1
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Bhagwat A, Haldar T, Kanojiya P, Saroj SD. Bacterial metabolism in the host and its association with virulence. Virulence 2025; 16:2459336. [PMID: 39890585 PMCID: PMC11792850 DOI: 10.1080/21505594.2025.2459336] [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: 10/16/2024] [Revised: 01/13/2025] [Accepted: 01/22/2025] [Indexed: 02/03/2025] Open
Abstract
The host restricted pathogens are competently dependent on their respective host for nutritional requirements. The bacterial metabolic pathways are surprisingly varied and remarkably flexible that in turn help them to successfully overcome competition and colonise their host. The metabolic adaptation plays pivotal role in bacterial pathogenesis. The understanding of host-pathogen metabolic crosstalk needs to be prioritized to decipher host-pathogen interactions. The review focuses on various aspects of host pathogen interactions that majorly involves adaptation of bacterial metabolism to counteract immune mechanisms by rectifying metabolic cues that provides pathogen the idea of different anatomical sites and the local physiology of the host. The key set of metabolites that are recognized as centre of competition between host and its pathogens are also briefly discussed. The factors that control the timely expression of virulence of bacterial pathogens is poorly understood. The perspective presented herein will facilitate us with a broader view of molecular mechanisms that modulates the expression of virulence factors in bacterial pathogens. The knowledge of crosslinked metabolic pathways of bacteria and their host will serve to develop novel potential therapeutics.
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Affiliation(s)
- Amrita Bhagwat
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Tiyasa Haldar
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Poonam Kanojiya
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Sunil D. Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
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2
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Nguyen TD, Winek MA, Rao MK, Dhyani SP, Lee MY. Nuclear envelope components in vascular mechanotransduction: emerging roles in vascular health and disease. Nucleus 2025; 16:2453752. [PMID: 39827403 DOI: 10.1080/19491034.2025.2453752] [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: 10/08/2024] [Revised: 01/08/2025] [Accepted: 01/09/2025] [Indexed: 01/22/2025] Open
Abstract
The vascular network, uniquely sensitive to mechanical changes, translates biophysical forces into biochemical signals for vessel function. This process relies on the cell's architectural integrity, enabling uniform responses to physical stimuli. Recently, the nuclear envelope (NE) has emerged as a key regulator of vascular cell function. Studies implicate nucleoskeletal elements (e.g. nuclear lamina) and the linker of nucleoskeleton and cytoskeleton (LINC) complex in force transmission, emphasizing nucleo-cytoskeletal communication in mechanotransduction. The nuclear pore complex (NPC) and its component proteins (i.e. nucleoporins) also play roles in cardiovascular disease (CVD) progression. We herein summarize evidence on the roles of nuclear lamina proteins, LINC complex members, and nucleoporins in endothelial and vascular cell mechanotransduction. Numerous studies attribute NE components in cytoskeletal-related cellular behaviors to insinuate dysregulation of nucleocytoskeletal feedback and nucleocytoplasmic transport as a mechanism of endothelial and vascular dysfunction, and hence implications for aging and vascular pathophysiology.
