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Liu W, Xu C, Li T, Ren Z, Hao S, Chen Z, Huang X, Wen X. Temporal Dynamics and Contribution of Phage Community to the Prevalence of Antibiotic Resistance Genes in a Full-Scale Sludge Anaerobic Digestion Plant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6296-6304. [PMID: 38556999 DOI: 10.1021/acs.est.4c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Anaerobic digestion (AD) is an important biological resource recovery process, where microorganisms play key roles for material transformation. There has been some knowledge about the prokaryotic community and antibiotic resistance genes (ARGs) in AD, but there has been very limited knowledge of phages. In this study, samples from a full-scale AD plant were collected over 13 months, sequenced, and analyzed for viral and prokaryotic metagenomes. Totally, 3015 viral operational taxonomic units (vOTUs) were detected, mostly assigned to Caudoviricetes. The phage community had faster temporal variation than the prokaryotic community. Warm seasons harbored a higher abundance of both temperate phages and broad host-range phages. Seven ARGs of 6 subtypes were carried by 20 vOTUs, a representative ermT gene was synthesized and expressed, and the resistance activity in the host was examined, confirming the real activity of virus-carried ARGs in the AD process. Some of the ARGs were horizontally transferred between the phage and prokaryotic genomes. However, phage infection was not found to contribute to ARG transfer. This study provided an insight into the ecological patterns of the phage community, confirmed the antibiotic resistance activity of virus-carried ARGs, evaluated the contribution of phages on the ARG prevalence, and laid the foundation for the control strategies of the community and antibiotic resistance in the AD process.
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Affiliation(s)
- Wei Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Chenyang Xu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tianle Li
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhengran Ren
- Research and Development Center, Beijing Drainage Group Co. Ltd., Beijing 100080, China
| | - Shan Hao
- Research and Development Center, Beijing Drainage Group Co. Ltd., Beijing 100080, China
| | - Zhan Chen
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Xia Huang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Xianghua Wen
- School of Environment, Tsinghua University, Beijing 100084, China
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Telhig S, Pham NP, Ben Said L, Rebuffat S, Ouellette M, Zirah S, Fliss I. Exploring the genetic basis of natural resistance to microcins. Microb Genom 2024; 10:001156. [PMID: 38407259 PMCID: PMC10926693 DOI: 10.1099/mgen.0.001156] [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: 03/29/2023] [Accepted: 11/28/2023] [Indexed: 02/27/2024] Open
Abstract
Enterobacteriaceae produce an arsenal of antimicrobial compounds including microcins, ribosomally produced antimicrobial peptides showing diverse structures and mechanisms of action. Microcins target close relatives of the producing strain to promote its survival. Their narrow spectrum of antibacterial activity makes them a promising alternative to conventional antibiotics, as it should decrease the probability of resistance dissemination and collateral damage to the host's microbiota. To assess the therapeutic potential of microcins, there is a need to understand the mechanisms of resistance to these molecules. In this study, we performed genomic analyses of the resistance to four microcins [microcin C, a nucleotide peptide; microcin J25, a lasso peptide; microcin B17, a linear azol(in)e-containing peptide; and microcin E492, a siderophore peptide] on a collection of 54 Enterobacteriaceae from three species: Escherichia coli, Salmonella enterica and Klebsiella pneumoniae. A gene-targeted analysis revealed that about half of the microcin-resistant strains presented mutations of genes involved in the microcin mechanism of action, especially those involved in their uptake (fhuA, fepA, cirA and ompF). A genome-wide association study did not reveal any significant correlations, yet relevant genetic elements were associated with microcin resistance. These were involved in stress responses, biofilm formation, transport systems and acquisition of immunity genes. Additionally, microcin-resistant strains exhibited several mutations within genes involved in specific metabolic pathways, especially for S. enterica and K. pneumoniae.
