Pub Date : 2025-12-04DOI: 10.1016/j.ijfoodmicro.2025.111567
Víctor Arcos-Limiñana , Marie Polet , Bavo Verhaegen , Arturo B. Soro , Brijesh K. Tiwari , Soledad Prats-Moya , Salvador Maestre-Pérez , Koenraad Van Hoorde
Ultraviolet light-emitting diodes (UV-LEDs) are being investigated for potential use in food disinfection due to their customisable wavelength and high energy efficiency. The objective of this study was to examine the impact of UV-LED treatments, for up to 30 min, at wavelengths of 280, 300, and 365 nm, as well as simultaneous irradiation with 280 and 300 nm, on the culturability of Escherichia coli, Bacillus cereus spores, and Salmonella enterica in black peppercorns. It resulted in a reduction of up to 1.65, 1.35 and 1 log colony-forming units per gram (CFU/g) for E. coli, S. enterica, and B. cereus spores, respectively. The viability of S. enterica was also evaluated in black pepper using a viability PCR method with DyeTox13. No significant differences were observed between active and inactive non-culturable states. This finding suggests that UV light did not cause substantial lethal damage to the bacteria, but instead rendered them non-culturable, potentially leading to an underestimation of the food safety risk. These findings are encouraging concerning the potential applications of UV-LEDs in the spice industry.
{"title":"Decontamination of black peppercorns using UV-LED technology and its effect on cell viability","authors":"Víctor Arcos-Limiñana , Marie Polet , Bavo Verhaegen , Arturo B. Soro , Brijesh K. Tiwari , Soledad Prats-Moya , Salvador Maestre-Pérez , Koenraad Van Hoorde","doi":"10.1016/j.ijfoodmicro.2025.111567","DOIUrl":"10.1016/j.ijfoodmicro.2025.111567","url":null,"abstract":"<div><div>Ultraviolet light-emitting diodes (UV-LEDs) are being investigated for potential use in food disinfection due to their customisable wavelength and high energy efficiency. The objective of this study was to examine the impact of UV-LED treatments, for up to 30 min, at wavelengths of 280, 300, and 365 nm, as well as simultaneous irradiation with 280 and 300 nm, on the culturability of <em>Escherichia coli</em>, <em>Bacillus cereus</em> spores, and <em>Salmonella enterica</em> in black peppercorns. It resulted in a reduction of up to 1.65, 1.35 and 1 log colony-forming units per gram (CFU/g) for <em>E. coli</em>, <em>S. enterica</em>, and <em>B. cereus</em> spores, respectively. The viability of <em>S. enterica</em> was also evaluated in black pepper using a viability PCR method with DyeTox13. No significant differences were observed between active and inactive non-culturable states. This finding suggests that UV light did not cause substantial lethal damage to the bacteria, but instead rendered them non-culturable, potentially leading to an underestimation of the food safety risk. These findings are encouraging concerning the potential applications of UV-LEDs in the spice industry.</div></div>","PeriodicalId":14095,"journal":{"name":"International journal of food microbiology","volume":"447 ","pages":"Article 111567"},"PeriodicalIF":5.2,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145692718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-03DOI: 10.1016/j.ijfoodmicro.2025.111563
Laura M. Nolan , James J. Lazenby , George M. Savva , Ryan Sweet , Gregory J. Wickham , Haider Al-Khanaq , Samuel J. Bloomfield , Alison E. Mather , Cynthia B. Whitchurch
Members of the Pseudomonas genus are common spoilers of a range of meat, dairy and vegetable products. While we have a good understanding of the Pseudomonas species typically responsible for spoilage, we know very little about how these bacteria interact with food surfaces during spoilage. Here we assessed the spoilage capabilities of a large panel (n = 124) of Pseudomonas species food-derived isolates on meat (chicken) and leafy greens (spinach). Most isolates (71/124) were capable of spoiling both foods, but some were only capable of spoiling only chicken (21/124) or spinach (23/124), or neither (9/124). Our data also demonstrated that the type of fresh food the strain was isolated from influenced spoilage capabilities: strains isolated from meat products were equally likely to spoil both chicken and spinach; isolates from seafood products were significantly more likely to spoil chicken; and those isolated from leafy greens were significantly more likely to spoil spinach. We used fluorescence microscopy to visualise how Pseudomonas spoilage species interacted with the meat or leaf tissue and observed significant tissue destruction associated with biofilm formation. For chicken, this was associated with the formation of dense biofilm pillars that penetrated deep into the tissue. For spinach we observed biofilms on the leaf in areas of tissue degradation. Finally, we explored the correlation between potentially relevant phenotypes (in vitro biofilm, motility and secreted enzyme production) and spoilage capabilities. After controlling for the phylogenetic relationships between samples there was no evidence for association between these phenotypes and spoilage capability in either product. Overall, this study increases our understanding of processes involved in food spoilage by Pseudomonas species.
