Foodborne pathogens and disease最新文献

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Clinical Manifestations and Molecular Identification of Giardia duodenalis in Pediatric and Adolescent Cancer Patients in Southwestern Iran. 伊朗西南部儿童和青少年癌症患者的临床表现和十二指肠贾第虫的分子鉴定。
IF 1.9 2区 农林科学
Foodborne pathogens and disease Pub Date : 2025-07-01 Epub Date: 2024-10-15 DOI: 10.1089/fpd.2024.0100
Farzad Mahdavi, Mohammad Reza Mohammadi, Kambiz Karimi, Laya Shamsi, Farajolah Maleki, Ali Asghari, Saeed Shahabi, Mohammad Hossein Motazedian, Hassan Nourmohammadi
{"title":"Clinical Manifestations and Molecular Identification of <i>Giardia duodenalis</i> in Pediatric and Adolescent Cancer Patients in Southwestern Iran.","authors":"Farzad Mahdavi, Mohammad Reza Mohammadi, Kambiz Karimi, Laya Shamsi, Farajolah Maleki, Ali Asghari, Saeed Shahabi, Mohammad Hossein Motazedian, Hassan Nourmohammadi","doi":"10.1089/fpd.2024.0100","DOIUrl":"10.1089/fpd.2024.0100","url":null,"abstract":"<p><p>This study aimed to investigate the clinical and molecular characteristics of <i>Giardia duodenalis</i> (<i>G. duodenalis</i>) infection and identify potential risk factors in children and teenagers with malignancies in Shiraz, southwestern Iran. A total of 200 fresh fecal samples were collected from children and adolescents suffering from 32 different cancer types at Amir, Nemazee, and Saadi hospitals affiliated with Shiraz University of Medical Sciences between October 2021 and May 2022. Direct microscopy using saline and iodine wet mount was conducted, and all fecal samples were rechecked by <i>SSU</i>-PCR. Subsequently, a specific fragment of the <i>tpi</i> gene was amplified on all samples for prevalence, sequencing, and assemblage identification. Our study found a 4% (8/200) prevalence of <i>G. duodenalis</i> using microscopy and PCR. The molecular findings were consistent with the microscopic results. All eight positive samples with <i>SSU-rRNA</i> gene were also detected as positive with <i>tpi</i> gene and were correctly sequenced. Among the examined cancer patients, two assemblages were identified: A [sub-assemblage AI (2/8, 25%) and sub-assemblage AII (3/8, 37.5%)] and B [sub-assemblage BIV (3/8, 37.5%)]. Notably, patients were more vulnerable to <i>G. duodenalis</i> infection after receiving at least 8 treatment episodes (<i>p</i> < 0.05) and displaying gastrointestinal symptoms (<i>p</i> > 0.05). The demographic characteristics of cancer patients with <i>G. duodenalis</i> infection and the statistical conclusions were separately detailed. The small sample size and low prevalence rate in this study hindered precise epidemiological conclusions. Nonetheless, the results suggest that <i>G. duodenalis</i> infection among cancer patients in Shiraz city originates from humans, without any specific animal groups (C-H) involved.</p>","PeriodicalId":12333,"journal":{"name":"Foodborne pathogens and disease","volume":" ","pages":"498-504"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142461625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcriptomic Analysis of the Effect of Glabridin on Biofilm Formation in Staphylococcus Aureus. 格拉布林对金黄色葡萄球菌生物膜形成影响的转录组分析
IF 1.9 2区 农林科学
Foodborne pathogens and disease Pub Date : 2025-07-01 Epub Date: 2024-10-17 DOI: 10.1089/fpd.2024.0038
Yanjun Ma, Yanni Mao, Xinyun Kang, Beibei Zhang, Jianchong Wang, Guiqin Wang, Guilai Wang
{"title":"Transcriptomic Analysis of the Effect of Glabridin on Biofilm Formation in <i>Staphylococcus Aureus</i>.","authors":"Yanjun Ma, Yanni Mao, Xinyun Kang, Beibei Zhang, Jianchong Wang, Guiqin Wang, Guilai Wang","doi":"10.1089/fpd.2024.0038","DOIUrl":"10.1089/fpd.2024.0038","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> (<i>S. aureus</i>) is among the major skin infection-causing pathogens in animals and humans. Its ability to form biofilms has become a foremost cause of bacterial infections and the extensive spread of drug resistance, which poses a great difficulty in clinical treatment. Glabridin (Glb), an extract of licorice with antibacterial and anti-infective properties, has