Molecular Epidemiology of Foodborne Pathogenic Bacteria

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

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 6642

Special Issue Editors


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Guest Editor
Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
Interests: food safety and quality; food microbiology; foodborne pathogens; allergens; molecular biology; PCR; isothermal amplification; antimicrobial resistance

E-Mail Website
Guest Editor
Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), Braga, Portugal
Interests: foodborne pathogens; microbiology; food microbiology; food safety; fast detection tools; PCR/ qPCR; fast multipathogen detection; food quality and safety
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The hazard associated with food contamination continues to be a serious worldwide human health concern, and the number of outbreaks related with food and water contamination has not shown any significant decrease in the past four years.

Contamination can occur by multiple routes, and the identification of the source can be challenging; this leads to delays in stopping the spread of pathogens and increases the possibilities for human infection. With the intensification of the food industry, new methodologies to improve the tracking of these causative agents are required, and molecular techniques are key for this depth assessment. Genotyping can allow the reconstruction of evolutionary patterns associated with specific outbreaks and identify the genetic potential and environmental risk factors of the bacteria identified.

This Special Issue will cover the different approaches used to study and trace pathogenic foodborne microorganisms; these will include, but not be limited to, molecular methods for the detection and characterization of microorganisms, bioinformatics analyses, among others. The aim is to expose the novelties in this area in order to improve the typing analysis in order to contain future outbreaks.

Dr. Sarah Azinheiro
Dr. Alejandro Garrido-Maestu
Guest Editors

Manuscript Submission Information

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Keywords

  • molecular epidemiology 
  • genotyping 
  • foodborne pathogens 
  • virulence 
  • outbreaks 
  • improved methodologies 
  • antimicrobial resistance

Published Papers (4 papers)