{"title":"Tissue destruction during food spoilage is associated with the formation of biofilms by Pseudomonas species","authors":"Laura M. Nolan , James J. Lazenby , George M. Savva , Ryan Sweet , Gregory J. Wickham , Haider Al-Khanaq , Samuel J. Bloomfield , Alison E. Mather , Cynthia B. Whitchurch","doi":"10.1016/j.ijfoodmicro.2025.111563","DOIUrl":"10.1016/j.ijfoodmicro.2025.111563","url":null,"abstract":"<div><div>Members of the <em>Pseudomonas</em> genus are common spoilers of a range of meat, dairy and vegetable products. While we have a good understanding of the <em>Pseudomonas</em> species typically responsible for spoilage, we know very little about how these bacteria interact with food surfaces during spoilage. Here we assessed the spoilage capabilities of a large panel (<em>n</em> = 124) of <em>Pseudomonas</em> species food-derived isolates on meat (chicken) and leafy greens (spinach). Most isolates (71/124) were capable of spoiling both foods, but some were only capable of spoiling only chicken (21/124) or spinach (23/124), or neither (9/124). Our data also demonstrated that the type of fresh food the strain was isolated from influenced spoilage capabilities: strains isolated from meat products were equally likely to spoil both chicken and spinach; isolates from seafood products were significantly more likely to spoil chicken; and those isolated from leafy greens were significantly more likely to spoil spinach. We used fluorescence microscopy to visualise how <em>Pseudomonas</em> spoilage species interacted with the meat or leaf tissue and observed significant tissue destruction associated with biofilm formation. For chicken, this was associated with the formation of dense biofilm pillars that penetrated deep into the tissue. For spinach we observed biofilms on the leaf in areas of tissue degradation. Finally, we explored the correlation between potentially relevant phenotypes (<em>in vitro</em> biofilm, motility and secreted enzyme production) and spoilage capabilities. After controlling for the phylogenetic relationships between samples there was no evidence for association between these phenotypes and spoilage capability in either product. Overall, this study increases our understanding of processes involved in food spoilage by <em>Pseudomonas</em> species.</div></div>","PeriodicalId":14095,"journal":{"name":"International journal of food microbiology","volume":"447 ","pages":"Article 111563"},"PeriodicalIF":5.2,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145742503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-03DOI: 10.1016/j.ijfoodmicro.2025.111564
Md Jisan Ahmed , Md Imran Hossain , Delower Hossain
Escherichia albertii (E. albertii) is a globally emerging zoonotic foodborne pathogen with underestimated public health significance due to misidentification challenges. This study systematically investigated the global epidemiology and host spectrum of E. albertii through a meta-analysis of its prevalence and associated epidemiological determinants across different sources. A total of 13 studies published between 2000 and 2025 were identified through comprehensive searches of Scopus, Web of Science, and PubMed, which were based on predefined inclusion criteria. The data were systematically extracted using Microsoft Excel, and the statistical analyses were performed in R (v4.5.0). To address substantial heterogeneity, a random effects model was applied to estimate the pooled prevalence. The meta-analysis included 13 studies comprising 5439 samples, 454 of which 454 were positive for E. albertii, resulting in a pooled prevalence of 15.49 % with significant heterogeneity (97 %). Subgroup differences by country (τ2 = 0.0008–0.0249), host (τ2 = 0.0032–0.1031), and sample (τ2 = 0.0076–0.0881) were statistically significant (p < 0.0001), whereas meta-regression identified no significant covariates. The highest prevalence was observed in Bangladesh (63.93 %), whereas the lowest was in Belgium (1.35 %). Host-specific analysis revealed the highest prevalence in chickens (26.75 %) and raccoons (25.61 %), whereas that in oysters (2.11 %) was the lowest. Meat (17.95 %) and fecal (17.43 %) samples presented the highest pooled prevalence among the samples. This study suggests that E. albertii is globally distributed and may exhibit underrecognized host diversity, highlighting its potentially underrecognized importance for public health. However, given the limited number of studies and substantial heterogeneity, these findings should be interpreted with caution.
