1
|
Zeng C, Wan SR, Guo M, Tan XZ, Zeng Y, Wu Q, Xie JJ, Yan P, Long Y, Zheng L, Jiang ZZ, Teng FY, Xu Y. Fecal virome transplantation: A promising strategy for the treatment of metabolic diseases. Biomed Pharmacother 2024; 177:117065. [PMID: 38971010 DOI: 10.1016/j.biopha.2024.117065] [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: 04/06/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/08/2024] Open
Abstract
Metabolic diseases are a group of disorders caused by metabolic abnormalities, including obesity, diabetes, non-alcoholic fatty liver disease, and more. Increasing research indicates that, beyond inherent metabolic irregularities, the onset and progression of metabolic diseases are closely linked to alterations in the gut microbiota, particularly gut bacteria. Additionally, fecal microbiota transplantation (FMT) has demonstrated effectiveness in clinically treating metabolic diseases, notably diabetes. Recent attention has also focused on the role of gut viruses in disease onset. This review first introduces the characteristics and influencing factors of gut viruses, then summarizes their potential mechanisms in disease development, highlighting their impact on gut bacteria and regulation of host immunity. We also compare FMT, fecal filtrate transplantation (FFT), washed microbiota transplantation (WMT), and fecal virome transplantation (FVT). Finally, we review the current understanding of gut viruses in metabolic diseases and the application of FVT in treating these conditions. In conclusion, FVT may provide a novel and promising treatment approach for metabolic diseases, warranting further validation through basic and clinical research.
Collapse
Affiliation(s)
- Chen Zeng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Sheng-Rong Wan
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xiao-Zhen Tan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yan Zeng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Qi Wu
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China; Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Jia-Jie Xie
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Pijun Yan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Institute of Cardiovascular Research, Peking University, Beijing 100871, China
| | - Yang Long
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Lemin Zheng
- Institute of Cardiovascular Research, Peking University, Beijing 100871, China
| | - Zong-Zhe Jiang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Fang-Yuan Teng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
| | - Yong Xu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
| |
Collapse
|
2
|
Kang Y, Wang J, Zhu C, Zheng M, Li Z. Unveiling the genomic diversity and ecological impact of phage communities in hospital wastewater. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135353. [PMID: 39094306 DOI: 10.1016/j.jhazmat.2024.135353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 07/13/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
Phages are pivotal in shaping microbial communities and biogeochemical cycles, while our understanding of the diversity, functions potential, and resistance gene carriage of phages in hospital wastewater (HWW) remains limited. We collected influent and effluent samples from the 3 hospital wastewater treatment plants (HWTPs) to assess the diversity and fate of phages, the interactions between phages and hosts, and the presence of resistance genes and auxiliary metabolic genes (AMGs) encoded by phages. Compared to influent, effluent showed reduced phage abundance and altered composition, with decreases in Microviridae and Inoviridae. The gene-sharing network highlights that many phages in HWW are not classified in known viral genera, suggesting HWW as a rich source of new viruses. There was a significant association between phages and microorganisms, with approximately 32.57 % of phages expected to be capable of infecting microbial hosts, characterized primarily by lytic activity. A total of 8 unique antibiotic resistance genes, 13 unique metal resistance genes, and 5 mobile genetic elements were detected in 3 HWTPs phageomes. Phage AMGs have the potential to influence carbon, nitrogen, phosphorus, and sulfur metabolism, impacting biogeochemical cycles. This study reveals the genomic diversity and ecological role of phages in HWTPs, highlighting their environmental and ecosystem impact.
Collapse
Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Caizhong Zhu
- The Fourth Medical Center of Chinese PLA General Hospital, China
| | - Meiqin Zheng
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China.
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102200, China.
| |
Collapse
|
3
|
Hou Y, Diao W, Jia R, Sun W, Feng W, Li B, Zhu J. Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem. ENVIRONMENTAL RESEARCH 2024; 251:118717. [PMID: 38518910 DOI: 10.1016/j.envres.2024.118717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/24/2024]
Abstract
Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.
