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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 76 - 100 of 286

  1. High-Content Screening, a Reliable System for Coxiella burnetii Isolation from Clinical Samples

    • Journal of Clinical Microbiology
    • Q fever, caused by Coxiella burnetii, is a worldwide zoonotic disease that may cause severe forms in humans and requires a specific and prolonged antibiotic treatment. Although current serological and molecular detection tools allow a reliable diagnosis of the disease, culture of C. burnetii strains is mandatory to assess their susceptibility to antibiotics and sequence their genome in order to optimize patient management and epidemiological studies.

      • Bacterial pathogens
  2. Evaluation of a Novel Multiplex PCR Panel Compared to Quantitative Bacterial Culture for Diagnosis of Lower Respiratory Tract Infections

    • Journal of Clinical Microbiology
    • Quantitative bacterial culture of bronchoalveolar lavage fluids (BALF) is labor-intensive, and the delay involved in performing culture, definitive identification, and susceptibility testing often results in prolonged use of broad-spectrum antibiotics. The Unyvero lower respiratory tract (LRT) panel (Curetis, Holzgerlingen, Germany) allows the multiplexed rapid detection and identification of 20 potential etiologic agents of pneumonia within 5 h of collection.

      • Staphylococcus aureus
      • Bacterial pathogens
  3. Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-{beta}-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit

    • Journal of Clinical Microbiology
    • Klebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which the sources of transmission may be challenging to elucidate. We describe the use of whole-genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates. Ceftriaxone-resistant Klebsiella spp.

      • Bacterial pathogens
  4. Multicenter Evaluation of a PCR-Based Digital Microfluidics and Electrochemical Detection System for the Rapid Identification of 15 Fungal Pathogens Directly from Positive Blood Cultures

    • Journal of Clinical Microbiology
    • Routine identification of fungal pathogens from positive blood cultures by culture-based methods can be time-consuming, delaying treatment with appropriate antifungal agents. The GenMark Dx ePlex investigational use only blood culture identification fungal pathogen panel (BCID-FP) rapidly detects 15 fungal targets simultaneously in blood culture samples positive for fungi by Gram staining. We aimed to determine the performance of the BCID-FP in a multicenter clinical study.

  5. Evaluation of the Revogene Carba C Assay for Detection and Differentiation of Carbapenemase-Producing Gram-Negative Bacteria

    • Journal of Clinical Microbiology
    • The Revogene Carba C assay (formerly GenePOC Carba assay) is a multiplex nucleic acid-based in vitro diagnostic test intended for the detection of carbapenemase-producing Enterobacterales (CPE) from cultured colonies. This assay was evaluated directly on colonies of 118 well-characterized Enterobacterales with reduced susceptibility to carbapenems and on 49 multidrug-resistant (MDR) Pseudomonas aeruginosa and 40 MDR Acinetobacter baumannii isolates.

      • Bacterial pathogens
  6. Validation of Aztreonam-Avibactam Susceptibility Testing Using Digitally Dispensed Custom Panels

    • Journal of Clinical Microbiology
    • Aztreonam-avibactam is a combination antimicrobial agent with activity against carbapenemase-producing Enterobacteriaceae (CPE) with metallo-β-lactamases (MβLs). Although aztreonam-avibactam is not yet approved by the U.S. Food and Drug Administration (FDA), clinicians can administer this combination by using two FDA-approved drugs: aztreonam and ceftazidime-avibactam.

      • Bacterial pathogens
  7. Evaluation of the NG-Test MCR-1 Lateral Flow Assay and EDTA-Colistin Broth Disk Elution Methods To Detect Plasmid-Mediated Colistin Resistance among Gram-Negative Bacterial Isolates

    • Journal of Clinical Microbiology
    • Plasmid-mediated colistin resistance (PMCR) is a global public health concern, given its ease of transmissibility. The purpose of this study was to evaluate two methods for the detection of PMCR from bacterial colonies: (i) the NG-Test MCR-1 lateral flow immunoassay (LFA; NG Biotech, Guipry, France) and (ii) the EDTA-colistin broth disk elution (EDTA-CBDE) screening test method. These methods were evaluated using a cohort of contemporary, clinical Gram-negative bacillus isolates from 3 U.S.

      • Bacterial pathogens
  8. Clinical Performance of the Novel GenMark Dx ePlex Blood Culture ID Gram-Positive Panel

    • Journal of Clinical Microbiology
    • Rapid identification from positive blood cultures is standard of care (SOC) in many clinical microbiology laboratories. The GenMark Dx ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a multiplex nucleic acid amplification assay based on competitive DNA hybridization and electrochemical detection using eSensor technology.

