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Guan P, Fan S, Dong W, Wang X, Li Z, Song M, Suo B. Comparative genomic analysis and multilocus sequence typing of Staphylococcus aureus reveals candidate genes for low-temperature tolerance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171331. [PMID: 38428609 DOI: 10.1016/j.scitotenv.2024.171331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
Staphylococcus aureus is one of the most frequently detected foodborne pathogens in cold chain foods. Worryingly, small colony variants (SCVs) can survive in cold environments for a long time and can revert to rapidly growing cells in suitable environments, causing serious food safety issues. This study investigated the underlying mechanism of SCV formation at low temperature (4 °C) via comparative genomics. Multilocus sequence typing (MLST) of 105 strains of S. aureus was divided into 9 sequence types. The ST352 strains exhibited the greatest tolerance to low temperature, with a mean reduction in survival rate of 10.34 % (p < 0.05). Comparative genomics revealed a total of 1941 core genes in the three S. aureus strains, and BB-1 had 468 specific genes, which were enriched mainly in translation, DNA recombination, DNA repair, metabolic pathways, two-component systems, and quorum sensing. Molecular docking analysis revealed that the binding of the RsbW protein to the SigB protein of BB-1 decreased due to base mutations in rsbW, while the binding to the RsbV protein was enhanced. In addition, the results of real-time quantitative PCR showed that the RsbV-RsbW/SigB system of BB-1 may play a role in the low-temperature survival of S. aureus and the formation of SCVs. These results suggest that genes specific to BB-1 may contribute to the mechanism of adaptation to low temperature and the formation of SCVs. This study helps elucidate the causes of SCV formation by S. aureus at low temperature at the molecular level and provides a basis for exploring the safety control of cold chain food environments.
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Affiliation(s)
- Peng Guan
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Shijia Fan
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Wenjing Dong
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Xiaojie Wang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Zhen Li
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Miao Song
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Biao Suo
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China.
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Werum V, Ehrmann M. Dellaglioa spp. an underestimated genus isolated from high-oxygen modified-atmosphere packaged meat. Food Microbiol 2024; 117:104398. [PMID: 37919006 DOI: 10.1016/j.fm.2023.104398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023]
Abstract
The genus Dellaglioa (D.) actually comprises two species, i.e., D. algida and the recently described species D. carnosa. Both species are adapted to cold and have been typically recovered from meat products. However, their importance has thus far been underestimated, since routine culture-based analysis failed to support their growth. Furthermore, their occurrence on meat packed under high-oxygen MA conditions (HiOx-MAP) is controversial because they have been described as being oxygen-sensitive. In this study, we focused on the targeted isolation of Dellaglioa spp. from HiOx-MAP meat samples and the characterization of our isolates regarding their adaption to HiOx-MAP conditions, their spoilage potential, as well as food safety aspects. We used a medium recently developed specifically for strains of this genus and investigated ten meat batches from seven different suppliers. Our study confirms that the occurrence of Dellaglioa spp. on HiOx-MAP meat is non-sporadic, reaching cell counts ranging from log10 5.8-7.1 CFU/cm2 at a late stage of chilled storage. Autochthonous Dellaglioa spp. and Leuconostoc (L.) gasicomitatum dominated the microbiota of the beef steaks with similar growth behavior. Our results suggest that Dellaglioa spp. benefits from the heme-dependent respiration of oxygen by L. gasicomitatum. Furthermore, whole genome analysis revealed the presence of genes predictively involved in oxidative stress defense, survival, and adaptation in meat environments. Moreover, we predict a weak aminogenic potential of D. algida strains. Tyramine production from tyrosine seems to be a species-specific characteristic of D. carnosa. The extent to which D. algida and D. carnosa occurrence is influenced by or even dependent on the composition of the entire microbiota remains to be investigated.
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Affiliation(s)
- Victoria Werum
- Lehrstuhl für Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354, Freising, Germany
| | - Matthias Ehrmann
- Lehrstuhl für Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354, Freising, Germany.
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Kim D, Jeon J, Kim M, Jeong J, Heo YM, Lee DG, Yon DK, Han K. Comparison of microbial molecular diagnosis efficiency within unstable template metagenomic DNA samples between qRT-PCR and chip-based digital PCR platforms. Genomics Inform 2023; 21:e52. [PMID: 38224719 PMCID: PMC10788361 DOI: 10.5808/gi.23068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 01/17/2024] Open
Abstract
Accurate and efficient microbial diagnosis is crucial for effective molecular diagnostics, especially in the field of human healthcare. The gold standard equipment widely employed for detecting specific microorganisms in molecular diagnosis is quantitative real-time polymerase chain reaction (qRT-PCR). However, its limitations in low metagenomic DNA yield samples necessitate exploring alternative approaches. Digital PCR, by quantifying the number of copies of the target sequence, provides absolute quantification results for the bacterial strain. In this study, we compared the diagnostic efficiency of qRT-PCR and digital PCR in detecting a particular bacterial strain (Staphylococcus aureus), focusing on skin-derived DNA samples. Experimentally, specific primer for S. aureus were designed at transcription elongation factor (greA) gene and the target amplicon were cloned and sequenced to validate efficiency of specificity to the greA gene of S. aureus. To quantify the absolute amount of microorganisms present on the skin, the variable region 5 (V5) of the 16S rRNA gene was used, and primers for S. aureus identification were used to relative their amount in the subject's skin. The findings demonstrate the absolute convenience and efficiency of digital PCR in microbial diagnostics. We suggest that the high sensitivity and precise quantification provided by digital PCR could be a promising tool for detecting specific microorganisms, especially in skin-derived DNA samples with low metagenomic DNA yields, and that further research and implementation is needed to improve medical practice and diagnosis.
