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Microbial Contamination and Food Safety (Volume II)

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A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (15 May 2026) | Viewed by 29465

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Dr. Joana Barbosa

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CBQF—Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, 4169-005 Porto, Portugal
Interests: food safety of edible insects; microbiological quality; hygiene practices; regulatory aspects; risk assess-ment; consumer safety; sustainable food systems
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Special Issue Information

Dear Colleagues,

Microbial contamination is one of the food chain's main challenges, from farm to fork/plate. According to the WHO, consuming contaminated food kills 420,000 people yearly and can cause more than 200 harmful diseases. Furthermore, microbial contamination of foods causes a huge economic impact due to product losses, increased insurance costs and consumer confidence loss. Since microbial contamination can occur at any step of the food chain, implementing effective food safety strategies is needed throughout production, postharvest handling, processing, distribution, and consumer handling to control and eliminate potential microbial hazards.

This Special Issue will collect comprehensive manuscripts dedicated to topics focused on food safety strategies, models that predict microbial behaviour, and the monitoring and prevention/elimination of microbial contamination along the farm-to-fork/consumer chain. Papers that present new approaches and innovative technologies are welcome for submission.

Dr. Joana Barbosa
Guest Editor

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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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology 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 2700 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 contamination
food safety practices
microbial inactivation
microbial safety
microbiological hazards

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Related Special Issue

Microbial Contamination and Food Safety in Biology (23 articles)

Published Papers (8 papers)

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Research

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21 pages, 364 KB

Open AccessArticle

Effectiveness of Some Natural Compounds Against Antibiotic-Resistant Listeria spp. and Salmonella enterica Strains

by David Jiménez-De-Juan, Félix Adanero-Jorge, Carlos Alonso-Calleja and Rosa Capita

Biology 2026, 15(14), 1141; https://doi.org/10.3390/biology15141141 - 13 Jul 2026

Viewed by 317

Abstract

The increasing prevalence of antibiotic resistance highlights the need to seek alternatives to currently used compounds. Minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) of nine ethanolic extracts of propolis (EEPs) from northwestern Spain and five phenolic compounds (carvacrol, eugenol, thymol, resveratrol, and trans-cinnamaldehyde) against Listeria spp. and Salmonella enterica strains were determined. All EEPs showed a strong antimicrobial effect against Listeria spp., with MICs (ppm) ranging between 78.00 ± 0.00 and 1041.67 ± 360.84 and MBCs (ppm) ranging between 312.50 ± 0.00 and 3333.33 ± 1443.38. The concentration of caffeic acid phenethyl ester (CAPE), isoprenyl caffeate (IPC), or total polyphenols did not influence the antimicrobial activity of EEPs. However, EEPs had only slight antimicrobial activity against S. enterica, with MICs ≥ 10,000 ppm and MBCs exceeding 10,000 ppm. MIC values (ppm) for phenolic compounds with respect to Listeria spp. strains ranged from 125.00 ± 0.00 to 2500.00 ± 0.00, and those for MBCs (ppm) ranged from 250.00 ± 0.00 to 5000.00 ± 0.00. For S. enterica, MICs (ppm) ranged from 250.00 ± 0.00 to 2500.00 ± 0.00 and MBCs (ppm) ranged from 416.67 ± 144.34 to 5000.00 ± 0.00. The results suggest that EEPs and phenolic compounds may offer natural alternatives to other antimicrobials in common use, with phenolic compounds being especially promising because of their antimicrobial activity against both Gram-positive and Gram-negative species. Full article

(This article belongs to the Special Issue Microbial Contamination and Food Safety (Volume II))

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17 pages, 2498 KB

Open AccessArticle

Harnessing a Lytic (Caudoviricetes with Podovirus-Like Morphology) Bacteriophage (ØAS2) for Biocontrol of Multidrug-Resistant Serratia marcescens Biofilms in Milk and Soft Cheese

by Dalia Kamal Rawy, Fawziah M. Albarakaty, Rehab M. A. El-Desoukey, Mayasar I. Al-Zaban, Alya Aljuaid, Mohammed Aladhadh, Khalid A. Alsaleem and Raghda M. S. Moawad

