Microbial Safety and Molecular Detection in Food Production and Processing

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: 15 September 2026 | Viewed by 1105

Special Issue Editor


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Guest Editor
Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillan 3780000, Chile
Interests: food safety; molecular epidemiology; food pathogens; public health; food hygiene

Special Issue Information

Dear Colleagues,

Foodborne diseases (FBDs) constitute a relevant public health problem due to their incidence and severity. The high costs associated with FBDs have required world health authorities (WHO-FAO) to design preventive measures that ensure adequate international trade and protect the health of consumers through food safety. Monitoring pathogenic microorganisms through traditional culture methods or viable counts provides direct evidence of microbial hazard. In some cases, these pathogens are not easily detectable due to a low concentration, heterogeneous distribution, and physiological stress conditions that characterize their presence in foods, among other reasons. However, current research in epidemiology and food-associated diseases has used a variety of techniques derived from immunology to genetics. Whole-genome sequencing (WGS) is currently the gold standard for epidemiological and molecular identification and typing. Studies using WGS have demonstrated high discrimination of the information content, which provides a more accurate view of taxonomic differences between pathogenic strains. This technique not only enables the identification of the causative microorganism, but also creates a link with the source of contamination. It provides a wealth of information regarding its virulence and antibiotic resistance, and enables the establishment of more precise epidemiological links.

Dr. Julio Parra-Flores
Guest Editor

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Keywords

  • microbiological quality of foods
  • pathogens and opportunistic foodborne pathogens
  • molecular epidemiology of foodborne illness
  • molecular characterization of foodborne pathogens
  • biofilm, sanitizers, and control of pathogens in food production plants
  • virulence factors
  • antibiotic resistance

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Published Papers (1 paper)

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Research

18 pages, 521 KB  
Article
Genotypic and Phenotypic Characterization of Cronobacter spp. Strains Isolated from Powdered Milk Formulas and Dairy Production Environments
by Julio Parra-Flores, Beatriz Daza-Prieto, Miriam Troncoso, Guillermo Figueroa, Maria I. Reyes-Fuentes, Ondrej Holy, Ariadnna Cruz-Córdova, Werner Ruppitsch and Stephen Forsythe
Microorganisms 2026, 14(3), 593; https://doi.org/10.3390/microorganisms14030593 - 6 Mar 2026
Viewed by 622
Abstract
Cronobacter spp. is a pathogenic genus comprising seven species, of which C. sakazakii is particularly notable for its association with neonatal outbreaks linked to powdered infant formula. The severity of infections is associated with virulence factors (VFs) and β-lactam antibiotic resistance genes (ARGs). [...] Read more.
Cronobacter spp. is a pathogenic genus comprising seven species, of which C. sakazakii is particularly notable for its association with neonatal outbreaks linked to powdered infant formula. The severity of infections is associated with virulence factors (VFs) and β-lactam antibiotic resistance genes (ARGs). Next-generation sequencing (NGS) has enabled precise strain typing through core genome multilocus sequence typing (cgMLST), enhancing discrimination and accuracy. This study aimed to use cgMLST (2831 genes) to genomically characterize 34 Cronobacter strains which had been isolated from powdered milk and production surfaces between 2011 and 2022. The identified strains included C. sakazakii ST1, ST4, ST13, ST31 and ST83, as well as C. malonaticus ST60. Overall, there were eight clusters of closely related strains. All strains exhibited resistance to cephalothin, 18 were resistant to ceftazidime and 11 to ampicillin. Various resistance genes (blaCSA, blaCMA, fos, qacJ, marA, AcrAB-TolC, and mcr-9.1) and virulence genes (cpa, nanAKT, fic, relB, fliC) were detected, with some genes being exclusive to C. sakazakii. All strains carried plasmids and mobile genetic elements. The multidrug resistance and presence of virulence genes in these isolates highlight the significant risk that C. sakazakii-contaminated powdered dairy products pose to public health, underscoring the need to adopt proper hygienic manufacturing practices and effectively implement HACCP in their production. Full article
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