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Affiliation(s)
- Dongwan Kim
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Junhyeon Jeon
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Minseo Kim
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Jinuk Jeong
- Department of Bioconvergence Engineering, Dankook University, Jukjeon 16890, Korea
| | | | - Dong-Geol Lee
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- R&I Center, COSMAX BTI, Seongnam 13486, Korea
| | - Dong Keon Yon
- Center for Digital Health, Medical Science Research Institute, Kyung Hee University Medical Center, Kyung Hee University College of Medicine, Seoul 02447, Korea
- Department of Pediatrics, Kyung Hee University College of Medicine, Seoul 02447, Korea
| | - Kyudong Han
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Department of Bioconvergence Engineering, Dankook University, Jukjeon 16890, Korea
- HuNbiome Co., Ltd, R&D Center, Seoul 08503, Korea
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Liang S, Jiang Y, Zhang M. Integrative analysis of the effects of organic and conventional farming methods on peanut based on transcriptome and metabolomics. Food Res Int 2023; 171:113065. [PMID: 37330858 DOI: 10.1016/j.foodres.2023.113065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/19/2023]
Abstract
To elucidate the nutritional quality of peanut under different farming methods, we selected two cultivars, "jihua13" and "jihua4", to grow in organic and conventional environments, respectively. After harvest, we measured physiological parameters and differential metabolites. Metabolomics showed that most of the amino acids, carbohydrates, and secondary metabolites in organically grown jihua4 were downregulated, which was completely the opposite in jihua13. Fatty acids associated with heart disease and hypertension are reduced in organically grown peanuts. In particular, the highly statistically significant tryptophan betaine seems to be used as a reference to distinguish between organic and conventional cultivation. Mechanisms leading to differences in crop chemical composition are explained by transcriptome analysis. The results of the transcriptome analysis indicated that organic cultivation largely affects the synthesis of amino acids and carbohydrates in jihua13. Combined analysis of transcriptome and metabolomics found that variety jihua13 is more sensitive to farming methods and produces more unsaturated fatty acids than jihua4.
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Affiliation(s)
- Shan Liang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Yangjie Jiang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Min Zhang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China.
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Fu T, Fan Z, Li Y, Li Z, Du B, Liu S, Cui X, Zhang R, Zhao H, Feng Y, Xue G, Cui J, Yan C, Gan L, Feng J, Xu Z, Yu Z, Tian Z, Ding Z, Chen J, Chen Y, Yuan J. ArcR contributes to tolerance to fluoroquinolone antibiotics by regulating katA in Staphylococcus aureus. Front Microbiol 2023; 14:1106340. [PMID: 36910210 PMCID: PMC9998937 DOI: 10.3389/fmicb.2023.1106340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/04/2023] [Indexed: 02/26/2023] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that shows a unique ability to quickly respond to a variety of antibiotics. The Crp/Fnr family transcriptional regulator ArcR controls expression of arginine deiminase pathway genes arcABDC, which enable the utilization of arginine as an energy source for cell growth under anaerobic conditions. However, ArcR shares low overall similarity with other Crp/Fnr family proteins, suggesting that they differ in the response to environmental stress. In this study, MIC and survival assays were performed to determine the role of ArcR in antibiotic resistance and tolerance. The results showed that deletion of arcR reduced tolerance of S.aureus to fluoroquinolone antibiotics, mainly through a defect in the response to oxidative stress. In ΔarcR mutant, the expression of the major catalase gene katA was downregulated, and katA overexpression restored bacterial resistance to oxidative stress and antibiotics. We showed that ArcR directly regulated katA transcription by binding to the promoter region of katA. Therefore, our results revealed the contribution of ArcR in bacterial tolerance to oxidative stress and subsequently to fluoroquinolones antibiotics. This study added our understanding on the role of Crp/Fnr family in bacterial susceptibility to antibiotics.
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Affiliation(s)
- Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yujie Li
- Department of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhoufei Li
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Bing Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shiyu Liu
- Military Supplies and Energy Quality Supervision Station of NV, PLA, Beijing, China
| | - Xiaohu Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zanbo Ding
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinfeng Chen
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yujie Chen
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
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Huang Z, Huang Y, Dong Z, Guan P, Wang X, Wang S, Lei M, Suo B. Modelling the growth of Staphylococcus aureus with different levels of resistance to low temperatures in glutinous rice dough. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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Cinnamaldehyde inactivates Listeria monocytogenes at a low temperature in ground pork by disturbing the expression of stress regulatory genes. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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