a partially understood biofilm-inhibitory mechanism. This study investigated the inhibitory and antibiofilm activities of subinhibitory concentrations of Glb against <i>S. aureus</i>. The crystal violet assay revealed that Glb significantly suppressed biofilm expression. Scanning electron microscopy observations unveiled that Glb reduced <i>S. aureus</i> adhesion and accumulation by disrupting the spatial structure of the biofilm. In vitro extracellular DNA (eDNA) inhibition assays demonstrated that Glb inhibited biofilm formation by <i>S. aureus by</i> suppressing eDNA secretion. In total, 184 differentially expressed genes were obtained through transcriptomic (RNA-seq) sequencing, of which 81 and 103 genes were upregulated and downregulated, respectively. Glb regulated the transcript levels of biofilm-related genes through the phosphatase transfer system, two-component regulatory system, and nitrogen metabolism. The qPCR analysis was performed to confirm whether Glb interfered with the expression of regulatory genes involved in <i>S. aureus</i> biofilm formation (<i>SarA, ArlR, FnbA, ClfA, icaD,</i> and <i>icaR</i>) as well as the virulence gene <i>Hla</i>. In conclusion, this study demonstrates that Glb has a significant inhibitory effect on biofilm activity and is expected to be a good antibiofilm drug.</p>","PeriodicalId":12333,"journal":{"name":"Foodborne pathogens and disease","volume":" ","pages":"489-497"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142461631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Do Temperature Abuses Along the Frozen Açaí Pulp Value Chain Increase Microbial Hazards? 冷冻阿萨伊果浆价值链中的温度滥用是否会增加微生物危害?
IF 1.9 2区 农林科学
Foodborne pathogens and disease Pub Date : 2025-07-01 Epub Date: 2024-10-11 DOI: 10.1089/fpd.2024.0073
Jéssica Caroline Araujo Silva Sandes, Eduardo Henrique Miranda Walter, Gustavo Luis de Paiva Anciens Ramos, Virgínia Martins da Matta, Lourdes Maria Correa Cabral
{"title":"Do Temperature Abuses Along the Frozen Açaí Pulp Value Chain Increase Microbial Hazards?","authors":"Jéssica Caroline Araujo Silva Sandes, Eduardo Henrique Miranda Walter, Gustavo Luis de Paiva Anciens Ramos, Virgínia Martins da Matta, Lourdes Maria Correa Cabral","doi":"10.1089/fpd.2024.0073","DOIUrl":"10.1089/fpd.2024.0073","url":null,"abstract":"<p><p>Does temperature abuse during storage, distribution, marketing, and consumption of unpasteurized frozen açaí pulp increase microbial hazards? This study investigated the behavior of potentially pathogenic (<i>Escherichia coli, Listeria monocytogenes and Salmonella</i> spp.) and spoilage (mesophilic bacteria, yeasts and molds) microorganisms in two simulated thawing conditions: under refrigeration and at room temperature. The effect of repeated cold chain abuse was observed by thawing and refreezing (-20°C) açaí pulp four times over a period of 90 days. Freezing resulted in inhibition of all microorganisms except for mesophilic aerobic bacteria in one single sample. After thawing at 5°C, the kinetic parameters obtained by the Weibull model indicated that mesophilic aerobic bacteria, yeasts and molds and <i>L. monocytogenes</i> showed a longer inactivation time with <i>δ</i> values reaching 35, 126, and 46 days, respectively. The shortest inactivation time for a reduction of 4 log CFU.g<sup>-1</sup> was for <i>E. coli</i>. The concentration of <i>Salmonella</i> spp. and <i>L. monocytogenes</i> in control samples was higher (<i>p</i> < 0.01) than in samples exposed to abusive conditions after 90 days of storage. The results indicate that the abusive thawing conditions studied do not increase the potential hazards of pathogens.</p>","PeriodicalId":12333,"journal":{"name":"Foodborne pathogens and disease","volume":" ","pages":"452-458"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Experience and Perspectives on Antibacterial Therapy for Listeriosis in a Tertiary Teaching Hospital in China: A Retrospective Study and Health Care Provider Survey. 中国某三级教学医院李斯特菌病抗菌治疗的经验与展望:回顾性研究与医护人员调查。
IF 1.9 2区 农林科学