{"title":"Emerging pathogen alert: Global epidemiology of the zoonotic potential of Escherichia albertii: A systematic review and meta-analysis","authors":"Md Jisan Ahmed , Md Imran Hossain , Delower Hossain","doi":"10.1016/j.ijfoodmicro.2025.111564","DOIUrl":"10.1016/j.ijfoodmicro.2025.111564","url":null,"abstract":"<div><div><em>Escherichia albertii</em> (<em>E. albertii</em>) is a globally emerging zoonotic foodborne pathogen with underestimated public health significance due to misidentification challenges. This study systematically investigated the global epidemiology and host spectrum of <em>E. albertii</em> through a meta-analysis of its prevalence and associated epidemiological determinants across different sources. A total of 13 studies published between 2000 and 2025 were identified through comprehensive searches of Scopus, Web of Science, and PubMed, which were based on predefined inclusion criteria. The data were systematically extracted using Microsoft Excel, and the statistical analyses were performed in R (v4.5.0). To address substantial heterogeneity, a random effects model was applied to estimate the pooled prevalence. The meta-analysis included 13 studies comprising 5439 samples, 454 of which 454 were positive for <em>E. albertii</em>, resulting in a pooled prevalence of 15.49 % with significant heterogeneity (97 %). Subgroup differences by country (τ<sup>2</sup> = 0.0008–0.0249), host (τ<sup>2</sup> = 0.0032–0.1031), and sample (τ<sup>2</sup> = 0.0076–0.0881) were statistically significant (<em>p</em> < 0.0001), whereas meta-regression identified no significant covariates. The highest prevalence was observed in Bangladesh (63.93 %), whereas the lowest was in Belgium (1.35 %). Host-specific analysis revealed the highest prevalence in chickens (26.75 %) and raccoons (25.61 %), whereas that in oysters (2.11 %) was the lowest. Meat (17.95 %) and fecal (17.43 %) samples presented the highest pooled prevalence among the samples. This study suggests that <em>E. albertii</em> is globally distributed and may exhibit underrecognized host diversity, highlighting its potentially underrecognized importance for public health. However, given the limited number of studies and substantial heterogeneity, these findings should be interpreted with caution.</div></div>","PeriodicalId":14095,"journal":{"name":"International journal of food microbiology","volume":"447 ","pages":"Article 111564"},"PeriodicalIF":5.2,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145714056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-03DOI: 10.1016/j.ijfoodmicro.2025.111562
Wenxin Zhao , Shenshen Liu , Haoxuan He , Huanhuan Zou , Xiaoyi Huang , Haiyan Zeng
Cronobacter spp. are important foodborne pathogens associated with severe neonatal infections and high mortality rates. CRISPR typing's higher resolution than multi-locus sequence typing (MLST) makes it powerful for tracing the source of Cronobacter contamination, yet its broader application is constrained by the technique's complexity. To address this challenge, we developed an automated CRISPR typing tool, CRISPRSpacerType, to perform CRISPR detection, classification, and CRISPR Type (CT) assignment. A local database was constructed for Cronobacter spp. as a reference, and all strains were subsequently typed using this tool. Furthermore, we conducted a detailed analysis of two major pathogenic sequence types, Cronobacter sakazakii ST1 and ST4, to assess the performance of CRISPRSpacerType. A total of 39 and 30 CTs were detected in ST1 and ST4 strains, respectively. Most importantly, significant associations were found linking specific CT types to both predominant colistin antibiotic resistance gene mcr-9.1 carriage and pathogenicity. Spacer analysis revealed potential plasmid transmission and specific phage driven adaptation. Ancestral spacer analysis of ST4 strains further identified a high-risk lineage, which includes both the pathogenic CT2 and mcr-9.1 positive CT325 strains, warranting heightened surveillance. Spacer sequences are closely associated with bacterial evolution and phenotype, making the development of a CRISPR typing tool of high biological significance. CRISPRSpacerType permits the broader application of high resolution CRISPR typing to contamination source tracing and evolutionary monitoring of Cronobacter. This advancement significantly strengthens outbreak prevention and surveillance efforts against this pathogen. Our tool is available from GitHub at https://github.com/zwxyo/CRISPRSpacerType.
{"title":"CRISPRSpacerType: Automated CRISPR typing of Cronobacter spp. for contamination tracing and evolutionary analysis via spacer profiles","authors":"Wenxin Zhao , Shenshen Liu , Haoxuan He , Huanhuan Zou , Xiaoyi Huang , Haiyan Zeng","doi":"10.1016/j.ijfoodmicro.2025.111562","DOIUrl":"10.1016/j.ijfoodmicro.2025.111562","url":null,"abstract":"<div><div><em>Cronobacter</em> spp. are important foodborne pathogens associated with severe neonatal infections and high mortality rates. CRISPR typing's higher resolution than multi-locus sequence typing (MLST) makes it powerful for tracing the source of <em>Cronobacter</em> contamination, yet its broader application is constrained by the technique's complexity. To address this challenge, we developed an automated CRISPR typing tool, CRISPRSpacerType, to perform CRISPR detection, classification, and CRISPR Type (CT) assignment. A local database was constructed for <em>Cronobacter</em> spp. as a reference, and all strains were subsequently typed using this tool. Furthermore, we conducted a detailed analysis of two major pathogenic sequence types, <em>Cronobacter sakazakii</em> ST1 and ST4, to assess the performance of CRISPRSpacerType. A total of 39 and 30 CTs were detected in ST1 and ST4 strains, respectively. Most importantly, significant associations were found linking specific CT types to both predominant colistin antibiotic resistance gene <em>mcr-9.1</em> carriage and pathogenicity. Spacer analysis revealed potential plasmid transmission and specific phage driven adaptation. Ancestral spacer analysis of ST4 strains further identified a high-risk lineage, which