      • Bacterial pathogens
      • Listeria monocytogenes
      • Bacillus cereus
      • Staphylococcus aureus
  9. Persistent Transmission of Shigellosis in England Is Associated with a Recently Emerged Multidrug-Resistant Strain of Shigella sonnei

    • Journal of Clinical Microbiology
    • Whole-genome sequencing has enhanced surveillance and facilitated detailed monitoring of the transmission of Shigella species in England. We undertook an epidemiological and phylogenetic analysis of isolates from all cases of shigellosis referred to Public Health England between 2015 and 2018 to explore recent strain characteristics and the transmission dynamics of Shigella species.

      • Bacterial pathogens
      • Shigella
  10. Validation of Bartonella henselae Western Immunoblotting for Serodiagnosis of Bartonelloses in Dogs

    • Journal of Clinical Microbiology
    • Bartonella spp. are etiological agents of life-threatening zoonotic diseases in dogs worldwide. Due to the poor sensitivity of immunofluorescent-antibody assays (IFAs), a reliable serodiagnostic test for canine bartonelloses is of clinical importance. The utility of Western blotting (WB) for the serodiagnosis of canine bartonelloses has not been critically investigated.

      • Bacterial pathogens
  11. Impact of a Rapid Blood Culture Diagnostic Test in a Children's Hospital Depends on Gram-Positive versus Gram-Negative Organism and Day versus Night Shift

    • Journal of Clinical Microbiology
    • Rapid diagnostic tests (RDTs) for bloodstream infections (BSIs) decrease the time to organism identification and resistance detection. RDTs are associated with early deescalation of therapy for Gram-positive BSIs. However, it is less clear how RDTs influence antibiotic management for Gram-negative BSIs and whether RDT results are acted on during off-hours. We performed a single-center, retrospective review of children with BSI and Verigene (VG) testing at a children’s hospital.

      • Bacterial pathogens
      • Staphylococcus aureus
  12. Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network

    • Journal of Clinical Microbiology
    • U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng.

  13. Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018: Impact and Lessons Learned

    • Journal of Clinical Microbiology
    • Candida auris is a multidrug-resistant yeast which has emerged in health care facilities worldwide; however, little is known about identification methods, patient colonization, environmental survival, spread, and drug resistance. Colonization on both biotic (patients) and abiotic (health care objects) surfaces, along with travel, appear to be the major factors for the spread of this pathogen across the globe. In this investigation, we present laboratory findings from an ongoing C.

  14. Direct Blood Culturing of Candida spp. on Solid Medium by a Rapid Enrichment Method with Magnetic Beads Coated with Recombinant Human Mannan-Binding Lectin

    • Journal of Clinical Microbiology
    • A rapid and accurate method to identify the species and antibiotic resistance of Candida spp. in blood is vital to increase the survival rates of patients with bloodstream infections. However, the extremely low levels of Candida spp. in blood make rapid diagnosis by standard blood culture difficult.

  15. Optimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine Samples

    • Journal of Clinical Microbiology
    • Empirical gonorrhea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance. We investigated if Nanopore sequencing can detect sufficient Neisseria gonorrhoeae DNA to reconstruct whole genomes directly from urine samples. We used N.

  16. Evaluation of the ResistancePlus MG FleXible Assay for Detection of Wild-Type and 23S rRNA-Mutated Mycoplasma genitalium Strains

    • Journal of Clinical Microbiology
    • Antibiotic resistance in Mycoplasma genitalium is rising globally, and resistance-guided diagnostics can facilitate targeted and timely treatment. The ResistancePlus MG FleXible (RPMG Flex) assay for the detection of M. genitalium and macrolide resistance-mediating mutations (MRMM) was evaluated for analytical sensitivity, specificity, reproducibility, and inhibition in the presence of interfering substances by simulating M. genitalium-negative pooled urine and swab matrices with M.

  17. Helicobacter pylori Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome Sequencing

    • Journal of Clinical Microbiology
    • The emergence of drug resistance in Helicobacter pylori has resulted in a greater need for susceptibility-guided treatment. While the alleles associated with resistance to clarithromycin and levofloxacin have been defined, there are limited data regarding the molecular mechanisms underlying resistance to other antimicrobials. Using H. pylori isolates from 42 clinical specimens, we compared phenotypic and whole-genome sequencing (WGS)-based detection of resistance.

  18. Single-Cell-Based Digital PCR Detection and Association of Shiga Toxin-Producing Escherichia coli Serogroups and Major Virulence Genes

    • Journal of Clinical Microbiology
    • Escherichia coli serogroups O157, O26, O45, O103, O111, O121, and O145, when carrying major virulence genes, the Shiga toxin genes stx1 and stx2 and the intimin gene eae, are important foodborne pathogens. They are referred to as the "top 7" Shiga toxin-producing E. coli (STEC) serogroups and were declared by the USDA as adulterants to human health. Since top 7 serogroup-positive cattle feces and ground beef can also contain nonadulterant E.

