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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 26 - 50 of 286

  1. Determination of Genomic Epidemiology of Historical Clostridium perfringens Outbreaks in New York State by Use of Two Web-Based Platforms: National Center for Biotechnology Information Pathogen Detection and FDA GalaxyTrakr

    • Journal of Clinical Microbiology
    • Clostridium perfringens is the second leading cause of bacterial foodborne illness in the United States. The Wadsworth Center (WC) at the New York State Department of Health enumerates infectious dose from primary patient and food samples and, until recently, identified C. perfringens to the species level only. We investigated whether whole-genome sequence-based subtyping could benefit epidemiological investigations of this pathogen, as it has with other enteric organisms.

      • Bacterial pathogens
      • Clostridium perfringens
  2. Method for Specific Identification of the Emerging Zoonotic Pathogen Vibrio vulnificus Lineage 3 (Formerly Biotype 3)

    • Journal of Clinical Microbiology
    • Vibrio vulnificus is a zoonotic pathogen that is spreading worldwide due to global warming. Lineage 3 (L3; formerly biotype 3) includes the strains of the species with the unique ability to cause fish farm-linked outbreaks of septicemia. The L3 strains emerged recently and are particularly virulent and difficult to identify.

      • Bacterial pathogens
      • Vibrio
  3. Clinical Performance of the Point-of-Care cobas Liat for Detection of SARS-CoV-2 in 20 Minutes: a Multicenter Study

    • Journal of Clinical Microbiology
    • Highly accurate testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the point of care (POC) is an unmet diagnostic need in emergency care and time-sensitive outpatient care settings. Reverse transcription-PCR (RT-PCR) technology is the gold standard for SARS-CoV-2 diagnostics. We performed a multisite U.S. study comparing the clinical performance of the first U.S.

  4. Diagnostic Accuracy of Four Commercial Triplex Immunochromatographic Tests for Rapid Detection of Rotavirus, Adenovirus, and Norovirus in Human Stool Samples

    • Journal of Clinical Microbiology
    • Noroviruses (NoV), rotaviruses (RVA), and adenoviruses (AdV) are the main viral agents responsible for acute gastroenteritis (AGE) in humans. We aimed to determine the diagnostic accuracy of four commercial immunochromatographic tests (ICTs) intended for the rapid and simultaneous detection of these three pathogens.

      • Viruses
      • Norovirus
  5. Cefiderocol Antimicrobial Susceptibility Testing against Multidrug-Resistant Gram-Negative Bacilli: a Comparison of Disk Diffusion to Broth Microdilution

    • Journal of Clinical Microbiology
    • Antimicrobial susceptibility testing (AST) of cefiderocol poses challenges because of its unique mechanism of action (i.e., requiring an iron-depleted state) and due to differences in interpretative criteria established by the Clinical and Laboratory Standards Institute (CLSI), U.S. Food and Drug Administration (FDA), and European Committee on Antimicrobial Susceptibility Testing (EUCAST).

      • Bacterial pathogens
  6. Assessing Nanopore Sequencing for Clinical Diagnostics: a Comparison of Next-Generation Sequencing (NGS) Methods for Mycobacterium tuberculosis

    • Journal of Clinical Microbiology
    • Next-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories. However, costs of operation and the need for specialized staff remain major hurdles for laboratories with limited resources for implementing these technologies.

      • Bacterial pathogens
  7. HIV-2 Drug Resistance Genotyping from Dried Blood Spots

    • Journal of Clinical Microbiology
    • The treatment of HIV-2 in resource-limited settings (RLS) is complicated by the limited availability of HIV-2-active antiretroviral drugs and inadequate access to HIV-2 viral load and drug resistance testing. Dried blood spots (DBS)-based drug resistance testing, widely studied for HIV-1, has not been reported for HIV-2 and could present an opportunity to improve care for HIV-2-infected individuals.