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Affiliation(s)
- Tung D Nguyen
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
- The Center for Cardiovascular Research, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Michael A Winek
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Mihir K Rao
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Shaiva P Dhyani
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Monica Y Lee
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
- The Center for Cardiovascular Research, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
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3
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Lin Y, Wang J, Bu F, Zhang R, Wang J, Wang Y, Huang M, Huang Y, Zheng L, Wang Q, Hu X. Bacterial extracellular vesicles in the initiation, progression and treatment of atherosclerosis. Gut Microbes 2025; 17:2452229. [PMID: 39840620 DOI: 10.1080/19490976.2025.2452229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 11/13/2024] [Accepted: 01/07/2025] [Indexed: 01/23/2025] Open
Abstract
Atherosclerosis is the primary cause of cardiovascular and cerebrovascular diseases. However, current anti-atherosclerosis drugs have shown conflicting therapeutic outcomes, thereby spurring the search for novel and effective treatments. Recent research indicates the crucial involvement of oral and gastrointestinal microbiota in atherosclerosis. While gut microbiota metabolites, such as choline derivatives, have been extensively studied and reviewed, emerging evidence suggests that bacterial extracellular vesicles (BEVs), which are membrane-derived lipid bilayers secreted by bacteria, also play a significant role in this process. However, the role of BEVs in host-microbiota interactions remains insufficiently explored. This review aims to elucidate the complex communication mediated by BEVs along the gut-heart axis. In this review, we summarize current knowledge on BEVs, with a specific focus on how pathogen-derived BEVs contribute to the promotion of atherosclerosis, as well as how BEVs from gut symbionts and probiotics may mitigate its progression. We also explore the potential and challenges associated with engineered BEVs in the prevention and treatment of atherosclerosis. Finally, we discuss the benefits and challenges of using BEVs in atherosclerosis diagnosis and treatment, and propose future research directions to address these issues.
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Affiliation(s)
- Yuling Lin
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jingyu Wang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fan Bu
- Institute of Hematology, Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Zhejiang University, Hangzhou, China
| | - Ruyi Zhang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Junhui Wang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yubing Wang
- Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Mei Huang
- Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yiyi Huang
- Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qian Wang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiumei Hu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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4
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Kwack KH, Jang EY, Kim C, Choi YS, Lee JH, Moon JH. Porphyromonas gulae and canine periodontal disease: Current understanding and future directions. Virulence 2025; 16:2449019. [PMID: 39834343 PMCID: PMC11756583 DOI: 10.1080/21505594.2024.2449019] [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: 08/29/2024] [Revised: 10/01/2024] [Accepted: 12/28/2024] [Indexed: 01/22/2025] Open
Abstract
Porphyromonas gulae has emerged as a notable pathogen in canine periodontal disease, akin to Porphyromonas gingivalis in human periodontitis. This review examines the initial isolation, phylogenetic analysis, habitat, host range, relationships with host health status and age, and key pathogenic determinants, including fimbriae, proteases, citrullinating enzyme, and lipopolysaccharide. Control strategies discussed include polyphosphate to disrupt haeme/iron utilization, clindamycin with interferon alpha to reduce bacterial load and enhance the immune response, and a protease inhibitor. Further research is needed to understand strain-level diversity of virulence factors and interactions between P. gulae and other oral bacteria, particularly Fusobacterium nucleatum, a common pathogen in both dogs and humans. The potential for interspecies transmission between dogs and humans warrants further research into these interactions. Extensive in vivo studies across various breeds are crucial to validate the effectiveness of proposed treatment strategies. This review emphasizes P. gulae's role in periodontal health and disease, setting the stage for future research and improved management of canine periodontal disease.