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Affiliation(s)
- Soufiane Telhig
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Nguyen Phuong Pham
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Laila Ben Said
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Ismaïl Fliss
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
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Xue S, Abdullahi R, Wu N, Zheng J, Su M, Xu M. Gut microecological regulation on bronchiolitis and asthma in children: A review. THE CLINICAL RESPIRATORY JOURNAL 2023; 17:975-985. [PMID: 37105551 PMCID: PMC10542989 DOI: 10.1111/crj.13622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/22/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023]
Abstract
INTRODUCTION Asthma and bronchiolitis in children are considered common clinical problems associated with gut microbiota. However, the exact relationship between gut microbiota and the above-mentioned diseases remains unclear. Here, we discussed recent advances in understanding the potential mechanism underlying immune regulation of gut microbiota on asthma and bronchiolitis in children as well as the role of the gut-lung axis. METHODS We retrieved and assessed all relevant original articles related to gut microbiota, airway inflammation-induced wheezing in children, and gut-lung axis studies from databases that have been published so far, including PubMed/MEDLINE, Scopus, Google Scholar, China National Knowledge Infrastructure (CNKI) and the Wanfang Database. RESULTS The infant period is critical for the development of gut microbiota, which can be influenced by gestational age, delivery mode, antibiotic exposure and feeding mode. The gut microbiota in children with asthma and bronchiolitis is significantly distinct from those in healthy subjects. Gut microbiota dysbiosis is implicated in asthma and bronchiolitis in children. The presence of intestinal disturbances in lung diseases highlights the importance of the gut-lung axis. CONCLUSION Gut microbiota dysbiosis potentially increases the risk of asthma and bronchiolitis in children. Moreover, a deeper understanding of the gut-lung axis with regard to the gut microbiota of children with respiratory diseases could contribute to clinical practice for pulmonary diseases.
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Affiliation(s)
- Sichen Xue
- Department of PediatricsThe First Affiliated Hospital of Ningbo UniversityNingboZhejiangChina
- Department of Pediatric Respiratory MedicineThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Rukkaiya Abdullahi
- Department of Pediatric Respiratory MedicineThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Naisheng Wu
- Department of PediatricsThe First Affiliated Hospital of Ningbo UniversityNingboZhejiangChina
| | - Jishan Zheng
- Department of PediatricsThe Ningbo Women and Children's HospitalNingboChina
| | - Miaoshang Su
- Department of Pediatric Respiratory MedicineThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Manhuan Xu
- College of Laboratory Medicine and Life ScienceWenzhou Medical UniversityWenzhouZhejiangChina
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Chen J, Zhu J, Lu W, Wang H, Pan M, Tian P, Zhao J, Zhang H, Chen W. Uncovering Predictive Factors and Interventions for Restoring Microecological Diversity after Antibiotic Disturbance. Nutrients 2023; 15:3925. [PMID: 37764709 PMCID: PMC10536327 DOI: 10.3390/nu15183925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic treatment can lead to a loss of diversity of gut microbiota and may adversely affect gut microbiota composition and host health. Previous studies have indicated that the recovery of gut microbes from antibiotic-induced disruption may be guided by specific microbial species. We expect to predict recovery or non-recovery using these crucial species or other indices after antibiotic treatment only when the gut microbiota changes. This study focused on this prediction problem using a novel ensemble learning framework to identify a set of common and reasonably predictive recovery-associated bacterial species (p-RABs), enabling us to predict the host microbiome recovery status under broad-spectrum antibiotic treatment. Our findings also propose other predictive indicators, suggesting that higher taxonomic and functional diversity may correlate with an increased likelihood of successful recovery. Furthermore, to explore the validity of p-RABs, we performed a metabolic support analysis and identified Akkermansia muciniphila and Bacteroides uniformis as potential key supporting species for reconstruction interventions. Experimental results from a C57BL/6J male mouse model demonstrated the effectiveness of p-RABs in facilitating intestinal microbial reconstitution. Thus, we proved the reliability of the new p-RABs and validated a practical intervention scheme for gut microbiota reconstruction under antibiotic disturbance.
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Affiliation(s)
- Jing Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jinlin Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mingluo Pan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Peijun Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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Usman SS, Uba AI, Christina E. Bacteriophage genome engineering for phage therapy to combat bacterial antimicrobial resistance as an alternative to antibiotics. Mol Biol Rep 2023; 50:7055-7067. [PMID: 37392288 DOI: 10.1007/s11033-023-08557-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
Bacteriophages (phages) are viruses that mainly infect bacteria and are ubiquitously distributed in nature, especially to their host. Phage engineering involves nucleic acids manipulation of phage genome for antimicrobial activity directed against pathogens through the applications of molecular biology techniques such as synthetic biology methods, homologous recombination, CRISPY-BRED and CRISPY-BRIP recombineering, rebooting phage-based engineering, and targeted nucleases including CRISPR/Cas9, zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Management of bacteria is widely achieved using antibiotics whose mechanism of action has been shown to target both the genetic dogma and the metabolism of pathogens. However, the overuse of antibiotics has caused the emergence of multidrug-resistant (MDR) bacteria which account for nearly 5 million deaths as of 2019 thereby posing threats to the public health sector, particularly by 2050. Lytic phages have drawn attention as a strong alternative to antibiotics owing to the promising efficacy and safety of phage therapy in various models in vivo and human studies. Therefore, harnessing phage genome engineering methods, particularly CRISPR/Cas9 to overcome the limitations such as phage narrow host range, phage resistance or any potential eukaryotic immune response for phage-based enzymes/proteins therapy may designate phage therapy as a strong alternative to antibiotics for combatting bacterial antimicrobial resistance (AMR). Here, the current trends and progress in phage genome engineering techniques and phage therapy are reviewed.