  8. Application, Verification, and Implementation of SARS-CoV-2 Serologic Assays with Emergency Use Authorization

    • Journal of Clinical Microbiology
    • Interest continues to grow regarding the role of serologic assays for the detection of prior infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The U.S. Food and Drug Administration (FDA) has granted emergency use authorization (EUA) status to many SARS-CoV-2 serologic assays.

  9. Genomic Serotyping, Clinical Manifestations, and Antimicrobial Resistance of Nontyphoidal Salmonella Gastroenteritis in Hospitalized Children in Ho Chi Minh City, Vietnam

    • Journal of Clinical Microbiology
    • Nontyphoidal Salmonella (NTS) are among the most common etiological agents of diarrheal diseases worldwide and have become the most commonly detected bacterial pathogen in children hospitalized with diarrhea in Vietnam.

      • Bacterial pathogens
      • Salmonella
  10. Additional Og-Typing PCR Techniques Targeting Escherichia coli-Novel and Shigella-Unique O-Antigen Biosynthesis Gene Clusters

    • Journal of Clinical Microbiology
    • The O-serogrouping of pathogenic Escherichia coli is a standard method for subtyping strains for epidemiological studies and controls. O-serogroup diversification shows a strong association with the genetic diversity in some O-antigen biosynthesis gene clusters. Through genomic studies, in addition to the types of O-antigen biosynthesis gene clusters (Og-types) from conventional O-serogroup strains, a number of novel Og-types have been found in E. coli isolates.

      • Bacterial pathogens
      • Shigella
  11. Laboratory Evaluation of a Lateral-Flow Cell for Molecular Detection of First-Line and Second-Line Antituberculosis Drug Resistance

    • Journal of Clinical Microbiology
    • Despite the WHO’s call for universal drug susceptibility testing for all patients being evaluated for tuberculosis (TB), a lack of rapid diagnostic tests which can fully describe TB resistance patterns is a major challenge in ensuring that all persons diagnosed with drug-resistant TB are started on an appropriate treatment regime.

      • Bacterial pathogens
  12. Performance Evaluation of the Novodiag Bacterial GE+ Multiplex PCR Assay

    • Journal of Clinical Microbiology
    • The bacteriological diagnosis of intestinal bacterial infections has historically been based on culture on agar plates. However, culture may lack sensitivity, and some enteropathogens, such as pathovars of Escherichia coli, may escape routine diagnosis. Our goal was to evaluate the analytical performance of the Novodiag Bacterial GE+ kit for the detection of enteropathogenic bacteria in acute community diarrhea. We included 251 stools in this study (198 retrospective and 53 prospective).

      • Salmonella
      • Yersinia
      • Shigella
      • Bacterial pathogens
      • Campylobacter
  13. Advances in Molecular Diagnosis of Tuberculosis

    • Journal of Clinical Microbiology
    • Molecular tests for tuberculosis (TB) have the potential to help reach the three million people with TB who are undiagnosed or not reported each year and to improve the quality of care TB patients receive by providing accurate, quick results, including rapid drug-susceptibility testing.

  14. Improved Early Detection of Focal Brucellosis Complications with Anti-Brucella IgG

    • Journal of Clinical Microbiology
    • To evaluate the associations of inflammatory factors and serological test results with complicated brucellosis, we recruited 285 patients with a diagnosis of brucellosis between May 2016 and September 2019. The patients were subsequently classified into two groups according to the presence of complications. We collected demographic and clinical information and routine laboratory test results in addition to anti-Brucella IgG and IgM levels.

      • Bacterial pathogens
  15. Comparison of Molecular Subtyping and Antimicrobial Resistance Detection Methods Used in a Large Multistate Outbreak of Extensively Drug-Resistant Campylobacter jejuni Infections Linked to Pet Store Puppies

    • Journal of Clinical Microbiology
    • Campylobacter jejuni is a leading cause of enteric bacterial illness in the United States. Traditional molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST), provided limited resolution to adequately identify C. jejuni outbreaks and separate out sporadic isolates during outbreak investigations. Whole-genome sequencing (WGS) has emerged as a powerful tool for C. jejuni outbreak detection.