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Affiliation(s)
- Kyu Hwan Kwack
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul, Republic of Korea
| | - Eun-Young Jang
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul, Republic of Korea
- Department of Dentistry, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Cheul Kim
- Research Institute of Oral Science, College of Dentistry, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Young-Suk Choi
- Department of Dental Hygiene, Kyung-In Women’s University, Incheon, Republic of Korea
| | - Jae-Hyung Lee
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul, Republic of Korea
| | - Ji-Hoi Moon
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul, Republic of Korea
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5
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Herzog MKM, Peters A, Shayya N, Cazzaniga M, Kaka Bra K, Arora T, Barthel M, Gül E, Maurer L, Kiefer P, Christen P, Endhardt K, Vorholt JA, Frankel G, Heimesaat MM, Bereswill S, Gahan CGM, Claesson MJ, Domingo-Almenara X, Hardt WD. Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM 12 mice reveals pathogen-specific host and microbiota responses. Gut Microbes 2025; 17:2447832. [PMID: 39835346 DOI: 10.1080/19490976.2024.2447832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 12/13/2024] [Accepted: 12/23/2024] [Indexed: 01/22/2025] Open
Abstract
Campylobacter jejuni, non-typhoidal Salmonella spp., Listeria monocytogenes and enteropathogenic/enterohemorrhagic Escherichia coli (EPEC/EHEC) are leading causes of food-borne illness worldwide. Citrobacter rodentium has been used to model EPEC and EHEC infection in mice. The gut microbiome is well-known to affect gut colonization and host responses to many food-borne pathogens. Recent progress has established gnotobiotic mice as valuable models to study how microbiota affect the enteric infections by S. Typhimurium, C. rodentium and L. monocytogenes. However, for C. jejuni, we are still lacking a suitable gnotobiotic mouse model. Moreover, the limited comparability of data across laboratories is often negatively affected by variations between different research facilities or murine microbiotas. In this study, we applied the standardized gnotobiotic OligoMM12 microbiota mouse model and compared the infections in the same facility. We provide evidence of robust colonization and significant pathological changes in OligoMM12 mice following infection with these pathogens. Moreover, we offer insights into pathogen-specific host responses and metabolite signatures, highlighting the advantages of a standardized mouse model for direct comparisons of factors influencing the pathogenesis of major food-borne pathogens. Notably, we reveal for the first time that C. jejuni stably colonizes OligoMM12 mice, triggering inflammation. Additionally, our comparative approach successfully identifies pathogen-specific responses, including the detection of genes uniquely associated with C. jejuni infection in humans. These findings underscore the potential of the OligoMM12 model as a versatile tool for advancing our understanding of food-borne pathogen interactions.
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Affiliation(s)
- Mathias K-M Herzog
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Audrey Peters
- Department of Life Sciences, MRC Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nizar Shayya
- Gastrointestinal Microbiology Research Group, Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Monica Cazzaniga
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Kardokh Kaka Bra
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Trisha Arora
- Omic Sciences Unit, EURECAT - Technology Centre of Catalonia, Reus, Spain
| | - Manja Barthel
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ersin Gül
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Luca Maurer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Philipp Christen
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Katharina Endhardt
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Gad Frankel
- Department of Life Sciences, MRC Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Markus M Heimesaat
- Gastrointestinal Microbiology Research Group, Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Stefan Bereswill
- Gastrointestinal Microbiology Research Group, Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Cormac G M Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- School of Pharmacy, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
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6
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Clyne M, Ó Cróinín T. Pathogenicity and virulence of Helicobacter pylori: A paradigm of chronic infection. Virulence 2025; 16:2438735. [PMID: 39725863 DOI: 10.1080/21505594.2024.2438735] [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: 05/13/2024] [Revised: 11/18/2024] [Accepted: 12/02/2024] [Indexed: 12/28/2024] Open
Abstract
Infection with Helicobacter pylori is one of the most common infections of mankind. Infection typically occurs in childhood and persists for the lifetime of the host unless eradicated with antimicrobials. The organism colonizes the stomach and causes gastritis. Most infected individuals are asymptomatic, but infection also causes gastric and duodenal ulceration, and gastric cancer. H. pylori possesses an arsenal of virulence factors, including a potent urease enzyme for protection from acid, flagella that mediate motility, an abundance of outer membrane proteins that can mediate attachment, several immunomodulatory proteins, and an ability to adapt to specific conditions in individual human stomachs. The presence of a type 4 secretion system that injects effector molecules into gastric cells and subverts host cell signalling is associated with virulence. In this review we discuss the interplay of H. pylori colonization and virulence factors with host and environmental factors to determine disease outcome in infected individuals.