Foodborne pathogens and disease Pub Date : 2025-07-01 Epub Date: 2025-01-08 DOI: 10.1089/fpd.2024.0079
Naiju Zhang, Zhenjie Wang, Zhijun Li, Yongzhong Xie, Jinchun Liu, Chunming Gao, Chuanmiao Liu, Tianping Chen
{"title":"Experience and Perspectives on Antibacterial Therapy for Listeriosis in a Tertiary Teaching Hospital in China: A Retrospective Study and Health Care Provider Survey.","authors":"Naiju Zhang, Zhenjie Wang, Zhijun Li, Yongzhong Xie, Jinchun Liu, Chunming Gao, Chuanmiao Liu, Tianping Chen","doi":"10.1089/fpd.2024.0079","DOIUrl":"10.1089/fpd.2024.0079","url":null,"abstract":"<p><p>Listeriosis is a rare, life-threatening bacterial infection. Prompt, appropriate antibiotic treatment is essential to save lives. We aimed to investigate antibiotic selection and listeriosis knowledge among health care providers. We first performed a retrospective study on patients with listeriosis who were treated in a hospital in China from January 2013 to March 2023. Patient characteristics and antibiotic selections were recorded. Antibiotics were classified as effective or ineffective based on the efficacy classifications listed in <i>The Sanford Guide to Antimicrobial Therapy</i> (50<sup>th</sup> edition). We then conducted a questionnaire survey of health care providers to investigate their listeriosis knowledge and practices between April 2023 to May 2023. Fifteen listeriosis patients were identified, with a case fatality rate of 26.7% (4/15). Empirical treatments assessed as effective antibiotics or ineffective antibiotics were given to 33.3% (5/15) and 66.7% (10/15) of the patients, respectively. After <i>Listeria monocytogenes</i> was identified, 40% (6/15) of the patients received an adjustment to their antibiotics, although 50% (3/6) patients still received ineffective antibiotics. The questionnaire survey of 77 participating health care providers showed that 32.9% (24/73) of the clinicians were unaware of the appropriate antibiotics for listeriosis. Most participants (83.1%, 64/77) would read the drug sensitivity report before selecting the antibiotics. The selection of effective antibiotics differed between the infectious diseases department and other departments (<i>p</i> < 0.001), but did not differ between junior title and other titles (<i>p</i> = 0.088). Most patients with listeriosis did not receive appropriate antibiotics, which might have accounted for the high fatality rate, and may have resulted from inadequate listeriosis knowledge. More education and correct reporting of drug sensitivity results are urgently needed.</p>","PeriodicalId":12333,"journal":{"name":"Foodborne pathogens and disease","volume":" ","pages":"505-513"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prevalence, Risk Factors, and Antimicrobial Resistance of Staphylococcus and Streptococcus Species Isolated from Subclinical Bovine Mastitis. 从亚临床牛乳腺炎中分离出的葡萄球菌和链球菌的流行率、风险因素和抗菌药耐药性。
IF 1.9 2区 农林科学
Foodborne pathogens and disease Pub Date : 2025-07-01 Epub Date: 2024-10-31 DOI: 10.1089/fpd.2024.0097
Abu Al Farabi, Hemayet Hossain, Khadiza A Brishty, Md Hafizar Rahman, Mostafizor Rahman, Md Saiful Islam Siddiqui, Mohammad Atikuzzaman, Asmaa Saleh, Reem Binsuwaidan, Heba Mohammed Refat M Selim, Ayman Noreddin, Yosra A Helmy, Md Mahfujur Rahman, Himel Barua, Mohamed E El Zowalaty
{"title":"Prevalence, Risk Factors, and Antimicrobial Resistance of <i>Staphylococcus</i> and <i>Streptococcus</i> Species Isolated from Subclinical Bovine Mastitis.","authors":"Abu Al Farabi, Hemayet Hossain, Khadiza A Brishty, Md Hafizar Rahman, Mostafizor Rahman, Md Saiful Islam Siddiqui, Mohammad Atikuzzaman, Asmaa Saleh, Reem Binsuwaidan, Heba Mohammed Refat M Selim, Ayman Noreddin, Yosra A Helmy, Md Mahfujur Rahman, Himel Barua, Mohamed E El Zowalaty","doi":"10.1089/fpd.2024.0097","DOIUrl":"10.1089/fpd.2024.0097","url":null,"abstract":"<p><p>Subclinical mastitis (SCM) is a prevalent serious disease among dairy cows worldwide. It poses a significant challenge to the dairy industry, animal welfare, and a threat to public health. The present study aimed to investigate the molecular detection, prevalence, and