Antibiotics

    • Journal of Clinical Microbiology
    • A fundamental, clinical, and scientific concern is how lytic bacteriophage, as well as antibiotics, impact diagnostic positivity. Cholera was chosen as a model disease to investigate this important question, because cholera outbreaks enable large enrollment, field methods are well established, and the predatory relationship between lytic bacteriophage and the etiologic agent Vibrio cholerae share commonalities across bacterial taxa.

      • Vibrio
      • Bacterial pathogens
  5. Diagnostic Accuracy of Nucleic Acid Amplification-Based Assays for Clostridium perfringens-Associated Diseases: a Systematic Review and Meta-analysis

    • Journal of Clinical Microbiology
    • Timely and accurate methods for detecting Clostridium perfringens-associated diseases (CPAD) are crucial to improve patient care. A number of studies have evaluated the accuracy of nucleic acid amplification tests (NAAT) in detecting CPAD, but decisive results about their effectiveness have not been reported. We conducted a meta-analysis to evaluate the diagnostic performance of NAAT for detecting C. perfringens in clinical diarrheal samples.

      • Clostridium perfringens
      • Bacterial pathogens
  6. Genomic Surveillance Enables Suitability Assessment of Salmonella Gene Targets Used for Culture-Independent Diagnostic Testing

    • Journal of Clinical Microbiology
    • Salmonella is a highly diverse genus consisting of over 2,600 serovars responsible for high-burden food- and waterborne gastroenteritis worldwide. Sensitivity and specificity of PCR-based culture-independent diagnostic testing (CIDT) systems for Salmonella, which depend on a highly conserved gene target, can be affected by single nucleotide polymorphisms (SNPs), indels, and genomic rearrangements within primer and probe sequences.

      • Salmonella
      • Bacterial pathogens
  7. Diagnostic Accuracy of Pan-Degenerate Amplification and Adaptation Assay for HIV-1 Drug Resistance Mutation Analysis in Low- and Middle-Income Countries

    • Journal of Clinical Microbiology
    • HIV drug resistance (HIVDR) is a barrier to sustained virologic suppression in low- and middle-income countries (LMICs). Point mutation assays targeting priority drug resistance mutations (DRMs) are being evaluated to improve access to HIVDR testing.

  8. Population Genomic Molecular Epidemiological Study of Macrolide-Resistant Streptococcus pyogenes in Iceland, 1995 to 2016: Identification of a Large Clonal Population with a pbp2x Mutation Conferring Reduced In Vitro {beta}-Lactam Susceptibility

    • Journal of Clinical Microbiology
    • Resistance to macrolide antibiotics is a global concern in the treatment of Streptococcus pyogenes (group A Streptococcus [GAS]) infections. In Iceland, since the detection of the first macrolide-resistant isolate in 1998, three epidemic waves of macrolide-resistant GAS infections have occurred, with peaks in 1999, 2004, and 2008.

  9. Evaluation of the FecalSwab for Stool Specimen Storage and Molecular Detection of Enteropathogens on the BD Max System

    • Journal of Clinical Microbiology
    • The FecalSwab system (Copan Italia, Brescia, Italy) is a convenient alternative to bulk stool for the diagnosis of enteric pathogens. Although the U.S. Food and Drug Administration (FDA) approved for transport and culture of enteric bacterial pathogens, the FecalSwab has not been well assessed for its suitability with molecular platforms.

  10. Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens

    • Journal of Clinical Microbiology
    • Several point-of-care (POC) molecular tests have received emergency use authorization (EUA) from the Food and Drug Administration (FDA) for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The test performance characteristics of the Accula (Mesa Biotech) SARS-CoV-2 POC test need to be evaluated to inform its optimal use. The aim of this study was to assess the test performance of the Accula SARS-CoV-2 test.