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Research

25 pages, 5045 KiB  
Article
Genomic and Transcriptomic Analyses Reveal Multiple Strategies for Vibrio parahaemolyticus to Tolerate Sub-Lethal Concentrations of Three Antibiotics
by Lianzhi Yang, Pan Yu, Juanjuan Wang, Taixia Zhao, Yong Zhao, Yingjie Pan and Lanming Chen
Foods 2024, 13(11), 1674; https://doi.org/10.3390/foods13111674 - 27 May 2024
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Abstract
Vibrio parahaemolyticus can cause acute gastroenteritis, wound infections, and septicemia in humans. The overuse of antibiotics in aquaculture may lead to a high incidence of the multidrug-resistant (MDR) pathogen. Nevertheless, the genome evolution of V. parahaemolyticus in aquatic animals and the mechanism of [...] Read more.
Vibrio parahaemolyticus can cause acute gastroenteritis, wound infections, and septicemia in humans. The overuse of antibiotics in aquaculture may lead to a high incidence of the multidrug-resistant (MDR) pathogen. Nevertheless, the genome evolution of V. parahaemolyticus in aquatic animals and the mechanism of its antibiotic tolerance remain to be further deciphered. Here, we investigated the molecular basis of the antibiotic tolerance of V. parahaemolyticus isolates (n = 3) originated from shellfish and crustaceans using comparative genomic and transcriptomic analyses. The genome sequences of the V. parahaemolyticus isolates were determined (5.0–5.3 Mb), and they contained 4709–5610 predicted protein-encoding genes, of which 823–1099 genes were of unknown functions. Comparative genomic analyses revealed a number of mobile genetic elements (MGEs, n = 69), antibiotic resistance-related genes (n = 7–9), and heavy metal tolerance-related genes (n = 2–4). The V. parahaemolyticus isolates were resistant to sub-lethal concentrations (sub-LCs) of ampicillin (AMP, 512 μg/mL), kanamycin (KAN, 64 μg/mL), and streptomycin (STR, 16 μg/mL) (p < 0.05). Comparative transcriptomic analyses revealed that there were significantly altered metabolic pathways elicited by the sub-LCs of the antibiotics (p < 0.05), suggesting the existence of multiple strategies for antibiotic tolerance in V. parahaemolyticus. The results of this study enriched the V. parahaemolyticus genome database and should be useful for controlling the MDR pathogen worldwide. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Foodborne Pathogenic Bacteria)
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15 pages, 4849 KiB  
Article
The Occurrence and Genomic Characteristics of mcr-1-Harboring Salmonella from Retail Meats and Eggs in Qingdao, China
by Changan Li, Xiulei Gu, Liping Zhang, Yuqing Liu, Yan Li, Ming Zou and Baotao Liu
Foods 2022, 11(23), 3854; https://doi.org/10.3390/foods11233854 - 29 Nov 2022
Cited by 7 | Viewed by 1244
Abstract
Salmonella are widely distributed foodborne pathogens and are often associated with food animal products. Colistin resistance mediated by mcr-1 is an increasing threat; however, data on the characteristics of mcr-1-harboring Salmonella among retail foods are still lacking. In this study, retail meats [...] Read more.
Salmonella are widely distributed foodborne pathogens and are often associated with food animal products. Colistin resistance mediated by mcr-1 is an increasing threat; however, data on the characteristics of mcr-1-harboring Salmonella among retail foods are still lacking. In this study, retail meats from 24 supermarkets and eggs from nine markets in Qingdao city were investigated to determine the presence and genomic characteristics of mcr-1-harboring Salmonella. We found the retail meats and eggs were highly contaminated by Salmonella, with detection rates of 17.5% (31/177) and 12.3% (16/130), respectively. A total of 76 Salmonella isolates were obtained in this study, and 77.6% showed multidrug resistance (MDR). The MDR proportion of egg isolates (97.5%) was significantly higher than that in meat isolates (55.6%) (p < 0.05). The most prevalent Salmonella serotypes were Typhimurium (56.6%) and Enteritidis (17.1%). Of the 76 Salmonella isolates, 40 possessed mcr-1. All 40 mcr-1-positive isolates were ST34 S. Typhimurium and were from eggs of eight brands. Different mcr-1-harboring isolates existed in the same egg, and some isolates from different egg samples or brands showed clonal relationships. The mcr-1 was located on similar IncHI2/HI2A MDR non-conjugative plasmids lacking transfer region, resulting in the failure of conjugation. The phylogenetic tree using genome sequences showed that the mcr-1-positive isolates from eggs clustered together with mcr-1-positive isolates from chicken and humans in China, revealing that mcr-1-positive egg-borne Salmonella might be derived from chicken and could potentially trigger outbreaks in humans. The high occurrence of mcr-1-harboring Salmonella in fresh eggs is alarming, and there is an urgent need to monitor mcr-1-harboring Salmonella in retail meats and eggs. We report for the first time the role of retail eggs in disseminating mcr-1-positive Salmonella and the risk of transmission of these MDR pathogens from retail food to humans should be evaluated comprehensively. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Foodborne Pathogenic Bacteria)