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Affiliation(s)
- Sani Sharif Usman
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144401, Punjab, India
- Department of Biological Sciences, Faculty of Science, Federal University of Kashere, P.M.B. 0182, Gombe, Nigeria
| | - Abdullahi Ibrahim Uba
- Department of Molecular Biology and Genetics, Istanbul AREL University, 34537, Istanbul, Türkiye
| | - Evangeline Christina
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144401, Punjab, India.
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Du S, Shang L, Zou X, Deng X, Sun A, Mu S, Zhao J, Wang Y, Feng X, Li B, Wang C, Liu S, Lu B, Liu Y, Zhang R, Tong Y, Cao B. Azithromycin Exposure Induces Transient Microbial Composition Shifts and Decreases the Airway Microbiota Resilience from Outdoor PM 2.5 Stress in Healthy Adults: a Randomized, Double-Blind, Placebo-Controlled Trial. Microbiol Spectr 2023; 11:e0206622. [PMID: 37093053 PMCID: PMC10269807 DOI: 10.1128/spectrum.02066-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 03/28/2023] [Indexed: 04/25/2023] Open
Abstract
Inappropriate antibiotic prescriptions are common for patients with upper respiratory tract infections (URTIs). Few data exist regarding the effects of antibiotic administration on airway microbiota among healthy adults. We conducted a randomized, double-blind, placebo-controlled trial to characterize the airway microbiota longitudinally in healthy adults using 16S rRNA gene sequencing and quantification. Both the induced sputum and oral wash samples were collected over a 60-day period following a 3-day intervention with 500 mg azithromycin or placebo. Environmental information, including air quality data (particulate matter [PM2.5] and PM10, air quality index [AQI] values), were also collected during the study. A total of 48 healthy volunteers were enrolled and randomly assigned into two groups. Azithromycin did not alter bacterial load but significantly reduced species richness and Shannon index. Azithromycin exposure resulted in a decrease in the detection rate and relative abundance of different genera belonging to Veillonellaceae, Leptotrichia, Fusobacterium, Neisseria, and Haemophilus. In contrast, the relative abundance of taxa belonging to Streptococcus increased immediately after azithromycin intervention. The shifts in the diversity of the microbiology composition took between 14 and 60 days to recover, depending on the measure used: either UniFrac phylogenetic distance or α-diversity. Outdoor environmental perturbations, especially the high concentration of PM2.5, contributed to novel variability in microbial community composition of the azithromycin group at D30 (30 days after baseline). The network analysis found that azithromycin altered the microbial interactions within airway microbiota. The influence was still obvious at D14 when the relative abundance of most taxa had returned to the baseline level. Compared to the sputum microbiota, oral cavity microbiota had a different pattern of change over time. The induced sputum microbial data can represent the airway microbiota composition in healthy adults. Azithromycin may have transient effects in the airway microbiota of healthy adults and decrease the airway microbiota resilience against outdoor environmental stress. The influence of azithromycin on microbial interactions is noteworthy, although the airway microbiota has returned to a near-baseline level. IMPORTANCE The influence of antibiotic administration on the airway microbiota of healthy adults remains unknown. This study is a randomized, double-blind, placebo-controlled trial aiming to investigate the microbial shifts in airways after exposure to azithromycin among heathy adults. We find that azithromycin changes the airway microbial community composition of healthy adults and decreases the airway microbiota resilience against outdoor environmental stress. This study depicts the longitudinal recovery trajectory of airway microbiota after the antibiotic perturbation and may provide reference for appropriate antibiotic prescription.