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Affiliation(s)
- Marguerite Clyne
- School of Medicine, University College Dublin, Dublin, Ireland
- The Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Tadhg Ó Cróinín
- The Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
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7
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Huang Y, Huang Y, Wu Z, Fan Z, Zheng F, Liu Y, Xu X. Characterization and genomic insights into bacteriophages Kpph1 and Kpph9 against hypervirulent carbapenem-resistant Klebsiella pneumoniae. Virulence 2025; 16:2450462. [PMID: 39803864 PMCID: PMC11730680 DOI: 10.1080/21505594.2025.2450462] [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: 04/23/2024] [Revised: 11/25/2024] [Accepted: 12/28/2024] [Indexed: 01/16/2025] Open
Abstract
The increasing incidence of infections attributed to hypervirulent carbapenem-resistant Klebsiella pneumoniae (Hv-CRKp) is of considerable concern. Bacteriophages, also known as phages, are viruses that specifically infect bacteria; thus, phage-based therapies offer promising alternatives to antibiotic treatments targeting Hv-CRKp infections. In this study, two isolated bacteriophages, Kpph1 and Kpph9, were characterized for their specificity against the Hv-CRKp K. pneumoniae NUHL30457 strain that possesses a K2 capsule serotype. Both phages exhibit remarkable environmental tolerance, displaying stability over a range of pH values (4-11) and temperatures (up to 50°C). The phages demonstrate potent antibacterial and antibiofilm efficacy, as indicated by their capacity to inhibit biofilm formation and to disrupt established biofilms of Hv-CRKp. Through phylogenetic analysis, it has been revealed that Kpph1 belongs to the new species of Webervirus genus, and Kpph9 to the Drulisvirus genus. Comparative genomic analysis suggests that the tail fiber protein region exhibits the greatest diversity in the genomes of phages within the same genus, which implies distinct co-evolution histories between phages and their corresponding hosts. Interestingly, both phages have been found to contain two tail fiber proteins that may exhibit potential depolymerase activities. However, the exact role of depolymerase in the interaction between phages and their hosts warrants further investigation. In summary, our findings emphasize the therapeutic promise of phages Kpph1 and Kpph9, as well as their encoded proteins, in the context of research on phage therapy targeting hypervirulent carbapenem-resistant Klebsiella pneumoniae.
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Affiliation(s)
- Ye Huang
- Jiangxi Institute of Respiratory Disease, Jiangxi Clinical Research Center for Respiratory Diseases, The Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, P.R. China
- Jiangxi Hospital of China-Japan Friendship Hospital, Jiangxi, P.R. China
| | - Yuan Huang
- Jiangxi Institute of Respiratory Disease, Jiangxi Clinical Research Center for Respiratory Diseases, The Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, P.R. China
- Gerontology Department of The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, P.R. China
| | - Zhiping Wu
- Central Sterile Supply Department of The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, P.R. China
| | - Ziyue Fan
- Queen Mary College, Nanchang University, Nanchang, Jiangxi, P.R. China
| | - Fanglin Zheng
- Jiangxi Institute of Respiratory Disease, Jiangxi Clinical Research Center for Respiratory Diseases, The Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, P.R. China
- Jiangxi Hospital of China-Japan Friendship Hospital, Jiangxi, P.R. China
| | - Yang Liu
- Jiangxi Hospital of China-Japan Friendship Hospital, Jiangxi, P.R. China
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, P.R China
- Jiangxi Medical Center for Critical Public Health Events, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, P.R. China
| | - Xinping Xu
- Jiangxi Institute of Respiratory Disease, Jiangxi Clinical Research Center for Respiratory Diseases, The Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, P.R. China
- Jiangxi Hospital of China-Japan Friendship Hospital, Jiangxi, P.R. China
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8
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Wang N, Meng F, Deng L, Wu L, Yang Y, Li H, Chen Y, Wei Z, Xie B, Gong L, Niu Q, Lei J, Gao J, Huang B, Wang Q, Lai X, Liu Z, Hu J. The epidemiology and gene mutation characteristics of pyrazinamide-resistant Mycobacterium tuberculosis clinical isolates in Southern China. Emerg Microbes Infect 2025; 14:2447607. [PMID: 39745172 PMCID: PMC11721771 DOI: 10.1080/22221751.2024.2447607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 12/03/2024] [Accepted: 12/22/2024] [Indexed: 01/30/2025]
Abstract