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20 pages, 2847 KiB  
Article
Relationships between Virulence Genes and Antibiotic Resistance Phenotypes/Genotypes in Campylobacter spp. Isolated from Layer Hens and Eggs in the North of Tunisia: Statistical and Computational Insights
by Manel Gharbi, Selim Kamoun, Chaima Hkimi, Kais Ghedira, Awatef Béjaoui and Abderrazak Maaroufi
Foods 2022, 11(22), 3554; https://doi.org/10.3390/foods11223554 - 8 Nov 2022
Cited by 5 | Viewed by 1750
Abstract
Globally, Campylobacter is a significant contributor to gastroenteritis. Efficient pathogens are qualified by their virulence power, resistance to antibiotics and epidemic spread. However, the correlation between antimicrobial resistance (AR) and the pathogenicity power of pathogens is complex and poorly understood. In this study, [...] Read more.
Globally, Campylobacter is a significant contributor to gastroenteritis. Efficient pathogens are qualified by their virulence power, resistance to antibiotics and epidemic spread. However, the correlation between antimicrobial resistance (AR) and the pathogenicity power of pathogens is complex and poorly understood. In this study, we aimed to investigate genes encoding virulence and AR mechanisms in 177 Campylobacter isolates collected from layer hens and eggs in Tunisia and to assess associations between AR and virulence characteristics. Virulotyping was determined by searching 13 virulence genes and AR-encoding genes were investigated by PCR and MAMA-PCR. The following genes were detected in C. jejuni and C. coli isolates: tet(O) (100%/100%), blaOXA-61 (18.82%/6.25%), and cmeB (100%/100%). All quinolone-resistant isolates harbored the Thr-86-Ile substitution in GyrA. Both the A2074C and A2075G mutations in 23S rRNA were found in all erythromycin-resistant isolates; however, the erm(B) gene was detected in 48.38% and 64.15% of the C. jejuni and C. coli isolates, respectively. The machine learning algorithm Random Forest was used to determine the association of virulence genes with AR phenotypes. This analysis showed that C. jejuni virulotypes with gene clusters encompassing the racR, ceuE, virB11, and pldA genes were strongly associated with the majority of phenotypic resistance. Our findings showed high rates of AR and virulence genes among poultry Campylobacter, which is a cause of concern to human health. In addition, the correlations of specific virulence genes with AR phenotypes were established by statistical analysis. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Foodborne Pathogenic Bacteria)
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15 pages, 823 KiB  
Article
Whole-Genome Analysis of Staphylococcus aureus Isolates from Ready-to-Eat Food in Russia
by Yulia Mikhaylova, Andrey Shelenkov, Aleksey Chernyshkov, Marina Tyumentseva, Stepan Saenko, Anna Egorova, Igor Manzeniuk and Vasiliy Akimkin
Foods 2022, 11(17), 2574; https://doi.org/10.3390/foods11172574 - 25 Aug 2022
Cited by 6 | Viewed by 2537
Abstract
This study provides a thorough investigation of a diverse set of antimicrobial resistant (AMR) Staphylococcus aureus isolates collected from a broad range of ready-to-eat (RTE) food in various geographic regions of Russia ranging from Pskov to Kamchatka. Thirty-five isolates were characterized using the [...] Read more.
This study provides a thorough investigation of a diverse set of antimicrobial resistant (AMR) Staphylococcus aureus isolates collected from a broad range of ready-to-eat (RTE) food in various geographic regions of Russia ranging from Pskov to Kamchatka. Thirty-five isolates were characterized using the whole genome sequencing (WGS) analysis in terms of clonal structure, the presence of resistance and virulence determinants, as well as plasmid replicon sequences and CRISPR/Cas systems. To the best of our knowledge, this is the first WGS-based surveillance of Russian RTE food-associated S. aureus isolates. The isolates belonged to fifteen different multilocus sequence typing (MLST)-based types with a predominant being the ones of clonal complex (CC) 22. The isolates studied can pose a threat to public health since about 40% of the isolates carried at least one enterotoxin gene, and 70% of methicillin-resistant (MRSA) isolates carried a tsst1 gene encoding a toxin that may cause severe acute disease. In addition, plasmid analysis revealed some important characteristics, e.g., Rep5 and Rep20 plasmid replicons were a “signature” of MRSA CC22. By analyzing the isolates belonging to the same/single strain based on cgMLST analysis, we were able to identify the differences in their accessory genomes marking their dynamics and plasticity. This data is very important since S. aureus isolates studied and RTE food, in general, represent an important route of transmission and dissemination of multiple pathogenic determinants. We believe that the results obtained will facilitate performing epidemiological surveillance and developing protection measures against this important pathogen in community settings. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Foodborne Pathogenic Bacteria)
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