Tracking Foodborne Pathogens and Antimicrobial Resistance

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: closed (15 December 2022) | Viewed by 4314

Special Issue Editor


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Guest Editor
1. Nutrition and Health Unit, Eurecat Technology Center of Catalonia, 43204 Reus, Catalonia, Spain
2. Department of Biochemistry and Biotechnology, University Rovira i Virgili, 43007 Tarragona, Catalonia, Spain
3. Department of Biology, University of Turku, 20500 Turku, Finland
Interests: computational biology; microbial evolution; evolutionary genomics; phylogenomics diversity; genome dynamics; prokaryotes; viruses
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Special Issue Information

Dear Colleagues,

Foodborne pathogens have been a problem for all human societies. Although standards in food treatment and production have improved in many countries, they still remain a global problem according to the World Health Organization (WHO). The WHO estimates that there are 31 types of foodborne infections that result in 600 million illnesses annually and more than 400,000 deaths. Foodborne illnesses are caused by the transmission of infectious agents (e.g., bacteria, viruses, fungi, and parasites) and their toxins. The growing presence of antimicrobial resistance (AMR), i.e., microorganisms able to withstand current antimicrobial treatments, leads to harder treatments of foodborne illnesses. In addition, there is an increased risk of transferring AMR genes from the food chain into other microorganisms. A key factor with which to tackle the spread of pathogenic microorganisms and AMR outbreaks in the food chain is the development of more reliable and accurate surveillance methods. The latest techniques of whole-genome sequencing combined with high-throughput data analyses have improved the speed and accuracy of surveillance systems. Moreover, the spread of AMR in the food chain causes the need to experiment on alternative methods to antibiotics.

This Special Issue welcomes groundbreaking articles that aim to improve the real-time detection and tracking of foodborne pathogens in addition to the spread of AMR, as well as alternative methods (e.g., bacteriophages) to overcome the current AMR problem. This Special Issue is open to a wide range of articles and reviews, including modeling (WGS biomarkers, AI, deep learning, etc.), basic science, and applied research articles. Articles that evaluate the social/economic impacts, well-being benefits, and potential improvements of current technologies are also welcome.

Dr. Pere Puigbò
Guest Editor

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Keywords

  • foodborne pathogens
  • antimicrobial resistance
  • antibiotic resistance
  • track foodborn pathogens
  • bacteriophages
  • alternative to antibiotics
  • genome tracking
  • genotyping
  • molecular typing
  • Multi-Locus sequence typing
  • real-time pathogen surveillance
  • Salmonella
  • Escherichia
  • Listeria
  • Campylobacter
  • Shigella
  • food safety
  • spatial-epidemiology

Published Papers (2 papers)