This study investigates the epidemic trend of pyrazinamide (PZA)-resistant tuberculosis in Southern China over 11 years (2012-2022) and evaluates the mutation characteristics of PZA resistance-related genes (pncA, rpsA, and panD) in clinical Mycobacterium tuberculosis (M. tuberculosis) isolates. To fulfil these goals, we analyzed the phenotypic PZA resistance characteristics of 14,927 clinical isolates for which Bactec MGIT 960 PZA drug susceptibility testing (DST) results were available, revealing that 2,054 (13.76%) isolates were resistant to PZA. After evaluating the annual variation in the PZA resistance rate among tuberculosis cases in this region, it was observed that it decreased from 37.21% to 6.45% throughout the initial 7 years (2012-2018) and then increased from 8.01% to 12.12% over the subsequent 4 years (2019-2022). Sequences of pncA were obtained from 402 clinical M. tuberculosis complex isolates. For rpsA and panD, sequences were obtained from 360 clinical M. tuberculosis complex isolates. Mutations in pncA were found in 8 out of 223 PZA-sensitive isolates (3.59%) and 105 of 179 (58.66%) PZA-resistant isolates. Conversely, non-synonymous mutations in rpsA were identified in 5 of 137 (3.65%) PZA-resistant isolates, whereas the mutation ratio of rpsA among PZA-sensitive isolates was high at 14.03% (31/221). This difference in the rpsA mutation rate was statistically significant (P = 0.001, chi-square test). No panD mutations were observed in the 137 PZA-resistant isolates, whereas two PZA-sensitive isolates harboured point mutations in panD, including one nonsense mutation (C433 T) and another C-69 T mutation. These findings indicate that rpsA and panD may not significantly contribute to the development of PZA resistance in clinical M. tuberculosis isolates.
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Affiliation(s)
- Nan Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Fanrong Meng
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Li Deng
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Ling Wu
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Yu Yang
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Hua Li
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Yuanjin Chen
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
- Guangzhou Medical University
| | - Zeyou Wei
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
- Guangzhou Medical University
| | - Bei Xie
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Lan Gong
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Qun Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Jie Lei
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Junwen Gao
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Bo Huang
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Qi Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Xiaomin Lai
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
- School of public health, Sun Yat-sen University, Shen Zhen, People’s Republic of China
| | - Zhihui Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Institute of Pulmonary Diseases, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
| | - Jinxing Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Department of Tuberculosis, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangdong, People’s Republic of China
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9
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El-Sayed SAES, Rizk MA, Li H, Mohanta UK, Zafar I, Ji S, Ma Z, Do T, Li Y, Kondoh D, Jaroszewski J, Xuan X. Preassembled complexes of hAgo2 and ssRNA delivered by nanoparticles: a novel silencing gene expression approach overcoming the absence of the canonical pathway of siRNA processing in the apicomplexan parasite Babesia microti, blood parasite of veterinary and zoonotic importance. Emerg Microbes Infect 2025; 14:2438658. [PMID: 39648859 PMCID: PMC11721618 DOI: 10.1080/22221751.2024.2438658] [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: 07/08/2024] [Revised: 11/13/2024] [Accepted: 12/01/2024] [Indexed: 12/10/2024]
Abstract
Due to the lack of efficacy of the currently used chemical drugs, poor tick control, and lack of effective vaccines against Babesia, novel control strategies are urgently needed. In this regard, searching for anti-Babesia gene therapy may facilitate the control of this infection. Following this pattern, small interfering RNAs (siRNAs) are widely used to study gene function and hence open the way to control the parasite. However, the primary constraint of this approach is the lack of Babesia to RNA-induced silencing complex (RISC) enzymes, making siRNA impractical. In this study, we preassembled complexes with the human enzyme argonaute 2 (hAgo2) and a small interfering RNA (siRNA)/single-stranded RNA (ssRNA) against B. gibsoni and B. microti metabolite transporters. The assembled complexes were generated by developing a gene delivery system with chitosan dehydroascorbic acid nanoparticles. The delivery system effectively protected the loaded RNAi and targeted Babesia-infected RBCs with a relatively high internalization rate. The assembled complexes were successfully transfected into live parasites for specific slicing of Babesia targets. We demonstrated a reduction in the expression of target genes at the mRNA level. Furthermore, this silencing inhibited Babesia growth in vitro and in vivo. For the first time, we used this method to confirm the role of the assembled complexes in manipulating the noncanonical pathway of RNAi in Babesia parasites. This novel method provides a means of silencing Babesia genes to study their role in host-parasite interactions and as potential targets for gene therapy and control.