      • Enterohemorrhagic Escherichia coli
      • Bacterial pathogens
  19. Multicenter Evaluation of the New Etest Gradient Diffusion Method for Piperacillin-Tazobactam Susceptibility Testing of Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii Complex

    • Journal of Clinical Microbiology
    • Piperacillin-tazobactam (P/T) is a β-lactam–β-lactamase inhibitor combination frequently used in the hospital setting. Etest is a gradient diffusion method that represents an alternative to broth microdilution (BMD) for performing antimicrobial susceptibility testing. We conducted a multicenter evaluation of the performance of the new P/T Etest compared to that of BMD following U.S.

      • Bacterial pathogens
  20. Comparison of Different Commercially Available Enzyme-Linked Immunosorbent Assays with Immunofluorescence Test for Detection of Phase II IgG and IgM Antibodies to Coxiella burnetii

    • Journal of Clinical Microbiology
    • Several commercially available enzyme-linked immunosorbent assays (ELISAs) for the detection of phase II IgG or IgM antibodies against Coxiella burnetii were compared. In addition, an indirect immunofluorescence test was used as a confirmation test. In all, 70 serum samples for IgG and 43 serum samples for IgM were tested. The ELISAs showed large differences in sensitivity and specificity, which led to a partially high ratio of false-negative determinations.

      • Bacterial pathogens
  21. Brucella Exposure Risk Events in 10 Clinical Laboratories, New York City, USA, 2015 to 2017

    • Journal of Clinical Microbiology
    • From 2015 to 2017, 11 confirmed brucellosis cases were reported in New York City, leading to 10 Brucella exposure risk events (Brucella events) in 7 clinical laboratories (CLs). Most patients had traveled to countries where brucellosis is endemic and presented with histories and findings consistent with brucellosis.

      • Bacterial pathogens
  22. Genotypic Characterization of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates of Clonal Complex 398 in Pigsty Visitors: Transient Carriage or Persistence?

    • Journal of Clinical Microbiology
    • Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) of clonal complex (CC) 398 has become a rising issue for public health. While it is known that >80% of pig farmers are colonized with LA-MRSA, only a few studies have assessed the situation for humans with occasional livestock contact. Recently it was shown that over 75% of scientific fieldworkers visiting pigsties were temporarily carrying LA-MRSA.

      • Staphylococcus aureus
      • Bacterial pathogens
  23. Origin and Evolution of Hybrid Shiga Toxin-Producing and Uropathogenic Escherichia coli Strains of Sequence Type 141

    • Journal of Clinical Microbiology
    • Hybrid Shiga toxin-producing Escherichia coli (STEC) and uropathogenic E. coli (UPEC) strains of multilocus sequence type 141 (ST141) cause both urinary tract infections and diarrhea in humans and are phylogenetically positioned between STEC and UPEC strains. We used comparative genomic analysis of 85 temporally and spatially diverse ST141 E. coli strains, including 14 STEC/UPEC hybrids, collected in Germany (n = 13) and the United States (n = 1) to reconstruct their molecular evolution.

      • Bacterial pathogens
  24. Multicenter Clinical Evaluation of Etest Meropenem-Vaborbactam (bioMerieux) for Susceptibility Testing of Enterobacterales (Enterobacteriaceae) and Pseudomonas aeruginosa

    • Journal of Clinical Microbiology
    • Meropenem-vaborbactam (MEV) is a novel carbapenem–beta-lactamase inhibitor combination antibiotic approved by the U.S. Food and Drug Administration (FDA) for treatment of complicated urinary tract infections, including pyelonephritis, in adults. In this study, we evaluated the performance of Etest MEV (bioMérieux, Marcy l’Etoile, France) compared to that of broth microdilution for 629 Enterobacterales and 163 Pseudomonas aeruginosa isolates.

      • Bacterial pathogens
  25. Screening for Human Immunodeficiency Virus Infection by Use of a Fourth-Generation Antigen/Antibody Assay and Dried Blood Spots: In-Depth Analysis of Sensitivity and Performance Assessment in a Cross-Sectional Study

    • Journal of Clinical Microbiology
    • We evaluated the performance of a fourth-generation antigen/antibody (Ag/Ab) assay for detecting HIV-1 infection on dried blood spots (DBS) both in a conventional laboratory environment and in an epidemiological survey corresponding to a real-life situation. Although a 2-log loss of sensitivity compared to that with plasma was observed when using DBS in an analytical analysis, the median delay of positivity between DBS and crude serum during the early phase postacute infection was 7 days.