includes both the pathogenic CT2 and <em>mcr-9.1</em> positive CT325 strains, warranting heightened surveillance. Spacer sequences are closely associated with bacterial evolution and phenotype, making the development of a CRISPR typing tool of high biological significance. CRISPRSpacerType permits the broader application of high resolution CRISPR typing to contamination source tracing and evolutionary monitoring of <em>Cronobacter</em>. This advancement significantly strengthens outbreak prevention and surveillance efforts against this pathogen. Our tool is available from GitHub at <span><span>https://github.com/zwxyo/CRISPRSpacerType</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":14095,"journal":{"name":"International journal of food microbiology","volume":"447 ","pages":"Article 111562"},"PeriodicalIF":5.2,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145742539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-02DOI: 10.1016/j.ijfoodmicro.2025.111553
Chenhan Geng , Shao Quan Liu , Yuyun Lu
Kombu (Saccharina japonica), a nutrient-rich brown seaweed, exhibits limited nutrient bioaccessibility/bioavailability and unfavorable sensory characteristics, particularly lipid-derived off-flavor volatiles, hindering its broader application in the food industry. Although enzymatic hydrolysis and lactic acid bacterial (LAB) fermentation have been applied to improve the nutritional quality of kombu, their effects on sensory improvement remain limited. In contrast, LAB-yeast co-fermentation, particularly involving non-Saccharomyces yeasts, has shown great potential to enhance probiotic viability and modulate flavor profiles; however, this approach has not yet been explored in seaweed substrate. Here, we report for the first time the co-fermentation of Lacticaseibacillus paracasei Shirota and Lactiplantibacillus plantarum 299v with the aroma-producing yeast Pichia kluyveri FrootZen in enzymatically hydrolyzed kombu slurry, under both monoculture and co-culture conditions. After 7 days of fermentation, co-cultures achieved significantly higher probiotic viability (7.36–7.48 log CFU/mL) than probiotic monocultures (6.10–6.40 log CFU/mL), with the L. plantarum-P. kluyveri co-culture additionally producing bioactive γ-aminobutyric acid (GABA). Co-cultures also reduced key off-flavor volatiles such as 1-octen-3-one, (E,Z)-2,6-nonadienal, and (E,E)-2,4-decadienal, by up to 41.5 % compared to the control group, while promoting the biosynthesis of desirable fruity esters, including isoamyl acetate (OAV ≥ 52.9), hexyl acetate (OAV ≥ 36.9), and 2-phenylethyl acetate (OAV ≥ 2.1). These findings highlight the synergistic benefits of LAB-yeast co-fermentation in improving fermentation performance and modulating odor-active volatiles, offering a promising strategy for developing high-quality fermented seaweed-based functional foods/beverages.
{"title":"Co-fermentation of probiotic lactic acid bacteria and Pichia kluyveri enhances the probiotic viability and flavor profile of enzyme-hydrolyzed kombu (Saccharina japonica) slurry","authors":"Chenhan Geng , Shao Quan Liu , Yuyun Lu","doi":"10.1016/j.ijfoodmicro.2025.111553","DOIUrl":"10.1016/j.ijfoodmicro.2025.111553","url":null,"abstract":"<div><div>Kombu (<em>Saccharina japonica</em>), a nutrient-rich brown seaweed, exhibits limited nutrient bioaccessibility/bioavailability and unfavorable sensory characteristics, particularly lipid-derived off-flavor volatiles, hindering its broader application in the food industry. Although enzymatic hydrolysis and lactic acid bacterial (LAB) fermentation have been applied to improve the nutritional quality of kombu, their effects on sensory improvement remain limited. In contrast, LAB-yeast co-fermentation, particularly involving non-<em>Saccharomyces</em> yeasts, has shown great potential to enhance probiotic viability and modulate flavor profiles; however, this approach has not yet been explored in seaweed substrate. Here, we report for the first time the co-fermentation of <em>Lacticaseibacillus paracasei</em> Shirota and <em>Lactiplantibacillus plantarum</em> 299v with the aroma-producing yeast <em>Pichia kluyveri</em> FrootZen in enzymatically hydrolyzed kombu slurry, under both monoculture and co-culture conditions. After 7 days of fermentation, co-cultures achieved significantly higher probiotic viability (7.36–7.48 log CFU/mL) than probiotic monocultures (6.10–6.40 log CFU/mL), with the <em>L. plantarum</em>-<em>P. kluyveri</em> co-culture additionally producing bioactive γ-aminobutyric acid (GABA). Co-cultures also reduced key off-flavor volatiles such as 1-octen-3-one, (<em>E</em>,<em>Z</em>)-2,6-nonadienal, and (<em>E</em>,<em>E</em>)-2,4-decadienal, by up to 41.5 % compared to the control group, while promoting the biosynthesis of desirable fruity esters, including isoamyl acetate (OAV ≥ 52.9), hexyl acetate (OAV ≥ 36.9), and 2-phenylethyl acetate (OAV ≥ 2.1). These findings highlight the synergistic benefits of LAB-yeast co-fermentation in improving fermentation performance and modulating odor-active volatiles, offering a promising strategy for developing high-quality fermented seaweed-based functional foods/beverages.</div></div>","PeriodicalId":14095,"journal":{"name":"International journal of food microbiology","volume":"447 ","pages":"Article 111553"},"PeriodicalIF":5.2,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145713996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-27DOI: 10.1016/j.ijfoodmicro.2025.111551
Jiaqi Ma , Xiaobao Bai , Siyue Wang , Yinuo Yang , Mei Li , Min Li , Wei Zhou , Shenghui Cui , Baowei Yang