antimicrobial resistance of <i>Staphylococcus</i> spp. and <i>Streptococcus</i> spp. isolated from raw composite milk samples obtained from SCM dairy cattle in Bangladesh. A total of 612 quarters milk samples obtained from 153 cows were analyzed for SCM using the California Mastitis Test. Bacterial isolation and identification were carried out and bacterial species were confirmed using molecular polymerase chain reaction methods. Antimicrobial susceptibility testing was performed using disc diffusion method. The findings revealed that the prevalence of SCM was 70.3% (26/37), 35.95% (55/153), and 23.04% (141/612) in the herd, cow, and quarter levels, respectively. Among the positive samples, 92.7% (51/55) were <i>Staphylococcus</i> spp. (<i>S. aureus, S. chromogenes</i>, and <i>S. simulans</i>) and the remaining isolates were 7.3% (4/55) <i>Streptococcus</i> spp. (<i>Streptococcus agalactiae</i> and <i>Streptococcus dysgalactiae</i>). The most prevalent species was <i>S. chromogenes,</i> accounting for 67.3% (37/55). Antimicrobial susceptibility testing showed that 65.5% of isolates were susceptible to cefoxitin, whereas, 89.1% were resistant to penicillin. Overall, 12 isolates (21.8%) out of 55 were resistant to more than three classes of antimicrobials and were defined as multidrug-resistant isolates. Methicillin-resistance gene was detected in 61.1% of the cefoxitin-resistant isolates. A multivariate logistic regression analysis identified five potential risk factors including the lack of post-milking teat disinfection (OR: 3.06), absence of immediate feeding after milking (OR: 9.81), poor udder hygiene (OR: 7.83), tick infestation (OR: 13.76), and absence of dry cow therapy (OR: 3.31). The findings of the current study underscore the urgent requirement for targeted interventions, considering the identified factors to effectively manage and control SCM in dairy cows.</p>","PeriodicalId":12333,"journal":{"name":"Foodborne pathogens and disease","volume":" ","pages":"467-476"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142544658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bovine Subclinical Mastitis Foodborne Pathogens: Risks and Mitigation of Microbial Safety of Raw Milk and Dairy Products. 牛亚临床乳腺炎食源性病原体:原料奶和乳制品微生物安全的风险和缓解。
IF 1.9 2区 农林科学
Foodborne pathogens and disease Pub Date : 2025-06-26 DOI: 10.1089/fpd.2025.0034
Della Della, Uma Tiwari, Geraldine Duffy, Pablo Silva Boloña, Mark Fenelon, Triona O'Brien
{"title":"Bovine Subclinical Mastitis Foodborne Pathogens: Risks and Mitigation of Microbial Safety of Raw Milk and Dairy Products.","authors":"Della Della, Uma Tiwari, Geraldine Duffy, Pablo Silva Boloña, Mark Fenelon, Triona O'Brien","doi":"10.1089/fpd.2025.0034","DOIUrl":"https://doi.org/10.1089/fpd.2025.0034","url":null,"abstract":"<p><p>Bovine subclinical mastitis (SCM), unlike clinical mastitis, characterized by the absence of visible symptoms such as swelling and abnormal milk, represents an under-recognized challenge for microbial safety within the dairy industry. Because SCM lacks visible signs, it can serve as a silent source of contamination that is not easily identified or managed during milk production. The review critically examines the multifaceted interplay between SCM and the transmission of such pathogens in milk, highlighting their entry routes, detection modalities, and contributory risk factors to the dairy industry, considering global and regional variability, the prevalence, diversity, and emerging trends in milk-borne pathogens are considered. To address these challenges, an integrative One Health-aligned mitigation framework that combines microbial risk assessment, genomic surveillance, and data-driven risk prioritization is recommended. Such strategies aim to harmonize detection protocols, optimize antimicrobial stewardship, and strengthen control measures across dairy value chains. By synthesizing current knowledge, this review article underscores the importance of SCM as a food safety issue and offers a critical foundation for developing comprehensive strategies to mitigate public health risks.</p>","PeriodicalId":12333,"journal":{"name":"Foodborne pathogens and disease","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144495452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Food Causes of Enteric Outbreaks in New South Wales, Australia, from 2000 to 2017. 2000年至2017年澳大利亚新南威尔士州肠道暴发的食物原因。