Collapse
Affiliation(s)
- Yiran Hou
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Weixu Diao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Rui Jia
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Wei Sun
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Wenrong Feng
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Bing Li
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China.
| | - Jian Zhu
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China.
| |
Collapse
|
4
|
Chu WC, Gao YY, Wu YX, Liu FF. Biofilm of petroleum-based and bio-based microplastics in seawater in response to Zn(II): Biofilm formation, community structure, and microbial function. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172397. [PMID: 38608889 DOI: 10.1016/j.scitotenv.2024.172397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/22/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024]
Abstract
Microplastic biofilms are novel vectors for the transport and spread of pathogenic and drug-resistant bacteria. With the increasing use of bio-based plastics, there is an urgent need to investigate the microbial colonization characteristics of these materials in seawater, particularly in comparison with conventional petroleum-based plastics. Furthermore, the effect of co-occurring contaminants, such as heavy metals, on the formation of microplastic biofilms and bacterial communities remains unclear. In this study, we compared the biofilm bacterial community structure of petroleum-based polyethylene (PE) and bio-based polylactic acid (PLA) in seawater under the influence of zinc ions (Zn2+). Our findings indicate that the biofilm on PLA microplastics in the late stage was impeded by the formation of a mildly acidic microenvironment resulting from the hydrolysis of the ester group on PLA. The PE surface had higher bacterial abundance and diversity, with a more intricate symbiotic pattern. The bacterial structures on the two types of microplastics were different; PE was more conducive to the colonization of anaerobic bacteria, whereas PLA was more favorable for the colonization of aerobic and acid-tolerant species. Furthermore, Zn increased the proportion of the dominant genera that could utilize microplastics as a carbon source, such as Alcanivorax and Nitratireductor. PLA had a greater propensity to harbor and disseminate pathogenic and drug-resistant bacteria, and Zn promoted the enrichment and spread of harmful bacteria such as, Pseudomonas and Clostridioides. Therefore, further research is essential to fully understand the potential environmental effects of bio-based microplastics and the role of heavy metals in the dynamics of bacterial colonization.
Collapse
Affiliation(s)
- Wang-Chao Chu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yuan-Yuan Gao
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yu-Xin Wu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Fei-Fei Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China.
| |
Collapse
|
5
|
Zhu DM, Yan YS, Wang H, Zhong Y, Inam, Gao YH, Li GM, Mu GD, Dong HF, Li Y, Liu DK, Ma HX, Kong LC. Transmission of human-pet antibiotic resistance via aerosols in pet hospitals of Changchun. One Health 2024; 18:100765. [PMID: 38855194 PMCID: PMC11157275 DOI: 10.1016/j.onehlt.2024.100765] [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: 03/22/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024] Open
Abstract
In recent years, aerosols have been recognized as a prominent medium for the transmission of antibiotic-resistant bacteria and genes. Among these, particles with a particle size of 2 μm (PM2.5) can directly penetrate the alveoli. However, the presence of antibiotic-resistant genes in aerosols from pet hospitals and the potential risks posed by antibiotic-resistant bacteria in these aerosols to humans and animals need to be investigated. In this study, cefotaxime-resistant bacteria were collected from 5 representative pet hospitals in Changchun using a Six-Stage Andersen Cascade Impactor. The distribution of bacteria in each stage was analyzed, and bacteria from stage 5 and 6 were isolated and identified. Minimal inhibitory concentrations of isolates against 12 antimicrobials were determined using broth microdilution method. Quantitative Polymerase Chain Reaction was employed to detect resistance genes and mobile genetic elements that could facilitate resistance spread. The results indicated that ARBs were enriched in stage 5 (1.1-2.1 μm) and stage 3 (3.3-4.7 μm) of the sampler. A total of 159 isolates were collected from stage 5 and 6. Among these isolates, the genera Enterococcus spp. (51%), Staphylococcus spp. (19%), and Bacillus spp. (14%) were the most prevalent. The isolates exhibited the highest resistance to tetracycline and the lowest resistance to cefquinome. Furthermore, 56 (73%) isolates were multidrug-resistant. Quantitative PCR revealed the expression of 165 genes in these isolates, with mobile genetic elements showing the highest expression levels. In conclusion, PM2.5 from pet hospitals harbor a significant number of antibiotic-resistant bacteria and carry mobile genetic elements, posing a potential risk for alveolar infections and the dissemination of antibiotic resistance genes.