<div><div><em>Salmonella</em> is a major foodborne pathogen, frequently linked to poultry and posing serious food safety and public health risks. To investigate its epidemiology in retail chicken in Shaanxi Province, China, we conducted a comprehensive study integrating whole-genome sequencing (WGS), Clusters of Orthologous Groups (COG) analysis, and machine learning (ML). Genomic data of 331 <em>S</em>. Kentucky and 614 <em>S. enteritidis</em> isolates from the NCBI database were also analyzed to assess genetic relatedness between local strains and those from other sources across China. From 280 chicken samples collected in seven cities, 92 (32.86 %) were <em>Salmonella</em>-positive, yielding 132 isolates representing 29 serotypes. <em>S.</em> Kentucky predominated in wet markets, whereas <em>S. enteritidis</em> dominated supermarkets. All isolates were resistant to at least one antibiotic, with 87.88 % showing multidrug resistance (MDR) and 38.64 % exhibiting extensive drug-resistance (XDR). WGS of 78 representative isolates identified 61 antimicrobial resistance genes (ARGs) and seven quinolone resistance-determining region (QRDR) mutations, with ParC (Thr57Ser) being most frequent. It is worth noting that the high prevalence (100.00 %) of Yersinia high-pathogenicity island (HPI) genes detected in <em>S. infantis</em> in this study has hardly been reported previously. Phylogenetic analysis revealed <em>S.</em> Kentucky and <em>S. enteritidis</em>, which are the predominant serotypes detected in the investigation, showing close genetic relationship (SNP < 10) with those from chicken, pork, aquatic products, and humans in other provinces and host sources. Pan-genomic analysis showed that the number of accessory genes in <em>S.</em> Kentucky was higher than that in <em>S. enteritidis</em>, and supermarket- and human-origin <em>Salmonella</em> isolates possessed a higher proportion of accessory genes. This indicates that the genomes of these isolates are more open and have greater potential for acquiring exogenous elements. Functional enrichment analysis on the core and auxiliary genomes of <em>S.</em> Kentucky and <em>S. enteritidis</em> based on COG clustering indicated that significant differences could be found in the functions of the accessory genomes between the two serotypes. ML-based screening identified <em>intS3</em>, which is implicated in genomic stability and DNA damage repair, as a key feature gene in wet market isolates. Key feature genes identified in <em>S.</em> Kentucky and <em>S. enteritidis</em> from chicken were <em>torI</em> and <em>rfaF</em>, respectively, both associated with environmental adaptability. In human-derived isolates, <em>ccmA</em> and <em>oadB1</em> were identified as feature genes, contributing to bacterial proliferation and host adaptation. This study provides comprehensive genomic and epidemiological insights into <em>Salmonella</em> in Shaanxi retail chicken, emphasizing the widespread MDR/XDR burden an
{"title":"Characteristics and genomics study of Salmonella isolates in retail chicken in Shaanxi, China: Focus on comparative genomics analysis of S. Kentucky and S. enteritidis isolates from Shaanxi with those from elsewhere in China","authors":"Jiaqi Ma , Xiaobao Bai , Siyue Wang , Yinuo Yang , Mei Li , Min Li , Wei Zhou , Shenghui Cui , Baowei Yang","doi":"10.1016/j.ijfoodmicro.2025.111551","DOIUrl":"10.1016/j.ijfoodmicro.2025.111551","url":null,"abstract":"<div><div><em>Salmonella</em> is a major foodborne pathogen, frequently linked to poultry and posing serious food safety and public health risks. To investigate its epidemiology in retail chicken in Shaanxi Province, China, we conducted a comprehensive study integrating whole-genome sequencing (WGS), Clusters of Orthologous Groups (COG) analysis, and machine learning (ML). Genomic data of 331 <em>S</em>. Kentucky and 614 <em>S. enteritidis</em> isolates from the NCBI database were also analyzed to assess genetic relatedness between local strains and those from other sources across China. From 280 chicken samples collected in seven cities, 92 (32.86 %) were <em>Salmonella</em>-positive, yielding 132 isolates representing 29 serotypes. <em>S.</em> Kentucky predominated in wet markets, whereas <em>S. enteritidis</em> dominated supermarkets. All isolates were resistant to at least one antibiotic, with 87.88 % showing multidrug resistance (MDR) and 38.64 % exhibiting extensive drug-resistance (XDR). WGS of 78 representative isolates identified 61 antimicrobial resistance genes (ARGs) and seven quinolone resistance-determining region (QRDR) mutations, with ParC (Thr57Ser) being most frequent. It is worth noting that the high prevalence (100.00 %) of Yersinia high-pathogenicity island (HPI) genes detected in <em>S. infantis</em> in this study has hardly been reported previously. Phylogenetic analysis revealed <em>S.</em> Kentucky and <em>S. enteritidis</em>, which are the predominant serotypes detected in the investigation, showing close genetic relationship (SNP < 10) with those from chicken, pork, aquatic products, and humans in other provinces and host sources. Pan-genomic analysis showed that the number of accessory genes in <em>S.</em> Kentucky was higher than that in <em>S. enteritidis</em>, and supermarket- and human-origin <em>Salmonella</em> isolates possessed a higher proportion of accessory genes. This indicates that the genomes of these isolates are more open and have greater potential for acquiring exogenous elements. Functional enrichment analysis on the core and auxiliary genomes of <em>S.</em> Kentucky and <em>S. enteritidis</em> based on COG clustering indicated that significant differences could be found in the functions of the accessory genomes between the two serotypes. ML-based screening identified <em>intS3</em>, which is implicated in genomic stability and DNA damage repair, as a key feature gene in wet market isolates. Key feature genes identified in <em>S.</em> Kentucky and <em>S. enteritidis</em> from chicken were <em>torI</em> and <em>rfaF</em>, respectively, both associated with environmental adaptability. In human-derived isolates, <em>ccmA</em> and <em>oadB1</em> were identified as feature genes, contributing to bacterial proliferation and host adaptation. This study provides comprehensive genomic and epidemiological insights into <em>Salmonella</em> in Shaanxi retail chicken, emphasizing the widespread MDR/XDR burden an","PeriodicalId":14095,"journal":{"name":"International journal of food microbiology","volume":"446 ","pages":"Article 111551"},"PeriodicalIF":5.2,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145661016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-27DOI: 10.1016/j.ijfoodmicro.2025.111552