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Affiliation(s)
- Sisi Du
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Lianhan Shang
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaohui Zou
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaoyan Deng
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Aihua Sun
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Shengrui Mu
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Jiankang Zhao
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Yimin Wang
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Jin Yin-tan Hospital, Wuhan, Hubei, China
| | - Xiaoxuan Feng
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Binbin Li
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Chunlei Wang
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Shuai Liu
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Binghuai Lu
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Yingmei Liu
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Rongrong Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Bin Cao
- China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
- Changping Laboratory, Beijing, China
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Pargin E, Roach MJ, Skye A, Papudeshi B, Inglis LK, Mallawaarachchi V, Grigson SR, Harker C, Edwards RA, Giles SK. The human gut virome: composition, colonization, interactions, and impacts on human health. Front Microbiol 2023; 14:963173. [PMID: 37293229 PMCID: PMC10244655 DOI: 10.3389/fmicb.2023.963173] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each individual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales). The stability of the virome's regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy individual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile. Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed 'viral dark matter', is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sarah K. Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
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Ding D, Wang B, Zhang X, Zhang J, Zhang H, Liu X, Gao Z, Yu Z. The spread of antibiotic resistance to humans and potential protection strategies. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 254:114734. [PMID: 36950985 DOI: 10.1016/j.ecoenv.2023.114734] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can exert selective pressure on antibiotic resistance bacteria (ARB) and antibiotic resistance gene (ARG), accelerating the flow of antibiotic resistance. As ARG spreads to the population, the burden of antibiotic resistance in humans increases, which may have potential health effects on people. Therefore, it is critical to mitigate the spread of antibiotic resistance to humans and reduce the load of antibiotic resistance in humans. This review briefly described the information of global antibiotic consumption information and national action plans (NAPs) to combat antibiotic resistance and provided a set of feasible control strategies for the transmission of ARB and ARG to humans in three areas including (a) Reducing the colonization capacity of exogenous ARB, (b) Enhancing human colonization resistance and mitigating the horizontal gene transfer (HGT) of ARG, (c) Reversing ARB antibiotic resistance. With the hope of achieving interdisciplinary one-health prevention and control of bacterial resistance.
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Affiliation(s)
- Dong Ding
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China; College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Bin Wang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaoan Zhang
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junxi Zhang
- NHC Key Laboratory of Birth Defects Prevention & Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Huanhuan Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xinxin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zhan Gao
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Zengli Yu
- College of Public Health, Zhengzhou University, Zhengzhou, China; The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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9
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von Gunten S, Schneider C, Imamovic L, Gorochov G. Antibody diversity in IVIG: Therapeutic opportunities for novel immunotherapeutic drugs. Front Immunol 2023; 14:1166821. [PMID: 37063852 PMCID: PMC10090664 DOI: 10.3389/fimmu.2023.1166821] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023] Open
Abstract
Significant progress has been made in the elucidation of human antibody repertoires. Furthermore, non-canonical functions of antibodies have been identified that reach beyond classical functions linked to protection from pathogens. Polyclonal immunoglobulin preparations such as IVIG and SCIG represent the IgG repertoire of the donor population and will likely remain the cornerstone of antibody replacement therapy in immunodeficiencies. However, novel evidence suggests that pooled IgA might promote orthobiotic microbial colonization in gut dysbiosis linked to mucosal IgA immunodeficiency. Plasma-derived polyclonal IgG and IgA exhibit immunoregulatory effects by a diversity of different mechanisms, which have inspired the development of novel drugs. Here we highlight recent insights into IgG and IgA repertoires and discuss potential implications for polyclonal immunoglobulin therapy and inspired drugs.
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Affiliation(s)
- Stephan von Gunten
- Institute of Pharmacology, University of Bern, Bern, Switzerland
- *Correspondence: Stephan von Gunten,
| | | | - Lejla Imamovic
- Sorbonne Université, Inserm, Assistance Publique Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Paris, France
| | - Guy Gorochov
- Sorbonne Université, Inserm, Assistance Publique Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Paris, France
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10
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Maves RC, Kalil AC. Which trial do we need? Doxycycline in combination with ceftriaxone for the treatment of community-acquired pneumonia. Clin Microbiol Infect 2023:S1198-743X(23)00090-3. [PMID: 36870434 DOI: 10.1016/j.cmi.2023.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/14/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023]
Affiliation(s)
- Ryan C Maves
- Section of Infectious Diseases, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA.