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Affiliation(s)
- Shimaa A. E-S. El-Sayed
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Mohamed A. Rizk
- Department of Internal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Hang Li
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Uday Kumar Mohanta
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Iqra Zafar
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
- Livestock and Dairy Development Department, Veterinary Research Institute, Lahore, Pakistan
| | - Shengwei Ji
- Department of Veterinary Medicine, Agriculture College of Yanbian University, Yanji, People’s Republic of China
| | - Zhuowei Ma
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Thom Do
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Yongchang Li
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Daisuke Kondoh
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Jerzy Jaroszewski
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Xuenan Xuan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Minato-ku, Japan
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10
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Meteyer CU, Boyles JG. Fungal chimera: A lethal mammalian fungus with invasion strategies of plant pathogens. Virulence 2025; 16:2439497. [PMID: 39726252 DOI: 10.1080/21505594.2024.2439497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 11/06/2024] [Accepted: 12/03/2024] [Indexed: 12/28/2024] Open
Affiliation(s)
| | - Justin G Boyles
- School of Biological Sciences, Southern Illinois University, Carbondale, IL, USA
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11
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Liang J, Yang F, Li Z, Li Q. Epigenetic regulation of the inflammatory response in stroke. Neural Regen Res 2025; 20:3045-3062. [PMID: 39589183 DOI: 10.4103/nrr.nrr-d-24-00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 09/20/2024] [Indexed: 11/27/2024] Open
Abstract
Stroke is classified as ischemic or hemorrhagic, and there are few effective treatments for either type. Immunologic mechanisms play a critical role in secondary brain injury following a stroke, which manifests as cytokine release, blood-brain barrier disruption, neuronal cell death, and ultimately behavioral impairment. Suppressing the inflammatory response has been shown to mitigate this cascade of events in experimental stroke models. However, in clinical trials of anti-inflammatory agents, long-term immunosuppression has not demonstrated significant clinical benefits for patients. This may be attributable to the dichotomous roles of inflammation in both tissue injury and repair, as well as the complex pathophysiologic inflammatory processes in stroke. Inhibiting acute harmful inflammatory responses or inducing a phenotypic shift from a pro-inflammatory to an anti-inflammatory state at specific time points after a stroke are alternative and promising therapeutic strategies. Identifying agents that can modulate inflammation requires a detailed understanding of the inflammatory processes of stroke. Furthermore, epigenetic reprogramming plays a crucial role in modulating post-stroke inflammation and can potentially be exploited for stroke management. In this review, we summarize current findings on the epigenetic regulation of the inflammatory response in stroke, focusing on key signaling pathways including nuclear factor-kappa B, Janus kinase/signal transducer and activator of transcription, and mitogen-activated protein kinase as well as inflammasome activation. We also discuss promising molecular targets for stroke treatment. The evidence to date indicates that therapeutic targeting of the epigenetic regulation of inflammation can shift the balance from inflammation-induced tissue injury to repair following stroke, leading to improved post-stroke outcomes.