Xinyu Cai , Kun Lan , Zhenlong Zhou , Shunxing Peng , Jinxiang Xiao , Pengzhen Li , Guanghao Chen , Penghui Fan , Jianyu Su
With the increasing threat of foodborne diseases, photodynamic inactivation (PDI) has attracted attention as a non-thermal sterilization technology that preserves food quality. But the efficiency of photosensitizers (PSs) is limited by short lifespan and limited diffusion distance of reactive oxygen species (ROS). Therefore, it is necessary to develop PSs capable of penetrating cell membranes and directly generating ROS within cells to effectively inactivate foodborne microorganisms. Among emerging materials, carbon dots (CDs) are small, water soluble, exhibit low photobleaching rates, and possess a core-shell structure with abundant surface functional groups, making them promising candidates for PDI. In this study, functional carbon dots (M-CDs) were synthesized from Cinnamomum burmannii waste. The M-CDs demonstrated strong fluorescence, excellent water solubility, and surface groups such as carboxyl and hydroxyl, which enhanced their biocompatibility and antimicrobial activity. With a diameter of approximately 3.355 nm, M-CDs efficiently penetrated cell membranes to generate ROS directly within cells, thereby inactivating foodborne microorganisms via multiple targets. The PDI efficacy of M-CDs against Escherichia coli 8739 was evaluated, demonstrating that 50 mg/L M-CDs reduced bacterial counts by 3.8 log10, and 200 mg/L achieved complete bacterial eradication. Transcriptome analysis revealed gene enrichment in pathways related to lipid metabolism, energy metabolism, DNA repair, and oxidative stress responses. Moreover, M-CDs effectively reduced microbial contamination in Psidium guajava (guavas) and extended their shelf life by eight days at room temperature. The findings of this study provide new insights for developing green, safe, and effective strategies to control foodborne pathogen.
{"title":"Cinnamomum burmannii waste-derived carbon dots as a novel photosensitizer for effective photodynamic inactivation of foodborne Escherichia coli","authors":"Xinyu Cai , Kun Lan , Zhenlong Zhou , Shunxing Peng , Jinxiang Xiao , Pengzhen Li , Guanghao Chen , Penghui Fan , Jianyu Su","doi":"10.1016/j.ijfoodmicro.2025.111552","DOIUrl":"10.1016/j.ijfoodmicro.2025.111552","url":null,"abstract":"<div><div>With the increasing threat of foodborne diseases, photodynamic inactivation (PDI) has attracted attention as a non-thermal sterilization technology that preserves food quality. But the efficiency of photosensitizers (PSs) is limited by short lifespan and limited diffusion distance of reactive oxygen species (ROS). Therefore, it is necessary to develop PSs capable of penetrating cell membranes and directly generating ROS within cells to effectively inactivate foodborne microorganisms. Among emerging materials, carbon dots (CDs) are small, water soluble, exhibit low photobleaching rates, and possess a core-shell structure with abundant surface functional groups, making them promising candidates for PDI. In this study, functional carbon dots (M-CDs) were synthesized from <em>Cinnamomum burmannii</em> waste. The M-CDs demonstrated strong fluorescence, excellent water solubility, and surface groups such as carboxyl and hydroxyl, which enhanced their biocompatibility and antimicrobial activity. With a diameter of approximately 3.355 nm, M-CDs efficiently penetrated cell membranes to generate ROS directly within cells, thereby inactivating foodborne microorganisms via multiple targets. The PDI efficacy of M-CDs against <em>Escherichia coli</em> 8739 was evaluated, demonstrating that 50 mg/L M-CDs reduced bacterial counts by 3.8 log<sub>10</sub>, and 200 mg/L achieved complete bacterial eradication. Transcriptome analysis revealed gene enrichment in pathways related to lipid metabolism, energy metabolism, DNA repair, and oxidative stress responses. Moreover, M-CDs effectively reduced microbial contamination in <em>Psidium guajava</em> (guavas) and extended their shelf life by eight days at room temperature. The findings of this study provide new insights for developing green, safe, and effective strategies to control foodborne pathogen.</div></div>","PeriodicalId":14095,"journal":{"name":"International journal of food microbiology","volume":"447 ","pages":"Article 111552"},"PeriodicalIF":5.2,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145668285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-27DOI: 10.1016/j.ijfoodmicro.2025.111542
Jinjin Pei , Jue Gong , Zhe Liu , Wengang Jin , Mingxin Hou , A.M. Abd El-Aty , Qi Deng
This study investigated the microbially driven spoilage mechanism of sturgeon (Acipenser baerii) under refrigerated (4 °C) aerobic storage. High-throughput sequencing analysis revealed that Pseudomonas and Shewanella dominated late-stage spoilage, which was strongly positively correlated with volatile base nitrogen (VBN) accumulation and microbial metabolic shifts toward amino acid degradation pathways. By applying machine learning (random forest coupled with SHAP analysis, AUROC = 0.96) and graph neural networks (GAT, recall = 89.7 %), we pinpointed key spoilage-associated taxa and their interaction dynamics. Furthermore, numerous chemical descriptors have revealed that spoilage-associated enzymes present elevated molecular electrostatic potential (MEPs >25 kcal/mol), which facilitates the nucleophilic attack of amino acids and accelerates spoilage reactions. Time series forecasting (multivariate Prophet model) accurately predicted critical spoilage thresholds (96.5 ± 4.2 h postprocessing) with high accuracy (MAPE = 12.3 %). Additionally, metabolic modeling has demonstrated microbial cold-adapted energy strategies, including a significant increase in succinate fermentation flux (3.8 ± 0.5 mmol·g−1 DW·h−1) and the suppression of TCA cycle activity. This study establishes a multiscale framework linking microbial ecology, enzymatic quantum mechanics, and metabolic dynamics, offering mechanistic insight into spoilage and providing a foundation for precise sturgeon preservation strategies in cold chain logistics.
