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Advances in Foodborne Pathogen Analysis

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A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: closed (15 June 2020) | Viewed by 47922

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Special Issue Editors

Prof. Dr. Arun K. Bhunia

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Guest Editor

1. Department of Food Science, Purdue University, West Lafayette, IN, USA
2. Department of Comparative Pathobiology (Courtesy), Purdue University, West Lafayette, IN, USA
Interests: microbiology; pathogenesis; host–pathogen interaction; nanobiotechnology; food safety
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Bledar Bisha

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Guest Editor

Interim Head and Associate Professor of Food Microbiology, Department of Animal Science, University of Wyoming, Laramie, WY 82071, USA
Interests: food microbiology and microbial safety of foods; ecology of foodborne pathogens; rapid diagnostics; sample preparation; study of microorganisms at the single cell level; antimicrobial resistance; microbial source tracking
Special Issues, Collections and Topics in MDPI journals

Dr. Andrew G. Gehring

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Guest Editor

Characterization and Interventions for Foodborne Pathogens, United States Department of Agriculture, Agricultural Research Service, Wyndmoor, PA 19038, USA
Interests: biosensors; food safety; immunoassays; nanopore sequencing; phage typing; rapid methods; sample preparation
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Byron F. Brehm-Stecher

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Guest Editor

Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, USA
Interests: rapid detection of pathogens; pre-analytical sample preparation; flow cytometry and other methods for single cell analysis; multicomponent antimicrobial systems for use in foods, on food contact surfaces or in environmental applications; leveraging advances in materials science and chemistry for detection or inactivation of pathogens

Special Issue Information

Dear Colleagues,

Traditional enrichment culture combined with differential and selective plating serve as gold standards for the detection and identification of foodborne bacterial pathogens. Although accurate and sensitive, culture-based methods are labor intensive and time consuming with the results often taking from days to weeks. There is a desire to replace these methods with “rapid methods” that typically employ highly sensitive and fast biosensor-based analysis. However, creative thought and/or diligent empirical effort are required to introduce paradigm shifts in the generation of rapid methods capable of replacing culture-based methods if the need for comparable sensitivity and accuracy is warranted. Therefore, this Special Issue will showcase contributions ranging from novel sample preparative techniques (like advances in filtration, centrifugation, chemical or particle-based separation, etc.) for the selective, rapid, efficient, and/or quantitative recovery and concentration of targeted bacterial analytes to the development and/or improvement of rapid biosensor-based detection and/or identification platforms (e.g., PCR, phage, immunoassays, optical imaging, luminescence, strip assays, flow cytometry, sequencing, etc.). A further challenge is the determination of live vs. dead organisms. Advances in this field are expected to impact the food production/testing industry and regulatory agencies alike.

Original and review papers dealing with all aspects of “Advances in Foodborne Pathogen Analysis” are welcome for inclusion in this Special Issue of Foods. Reports will focus on the following areas: development and/or improvement of rapid methods for the detection and/or identification of foodborne pathogens (methods, reagents, instrumentation); sample preparation techniques for the rapid and quantitative concentration of targeted microbes in food matrices; new approaches for determining or characterizing pathogen activity, metabolic state or viability.

Prof. Dr. Arun K. Bhunia
Prof. Bledar Bisha
Dr. Andrew Gehring
Prof. Dr. Byron F. Brehm-Stecher
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Foods is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

food safety
food pathogens
sample preparation
biosensors
rapid methods
detection
identification
food biosecurity

Published Papers (9 papers)

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Editorial

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5 pages, 176 KiB

Open AccessEditorial

Advances in Foodborne Pathogen Analysis

by Arun K. Bhunia, Bledar Bisha, Andrew G. Gehring and Byron F. Brehm-Stecher

Foods 2020, 9(11), 1635; https://doi.org/10.3390/foods9111635 - 10 Nov 2020

Cited by 3 | Viewed by 6544

Abstract

As the world population has grown, new demands on the production of foods have been met by increased efficiencies in production, from planting and harvesting to processing, packaging and distribution to retail locations. These efficiencies enable rapid intranational and global dissemination of foods, providing longer “face time” for products on retail shelves and allowing consumers to make healthy dietary choices year-round. However, our food production capabilities have outpaced the capacity of traditional detection methods to ensure our foods are safe. Traditional methods for culture-based detection and characterization of microorganisms are time-, labor- and, in some instances, space- and infrastructure-intensive, and are therefore not compatible with current (or future) production and processing realities. New and versatile detection methods requiring fewer overall resources (time, labor, space, equipment, cost, etc.) are needed to transform the throughput and safety dimensions of the food industry. Access to new, user-friendly, and point-of-care testing technologies may help expand the use and ease of testing, allowing stakeholders to leverage the data obtained to reduce their operating risk and health risks to the public. The papers in this Special Issue on “Advances in Foodborne Pathogen Analysis” address critical issues in rapid pathogen analysis, including preanalytical sample preparation, portable and field-capable test methods, the prevalence of antibiotic resistance in zoonotic pathogens and non-bacterial pathogens, such as viruses and protozoa. Full article

