New Tools, Old Enemies: Introducing a New Era of Methods for Detecting, Tracking, and Controlling Foodborne Pathogens

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 5913

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Guest Editor
Department of Dairy Research, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “DEMETER”, Ethnikis Antistaseos 3, 45221 Ioannina, Greece
Interests: molecular microbiology; bioinformatics; ecology of fermented foods; food safety and quality control; foodborne pathogens; predictive microbiology; microbial risk assessment; statistical process and quality control; udder health of ruminants; dairy farming precision
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Special Issue Information

Dear Colleagues,

Molecular microbiology techniques, such as whole genome sequencing or PCR-based techniques, as well as bioinformatics and modelling, such as source attribution or predictive microbiology, have major impacts on food safety as they can be used with high accuracy for the detection, tracking, characterization, and identification of pathogens. The rapid emergence and adoption of these tools marks the beginning of a new era in food safety by the application of new molecular and statistical techniques for evidence-based decision-making, and a more effective assessment of microbiological risks. Genomics and other omics technologies (metagenomics, metatranscriptomics, etc.) will be an integral part of the toolkit for the assessment and systematic monitoring of microbiological risks in foods. These technologies will be used to improve the phylogenetic and genetic classification of pathogens by identifying, with high precision, genes related to virulence and/or resistance to antibiotics (antimicrobial resistance). Therefore, articles dealing with these topics as they relate to various foodborne pathogens are welcome for submission to this Special Issue.

Dr. Marios Mataragas
Guest Editor

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Keywords

  • molecular microbiology
  • next generation sequencing
  • whole genome sequencing
  • PCR-based methods
  • bioinformatics
  • foodborne pathogens
  • antimicrobial resistance
  • modelling
  • risk assessment
  • source attribution

Published Papers (2 papers)

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Research

17 pages, 2888 KiB  
Article
Characterization and Antibiotic Resistance of Listeria monocytogenes Strains Isolated from Greek Myzithra Soft Whey Cheese and Related Food Processing Surfaces over Two-and-a-Half Years of Safety Monitoring in a Cheese Processing Facility
by Nikolaos D. Andritsos and Marios Mataragas
Foods 2023, 12(6), 1200; https://doi.org/10.3390/foods12061200 - 12 Mar 2023
Cited by 5 | Viewed by 2555
Abstract
Listeriosis is a serious infectious disease with one of the highest case fatality rates (ca. 20%) among the diseases manifested from bacterial foodborne pathogens in humans, while dairy products are often implicated as sources of human infection with Listeria monocytogenes. In [...] Read more.
Listeriosis is a serious infectious disease with one of the highest case fatality rates (ca. 20%) among the diseases manifested from bacterial foodborne pathogens in humans, while dairy products are often implicated as sources of human infection with Listeria monocytogenes. In this study, we characterized phenotypically and genetically by whole-genome sequencing (WGS) 54 L. monocytogenes strains isolated from Myzithra, a traditional Greek soft whey cheese (48 isolates), and swabs collected from surfaces of a cheese processing plant (six isolates) in the Epirus region of Greece. All but one strain of L. monocytogenes belonged to the polymerase chain reaction (PCR) serogroups IIa (16.7%) and IIb (81.5%), corresponding to serotypes 1/2a, 3a and 1/2b, 3b, 7, respectively. The latter was identified as a PCR-serogroup IVb strain (1.8%) of serotypes 4b, 4d, 4e. Bioinformatics analysis revealed the presence of five sequence types (STs) and clonal complexes (CCs); ST1, ST3, ST121, ST 155, ST398 and CC1, CC3, CC121, CC155, CC398 were thus detected in 1.9, 83.3, 11.0, 1.9, and 1.9% of the L. monocytogenes isolates, respectively. Antibiograms of the pathogen against a panel of seven selected antibiotics (erythromycin, tetracycline, benzylpenicillin, trimethoprim-sulfamethoxazole, ampicillin, ciprofloxacin, and meropenem) showed that 50 strains (92.6%), the six surface isolates also included, were intermediately resistant to ciprofloxacin and susceptible to the rest of the six antimicrobial agents tested, whereas strong resistance against the use of a single from three implicated antibiotics was recorded to four strains (7.4%) of the pathogen isolated from Myzithra cheese samples. Thence, the minimum inhibitory concentrations (MICs) were determined for erythromycin (MIC = 0.19 μg/mL), ciprofloxacin (MIC ≥ 0.19 μg/mL), and meropenem (MIC = 0.64 μg/mL), and finally, just one strain was deemed resistant to the latter antibiotic. The phylogenetic positions of the L. monocytogenes strains and their genetic variability were determined through WGS, whilst also stress response and virulence gene analysis for the isolates was conducted. Findings of this work should be useful as they could be utilized for epidemiological investigations of L. monocytogenes in the food processing environment, revealing possible contamination scenarios, and acquired antimicrobial resistance along the food production chain. Full article
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13 pages, 2026 KiB  
Article
Development of an RNA Extraction Protocol for Norovirus from Raw Oysters and Detection by qRT-PCR and Droplet-Digital RT-PCR
by Daniel Plante, Julio Alexander Bran Barrera, Maude Lord, Irène Iugovaz and Neda Nasheri
Foods 2021, 10(8), 1804; https://doi.org/10.3390/foods10081804 - 4 Aug 2021
Cited by 12 | Viewed by 2684
Abstract
Foodborne viruses such as norovirus and hepatitis A virus cause frequent outbreaks associated with the consumption of raw or undercooked oysters. Viral particles are bioaccumulated in the oyster’s digestive glands, making RNA extraction and RT-PCR detection difficult due to the complex nature of [...] Read more.
Foodborne viruses such as norovirus and hepatitis A virus cause frequent outbreaks associated with the consumption of raw or undercooked oysters. Viral particles are bioaccumulated in the oyster’s digestive glands, making RNA extraction and RT-PCR detection difficult due to the complex nature of the food matrix and the presence of RT-PCR inhibitors. Herein, we have developed a viral RNA extraction protocol from raw oysters using murine norovirus (MNV) as a surrogate for human noroviruses. The method combines lysis in Tri-Reagent reagent, followed by RNA extraction using Direct-Zol purification columns and lithium chloride precipitation. Viral load quantification was performed by both qRT-PCR and droplet-digital RT-PCR. We have demonstrated that this method can efficiently remove RT-PCR inhibitors, and is sensitive enough to reliably detect viral contamination at 25 PFU/0.2 g. We have also compared the efficiency of this method with the ISO 15216-1:2017 method and Method E developed by Quang and colleagues, and observed significantly higher efficiency compared with the ISO 15216-1 method and comparable efficiency with Method E, with less steps, and shorter hands-on time. Full article
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