Biology 2026, 15(13), 1055; https://doi.org/10.3390/biology15131055 - 2 Jul 2026

Viewed by 413

Abstract

Serratia marcescens is a nosocomial pathogen that has acquired resistance to multiple antibiotics, necessitating alternative antimicrobial strategies. The aim of this study was to isolate and characterize a novel phage (ØAS2) against Serratia marcescens and evaluate its biocontrol potential in dairy matrices. In this study, a lytic bacteriophage specific to S. marcescens, designated ØAS2, was isolated from sewage samples collected in Assiut, Egypt. Phage ØAS2 was characterized using plaque assays, transmission electron microscopy (TEM), host range determination, pH and thermal stability tests, and one-step growth curve analysis. Its ability to inhibit bacterial growth and disrupt biofilms was also evaluated in vitro. TEM revealed that ØAS2 possesses an icosahedral head approximately 47.2 nm in diameter and a very short tail, consistent with the morphology of a member of the class Caudoviricetes that exhibits podovirus-like morphology. The phage exhibited a broad host range, infecting various Serratia strains as well as other Gram-negative bacteria, including Klebsiella spp., Escherichia coli, Salmonella typhi, and Shigella spp. ØAS2 was thermostable up to 60 °C and showed maximum activity at pH 8. One-step growth curve analysis revealed a short latent period of 10 min and a burst size of 115 PFU per infected cell. ØAS2 effectively inhibited the growth of S. marcescens SM02 in vitro and significantly reduced preformed biofilms at different multiplicities of infection (MOIs). When applied to skim milk and fresh soft cheese at various MOIs (Multiplicities of Infection), the phage successfully controlled bacterial contamination under refrigerated storage (7 °C for 7–10 days). At MOI 5.0, phage ØAS2 reduced biofilm biomass by 25.6%, planktonic growth by 85.7%, and achieved a reduction of 2.1 log₁₀ CFU/mL in skim milk. These findings indicate that ØAS2 is a promising biocontrol candidate for managing S. marcescens spoilage in dairy products. Full article

(This article belongs to the Special Issue Microbial Contamination and Food Safety (Volume II))

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16 pages, 2585 KB

Open AccessArticle

Cross-Contamination of Foodborne Pathogens During Juice Processing

by Isma Neggazi, Pilar Colás-Medà, Inmaculada Viñas and Isabel Alegre

Biology 2025, 14(8), 932; https://doi.org/10.3390/biology14080932 - 24 Jul 2025

Viewed by 3124

Abstract

The demand for unpasteurized fruit juices has grown due to their natural nutritional benefits, but this also increases the risk of foodborne illnesses. This study evaluated the transfer of three pathogens (Salmonella enterica, Escherichia coli O157:H7, and Listeria monocytogenes) from different surfaces (cutting boards, knives, and gloves) to produce and subsequently across different juice batches. Cutting boards and gloves showed the highest pathogen transfer rates (ranging from 2.03 ± 4.36 to 70.69 ± 23.58% for cutting boards, and from 0.04 ± 0.05 to 70.61 ± 23.51% for gloves), while knives exhibited the lowest (from 1.27 ± 1.35 to 7.87 ± 5.33%), when surface-to-produce transference was evaluated. Among the tested produce, beetroot had the highest pathogen transfer for all the tested pathogens (for the cutting board, from 48.55 ± 21.66 to 70.69 ± 23.58%, for the knife from 7.17 ± 6.17 to 7.87 ± 5.33%, and for the gloves from 48.85 ± 21.66 to 70.61 ± 23.51%). Beetroot juice provided the most favorable conditions for bacterial transfer (δ = 0.53–0.56; k_max1 = 3.09–3.20), whereas strawberry juice led to the fastest microbial decrease (δ = 1.10–1.26; k_max1 = 2.08–2.28) throughout processed juices. Apple juice demonstrated intermediate bacterial decline rates (δ = 0.75–1.10; k_max1 = 2.20–2.61). These findings highlight the need for improved hygiene practices and contamination control in juice processing to minimize food safety risks associated with unpasteurized fruit or vegetable juices. Full article

(This article belongs to the Special Issue Microbial Contamination and Food Safety (Volume II))

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17 pages, 3443 KB

Open AccessArticle

Neem Oil (Azadirachta indica L.) Response Surface Methodology (RSM)-Optimized Nanoemulsions for Sensory Quality Preservation of Oreochromis niloticus Fillets

by Jamal Kazam, Khalid Javed Iqbal, Afshan Shafi, Usman Majeed and Maximilian Lackner