(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis)

Research

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13 pages, 2504 KiB

Open AccessFeature PaperArticle

High-Throughput Detection and Characterization of Antimicrobial Resistant Enterococcus sp. Isolates from GI Tracts of European Starlings Visiting Concentrated Animal Feeding Operations

by Jennifer Anders and Bledar Bisha

Foods 2020, 9(7), 890; https://doi.org/10.3390/foods9070890 - 07 Jul 2020

Cited by 5 | Viewed by 2616

Abstract

Antimicrobial resistant enteric bacteria can easily contaminate the environment and other vehicles through the deposition of human and animal feces. In turn, humans can be exposed to these antimicrobial resistant (AMR) bacteria through contaminated food products and/or contaminated drinking water. As wildlife are firmly established as reservoirs of AMR bacteria and serve as potential vectors in the constant spread of AMR, limiting contact between wildlife and livestock and effective tracking of AMR bacteria can help minimize AMR dissemination to humans through contaminated food and water. Enterococcus spp., which are known opportunistic pathogens, constantly found in gastrointestinal tracts of mammalian and avian species, swiftly evolve and cultivate AMR genotypes and phenotypes, which they easily distribute to other bacteria, including several major bacterial pathogens. In this study, we evaluated the use of high throughput detection and characterization of enterococci from wildlife [European starlings (Sturnus vulgaris)] by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) following culture-based isolation. MALDI-TOF MS successfully identified 658 Enterococcus spp. isolates out of 718 presumptive isolates collected from gastrointestinal tracts of European starlings, which were captured near livestock operations in Colorado, Iowa, Kansas, Missouri, and Texas; antimicrobial susceptibility testing was then performed using 13 clinically significant antibiotics. Full article

(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis)

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15 pages, 1805 KiB

Open AccessArticle

Multiplex Recombinase Polymerase Amplification Assay for the Simultaneous Detection of Three Foodborne Pathogens in Seafood

by Biao Ma, Jiali Li, Kai Chen, Xiaoping Yu, Chuanxin Sun and Mingzhou Zhang

Foods 2020, 9(3), 278; https://doi.org/10.3390/foods9030278 - 03 Mar 2020

Cited by 46 | Viewed by 6231

Abstract

Foodborne pathogens can cause foodborne illness. In reality, one food sample may carry more than one pathogen. A rapid, sensitive, and multiple target method for bacteria detection is crucial in food safety. For the simultaneous detection of Staphylococcus aureus, Vibrio parahaemolyticus, and Salmonella Enteritidis, multi-objective recombinase polymerase amplification (RPA) combined with a lateral flow dipstick (LFD) was developed in this study. The whole process, including amplification and reading, can be completed in 15 min at 37 °C. The detection limits were 2.6 × 10¹ CFU/mL for Staphylococcus aureus, 7.6 × 10¹ CFU/mL for Vibrio parahaemolyticus, and 1.29 × 10¹ CFU/mL for Salmonella Enteritidis. Moreover, colored signal intensities on test lines were measured by a test strip reader to achieve quantitative detection for Staphylococcus aureus (R² = 0.9903), Vibrio parahaemolyticus (R² = 0.9928), and Salmonella Enteritidis (R² = 0.9945). In addition, the method demonstrated good recoveries (92.00%–107.95%) in the testing of spiked food samples. Therefore, the multiplex LFD-RPA assay is a feasible method for the rapid, sensitive, and quantitative detection of bacterial pathogens in seafood. Full article

(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis)

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11 pages, 2332 KiB

Open AccessArticle

A Molecular Tool for Rapid Detection and Traceability of Cyclospora cayetanensis in Fresh Berries and Berry Farm Soils

by Carolina N. Resendiz-Nava, Guadalupe E. Orozco-Mosqueda, Edmundo M. Mercado-Silva, Susana Flores-Robles, Hilda V. Silva-Rojas and Gerardo M. Nava