      • Bacterial pathogens
      • Campylobacter
  16. Imipenem-Relebactam Susceptibility Testing of Gram-Negative Bacilli by Agar Dilution, Disk Diffusion, and Gradient Strip Methods Compared with Broth Microdilution

    • Journal of Clinical Microbiology
    • This study aimed to determine whether agar dilution, research-use-only disk diffusion (Mast Group Ltd., Bootle Merseyside, UK), Etest (bioMérieux, Inc., Durham, NC), and MIC test strip (MTS) (Liofilchem, Inc., Waltham, MA) methods yield equivalent results to those of broth microdilution (BMD) for imipenem-relebactam susceptibility testing using a collection of 297 Gram-negative bacilli, including members of the order Enterobacterales and Pseudomonas aeruginosa, enriched for drug resistance.

      • Bacterial pathogens
  17. Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples

    • Journal of Clinical Microbiology
    • Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resistant tuberculosis (DR-TB). However, the complexity of sequencing platforms has limited their uptake in low-resource settings.

      • Bacterial pathogens
  18. Rapid Salivary IgG Antibody Screening for Hepatitis A

    • Journal of Clinical Microbiology
    • Hepatitis A virus (HAV) is a common infection that is transmitted through the fecal-oral route, shed in the stool of infected individuals, and spread either by direct contact or by ingesting contaminated food or water. Each year, approximately 1.4 million acute cases are reported globally with a major risk factor for exposure being low household socioeconomic status.

      • Hepatitis
      • Viruses
  19. Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays

    • Journal of Clinical Microbiology
    • Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material quantified with droplet digital PCR.

      • COVID-19
      • Viruses
  20. Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription-Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19

    • Journal of Clinical Microbiology
    • The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. Saliva samples from 103 patients with laboratory-confirmed COVID-19 (15 asymptomatic and 88 symptomatic) were collected on the day of hospital admission.

      • COVID-19
      • Viruses
  21. Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms

    • Journal of Clinical Microbiology
    • The ability to detect SARS-CoV-2 in the upper respiratory tract ceases after 2 to 3 weeks post-symptom-onset in most patients. In contrast, SARS-CoV-2 can be detected in the stool of some patients for greater than 4 weeks, suggesting that stool may hold utility as an additional source for diagnosis. We validated the Cepheid Xpert Xpress SARS-CoV-2 and Hologic Panther Fusion real-time RT-PCR assays for detection of viral RNA in stool specimens and compared performance.

      • COVID-19
      • Viruses
  22. Clinical and Analytical Performance of an Automated Serological Test That Identifies S1/S2-Neutralizing IgG in COVID-19 Patients Semiquantitatively

    • Journal of Clinical Microbiology
    • In the coronavirus (CoV) disease 2019 (COVID-19) pandemic, highly selective serological testing is essential to define exposure to severe acute respiratory syndrome CoV 2 (SARS-CoV-2). Many tests have been developed, yet with variable speeds to first results, and are of unknown quality, particularly when considering the prediction of neutralizing capacity.

      • COVID-19
      • Viruses
  23. Changing from Clinician-Collected to Self-Collected Throat Swabs for Oropharyngeal Gonorrhea and Chlamydia Screening among Men Who Have Sex with Men

    • Journal of Clinical Microbiology
    • The coronavirus disease 2019 (COVID-19) pandemic has led many clinics to move from clinician-collected to self-collected oropharyngeal swabs for the detection of sexually transmitted infections (STIs). Before this change, however, self-collection was used primarily for genital and anorectal infections, with only limited studies on the performance of self-collection of oropharyngeal swabs for oropharyngeal STI detection.

      • COVID-19
      • Viruses
  24. When To Retest: an Examination of Repeat COVID-19 PCR Patterns in an Ambulatory Population

    • Journal of Clinical Microbiology
      • COVID-19
      • Viruses
  25. Under-allocation: Critical Supply Chain Hurdles Negatively Impact the Ability of Community Hospitals To Perform Repeat SARS-CoV-2 Testing

    • Journal of Clinical Microbiology
      • COVID-19
      • Viruses