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Research

13 pages, 764 KiB  
Article
Prevalence and Antibiotic Resistance of Salmonella and Campylobacter Isolates from Raw Chicken Breasts in Retail Markets in the United States and Comparison to Data from the Plant Level
by Sana Mujahid, Michael Hansen, Robyn Miranda, Keith Newsom-Stewart and James E. Rogers
Life 2023, 13(3), 642; https://doi.org/10.3390/life13030642 - 25 Feb 2023
Cited by 2 | Viewed by 2174
Abstract
Chicken is the most popular meat in the United States, and consumers may be exposed to multidrug resistant Salmonella and Campylobacter through consumption of retail chicken breasts. This study aimed to (i) determine the percentage of raw, packaged, retail chicken breasts from 27 [...] Read more.
Chicken is the most popular meat in the United States, and consumers may be exposed to multidrug resistant Salmonella and Campylobacter through consumption of retail chicken breasts. This study aimed to (i) determine the percentage of raw, packaged, retail chicken breasts from 27 metro areas that tested positive for Salmonella and Campylobacter; (ii) investigate the antibiotic susceptibility profiles of a subset of the isolates; and (iii) compare the Salmonella prevalence data to establishment level Salmonella categorization data published by the U.S. Department of Agriculture (USDA). USDA Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook (MLG) methodology was used to isolate and identify Salmonella (n = 672), Campylobacter (n = 499) from 400 g samples. National Antimicrobial Resistance Monitoring System (NARMS) methodology was followed for antimicrobial susceptibility testing of Salmonella (n = 52) and Campylobacter (n = 16) isolates. Salmonella was found in 8.6% of samples and Campylobacter in 4.2%. Having a 3 rating in USDA’s Salmonella Categorization of Individual Establishments for chicken parts was predictive of having a higher Salmonella percent positive in our data set (p ≤ 0.05). A total of 73.1% of Salmonella isolates, and 62.5% of Campylobacter isolates were resistant to ≥one class of antibiotics, with 48.1% of Salmonella isolates resistant to ≥three classes. Current results support interventions that take a ‘farm-to-fork’ approach with distinction by poultry types and parts as well as serovars, to lower antibiotic resistant Salmonella infections in humans due to poultry. Highlights: Salmonella was found in 8.6% and Campylobacter in 4.2% of chicken breasts tested; A 3 rating by USDA was predictive of a higher Salmonella percent positive; 48.1% of Salmonella isolates were resistant to 3 or more classes of antibiotics. Full article
(This article belongs to the Special Issue Tracking Foodborne Pathogens and Antimicrobial Resistance)
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21 pages, 1606 KiB  
Article
High Biofilm-Forming Ability and Clonal Dissemination among Colistin-Resistant Escherichia coli Isolates Recovered from Cows with Mastitis, Diarrheic Calves, and Chickens with Colibacillosis in Tunisia
by Sana Dhaouadi, Amel Romdhani, Wafa Bouglita, Salsabil Chedli, Soufiene Chaari, Leila Soufi, Ameur Cherif, Wissem Mnif, Mohamed Salah Abbassi and Ramzi Boubaker Elandoulsi
Life 2023, 13(2), 299; https://doi.org/10.3390/life13020299 - 20 Jan 2023
Cited by 3 | Viewed by 1326
Abstract
Background: Escherichia coli (E. coli) is one of the main etiological agents responsible for bovine mastitis (BM), neonatal calf diarrhea (NCD), and avian colibacillosis (AC). This study aimed to assess resistance and virulence genes content, biofilm-forming ability, phylogenetic groups, and genetic [...] Read more.
Background: Escherichia coli (E. coli) is one of the main etiological agents responsible for bovine mastitis (BM), neonatal calf diarrhea (NCD), and avian colibacillosis (AC). This study aimed to assess resistance and virulence genes content, biofilm-forming ability, phylogenetic groups, and genetic relatedness in E. coli isolates recovered from clinical cases of BM, NCD, and AC. Materials/Methods: A total of 120 samples including samples of milk (n = 70) and feces (n = 50) from cows with BM and calves with NCD, respectively, were collected from different farms in Northern Tunisia. Bacterial isolation and identification were performed. Then, E. coli isolates were examined by disk diffusion and broth microdilution method for their antimicrobial susceptibility and biofilm-forming ability. PCR was used to detect antimicrobial resistance genes (ARGs), virulence genes (VGs), phylogenetic groups, and Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) for their clonal relationship. Results: Among the 120 samples, 67 E. coli isolates (25 from BM, 22 from AC, and 20 from NCD) were collected. Overall, 83.6% of isolates were multidrug resistant. Thirty-six (53.73%) isolates were phenotypically colistin-resistant (CREC), 28.3% (19/67) were ESBL producers (ESBL-EC), and forty-nine (73.1%) formed biofilm. The blaTEM gene was found in 73.7% (14/19) of isolates from the three diseases, whilst the blaCTXM-g-1 gene was detected in 47.3% (9/19) of isolates, all from AC. The most common VG was the fimA gene (26/36, 72.2%), followed by aer (12/36, 33.3%), cnf1 (6/36, 16.6%), papC (4/36, 11.1%), and stx1 and stx2 genes (2/36; 5.5% for each). Phylogenetic analysis showed that isolates belonged to three groups: A (20/36; 55.5%), B2 (7/36; 19.4%), and D (6/36; 16.6%). Molecular typing by ERIC-PCR showed high genetic diversity of CREC and ESBL E. coli isolates from the three animal diseases and gave evidence of their clonal dissemination within farms in Tunisia. Conclusion: The present study sheds new light on the biofilm-forming ability and clonality within CREC and ESBL-EC isolated from three different animal diseases in Tunisian farm animals. Full article
(This article belongs to the Special Issue Tracking Foodborne Pathogens and Antimicrobial Resistance)
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