Foods 2020, 9(3), 261; https://doi.org/10.3390/foods9030261 - 02 Mar 2020

Cited by 9 | Viewed by 3243

Abstract

Due to recent outbreaks of cyclosporiasis associated with consumption of fresh berries, producers are demanding modern microbiological tools for the rapid and accurate identification of the human pathogen Cyclospora cayetanensis in berries and environmental samples. The aim of the present work was to develop a molecular tool based on a PCR approach for the rapid and accurate detection of C. cayetanensis. A nested PCR assay was validated for the amplification of a 294 bp size region of the 18S rRNA gene from C. cayetanensis. The limit of detection for the nested PCR assay was validated using 48 berry samples spiked with ~0, 10, 100, and 1000 oocyst per gram of sample. With this assay, it was possible to detect as few as 1 oocyst per gram of berry, in a 50 g sample. Sanger DNA sequencing and phylogenetic analysis were carried out to confirm the presence of C. cayetanensis in berry (n = 17) and soil (n = 5) samples. The phylogenetic analysis revealed that the C. cayetanensis sequences obtained from Mexico clustered within a group recovered from China, Peru, Guatemala-Haiti, and Japan. The PCR protocol designed in the present study could be an important tool for the rapid and accurate detection of this human pathogen in environmental and food samples. Full article

(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis)

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12 pages, 2472 KiB

Open AccessEditor’s ChoiceArticle

Recombinase Polymerase Amplification (RPA) Combined with Lateral Flow Immunoassay for Rapid Detection of Salmonella in Food

by Jiali Li, Biao Ma, Jiehong Fang, Antong Zhi, Erjing Chen, Ying Xu, Xiaoping Yu, Chuanxin Sun and Mingzhou Zhang

Foods 2020, 9(1), 27; https://doi.org/10.3390/foods9010027 - 26 Dec 2019

Cited by 59 | Viewed by 8532

Abstract

Salmonella can cause serious foodborne diseases. We have developed a lateral flow immunoassay combined with recombinase polymerase amplification (LFD-RPA) for detection of Salmonella in food. The conserved fragment (fimY) was selected as the target gene. Under an optimal condition (37 °C, 10 min), the sensitivity was 12 colony-forming units (CFU)/mL in a pure culture. Testing with 16 non-Salmonella strains as controls revealed that LFD-RPA was specific to the fimY gene of Salmonella. The established assay could detect Salmonella at concentrations as low as 1.29 × 10² CFU/mL in artificially contaminated samples. This detection was at a slightly higher level than that for a pure bacterial culture. Combined with the test strip reader, the LFD-RPA is a feasible method for quantitative detection of Salmonella based on the test line intensity, which was the ratio for the test line and control line of the reflected light. The method could be a potential point-of-care test in limited resource areas and provides a new approach and technical support for the diagnosis of food safety. Full article

(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis)

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14 pages, 4118 KiB

Open AccessArticle

Efficacy of Commercial Sanitizers Used in Food Processing Facilities for Inactivation of Listeria monocytogenes, E. Coli O157:H7, and Salmonella Biofilms

by Manish Aryal and Peter M. Muriana

Foods 2019, 8(12), 639; https://doi.org/10.3390/foods8120639 - 04 Dec 2019

Cited by 45 | Viewed by 6332

Abstract

Bacteria entrapped in biofilms are a source of recurring problems in food processing environments. We recently developed a robust, 7-day biofilm microplate protocol for creating biofilms with strongly adherent strains of Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella serovars that could be used to examine the effectiveness of various commercial sanitizers. Listeria monocytogenes 99-38, E.coli O157:H7 F4546, and Salmonella Montevideo FSIS 051 were determined from prior studies to be good biofilm formers and could be recovered and enumerated from biofilms following treatment with trypsin. Extended biofilms were generated by cycles of growth and washing daily, for 7 days, to remove planktonic cells. We examined five different sanitizers (three used at two different concentrations) for efficacy against the three pathogenic biofilms. Quaternary ammonium chloride (QAC) and chlorine-based sanitizers were the least effective, showing partial inhibition of the various biofilms within 2 h (1–2 log reduction). The best performing sanitizer across all three pathogens was a combination of modified QAC, hydrogen peroxide, and diacetin which resulted in ~6–7 log reduction, reaching levels below our limit of detection (LOD) within 1–2.5 min. All treatments were performed in triplicate replication and analyzed by one way repeated measures analysis of variance (RM-ANOVA) to determine significant differences (p < 0.05) in the response to sanitizer treatment over time. Analysis of 7-day biofilms by scanning electron microscopy (SEM) suggests the involvement of extracellular polysaccharides with Salmonella and E. coli, which may make their biofilms more impervious to sanitizers than L. monocytogenes. Full article

(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis)

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17 pages, 3394 KiB

Open AccessArticle

Impacts of Clarification Techniques on Sample Constituents and Pathogen Retention

by Cheryl M. Armstrong, Andrew G. Gehring, George C. Paoli, Chin-Yi Chen, Yiping He and Joseph A. Capobianco