Collapse
Affiliation(s)
- Dao Mi Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
| | - Ya Song Yan
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
| | - Hao Wang
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
| | - Yue Zhong
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
| | - Inam
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
| | - Yun Hang Gao
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
| | - Gong Mei Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
| | - Guo Dong Mu
- Jilin Provincial Animal Disease Prevention and Control Center, Jilin Animal Husbandry Building, Xi'an Road No. 4510, Changchun, PR China
| | - Hui Feng Dong
- Tianjin Key Laboratory of Biological Feed Additive Enterprise, S&E Burgeoning Biotechnology (Tianjin) Co., Ltd, No.27, Shengda Second Branch Road, Wangwenzhuang Industrial Park, Xiqing District, Tianjin 300383, PR China
| | - Yuan Li
- Tianjin Key Laboratory of Biological Feed Additive Enterprise, S&E Burgeoning Biotechnology (Tianjin) Co., Ltd, No.27, Shengda Second Branch Road, Wangwenzhuang Industrial Park, Xiqing District, Tianjin 300383, PR China
| | - Ding Kuo Liu
- Tianjin Key Laboratory of Biological Feed Additive Enterprise, S&E Burgeoning Biotechnology (Tianjin) Co., Ltd, No.27, Shengda Second Branch Road, Wangwenzhuang Industrial Park, Xiqing District, Tianjin 300383, PR China
| | - Hong Xia Ma
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
| | - Ling Cong Kong
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, PR China
| |
Collapse
|
6
|
Dantas CWD, Martins DT, Nogueira WG, Alegria OVC, Ramos RTJ. Tools and methodology to in silico phage discovery in freshwater environments. Front Microbiol 2024; 15:1390726. [PMID: 38881659 PMCID: PMC11176557 DOI: 10.3389/fmicb.2024.1390726] [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: 02/23/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms. Current water treatment methods cannot keep pace with bacterial evolution, which increasingly exhibits a profile of multidrug resistance to antibiotics. Furthermore, using more powerful disinfectants may affect the balance of aquatic ecosystems. Therefore, there is a need to explore sustainable ways to control the spreading of pathogenic bacteria. Bacteriophages can infect bacteria and archaea, hijacking their host machinery to favor their replication. They are widely abundant globally and provide a biological alternative to bacterial treatment with antibiotics. In contrast to common disinfectants and antibiotics, bacteriophages are highly specific, minimizing adverse effects on aquatic microbial communities and offering a lower cost-benefit ratio in production compared to antibiotics. However, due to the difficulty involving cultivating and identifying environmental bacteriophages, alternative approaches using NGS metagenomics in combination with some bioinformatic tools can help identify new bacteriophages that can be useful as an alternative treatment against resistant bacteria. In this review, we discuss advances in exploring the virome of freshwater, as well as current applications of bacteriophages in freshwater treatment, along with current challenges and future perspectives.
Collapse
Affiliation(s)
- Carlos Willian Dias Dantas
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - David Tavares Martins
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Wylerson Guimarães Nogueira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Oscar Victor Cardenas Alegria
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel Thiago Jucá Ramos
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| |
Collapse
|
7
|
Kang Y, Wang J, Wang Y, Li Z. Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171766. [PMID: 38513871 DOI: 10.1016/j.scitotenv.2024.171766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.
Collapse
Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- North China University of Science and Technology, Basic Medical College, Tangshan, Hebei 063210, P.R. China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China.
| |
Collapse
|
8
|
Li Y, Xu Y, Zhou X, Huang L, Wang G, Liao J, Dai R. From "resistance genes expression" to "horizontal migration" as well as over secretion of Extracellular Polymeric Substances: Sludge microorganism's response to the increasing of long-term disinfectant stress. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133940. [PMID: 38457979 DOI: 10.1016/j.jhazmat.2024.133940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/16/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
Glutaraldehyde-Didecyldimethylammonium bromides (GDs) has been frequently and widely employed in livestock and poultry breeding farms to avoid epidemics such as African swine fever, but its long-term effect on the active sludge microorganisms of the receiving wastewater treatment plant was keep unclear. Four simulation systems were built here to explore the performance of aerobic activated sludge with the long-term exposure of GDs and its mechanism by analyzing water qualities, resistance genes, extracellular polymeric substances and microbial community structure. The results showed that the removal rates of CODCr and ammonia nitrogen decreased with the exposure concentration of GDs increasing. It is worth noting that long-term exposure to GDs can induce the horizontal transfer and coordinated expression of a large number of resistance genes, such as qacE, sul1, tetx, and int1, in drug-resistant microorganisms. Additionally, it promotes the secretion of more extracellular proteins, including arginine, forming a "barrier-like" protection. Therefore, long-term exposure to disinfectants can alter the treatment capacity of activated sludge receiving systems, and the abundance of resistance genes generated through horizontal transfer and coordinated expression by drug-resistant microorganisms does pose a significant threat to ecosystems and health. It is recommended to develop effective pretreatment methods to eliminate disinfectants.