  11. The Role of Antibody Testing for SARS-CoV-2: Is There One?

    • Journal of Clinical Microbiology
    • The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) brought with it rapid development of both molecular and serologic assays for identification of COVID-19 infections. While Food and Drug Administration (FDA) emergency use authorization (EUA) is required for clinical application of SARS-CoV-2 molecular tests, submission for EUA is currently a voluntary process for manufacturers of serologic assays.

  12. Clinical Evaluation of Three Sample-to-Answer Platforms for Detection of SARS-CoV-2

    • Journal of Clinical Microbiology
    • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread across the globe. As part of the worldwide response, many molecular diagnostic platforms have been granted emergency use authorization (EUA) by the Food and Drug Administration (FDA) to identify SARS-CoV-2 positive patients.

  13. Understanding, Verifying, and Implementing Emergency Use Authorization Molecular Diagnostics for the Detection of SARS-CoV-2 RNA

    • Journal of Clinical Microbiology
    • The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has brought a new wave of challenges to health care, particularly in the area of rapid diagnostic test development and implementation. The diagnosis of acute coronavirus disease 2019 (COVID-19) is critically dependent on the detection of SARS-CoV-2 RNA from clinical specimens (e.g., nasopharyngeal swabs).

  14. Chimeric Protein Designed by Genome-Scale Immunoinformatics Enhances Serodiagnosis of Bovine Neosporosis

    • Journal of Clinical Microbiology
    • Neosporosis has become a concern since it is associated with abortion in cattle. Currently, in situ diagnosis is determined through anamnesis, evaluation of the history, and perception of the clinical signs of the herd. There is no practical and noninvasive test adapted to a large number of samples, which represents a gap for the use of new approaches that provide information about infections and the risks of herds.

      • Parasites
      • Toxoplasma gondii
      • Bacterial pathogens
  15. Multicenter Clinical Evaluation of the Revogene Strep A Molecular Assay for Detection of Streptococcus pyogenes from Throat Swab Specimens

    • Journal of Clinical Microbiology
    • Group A streptococcus (GAS) species cause bacterial pharyngitis in both adults and children. Early and accurate diagnosis of GAS is important for appropriate antibiotic therapy to prevent GAS sequalae. The Revogene Strep A molecular assay (Meridian Bioscience Canada Inc, Quebec City, QC, Canada) is an automated real-time PCR assay for GAS detection from throat swab specimens within approximately 70 min.

  16. Evaluation of NG-Test Carba 5 for Rapid Phenotypic Detection and Differentiation of Five Common Carbapenemase Families: Results of a Multicenter Clinical Evaluation

    • Journal of Clinical Microbiology
    • NG-Test Carba 5 is a rapid in vitro multiplex immunoassay for the phenotypic detection and differentiation of five common carbapenemase families (KPC, OXA-48-like, VIM, IMP, and NDM) directly from bacterial colonies. The assay is simple to perform and has recently received U.S. Food and Drug Administration clearance.

      • Bacterial pathogens
  17. Assessing the Use of PCR To Screen for Shedding of Salmonella enterica in Infected Humans

    • Journal of Clinical Microbiology
    • Recovery from enteric bacterial illness often includes a phase of organismal shedding over a period of days to months. The monitoring of this process through laboratory testing forms the foundation of public health action to prevent further transmission. Regulations in most jurisdictions in the United States exclude individuals who continue to shed certain organisms from sensitive occupations and situations, such as food handling, providing direct patient care, or attending day care.

      • Salmonella
      • Bacterial pathogens
  18. Genomic Analysis of Mycobacterium abscessus Complex Isolates Collected in Ireland between 2006 and 2017

    • Journal of Clinical Microbiology
    • Members of the Mycobacterium abscessus complex (MABC) are multidrug-resistant nontuberculous mycobacteria and cause opportunistic pulmonary infections in individuals with cystic fibrosis (CF). In this study, genomic analysis of MABC isolates was performed to gain greater insights into the epidemiology of circulating strains in Ireland.