Foods 2019, 8(12), 636; https://doi.org/10.3390/foods8120636 - 03 Dec 2019

Cited by 8 | Viewed by 3759

Abstract

Determination of the microbial content in foods is important, not only for safe consumption, but also for food quality, value, and yield. A variety of molecular techniques are currently available for both identification and quantification of microbial content within samples; however, their success is often contingent upon proper sample preparation when the subject of investigation is a complex mixture of components such as foods. Because of the importance of sample preparation, the present study employs a systematic approach to compare the effects of four different separation techniques (glass wool, 50 μm polypropylene filters, graphite felt, and continuous flow centrifugation (CFC)) on sample preparation. To define the physical effects associated with the use of these separation methods, a multifactorial analysis was performed where particle size and composition, both pre- and post- processing, were analyzed for four different food matrices including lean ground beef, ground pork, ground turkey and spinach. Retention of three important foodborne bacterial pathogens (Escherichia coli O157:H7, Salmonella enterica, and Listeria monocytogenes) was also examined to evaluate the feasibility of the aforementioned methods to be utilized within the context of foodborne pathogen detection. Data from the multifactorial analysis not only delineated the particle size ranges but also defined the unique compositional profiles and quantified the bacterial retention. The three filtration membranes allowed for the passage of bacteria with minimal loss while CFC concentrated the inoculated bacteria. In addition, the deposition and therefore concentration of food matrix observed with CFC was considerably higher for meat samples relative to spinach. However, filtration with glass wool prior to CFC helped clarify meat samples, which led to considerably lower amounts of solids in the CFC vessel post processing and an increase in the recovery of the bacteria. Overall, by laying a framework for the deductive selection of sample preparation techniques, the results of the study can be applied to a range of applications where it would be beneficial to scientifically guide the pairing of the criteria associated with a downstream detection method with the most advantageous sample preparation techniques for complex matrices such as foods. Full article

(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis)

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13 pages, 2748 KiB

Open AccessArticle

Optimization of a Microplate Assay for Generating Listeria Monocytogenes, E. Coli O157:H7, and Salmonella Biofilms and Enzymatic Recovery for Enumeration

by Manish Aryal, Preetty Pranatharthiharan and Peter M. Muriana

Foods 2019, 8(11), 541; https://doi.org/10.3390/foods8110541 - 02 Nov 2019

Cited by 5 | Viewed by 3566

Abstract

Biofilms enable the persistence of pathogens in food processing environments. Sanitizing agents are needed that are effective against pathogens entrapped in biofilms that are more difficult to inactivate than planktonic cells that are displaced and found on equipment surfaces. We examined conditions to develop, analyze, and enumerate the enhanced biofilms of three different foodborne pathogens assisted by fluorescence adherence assay and enzymatic detachment. We compared three different isomeric forms of fluorescent substrates that are readily taken up by bacterial cells based on carboxy-fluorescein diacetate (5-CFDA, 5,6-CFDA, 5,6-CFDA, SE). Biofilm-forming strains of Escherichia coli O157:H7 F4546 and Salmonella Montevideo FSIS 051 were identified using a microplate fluorescence assay defined previously for L. monocytogenes. Adherence levels were determined by differences in relative fluorescence units (RFU) as well as recovered bacterial cells. Multiple hydrolytic enzymes were examined for each representative pathogen for the most suitable enzyme for detachment and enumeration to confirm adherence data obtained by fluorescence assay. Cultures were grown overnight in microplates, incubated, washed and replenished with fresh sterile growth medium; this cycle was repeated for seven consecutive days to enrich for robust biofilms. Treatments were performed in triplicate and compared by one-way analysis of variance (ANOVA) to determine significant differences (p < 0.05). Full article

(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis)

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Review

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37 pages, 3087 KiB

Open AccessReview

A Survey of Analytical Techniques for Noroviruses

by Lingling Liu and Matthew D. Moore

Foods 2020, 9(3), 318; https://doi.org/10.3390/foods9030318 - 10 Mar 2020

Cited by 27 | Viewed by 5770

Abstract

As the leading cause of acute gastroenteritis worldwide, human noroviruses (HuNoVs) have caused around 685 million cases of infection and nearly $60 billion in losses every year. Despite their highly contagious nature, an effective vaccine for HuNoVs has yet to become commercially available. Therefore, rapid detection and subtyping of noroviruses is crucial for preventing viral spread. Over the past half century, there has been monumental progress in the development of techniques for the detection and analysis of noroviruses. However, currently no rapid, portable assays are available to detect and subtype infectious HuNoVs. The purpose of this review is to survey and present different analytical techniques for the detection and characterization of noroviruses. Full article

(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis)

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