Collapse
Affiliation(s)
- Yuxin Li
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yanbin Xu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Xiao Zhou
- Analysis and Test Center, Guangdong University of Technology, Guangzhou 510006, China
| | - Lu Huang
- Analysis and Test Center, Guangdong University of Technology, Guangzhou 510006, China
| | - Guan Wang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Jingsong Liao
- Yikangsheng Environmental Science and Technology Limited Company of Guangdong, Yunfu 527400, China
| | - Ruizhi Dai
- Yikangsheng Environmental Science and Technology Limited Company of Guangdong, Yunfu 527400, China
| |
Collapse
|
9
|
Nair S, Barker CR, Bird M, Greig DR, Collins C, Painset A, Chattaway M, Pickard D, Larkin L, Gharbia S, Didelot X, Ribeca P. Presence of phage-plasmids in multiple serovars of Salmonella enterica. Microb Genom 2024; 10:001247. [PMID: 38717818 PMCID: PMC11165635 DOI: 10.1099/mgen.0.001247] [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: 01/05/2024] [Accepted: 04/17/2024] [Indexed: 06/13/2024] Open
Abstract
Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterized a circular P1-like phage-plasmid harbouring a bla CTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in Salmonella enterica serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales, in this study we carried out a follow-up retrospective analysis of UK Salmonella isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47 784 isolates for the presence of the P1 lytic replication gene repL, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to S. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8 and 98.2 kb in size, with an average length of 92.1 kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. In total, 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in Salmonella, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.
Collapse
Affiliation(s)
| | - Clare R. Barker
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
| | - Matthew Bird
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - David R. Greig
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Caitlin Collins
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Marie Chattaway
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
| | - Derek Pickard
- The Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
| | | | - Saheer Gharbia
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Xavier Didelot
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- School of Public Health and Department of Statistics, University of Warwick, Warwick, UK
| | - Paolo Ribeca
- UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- Biomathematics and Statistics Scotland, The James Hutton Institute, Edinburgh, UK
| |
Collapse
|
10
|
Hu L, Meng A, Tu Z, Jia S, Liu Q, Chen F. The analysis of complete genome sequence and comparative genomics of Vibrio parahaemolyticus LF1113 in Hainan. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 119:105574. [PMID: 38373468 DOI: 10.1016/j.meegid.2024.105574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/28/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Vibrio parahaemolyticus is a Gram-negative, halophilic and polymorphic coccobacillus. It is world-widely distributed and has resulted in great economic losses since its first appearance. In this study, a pathogenic strain was isolated from diseased pearl gentian grouper and identified as V. parahaemolyticus based on the sequencing results of 16S rDNA gene. In order to gain a comprehensive understanding of this isolation, the whole genome sequencing was conducted. Phylogenetic analysis of the complete genomes of 16 Vibrio species showed that LF1113, ATCC17802, ATCC33787, 2210633, FORC 004, and 160807 were the most closely related. Animal experiments demonstrated that the isolated LF1113 strain was pathogenic in a fish model. This study is the first study to describe the complete genome sequence of a V. parahaemolyticus isolate, which infected pearl gentian grouper from an outbreak in a fish factory farm in Hainan. The results will expand our understanding of genetic characteristics, pathogenesis, diagnostics and disease prevention of V. parahaemolyticus, and lay the foundation for further study.