{"title":"High-throughput sequencing reveals microbial transitions in refrigerated sturgeon meat: Implications for quality assurance","authors":"Jinjin Pei , Jue Gong , Zhe Liu , Wengang Jin , Mingxin Hou , A.M. Abd El-Aty , Qi Deng","doi":"10.1016/j.ijfoodmicro.2025.111542","DOIUrl":"10.1016/j.ijfoodmicro.2025.111542","url":null,"abstract":"<div><div>This study investigated the microbially driven spoilage mechanism of sturgeon (<em>Acipenser baerii</em>) under refrigerated (4 °C) aerobic storage. High-throughput sequencing analysis revealed that Pseudomonas and Shewanella dominated late-stage spoilage, which was strongly positively correlated with volatile base nitrogen (VBN) accumulation and microbial metabolic shifts toward amino acid degradation pathways. By applying machine learning (random forest coupled with SHAP analysis, AUROC = 0.96) and graph neural networks (GAT, recall = 89.7 %), we pinpointed key spoilage-associated taxa and their interaction dynamics. Furthermore, numerous chemical descriptors have revealed that spoilage-associated enzymes present elevated molecular electrostatic potential (MEPs >25 kcal/mol), which facilitates the nucleophilic attack of amino acids and accelerates spoilage reactions. Time series forecasting (multivariate Prophet model) accurately predicted critical spoilage thresholds (96.5 ± 4.2 h postprocessing) with high accuracy (MAPE = 12.3 %). Additionally, metabolic modeling has demonstrated microbial cold-adapted energy strategies, including a significant increase in succinate fermentation flux (3.8 ± 0.5 mmol·g<sup>−1</sup> DW·h<sup>−1</sup>) and the suppression of TCA cycle activity. This study establishes a multiscale framework linking microbial ecology, enzymatic quantum mechanics, and metabolic dynamics, offering mechanistic insight into spoilage and providing a foundation for precise sturgeon preservation strategies in cold chain logistics.</div></div>","PeriodicalId":14095,"journal":{"name":"International journal of food microbiology","volume":"448 ","pages":"Article 111542"},"PeriodicalIF":5.2,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145719041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-26DOI: 10.1016/j.ijfoodmicro.2025.111533
Weiye Cheng , Qingyang Zhang , Xuan Wang , Yun Cen , Zifan Li , Yunjing Gu , Hui Guan , Kanghee Ko , Wenli Liu , Huamin Li
The inoculation timing of starter cultures is a critical factor influencing the quality of fermented foods, yet it remains underexplored. This study evaluated how simultaneous (T1) and sequential (X1) inoculation of Leuconostoc, Levilactobacillus, and Lactiplantibacillus affects inter-species competition and fermentation dynamics in Chinese spicy cabbage (CSC). While the T1 strategy accelerated fermentation kinetics with Leuconostoc acting as the primary fermenter, the inoculation sequence altered the competitive hierarchy of the secondary fermenters: Levilactobacillus dominated in T1, whereas Lactiplantibacillus prevailed in X1. This differential microbial succession resulted in distinct aromatic signatures, with Random Forest modeling identifying methyl allyl disulfide (Day 6) and dimethyl trisulfide (Day 13) as key differential compounds driving these flavor differences. Although the T1 group developed a more intense fermented flavor, sensory analysis indicated that the sequential (X1) strategy achieved higher overall acceptability by yielding a more desirable balance between moderate flavor and preserved texture. These findings demonstrate that adjusting inoculation timing is an effective method to engineer microbial succession and systematically modify the final sensory profile of fermented vegetables.