IF 1.9 2区 农林科学
Foodborne pathogens and disease Pub Date : 2025-06-25 DOI: 10.1089/fpd.2025.0030
Neil Franklin, Kirsty Hope, Kathryn Glass, Martyn Kirk
{"title":"Food Causes of Enteric Outbreaks in New South Wales, Australia, from 2000 to 2017.","authors":"Neil Franklin, Kirsty Hope, Kathryn Glass, Martyn Kirk","doi":"10.1089/fpd.2025.0030","DOIUrl":"https://doi.org/10.1089/fpd.2025.0030","url":null,"abstract":"<p><p>There are an estimated 4.7 million cases of foodborne illness in Australia each year, but the contaminated food items that are the source of these illnesses are rarely identified. Current knowledge relies largely on the few foodborne outbreaks where the implicated food commodity was identified. To better understand which foods cause outbreaks, we analyzed 18 years of foodborne outbreak data collected in New South Wales (NSW) and classified the food dishes responsible for the outbreaks into standardized categories based on type of dish and preparation method. A total of 869 outbreaks were reported in NSW from 2000 to 2017. Outbreaks with a suspected contaminated food or dish reported (57.1%) underwent dish reclassification that assigned the implicated food into two groupings that characterized the food consumed into commonly understood dish types (e.g., sandwich, stew, etc.) and how it was prepared (e.g., sliced, heated, etc.). The dish type associated with the most outbreaks was sandwiches (18.8%) followed by desserts (13.1%) and then stir fries (9.1%). The dishes associated with more serious outbreak outcomes (higher numbers of cases, hospitalizations, and deaths per outbreak) were those associated with ready to eat fresh produce. Dish preparations that did not involve a cooking step also resulted in more serious outcomes. While identifying contaminated food is crucial for food safety reasons, people rarely consider these risks when eating. Food carries the combined risks posed by the ingredients and preparation method followed. Education of food business operators and consumers needs to promote a view of food safety risk that goes beyond unsafe commodities, encouraging a holistic perspective that considers ingredients and preparation methods.</p>","PeriodicalId":12333,"journal":{"name":"Foodborne pathogens and disease","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144495453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prediction of Antibiotic Resistance Phenotypes and Minimum Inhibitory Concentrations in Salmonella Using Machine Learning Analysis of Its Pan-Genome and Pan-Resistome Features. 利用机器学习分析沙门氏菌泛基因组和泛抵抗组特征预测抗生素耐药表型和最低抑菌浓度。
IF 1.9 2区 农林科学
Foodborne pathogens and disease Pub Date : 2025-06-13 DOI: 10.1089/fpd.2024.0170
Yichen He, Xiujuan Zhou, Lida Zhang, Yan Cui, Yiping He, Andrew Gehring, Xiangyu Deng, Xianming Shi
{"title":"Prediction of Antibiotic Resistance Phenotypes and Minimum Inhibitory Concentrations in <i>Salmonella</i> Using Machine Learning Analysis of Its Pan-Genome and Pan-Resistome Features.","authors":"Yichen He, Xiujuan Zhou, Lida Zhang, Yan Cui, Yiping He, Andrew Gehring, Xiangyu Deng, Xianming Shi","doi":"10.1089/fpd.2024.0170","DOIUrl":"https://doi.org/10.1089/fpd.2024.0170","url":null,"abstract":"<p><p>Traditional experimental methods for determining antibiotic resistance phenotypes (ARPs) and minimum inhibitory concentrations (MICs) in bacteria are laborious and time consuming. This study aims to explore the potential of whole-genome sequencing data combined with machine learning models for robustly predicting ARPs and MICs in <i>Salmonella</i>. Using a training set of 6394 <i>Salmonella</i> genomes alongside antimicrobial susceptibility testing results, we built two machine learning (ML) predictive models based on the pan-genome