Collapse
Affiliation(s)
- Linlin Hu
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China; Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Tropical Ocean University, Sanya 572022, China, Haikou 570228, China.
| | - Aiyun Meng
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China; Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Tropical Ocean University, Sanya 572022, China, Haikou 570228, China
| | - Zhigang Tu
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China; Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Tropical Ocean University, Sanya 572022, China, Haikou 570228, China
| | - Shuwen Jia
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China
| | - Qingming Liu
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China
| | - Fuxiao Chen
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China; Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Tropical Ocean University, Sanya 572022, China, Haikou 570228, China
| |
Collapse
|
11
|
Li Z, Guo X, Liu B, Huang T, Liu R, Liu X. Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants. WATER RESEARCH 2024; 253:121289. [PMID: 38341975 DOI: 10.1016/j.watres.2024.121289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/13/2024]
Abstract
Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.
Collapse
Affiliation(s)
- Zong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China
| | - Xiaoxiao Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China
| | - Bingxin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Huang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China.
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China.
| |
Collapse
|
12
|
Ji Y, Xi H, Chen C, Sun C, Feng X, Lei L, Han W, Gu J. The pig intestinal phageome is an important reservoir and transfer vector for virulence genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170076. [PMID: 38220020 DOI: 10.1016/j.scitotenv.2024.170076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
Bacteriophages (phages) can significantly influence the composition and functions of their host communities, and enhance host pathogenicity via the transport of phage-encoded virulence genes. Phages are the main component of animal gut viruses, however, there are few reports on the piglet gut phageome and its contribution to virulence genes. Here, a total of 185 virulence genes from 59,955 predicted genes of gut phages in weaned piglets were identified, with 0.688 % of the phage contigs coding for at least one virulence gene. The virulence gene pblA was the most abundant, with various virulence genes significantly correlated with gut phages and their encoded mobile gene element (MGE) genes. Importantly, multiple virulence genes and MGE genes coexist in some phage sequences, and up to 12 virulence genes were detected in a single phage sequence, greatly increasing the risk of phage-mediated transmission of virulence genes into the bacterial genome. In addition, diarrhoea has driven changes in the composition and structure of phage and bacterial communities in the intestinal tract of weaned piglets, significantly increasing the abundance of phage contigs encoding both virulence genes and MGE genes in faecal samples, which potentially increases the risk of phage-mediated virulence genes being transfected into the gut bacterial genome. In summary, this study expands our understanding of the gut microbiome of piglets, advances our understanding of the potential role of phages in driving host pathogenesis in the gut system, and provides new insights into the sources of virulence genes and genetic evolution of bacteria in pig farm environments.
Collapse
Affiliation(s)
- Yalu Ji
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hengyu Xi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Chong Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Changjiang Sun
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xin Feng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Liancheng Lei
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenyu Han
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jingmin Gu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
| |
Collapse
|
13
|
Samson R, Dharne M, Khairnar K. Bacteriophages: Status quo and emerging trends toward one health approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168461. [PMID: 37967634 DOI: 10.1016/j.scitotenv.2023.168461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.
Collapse
Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Krishna Khairnar
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
| |
Collapse
|
14
|
Bin Hafeez A, Pełka K, Worobo R, Szweda P. In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates. Int J Mol Sci 2024; 25:666. [PMID: 38203838 PMCID: PMC10780176 DOI: 10.3390/ijms25010666] [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: 12/11/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.
Collapse
Affiliation(s)
- Ahmer Bin Hafeez
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Karolina Pełka
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Randy Worobo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| |
Collapse
|
15
|
Singh K, Park S. Construction of prophage-free and highly-transformable Limosilactobacillus reuteri strains and their use for production of 1,3-propanediol. Biotechnol Bioeng 2024; 121:317-328. [PMID: 37747698 DOI: 10.1002/bit.28559] [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: 02/21/2023] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
The lactic acid bacterium Limosilactobacillus reuteri (formerly Lactobacillus reuteri) is a desirable host for the production of 1,3-propanediol (1,3-PDO) from glycerol when 1,3-PDO is used in the food or cosmetic industry. However, the production is hindered by strain instability, causing cell lysis, and difficult gene manipulation. This study reveals that the stability of L. reuteri DSM 20016 and its 1,3-PDO production, especially in the alcohol dehydrogenases (ADHs)-deletion mutants, are greatly enhanced after the deletion of two prophages (Φ3 and Φ4) present in the L. reuteri's chromosome. The resulting phage-free and ADHs-deletion mutant could produce >825 mM 1,3-PDO in 48 h without cell lysis at the theoretical maximum yield on glucose of ~2 mol/mol. Compared to the wild-type strain, the mutant exhibited a 45.2% increase in 1,3-PDO production titer and a 2.1-fold increase in yield. In addition, this study reports that the transformation efficiency of L. reuteri Δadh2Δadh6 mutant strains were greatly enhanced by >300-fold after the deletion of prophage Φ3, probably due to the removal of a restriction-modification (RM) system which resides in the phage genome. With improved stability and higher transformation efficiency, recombinant L. reuteri DSM 20016 Δadh2Δadh6ΔΦ3ΔΦ4 can be a more reliable and amenable host for industrial applications.