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Affiliation(s)
- Jingyi Liang
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Fei Yang
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
- Laboratory for Clinical Medicine, Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, China
| | - Zixiao Li
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- National Center for Healthcare Quality Management in Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Research Unit of Artificial Intelligence in Cerebrovascular Disease, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Engineering Research Center of Digital Healthcare for Neurological Diseases, Beijing, China
| | - Qian Li
- Laboratory for Clinical Medicine, Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Capital Medical University, Beijing, China
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12
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Hetta HF, Ahmed R, Ramadan YN, Fathy H, Khorshid M, Mabrouk MM, Hashem M. Gut virome: New key players in the pathogenesis of inflammatory bowel disease. World J Methodol 2025; 15:92592. [DOI: 10.5662/wjm.v15.i2.92592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/28/2024] [Accepted: 07/23/2024] [Indexed: 11/27/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory illness of the intestine. While the mechanism underlying the pathogenesis of IBD is not fully understood, it is believed that a complex combination of host immunological response, environmental exposure, particularly the gut microbiota, and genetic susceptibility represents the major determinants. The gut virome is a group of viruses found in great frequency in the gastrointestinal tract of humans. The gut virome varies greatly among individuals and is influenced by factors including lifestyle, diet, health and disease conditions, geography, and urbanization. The majority of research has focused on the significance of gut bacteria in the progression of IBD, although viral populations represent an important component of the microbiome. We conducted this review to highlight the viral communities in the gut and their expected roles in the etiopathogenesis of IBD regarding published research to date.
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Affiliation(s)
- Helal F Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
- Division of Microbiology, Immunology and Biotechnology, Faculty of pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Rehab Ahmed
- Division of Microbiology, Immunology and Biotechnology, Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Yasmin N Ramadan
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Hayam Fathy
- Department of Internal Medicine, Division Hepatogastroenterology, Assiut University, Assiut 71515, Egypt
| | - Mohammed Khorshid
- Department of Clinical Research, Egyptian Developers of Gastroenterology and Endoscopy Foundation, Cairo 11936, Egypt
| | - Mohamed M Mabrouk
- Department of Internal Medicine, Faculty of Medicine. Tanta University, Tanta 31527, Egypt
| | - Mai Hashem
- Department of Tropical Medicine, Gastroenterology and Hepatology, Assiut University Hospital, Assiut 71515, Egypt
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13
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O'Brien B, Yushchenko A, Suh J, Jung D, Cai Z, Nguyen NS, Semret M, Dufour S, Fanning S, Ronholm J. Subtle genomic differences in Klebsiella pneumoniae sensu stricto isolates indicate host adaptation. One Health 2025; 20:100970. [PMID: 39898312 PMCID: PMC11787494 DOI: 10.1016/j.onehlt.2025.100970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 11/15/2024] [Accepted: 01/07/2025] [Indexed: 02/04/2025] Open
Abstract
Klebsiella pneumoniae sensu stricto (KpI) is an opportunistic pathogen capable of residing as a commensal in both human and bovine intestinal tracts and can cause serious systemic infections in humans and severe clinical mastitis in dairy cattle. It is unclear what role zoonotic and anthroponotic transmission play in the dissemination of KpI. In this study, we use a comparative genomic approach to identify differences between KpI associated with disease in humans and cattle and aimed to identify any potential genetic barriers limiting transmission of KpI between these two hosts. A total of 128 KpI strains (bovine n = 65; human n = 63) were whole genome sequenced and human and bovine strains were compared based on phylogenomics, the pangenome, mobile genetic elements, and differential gene abundance. No obvious phylogenomic differentiation was observed between isolates from these hosts. However, subtle genetic differences exist between bovine and human KpI which likely reflect environmental adaptation to different host niches, including a higher representation of gene clusters encoding ferric citrate uptake transporters, as well as histidine, arginine, and lactose utilization pathways in bovine isolates. These gene clusters may be positively selected due to the unique metabolic environment of the mammary gland, where lactose, citrate-bound iron, and amino acids like histidine and arginine provide growth advantages for KpI during mastitis. Overall, our study identified no obvious genetic barriers to zoonotic transmission of KpI within the dairy environment and provides insight into the development of host-specific therapeutic options for KpI infections in humans and bovine.