| | - Andre C Kalil
- Division of Infectious Diseases, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
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11
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Sun T, Liu X, Su Y, Wang Z, Cheng B, Dong N, Wang J, Shan A. The efficacy of anti-proteolytic peptide R7I in intestinal inflammation, function, microbiota, and metabolites by multi-omics analysis in murine bacterial enteritis. Bioeng Transl Med 2023; 8:e10446. [PMID: 36925697 PMCID: PMC10013768 DOI: 10.1002/btm2.10446] [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: 08/13/2022] [Revised: 10/21/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022] Open
Abstract
Increased antibiotic resistance poses a major limitation in tackling inflammatory bowel disease and presents a large challenge for global health care. Antimicrobial peptides (AMPs) are a potential class of antimicrobial agents. Here, we have designed the potential oral route for antimicrobial peptide R7I with anti-proteolytic properties to deal with bacterial enteritis in mice. The results revealed that R7I protected the liver and gut from damage caused by inflammation. RNA-Seq analysis indicated that R7I promoted digestion and absorption in the small intestine by upregulating transmembrane transporter activity, lipid and small molecule metabolic processes and other pathways, in addition to upregulating hepatic steroid biosynthesis and fatty acid degradation. For the gut microbiota, Clostridia were significantly reduced in the R7I-treated group, and Odoribacteraceae, an efficient isoalloLCA-synthesizing strain, was the main dominant strain, protecting the gut from potential pathogens. In addition, we further discovered that R7I reduced the accumulation of negative organic acid metabolites. Overall, R7I exerted better therapeutic and immunomodulatory potential in the bacterial enteritis model, greatly reduced the risk of disease onset, and provided a reference for the in vivo application of antimicrobial peptides.
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Affiliation(s)
- Taotao Sun
- Laboratory of Molecular Nutrition and Immunity, the Institute of Animal NutritionNortheast Agricultural UniversityHarbinChina
| | - Xuesheng Liu
- Laboratory of Molecular Nutrition and Immunity, the Institute of Animal NutritionNortheast Agricultural UniversityHarbinChina
| | - Yunzhe Su
- Laboratory of Molecular Nutrition and Immunity, the Institute of Animal NutritionNortheast Agricultural UniversityHarbinChina
| | - Zihang Wang
- Laboratory of Molecular Nutrition and Immunity, the Institute of Animal NutritionNortheast Agricultural UniversityHarbinChina
| | - Baojing Cheng
- Laboratory of Molecular Nutrition and Immunity, the Institute of Animal NutritionNortheast Agricultural UniversityHarbinChina
| | - Na Dong
- Laboratory of Molecular Nutrition and Immunity, the Institute of Animal NutritionNortheast Agricultural UniversityHarbinChina
| | - Jiajun Wang
- Laboratory of Molecular Nutrition and Immunity, the Institute of Animal NutritionNortheast Agricultural UniversityHarbinChina
| | - Anshan Shan
- Laboratory of Molecular Nutrition and Immunity, the Institute of Animal NutritionNortheast Agricultural UniversityHarbinChina
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12
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Double-edged sword: impact of fecal microbiome transplants on the gut resistome. Curr Opin Gastroenterol 2023; 39:16-22. [PMID: 36504032 DOI: 10.1097/mog.0000000000000894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW Fecal microbiome transplants (FMT) show promise in treating various diseases, such as Clostridioides difficile infections. FMT have also demonstrated the capacity to modulate the collection of antibiotic resistance genes (ARGs), termed the resistome, within the gut. The purpose of this review was to critically evaluate the literature regarding the interaction between FMT and the gut resistome and determine whether FMT could be used specifically to reduce ARG carriage in the gut. RECENT FINDINGS Several studies have demonstrated a decrease in ARG carriage post-FMT administration in various disease states, including recurrent C. difficile infection and after antibiotic usage. However, other studies have reported an expansion of the resistome following FMT. Most studies contained small patient cohorts regardless of the outcome and showed heterogeneity in responses. SUMMARY Research on resistome modulation by FMT is preliminary, and human studies currently lack consensus regarding benefits and risks. From a safety perspective, screening donor samples for ARGs in addition to antibiotic-resistant organisms may be advisable. Additional studies on the mechanisms underlying heterogeneity between studies and individuals are required before FMT is considered an efficient approach for resistome amelioration.