Biology 2025, 14(4), 400; https://doi.org/10.3390/biology14040400 - 10 Apr 2025

Cited by 1 | Viewed by 3411

Abstract

Neem oil nanoemulsions (NO NEs) have gained attention as natural antibacterial agents due to toxicity concerns surrounding synthetic preservatives. This study aimed to prepare a response surface methodology (RSM)-optimized NO NE < 200 nm to achieve a stable dip solution to maintain the sensory quality of Oreochromis niloticus fillets. The NO NE achieved a stable formulation with a particle size of 160.2 ± 0.04 nm on average. The polydispersity index (PDI) was 0.1 ± 0.05, and the zeta potential was found to be 18.2 ± 0.09 mV. Gas chromatography confirmed the presence of nimbiol, nimbandiol, 6-deacetyl nimbinene, and azadirachtin in NO after ultrasonic homogenization for 10 min (alternating between 30 s rest and 30 s work time). The NE had a spherical shape with a smooth surface, as was evident from transmission electron microscopy (TEM). Furthermore, NO:PM (neem oil–potassium metabisulphite) had an MIC (minimum inhibitory concentration) value of 150 ppm, compared to 210 ppm for the NO NE alone, against Staphylococcus aureus. Time–kill dynamics revealed the more effective control of S. aureus until 72 h with NO:PM. Moreover, DNA and protein leakage also increased from 0.145 ± 0.001 to 0.769 ± 0.002 OD (optical density) and from 0.142 ± 0.002 to 0.740 ± 0.001 OD, respectively, with the co-formulation of NO:PM. Conclusively, NO:PM inhibited S. aureus at a lower dose compared to the NO NE alone. Time–kill dynamics revealed complete inhibition of S. aureus in vitro for a period of 72 h. On the other hand, a proximate analysis of O. niloticus fillets showed no alteration in pH, no protein loss, and juiciness/moisture retention during 30 days of storage (4 °C). Sensory panelists reported that O. niloticus fillets treated with NE NO had improved color, flavor, juiciness, aroma, and overall quality. These results show that NE NO is a suitable green preservative for fish and possibly other meat-based products. Full article

(This article belongs to the Special Issue Microbial Contamination and Food Safety (Volume II))

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20 pages, 3181 KB

Open AccessArticle

Foodborne Pathogen Prevalence and Biomarker Identification for Microbial Contamination in Mutton Meat

by Gayathri Muthusamy, Subburamu Karthikeyan, Veeranan Arun Giridhari, Ahmad R. Alhimaidi, Dananjeyan Balachandar, Aiman A. Ammari, Vaikuntavasan Paranidharan and Thirunavukkarasu Maruthamuthu

Biology 2024, 13(12), 1054; https://doi.org/10.3390/biology13121054 - 16 Dec 2024

Cited by 2 | Viewed by 3142

Abstract

Microbial contamination and the prevalence of foodborne pathogens in mutton meat and during its slaughtering process were investigated through microbial source tracking and automated pathogen identification techniques. Samples from mutton meat, cutting boards, hand swabs, knives, weighing balances, and water sources were collected from four different retail sites in Coimbatore. Total plate count (TPC), yeast and mold count (YMC), coliforms, E. coli, Pseudomonas aeruginosa, Salmonella, and Staphylococcus were examined across 91 samples. The highest microbial loads were found in the mutton-washed water, mutton meat, and cutting board samples. The automated pathogen identification system identified Staphylococcus species as the predominant contaminant and also revealed a 57% prevalence of Salmonella. Further analysis of goat meat inoculated with specific pathogens showed distinct volatile and metabolite profiles, identified using gas chromatography-mass spectrometry (GC-MS). Multivariate statistical analyses, including principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA), and sparse partial least squares discriminant analysis (sPLS-DA), identified potential biomarkers for pathogen contamination. The results highlight the significance of cross-contamination in the slaughtering process and suggest the use of volatile compounds as potential biomarkers for pathogen detection. Full article

(This article belongs to the Special Issue Microbial Contamination and Food Safety (Volume II))

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23 pages, 3365 KB

Open AccessArticle

Phytochemical Profiles and Biological Activities of Plant Extracts from Aromatic Plants Cultivated in Cyprus

by Antonios Chrysargyris, Jovana D. Petrovic, Ekaterina-Michaela Tomou, Kalia Kyriakou, Panayiota Xylia, Andria Kotsoni, Vasiliki Gkretsi, Panagiota Miltiadous, Helen Skaltsa, Marina D. Soković and Nikolaos Tzortzakis

Biology 2024, 13(1), 45; https://doi.org/10.3390/biology13010045 - 15 Jan 2024

Cited by 25 | Viewed by 7424

Abstract

Medicinal and aromatic plants’ properties, still an interesting research area, are attributed to the presence of various specialized products that possess important pharmacological activities. In the present study, six medicinal/aromatic plants (Sideritis cypria, Origanum dubium, Melissa officinalis, Mentha piperita, Thymus capitatus, and Salvia fruticosa) were evaluated for their phytochemical and nutritive composition, as well as their biological activities, including antioxidant, antimicrobial, and cytotoxic properties. The results obtained indicate that M. piperita was rich in proteins and minerals such as N and Mg, while S. cypria accumulated more K, Na, P, and Ca. The highest content of phenols and flavonoids was observed in M. piperita, followed by O. dubium and T. capitatus, which eventually influenced their high antioxidant capacity. NMR screening revealed the presence of (i) triterpenoids and hydroxycinnamic acid derivatives in M. officinalis; (ii) terpenoids, flavonoids, and phenolic acid derivatives in S. fruticosa; (iii) flavonoids and phenolic acid derivatives in M. piperita; (iv) phenolic monoterpenes in O. dubium and T. capitatus; and (v) terpenoids, flavones, and phenylethanoid glycosides in S. cypria. The results of the antimicrobial activity showed that the tested samples overall had quite good antimicrobial potential. High antibacterial activity was found in O. dubium and T. capitatus, while O. dubium and S. cypria exhibited great antifungal activities. The studied species also had an important effect on the viability of female-derived and colon cancer cells. In particular, in colon cancer cells, the extracts from T. capitatus, M. officinalis, M. piperita, and S. fruticosa exhibited a stronger effect on cell viability in the more metastatic cell line at significantly lower concentrations, indicating an important therapeutic potential in targeting highly metastatic tumors. This finding is worth further investigation. The present study unveiled interesting phytochemical profiles and biological properties of the six medicinal/aromatic plants, which should be further explored, contributing to green chemistry and the possible creation of natural health products for humans’ health/nutrition and additives in cosmetics. Full article