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Affiliation(s)
- Bridget O'Brien
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, Quebec, Canada
| | - Alla Yushchenko
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, Quebec, Canada
| | - Jinha Suh
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, Quebec, Canada
| | - Dongyun Jung
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, Quebec, Canada
- Mastitis Network, Saint-Hyacinthe, Quebec, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Quebec, Canada
| | - Zhangbin Cai
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, Quebec, Canada
| | - Ngoc Sang Nguyen
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, Quebec, Canada
| | - Makeda Semret
- McGill University Health Centre (Infectious Diseases and Medical Microbiology), Montreal, Quebec, Canada
| | - Simon Dufour
- Mastitis Network, Saint-Hyacinthe, Quebec, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Quebec, Canada
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Séamus Fanning
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Ireland
| | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, Quebec, Canada
- Mastitis Network, Saint-Hyacinthe, Quebec, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Quebec, Canada
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14
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Girma A. Staphylococcus aureus: Current perspectives on molecular pathogenesis and virulence. Cell Surf 2025; 13:100137. [PMID: 39758277 PMCID: PMC11699754 DOI: 10.1016/j.tcsw.2024.100137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Revised: 12/04/2024] [Accepted: 12/07/2024] [Indexed: 01/07/2025] Open
Abstract
Staphylococcus aureus has evolved a sophisticated regulatory system to control its virulence. One of the main roles of this interconnected network is to sense and respond to diverse environmental signals by altering the synthesis of virulence components required for survival in the host, including cell surface adhesins, extracellular enzymes and toxins. The accessory gene regulator (agr), a quorum sensing system that detects the local concentration of a cyclic peptide signaling molecule, is one of the well-studied of these S. aureus regulatory mechanisms. By using this system, S. aureus is able to sense its own population density and translate this information into a specific pattern of gene expression. In addition to Agr, this pathogen senses specific stimuli through various two-component systems and synchronizes responses with alternative sigma factors and cytoplasmic regulators of the SarA protein family. These different regulatory mechanisms combine host and environmental information into a network that guarantees the best possible response of pathogens to changing circumstances. In this article, an overview of the most significant and thoroughly studied regulatory systems of S. aureus is provided, along with a summary of their roles in host interactions.
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Affiliation(s)
- Abayeneh Girma
- Department of Biology, College of Natural and Computational Science, Mekdela Amba University, P.O. Box 32, Tulu Awuliya, Ethiopia
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15
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Cousson A, Pablo AL, Cournac L, Piton G, Dezette D, Robin A, Taschen E, Bernard L. Ultra pure high molecular weight DNA from soil for Nanopore shotgun metagenomics and metabarcoding sequencing. MethodsX 2025; 14:103134. [PMID: 39846015 PMCID: PMC11751509 DOI: 10.1016/j.mex.2024.103134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 12/25/2024] [Indexed: 01/24/2025] Open
Abstract
Soil microbes are among the most abundant and diverse organisms on Earth but remain poorly characterized. New technologies have made possible to sequence the DNA of uncultivated microorganisms in soil and other complex ecosystems. Genome assembly is crucial for understanding their functional potential. Nanopore sequencing technologies allow to sequence long DNA fragments, optimizing production of metagenome-assembled genomes compared to short-read technology. Extracting DNA with a very high purity and high molecular weight is key to get the most out of this long read technologies. Here we present two extraction protocols to get DNA with high purity. First protocol is optimized to reach DNA quality suiting Nanopore shotgun metagenomics. It uses a non-toxic centrifugation gradient to separate bacterial cells from soil to extract DNA directly on cells. The median length of the acquired DNA sequences (N50) was 3 to 7 times greater than previously published in the literature, achieving an N50 of ∼14 kb. The other, a modification of a commercially available MP Biomedical DNA extraction kit, yielded high-purity DNA for full-length 16S Oxford Nanopore metabarcoding, with an N50 of ∼8 kb. The MP-based protocol achieves higher yields of ultra-pure DNA compared to the Nycodenz protocol, at the expense of shorter fragment lengths.
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