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13
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Mahmud H, Keenan JD, Gonzales J, Schallhorn J, Chan M, Arnold B, Cavallino V, Lietman TM, Doan T, Seitzman GD. Ocular Rosacea microBiome Study (ORBS)-sub-microbial versus antibiotic dosing of doxycycline versus placebo in treatment of symptomatic ocular rosacea: study protocol for a parallel-arm randomized clinical trial. Trials 2022; 23:1033. [PMID: 36539810 PMCID: PMC9769060 DOI: 10.1186/s13063-022-06948-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Ocular rosacea is common and is often managed with long-term antibiotic treatment. Doxycycline is the most commonly selected antibiotic for the treatment of rosacea. As there is no established standard of care treatment dose for rosacea, prescribed doses of doxycycline vary widely. The FDA classifies 40 mg daily dose of doxycycline for ocular rosacea as sub-microbial in comparison to an antibiotic dose of 200 mg daily. However, this "sub-microbial" dose has never been evaluated in patients with ocular rosacea, and even the sub-microbial dose has potential to alter systemic mucosa flora. Here, we present a randomized controlled trial using RNA sequencing to fully characterize the impact of sub-microbial antibiotic dosing of doxycycline on antimicrobial resistance and bacterial composition of the ocular and gut flora. METHODS In a triple-masked parallel randomized control trial, patients with ocular rosacea will be randomized to three arms: a 40-mg dose of doxycycline, a 200-mg antibiotic dose of doxycycline, or placebo. Collected rectal and lower eyelid samples will be compared for frequency of antimicrobial resistance genetic determinants and microbiome diversity. A subjective ocular surface disease index survey and objective tear breakup time measurement will be determined. DISCUSSION These results will enhance our understanding of the overall systemic impact of long-term systemic sub-microbial antibiotic dosing for the treatment of chronic recurrent ocular inflammatory diseases. TRIAL REGISTRATION This trial was registered on ClinicalTrials.org (NCT05296837) on March 22, 2022.
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Affiliation(s)
- Hamidah Mahmud
- grid.266102.10000 0001 2297 6811San Francisco School of Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Francis I. Proctor Foundation, University of California, San Francisco, CA USA
| | - Jeremy D. Keenan
- grid.266102.10000 0001 2297 6811Francis I. Proctor Foundation, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Ophthalmology, University of California, San Francisco, CA USA
| | - John Gonzales
- grid.266102.10000 0001 2297 6811Francis I. Proctor Foundation, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Ophthalmology, University of California, San Francisco, CA USA
| | - Julie Schallhorn
- grid.266102.10000 0001 2297 6811Francis I. Proctor Foundation, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Ophthalmology, University of California, San Francisco, CA USA
| | - Matilda Chan
- grid.266102.10000 0001 2297 6811Francis I. Proctor Foundation, University of California, San Francisco, CA USA
| | - Benjamin Arnold
- grid.266102.10000 0001 2297 6811Francis I. Proctor Foundation, University of California, San Francisco, CA USA
| | - Victoria Cavallino
- grid.266102.10000 0001 2297 6811Francis I. Proctor Foundation, University of California, San Francisco, CA USA
| | - Thomas M. Lietman
- grid.266102.10000 0001 2297 6811Francis I. Proctor Foundation, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Ophthalmology, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Epidemiology and Biostatistics, University of California, San Francisco, CA USA
| | - Thuy Doan
- grid.266102.10000 0001 2297 6811Francis I. Proctor Foundation, University of California, San Francisco, CA USA
| | - Gerami D. Seitzman
- grid.266102.10000 0001 2297 6811Francis I. Proctor Foundation, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Ophthalmology, University of California, San Francisco, CA USA
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14
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Gelli HP, Vazquez-Uribe R, Sommer MOA. Screening for effective cell-penetrating peptides with minimal impact on epithelial cells and gut commensals in vitro. Front Pharmacol 2022; 13:1049324. [PMID: 36408245 PMCID: PMC9666501 DOI: 10.3389/fphar.2022.1049324] [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: 09/20/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023] Open
Abstract
One of the biggest challenges for oral drug absorption is the epithelial barrier of the gastrointestinal tract. The use of cell-penetrating peptides (CPPs) to modulate the epithelial barrier function is known to be an effective strategy to improve drug absorption and bioavailability. In this study we compare side-by-side, 9 most promising CPPs to study their cytotoxicity (Cytotox Red dye staining) and cell viability (AlamarBlue staining) on epithelial cells and their effects on paracellular permeability of the intestinal barrier in vitro in a differentiated Caco-2 epithelial monolayer model. The data revealed that 4 out of 9 well-studied CPPs significantly improved Caco-2 paracellular permeability without compromising on cellular health. To assess the impact of CPPs on the human microbiota we studied the antimicrobial effects of the 4 effective CPPs from our permeation studies against 10 representative strains of the gut microbiota in vitro using microbroth dilution. Our data revealed that these 4 CPPs affected the growth of almost all tested commensal strains. Interestingly, we found that two synthetic CPPs (Shuffle and Penetramax) outperformed all the other CPPs in their ability to increase intestinal paracellular permeability at 50 µM and had only a small to moderate effect on the tested gut commensal strains. Based on these data Shuffle and Penetramax represent relevant CPPs to be further characterized in vivo for safe delivery of poorly absorbed therapeutics while minimizing negative impacts on the gut microbiota.