and pan-resistome. Each model was implemented using three algorithms: random forest, extreme gradient boosting (XGB), and convolutional neural network. Among them, XGB achieved the highest overall accuracy, with the pan-genome and pan-resistome models accurately predicting ARPs (98.51% and 97.77%) and MICs (81.42% and 78.99%) for 15 commonly used antibiotics. Feature extraction from pan-genome and pan-resistome data effectively reduced computational complexity and significantly decreased computation time. Notably, fewer than 10 key genomic features, often linked to known resistance or mobile genes, were sufficient for robust predictions for each antibiotic. This study also identified challenges, including imbalanced resistance classes and imprecise MIC measurements, which impacted prediction accuracy. These findings highlight the importance of using multiple evaluation metrics to assess model performance comprehensively. Overall, our findings demonstrated that ML, utilizing pan-genome or pan-resistome features, was highly effective in predicting antibiotic resistance and identifying correlated genetic features in <i>Salmonella</i>. This approach holds great potential to supplement conventional culture-based methods for routine surveillance of antibiotic-resistant bacteria.</p>","PeriodicalId":12333,"journal":{"name":"Foodborne pathogens and disease","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144289427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mycobiota and Their Mycotoxins in Egyptian Dried Figs. 埃及无花果干真菌菌群及其真菌毒素。
IF 1.9 2区 农林科学
Foodborne pathogens and disease Pub Date : 2025-06-12 DOI: 10.1089/fpd.2025.0048
Helal F Al-Harthi, Hanan AlOmari, Ioan Pet, Youssuf A Gherbawy
{"title":"Mycobiota and Their Mycotoxins in Egyptian Dried Figs.","authors":"Helal F Al-Harthi, Hanan AlOmari, Ioan Pet, Youssuf A Gherbawy","doi":"10.1089/fpd.2025.0048","DOIUrl":"10.1089/fpd.2025.0048","url":null,"abstract":"<p><p>This study evaluates the impact of traditional sun drying and modern industrial drying techniques on fungal contamination and mycotoxin production in dried figs. A total of 80 samples (40 per drying method), collected from various retail sources in Upper Egypt, were analyzed. Fungal isolation was performed on Dichloran Rose Bengal Chloramphenicol agar medium and incubated at 28°C. Sun-dried figs exhibited significantly higher fungal loads (1395 colony-forming unit [CFU]/g) compared with industrially dried figs (750 CFU/g). Mycobiota analysis identified 33 fungal species across 12 genera in sun-dried figs, whereas industrial drying yielded 21 species. Internal transcribed spacer sequencing facilitated species identification, with accession numbers PV065865 to PV065896 deposited in GenBank. <i>Aspergillus</i> spp. were dominant in both drying methods, with <i>Aspergillus welwitschiae</i>, <i>A. flavus</i>, and <i>A. niger</i> being the most prevalent. Mycotoxin analysis revealed aflatoxin contamination in 37.5% of sun-dried and 15% of industrially dried figs, while ochratoxin A was detected in 57.5% and 27.5% of samples, respectively, for sun-dried and industrially dried figs. Total fumonisins were present in 12.5% of sun-dried and 5% of industrially dried figs. These findings highlight the efficacy of industrial drying techniques in mitigating fungal contamination and mycotoxin accumulation, thereby improving the microbiological safety of dried figs.</p>","PeriodicalId":12333,"journal":{"name":"Foodborne pathogens and disease","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144274614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Targeted Antimicrobial Resistance Gene Screening from Metagenomic DNA of Raw Milk Samples Identifies the Presence of Multiple Genes Including the mcr9. 从原料奶样品的宏基因组DNA中筛选靶向抗微生物药物耐药基因,确定包括mcr9在内的多个基因的存在。
IF 1.9 2区 农林科学
Foodborne pathogens and disease Pub Date : 2025-06-09 DOI: 10.1089/fpd.2024.0187
Remina M Shajahan, Athul M, Farhana T A, Sreejith Sreekumaran, Divya Lakshmanan, Mithilesh Jaiswal, Radhakrishnan E K
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