Collapse
Affiliation(s)
- Kalpana Singh
- School of Energy and Chemical Engineering, UNIST, Ulsan, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, UNIST, Ulsan, Republic of Korea
| |
Collapse
|
16
|
Shuai X, Zhou Z, Ba X, Lin Y, Lin Z, Liu Z, Yu X, Zhou J, Zeng G, Ge Z, Chen H. Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems? WATER RESEARCH 2024; 248:120833. [PMID: 37952327 DOI: 10.1016/j.watres.2023.120833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Antimicrobial resistance poses a serious threat to human health and is responsible for the death of millions of people annually. Hospital wastewater is an important hotspot for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). However, little is known about the relationship between phages and ARGs in hospital wastewater systems (HWS). In the present study, the viral diversity of 12 HWSs using data from public metagenomic databases was investigated. Viruses were widely found in both the influent and effluent of each HWS. A total of 45 unique ARGs were carried by 85 viral contigs, which accounted for only 0.14% of the total viral populations, implying that ARGs were not commonly present in phages. Three efflux pump genes were identified as shared between phages and bacterial genomes. However, the predominant types of ARGs in HWS such as aminoglycoside- and beta-lactam-resistance genes were rarely found in phages. Based on CRISPR spacer and tRNA matches, interactions between 171 viral contigs and 60 antibiotic-resistant genomes were predicted, including interactions involving phages and vancomycin-resistant Enterococcus_B faecium or beta-lactam-resistant Klebsiella pneumoniae. More than half (56.1%) of these viral contigs indicated lytic and none of them carried ARGs. As the vOTUs in this study had few ARGs and were primarily lytic, HWS may be a valuable source for phage discovery. Future studies will be able to experimentally validate these sequence-based results to confirm the suitability of HWS phages for pathogen control measures in wastewater.
Collapse
Affiliation(s)
- Xinyi Shuai
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yanhan Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zejun Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhe Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xi Yu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinyu Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangshu Zeng
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ziye Ge
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; International Cooperation Base of Environmental Pollution and Ecological Health, Science and Technology Agency of Zhejiang, Zhejiang University, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
| |
Collapse
|
17
|
Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
Collapse
Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
| |
Collapse
|
18
|
Coxe T, Azad RK. Silicon versus Superbug: Assessing Machine Learning's Role in the Fight against Antimicrobial Resistance. Antibiotics (Basel) 2023; 12:1604. [PMID: 37998806 PMCID: PMC10669088 DOI: 10.3390/antibiotics12111604] [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: 09/30/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/25/2023] Open
Abstract
In his 1945 Nobel Prize acceptance speech, Sir Alexander Fleming warned of antimicrobial resistance (AMR) if the necessary precautions were not taken diligently. As the growing threat of AMR continues to loom over humanity, we must look forward to alternative diagnostic tools and preventive measures to thwart looming economic collapse and untold mortality worldwide. The integration of machine learning (ML) methodologies within the framework of such tools/pipelines presents a promising avenue, offering unprecedented insights into the underlying mechanisms of resistance and enabling the development of more targeted and effective treatments. This paper explores the applications of ML in predicting and understanding AMR, highlighting its potential in revolutionizing healthcare practices. From the utilization of supervised-learning approaches to analyze genetic signatures of antibiotic resistance to the development of tools and databases, such as the Comprehensive Antibiotic Resistance Database (CARD), ML is actively shaping the future of AMR research. However, the successful implementation of ML in this domain is not without challenges. The dependence on high-quality data, the risk of overfitting, model selection, and potential bias in training data are issues that must be systematically addressed. Despite these challenges, the synergy between ML and biomedical research shows great promise in combating the growing menace of antibiotic resistance.