(This article belongs to the Special Issue Microbial Contamination and Food Safety (Volume II))

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Review

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32 pages, 1306 KB

Open AccessReview

Stress-Driven Tolerance and Persistence of Listeria monocytogenes Across the Farm-to-Fork Continuum

by Ayman Elbehiry, Eman Marzouk and Adil Abalkhail

Biology 2026, 15(4), 310; https://doi.org/10.3390/biology15040310 - 10 Feb 2026

Cited by 2 | Viewed by 1366

Abstract

Food systems expose bacteria to repeated nonlethal stresses during primary production, processing, storage, and sanitation. Depending on the type, intensity, and sequence of exposure, these stresses may weaken cells, act synergistically to promote inactivation, or fail to eliminate contamination. Instead, they can alter bacterial physiology in ways that affect survival, recovery, detection, and responses to control measures. This review examines how stress history contributes to persistent food safety challenges. Listeria monocytogenes is used as a central biological model, with relevant comparisons to other foodborne pathogens. Evidence from food-processing and environmental studies shows that repeated sublethal stress can shift bacterial populations toward stress-hardened states. Here, “stress-hardened” refers to reversible physiological changes and the survival of more tolerant cells, not permanent genetic adaptation. These states include sublethal injury, delayed growth, viable but nonculturable cells, biofilm formation, and increased tolerance to later stresses. These outcomes contribute to, but do not fully explain, the persistence of L. monocytogenes in food environments; intrinsic traits such as psychrotrophic growth and interactions with endogenous microflora also play important roles. These factors help explain repeated recovery of L. monocytogenes after sanitation and the underestimation of viable cells by routine culture-based methods, which do not reliably indicate whether pre-stressed cells retain the potential to cause foodborne illness. Many monitoring and validation approaches rely on unstressed laboratory cultures and fixed enrichment protocols. These conditions do not reflect the physiological states encountered in real food systems. As a result, negative test results may reflect limited recovery rather than true absence, and control performance may be overestimated when stress-conditioned populations are not considered. Across the farm-to-fork continuum, stress responses, persistence mechanisms, and detection limitations are closely linked, indicating that stress history should be considered a core element of hazard characterization, monitoring, and control validation. Incorporating stress biology into food safety assessment can improve the realism of verification strategies when combined with risk characterization that considers infectious dose and host susceptibility, and support control strategies under real-world processing and environmental conditions. Full article

(This article belongs to the Special Issue Microbial Contamination and Food Safety (Volume II))

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20 pages, 337 KB

Open AccessEditor’s ChoiceReview

Assessing Antimicrobial Efficacy on Plastics and Other Non-Porous Surfaces: A Closer Look at Studies Using the ISO 22196:2011 Standard

by Teresa Bento de Carvalho, Joana Bastos Barbosa and Paula Teixeira

Biology 2024, 13(1), 59; https://doi.org/10.3390/biology13010059 - 20 Jan 2024

Cited by 34 | Viewed by 7755

Abstract

The survival and spread of foodborne and nosocomial-associated bacteria through high-touch surfaces or contamination-prone sites, in either healthcare, domestic or food industry settings, are not always prevented by the employment of sanitary hygiene protocols. Antimicrobial surface coatings have emerged as a solution to eradicate pathogenic bacteria and prevent future infections and even outbreaks. Standardised antimicrobial testing methods play a crucial role in validating the effectiveness of these materials and enabling their application in real-life settings, providing reliable results that allow for comparison between antimicrobial surfaces while assuring end-use product safety. This review provides an insight into the studies using ISO 22196, which is considered the gold standard for antimicrobial surface coatings and examines the current state of the art in antimicrobial testing methods. It primarily focuses on identifying pitfalls and how even small variations in methods can lead to different results, affecting the assessment of the antimicrobial activity of a particular product. Full article

(This article belongs to the Special Issue Microbial Contamination and Food Safety (Volume II))

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