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15
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Pan X, Zhou Z, Liu B, Wu Z. A novel therapeutic concern: Antibiotic resistance genes in common chronic diseases. Front Microbiol 2022; 13:1037389. [DOI: 10.3389/fmicb.2022.1037389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Infections caused by multidrug-resistant bacteria carrying antibiotic resistance genes pose a severe threat to global public health and human health. In clinical practice, it has been found that human gut microbiota act as a “reservoir” of antibiotic resistance genes (ARGs) since gut microbiota contain a wide variety of ARGs, and that the structure of the gut microbiome is influenced by the profile of the drug resistance genes present. In addition, ARGs can spread within and between species of the gut microbiome in multiple ways. To better understand gut microbiota ARGs and their effects on patients with chronic diseases, this article reviews the generation of ARGs, common vectors that transmit ARGs, the characteristics of gut microbiota ARGs in common chronic diseases, their impact on prognosis, the current state of treatment for ARGs, and what should be addressed in future research.
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16
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Huang P, Cao J, Chen J, Luo Y, Gong X, Wu C, Wang Y. Crosstalk between gut microbiota and renal ischemia/reperfusion injury. Front Cell Infect Microbiol 2022; 12:1015825. [PMID: 36132990 PMCID: PMC9483100 DOI: 10.3389/fcimb.2022.1015825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Renal ischemia-reperfusion injury (IRI) is the main cause of acute kidney injury and the cause of rapid renal dysfunction and high mortality. In recent years, with the gradual deepening of the understanding of the intestinal flora, exploring renal IRI from the perspective of the intestinal flora has become a research hotspot. It is well known that the intestinal flora plays an important role in maintaining human health, and dysbiosis is the change in the composition and function of the intestinal tract, which in turn causes intestinal barrier dysfunction. Studies have shown that there are significant differences in the composition of intestinal flora before and after renal IRI, and this difference is closely related to the occurrence and development of renal IRI and affects prognosis. In addition, toxins produced by dysregulated gut microbes enter the bloodstream, which in turn exacerbates kidney damage. This article reviews the research progress of intestinal flora and renal IRI, in order to provide new treatment ideas and strategies for renal IRI.
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Affiliation(s)
- Peng Huang
- Department of Anesthesiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jianwei Cao
- Department of Microscopic Orthopedics of Hand and Foot, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jingyi Chen
- Department of Anesthesiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Jingyi Chen, ; Yu Wang, ; Chengyi Wu,
| | - Yanrong Luo
- Physical examination center, Shiyan Hospital of Integrated Traditional and Western Medicine, Shiyan, China
| | - Xiaofang Gong
- Department of Anesthesiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Chengyi Wu
- Department of Anesthesiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Jingyi Chen, ; Yu Wang, ; Chengyi Wu,
| | - Yu Wang
- Department of Anesthesiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Jingyi Chen, ; Yu Wang, ; Chengyi Wu,
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17
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Antibiotic resistance in the commensal human gut microbiota. Curr Opin Microbiol 2022; 68:102150. [DOI: 10.1016/j.mib.2022.102150] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 12/24/2022]
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18
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Telhig S, Ben Said L, Torres C, Rebuffat S, Zirah S, Fliss I. Evaluating the Potential and Synergetic Effects of Microcins against Multidrug-Resistant Enterobacteriaceae. Microbiol Spectr 2022; 10:e0275221. [PMID: 35543514 PMCID: PMC9241698 DOI: 10.1128/spectrum.02752-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/12/2022] [Indexed: 11/20/2022] Open
Abstract