Collapse
Affiliation(s)
- Tallon Coxe
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA;
- BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA
| | - Rajeev K. Azad
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA;
- BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA
| |
Collapse
|
19
|
Bai Y, Sun X, Guo Y, Qiu T, Xin H, Yu A, Wang X, Gao M. Particle-size stratification of airborne antibiotic resistant genes, mobile genetic elements, and bacterial pathogens within layer and broiler farms in Beijing, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:112799-112812. [PMID: 37843709 DOI: 10.1007/s11356-023-29975-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023]
Abstract
The particle-size distribution of antimicrobial resistant (AMR) elements is crucial in evaluating their environmental behavior and health risks, and exposure to the fecal microbiome via particle mass (PM) is an important route of transmission of AMR from livestock to humans. However, few studies have explored the association between air and fecal AMR in farm environments from the perspective of particle-size stratification. We collected feces and PMs of different sizes from layer and broiler farms, quantified antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and human pathogenic bacteria (HPB) using Droplet digital PCR (ddPCR), and analyzed the bacterial communities based on 16S rRNA sequencing. The particle-size distributions of 16S rRNA and AMR elements were similar and generally increased with larger particle sizes in chicken farms. In broiler farms, we observed a bimodal distribution with two peaks at 5.8-9.0 μm and 3.3-4.7 μm. The dominant airborne bacterial phyla were Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The dominant phyla in the feces were the same as those in the air, but the order of relative abundance varied. The particle-size distributions of specific bacterial genera differed between the animal-farm types. Overall, the degree of association between feces and different particulates increased with increasing particle size. The microbial communities in the coarse particles were similar to those in fecal samples. Escherichia coli, Staphylococcus spp., Campylobacter spp., and sul 2 (sulfonamide ARGs) tended to attach to small particles. We highlight the particle size-specific relationship between fecal and air microbes involving ARGs, MGEs, and HPB and provide valuable information for comprehensively assessing the transmission of fecal microorganisms through the airpath and its environmental and occupational health risks.
Collapse
Affiliation(s)
- Yuqiao Bai
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
- College of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Xingbin Sun
- College of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Yajie Guo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
| | - Tianlei Qiu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
| | - Huibo Xin
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
| | - Aoyuan Yu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
| | - Xuming Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
| | - Min Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China.
| |
Collapse
|
20
|
Zhang Y, Kitazumi A, Liao YT, de Los Reyes BG, Wu VCH. Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem. Microbiol Spectr 2023; 11:e0022623. [PMID: 37754684 PMCID: PMC10581182 DOI: 10.1128/spectrum.00226-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/10/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.
Collapse
Affiliation(s)
- Yujie Zhang
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center , Albany, California, USA
| | - Ai Kitazumi
- Department of Plant and Soil Science, Texas Tech University , Lubbock, Texas, USA
| | - Yen-Te Liao
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center , Albany, California, USA
| | | | - Vivian C H Wu
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center , Albany, California, USA
| |
Collapse
|
21
|
Zhu M, Li Y, Wang L, Zhang W, Niu L, Hu T. Unraveling antibiotic resistomes associated with bacterial and viral communities in intertidal mudflat aquaculture area. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132087. [PMID: 37506645 DOI: 10.1016/j.jhazmat.2023.132087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/22/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
The extensive use of antibiotics in intertidal mudflat aquaculture area has substantially increased the dissemination risk of antibiotic resistance genes (ARGs). As hosts of ARGs, bacteria and virus exert vital effects on ARG dissemination. However, the insights for the interrelationships among ARGs, bacteria, and virus have not been thoroughly explored in intertidal mudflat. Therefore, this study attempts to unravel the occurrence, dissemination, evolution, and driving mechanisms of ARGs associated with bacterial and viral communities using metagenomic sequencing in a typical intertidal mudflat. Abundant and diverse ARGs (22 types and 437 subtypes) were identified and those of ARGs were higher in spring than in autumn. It is worthy noted that virus occupied a more essential position than bacteria for ARGs dissemination through network analysis. Meanwhile, nitrogen exerted indirect effect on ARG profiles by shaping viral and bacterial diversity. According to the results of neutral and null models, deterministic processes dominated the ARG community assembly by controlling sediment nitrogen and antibiotics. Homogeneous and variable selection dominated phylogenetic turnover of ARG community, contributing 46.15% and 45.90% of the total processes, respectively. This study can hence theoretically support for the ARG pollution control and management in intertidal mudflat aquaculture area.