  19. Practical Comparison of the BioFire FilmArray Pneumonia Panel to Routine Diagnostic Methods and Potential Impact on Antimicrobial Stewardship in Adult Hospitalized Patients with Lower Respiratory Tract Infections

    • Journal of Clinical Microbiology
    • Lower respiratory tract infections, including hospital-acquired and ventilator-associated pneumonia, are common in hospitalized patient populations. Standard methods frequently fail to identify the infectious etiology due to the polymicrobial nature of respiratory specimens and the necessity of ordering specific tests to identify viral agents.

  20. Genomic Epidemiology and Evolution of Diverse Lineages of Clinical Campylobacter jejuni Cocirculating in New Hampshire, USA, 2017

    • Journal of Clinical Microbiology
    • Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis worldwide. In the United States, New Hampshire was one of the 18 states that reported cases in the 2016 to 2018 multistate outbreak of multidrug-resistant C. jejuni. Here, we aimed to elucidate the baseline diversity of the wider New Hampshire C. jejuni population during the outbreak. We used genome sequences of 52 clinical isolates sampled in New Hampshire in 2017, including 1 of the 2 isolates from the outbreak.

      • Bacterial pathogens
      • Campylobacter
  21. Clinical Evaluation of the cobas SARS-CoV-2 Test and a Diagnostic Platform Switch during 48 Hours in the Midst of the COVID-19 Pandemic

    • Journal of Clinical Microbiology
    • Laboratories are currently witnessing extraordinary demand globally for sampling devices, reagents, consumables, and diagnostic instruments needed for timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To meet diagnostic needs as the pandemic grows, the U.S. Food and Drug Administration (FDA) recently granted several commercial SARS-CoV-2 tests Emergency Use Authorization (EUA), but manufacturer-independent evaluation data are scarce.

  22. Updates in Laboratory Diagnostics for Invasive Fungal Infections

    • Journal of Clinical Microbiology
    • Appropriate diagnosis of invasive fungal infections (IFIs) is critical due to the high rates of morbidity and mortality, as well as the substantial economic burden, associated with the management of these diseases.

  23. Evaluation and Optimization of the Clinical Accuracy of Hybribio's 14 High-Risk HPV with 16/18 Genotyping Assay within the VALGENT-3 Framework

    • Journal of Clinical Microbiology
    • Hybribio’s 14 High-Risk HPV with 16/18 genotyping real-time PCR (HBRT-H14) is a human papillomavirus (HPV) assay with approval from the China Food and Drug Administration that is widely used in China. VALGENT (VALidation of HPV GENotyping Tests) is an established framework for evaluating HPV tests’ clinical performance relative to validated comparators. The aim of this study was to assess the clinical accuracy of HBRT-H14 following international validation criteria.

  24. Development of an RNA Strand-Specific Hybridization Assay To Differentiate Replicating versus Nonreplicating Influenza A Viruses

    • Journal of Clinical Microbiology
    • Replication of influenza A virus (IAV) from negative-sense viral RNA (vRNA) requires the generation of positive-sense RNA (+RNA). Most molecular assays, such as conventional real-time reverse transcriptase PCR (rRT-PCR), detect total RNA in a sample without differentiating vRNA from +RNA. These assays are not designed to distinguish IAV infection versus exposure of an individual to an environment enriched with IAVs but wherein no viral replication occurs.

  25. Differentiation of Community-Associated and Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates and Identification of spa Types by Use of PCR and High-Resolution Melt Curve Analysis

    • Journal of Clinical Microbiology
    • Infections due to methicillin-resistant Staphylococcus aureus (MRSA) are present worldwide and represent a major public health concern. The capability of PCR followed by high-resolution melt (HRM) curve analysis for the detection of community-associated and livestock-associated MRSA strains and the identification of staphylococcal protein A (spa) locus was evaluated in 74 MRSA samples which were isolated from the environment, humans, and pigs on a single piggery.

      • Staphylococcus aureus
      • Bacterial pathogens