The advent of multidrug-resistant bacteria has hampered the development of new antibiotics, exacerbating their morbidity and mortality. In this context, the gastrointestinal tract reveals a valuable source of novel antimicrobials. Microcins are bacteriocins produced by members of the family Enterobacteriaceae, which are endowed with a wide diversity of structures and mechanisms of action, and exert potent antibacterial activity against closely related bacteria. In this study, we investigated the antibacterial activities of four microcins against 54 Enterobacteriaceae isolates from three species (Escherichia coli, Klebsiella pneumoniae, and Salmonella enterica). The selected microcins, microcin C (McC, nucleotide peptide), microcin J25 (MccJ25, lasso peptide), microcin B17 (MccB17, linear azol(in)e-containing peptide), and microcin E492 (MccE492, siderophore peptide) carry different post-translational modifications and have distinct mechanisms of action. MICs and minimal bactericidal concentrations (MBC) of the microcins were measured and the efficacy of combinations of the microcins together or with antibiotics was assessed to identify potential synergies. Every isolate showed sensitivity to at least one microcin with MIC values ranging between 0.02 μM and 42.5 μM. Among the microcins tested, McC exhibited the broadest spectrum of inhibition with 46 strains inhibited, closely followed by MccE492 with 38 strains inhibited, while MccJ25 showed the highest activity. In general, microcin activity was observed to be independent of antibiotic resistance profile and strain genus. Of the 42 tested combinations, 20 provided enhanced activity (18 out of 20 being microcin-antibiotic combinations), with two being synergetic. IMPORTANCE With their wide range of structures and mechanisms of action, microcins are shown to exert antibacterial activities against Enterobacteriaceae resistant to antibiotics together with synergies with antibiotics and in particular colistin.
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Affiliation(s)
- Soufiane Telhig
- Food Science Department, Food and Agriculture Faculty, Laval University, Québec City, Québec, Canada
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Laila Ben Said
- Food Science Department, Food and Agriculture Faculty, Laval University, Québec City, Québec, Canada
| | - Carmen Torres
- Department of Food and Agriculture, University of La Rioja, Logrono, Spain
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Ismail Fliss
- Food Science Department, Food and Agriculture Faculty, Laval University, Québec City, Québec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Québec City, Québec, Canada
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Blanco-Picazo P, Gómez-Gómez C, Tormo M, Ramos-Barbero MD, Rodríguez-Rubio L, Muniesa M. Prevalence of bacterial genes in the phage fraction of food viromes. Food Res Int 2022; 156:111342. [DOI: 10.1016/j.foodres.2022.111342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/15/2022] [Accepted: 05/03/2022] [Indexed: 11/04/2022]
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20
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Bornbusch SL, Drea CM. Antibiotic Resistance Genes in Lemur Gut and Soil Microbiota Along a Gradient of Anthropogenic Disturbance. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.704070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The overuse of man-made antibiotics has facilitated the global propagation of antibiotic resistance genes in animals, across natural and anthropogenically disturbed environments. Although antibiotic treatment is the most well-studied route by which resistance genes can develop and spread within host-associated microbiota, resistomes also can be acquired or enriched via more indirect routes, such as via transmission between hosts or via contact with antibiotic-contaminated matter within the environment. Relatively little is known about the impacts of anthropogenic disturbance on reservoirs of resistance genes in wildlife and their environments. We therefore tested for (a) antibiotic resistance genes in primate hosts experiencing different severities and types of anthropogenic disturbance (i.e., non-wildlife animal presence, human presence, direct human contact, and antibiotic treatment), and (b) covariation between host-associated and environmental resistomes. We used shotgun metagenomic sequencing of ring-tailed lemur (Lemur catta) gut resistomes and associated soil resistomes sampled from up to 10 sites: seven in the wilderness of Madagascar and three in captivity in Madagascar or the United States. We found that, compared to wild lemurs, captive lemurs harbored greater abundances of resistance genes, but not necessarily more diverse resistomes. Abundances of resistance genes were positively correlated with our assessments of anthropogenic disturbance, a pattern that was robust across all ten lemur populations. The composition of lemur resistomes was site-specific and the types of resistance genes reflected antibiotic usage in the country of origin, such as vancomycin use in Madagascar. We found support for multiple routes of ARG enrichment (e.g., via human contact, antibiotic treatment, and environmental acquisition) that differed across lemur populations, but could result in similar degrees of enrichment. Soil resistomes varied across natural habitats in Madagascar and, at sites with greater anthropogenic disturbance, lemurs and soil resistomes covaried. As one of the broadest, single-species investigations of wildlife resistomes to date, we show that the transmission and enrichment of antibiotic resistance genes varies across environments, thereby adding to the mounting evidence that the resistance crisis extends outside of traditional clinical settings.
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