{"title":"Simultaneous and sequential inoculation of lactic acid bacteria to engineer the flavor profile of Chinese spicy cabbage: A machine learning and modeling study","authors":"Weiye Cheng , Qingyang Zhang , Xuan Wang , Yun Cen , Zifan Li , Yunjing Gu , Hui Guan , Kanghee Ko , Wenli Liu , Huamin Li","doi":"10.1016/j.ijfoodmicro.2025.111533","DOIUrl":"10.1016/j.ijfoodmicro.2025.111533","url":null,"abstract":"<div><div>The inoculation timing of starter cultures is a critical factor influencing the quality of fermented foods, yet it remains underexplored. This study evaluated how simultaneous (T1) and sequential (X1) inoculation of <em>Leuconostoc</em>, <em>Levilactobacillus</em>, and <em>Lactiplantibacillus</em> affects inter-species competition and fermentation dynamics in Chinese spicy cabbage (CSC). While the T1 strategy accelerated fermentation kinetics with <em>Leuconostoc</em> acting as the primary fermenter, the inoculation sequence altered the competitive hierarchy of the secondary fermenters: <em>Levilactobacillus</em> dominated in T1, whereas <em>Lactiplantibacillus</em> prevailed in X1. This differential microbial succession resulted in distinct aromatic signatures, with Random Forest modeling identifying methyl allyl disulfide (Day 6) and dimethyl trisulfide (Day 13) as key differential compounds driving these flavor differences. Although the T1 group developed a more intense fermented flavor, sensory analysis indicated that the sequential (X1) strategy achieved higher overall acceptability by yielding a more desirable balance between moderate flavor and preserved texture. These findings demonstrate that adjusting inoculation timing is an effective method to engineer microbial succession and systematically modify the final sensory profile of fermented vegetables.</div></div>","PeriodicalId":14095,"journal":{"name":"International journal of food microbiology","volume":"446 ","pages":"Article 111533"},"PeriodicalIF":5.2,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145615353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-25DOI: 10.1016/j.ijfoodmicro.2025.111536
Alejandro Piña-Iturbe , Daniel Tichy-Navarro , Josefina Miranda-Riveros , María José Navarrete , Andrea I. Moreno-Switt
Multidrug-resistant Salmonella Infantis carrying pESI-like megaplasmids have disseminated worldwide representing a serious threat to public health. Previous studies have investigated its population structure and temporal dynamics above the continental level. However, their conclusions were constrained by limited datasets and sampling biases. To address these issues, we analyzed all publicly available Salmonella Infantis genomes to characterize its global population structure and phylogeographic dispersal. We selected a non-redundant dataset of 14,010 genomes representing the temporal, geographic, isolation source, and genomic diversity of Salmonella Infantis from 77 countries across five continents, collected from 1910 to 2024. Phylogenomic analyses showed that emergent megaplasmid-positive Salmonella Infantis forms a monophyletic lineage with significant geographic structuring. The megaplasmid-positive lineage was inferred to have originated in Western Asia around 1990, followed by multiple introductions into Europe and a single transmission to South America which resulted in the dissemination of this pathogen to Northern America, and from there to the rest of the continent. Multiple recent transmission events of the American lineage to all continents were observed, driving the dispersal of the blaCTX-M-65 gene encoding extended-spectrum β-lactamases. Moreover, genomic evidence also suggests that the emergence of ESBL-producing strains in parts of Asia and Africa may be associated with poultry trading from the Americas. Our findings underscore the urgent need for integrating global human, animal, and environmental surveillance data with population genomic analyses to contain the threats posed by ESBL-producing Salmonella Infantis.
{"title":"Emergent Salmonella enterica serovar Infantis forms a monophyletic lineage shaped by geographic structuring","authors":"Alejandro Piña-Iturbe , Daniel Tichy-Navarro , Josefina Miranda-Riveros , María José Navarrete , Andrea I. Moreno-Switt","doi":"10.1016/j.ijfoodmicro.2025.111536","DOIUrl":"10.1016/j.ijfoodmicro.2025.111536","url":null,"abstract":"<div><div>Multidrug-resistant <em>Salmonella</em> Infantis carrying pESI-like megaplasmids have disseminated worldwide representing a serious threat to public health. Previous studies have investigated its population structure and temporal dynamics above the continental level. However, their conclusions were constrained by limited datasets and sampling biases. To address these issues, we analyzed all publicly available <em>Salmonella</em> Infantis genomes to characterize its global population structure and phylogeographic dispersal. We selected a non-redundant dataset of 14,010 genomes representing the temporal, geographic, isolation source, and genomic diversity of <em>Salmonella</em> Infantis from 77 countries across five continents, collected from 1910 to 2024. Phylogenomic analyses showed that emergent megaplasmid-positive <em>Salmonella</em> Infantis forms a monophyletic lineage with significant geographic structuring. The megaplasmid-positive lineage was inferred to have originated in Western Asia around 1990, followed by multiple introductions into Europe and a single transmission to South America which resulted in the dissemination of this pathogen to Northern America, and from there to the rest of the continent. Multiple recent transmission events of the American lineage to all continents were observed, driving the dispersal of the <em>bla</em><sub>CTX-M-65</sub> gene encoding extended-spectrum β-lactamases. Moreover, genomic evidence also suggests that the emergence of ESBL-producing strains in parts of Asia and Africa may be associated with poultry trading from the Americas. Our findings underscore the urgent need for integrating global human, animal, and environmental surveillance data with population genomic analyses to contain the threats posed by ESBL-producing <em>Salmonella</em> Infantis.</div></div>","PeriodicalId":14095,"journal":{"name":"International journal of food microbiology","volume":"446 ","pages":"Article 111536"},"PeriodicalIF":5.2,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145661081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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