Collapse
Affiliation(s)
- Mengjie Zhu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Linqiong Wang
- College of Oceanography, Hohai University, Nanjing 210098, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Tong Hu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| |
Collapse
|
22
|
Mahdavi S, Sadeghi M, Shokri R, Kalantari M. Molecular characterization of PMQR carrying bacteriophages in effluent discharge samples of Azerbaijan hospitals. Braz J Microbiol 2023; 54:1769-1781. [PMID: 37599326 PMCID: PMC10484843 DOI: 10.1007/s42770-023-01084-1] [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: 10/27/2022] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Quinolones are one of the most widely used drugs in medicine. Resistance to this agent has been increased significantly among the nosocomial isolates. The objective of this research was to study generalized transduction, as a potential mechanism for plasmid-mediated quinolone resistance (PMQR) genes acquisition among hospital effluent isolates. Discharge samples from hospital effluent were taken from four medical centers in Azerbaijan. Resident phages were enriched against resident enterobacterial hosts using standard phage enrichment protocols. Polymerase chain reaction (PCR) was used to examine phage stocks and bacterial isolates for the presence of PMQR determinants. All positive bacterial isolates for target genes were subjected to transduction assays. Restriction fragment length polymorphism (RFLP) profiles were determined for cluster analysis. A total of 55 pure phage stocks were prepared from 42 effluents. A total of 95 non-duplicated Gram-negative bacteria were isolated. Thirty-two EcoRV-RFLP profiles were determined for the 40 Escherichia coli phage stocks. Twenty-six of 40 (65%) E. coli phages were positive for qnrB (n = 15), qnrD (n = 7), qnrA (n = 3), and qnrC (n = 2) genes. A total of 34 (35.7%) bacterial isolates were recognized to have any PMQR genes including qnrB (n = 23), qnrD (n = 8), qnrA (n = 5), and qnrC (n = 3) genes. Present research provided a strong evidence for potential role of generalized transduction in persistence and circulation of PMQR genes in health care settings of Azerbaijan.
Collapse
Affiliation(s)
- Sahar Mahdavi
- Biology Research Center, Zanjan branch, Islamic Azad University, Zanjan, Iran
| | - Mohammadreza Sadeghi
- Department of Clinical Microbiology, Maku branch, Islamic Azad University, Maku, Iran.
| | - Rasoul Shokri
- Biology Research Center, Zanjan branch, Islamic Azad University, Zanjan, Iran.
| | - Mohsen Kalantari
- Biology Research Center, Zanjan branch, Islamic Azad University, Zanjan, Iran
| |
Collapse
|
23
|
Zang X, Lv H, Huang P, Sun Z, Gu C, Ding W, Jiao X, Huang J. Genomic Insights into Pangenome and Antimicrobial Resistance in Campylobacter spp. Isolated from Chickens at Specific Growth Stages. Foodborne Pathog Dis 2023; 20:303-312. [PMID: 37318846 DOI: 10.1089/fpd.2023.0008] [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] [Indexed: 06/17/2023] Open
Abstract
Improved understanding of the genetic basis of Campylobacter spp. colonization of poultry at specific growth stage is the key to developing a farm-based strategy to prevent flock colonization. In this study, 39 Campylobacter spp. strains (chicken isolates, n = 29; environmental isolates, n = 10) were collected from six marked chickens at the growth stage from week 7 to week 13. Then, we use comparative genomics techniques to analyze the temporal genomic characteristics of Campylobacter spp. in individual chickens across a production cycle. Genotype, average nucleotide identity (ANI), and phylogenetic trees all indicated the evolutionary relationships between the strains from different sampling weeks. The clustering of isolates was not dependent on sampling time and sample source, indicating that strains could persist over several weeks in a flock. Notably, 10 antimicrobial resistance (AMR) genes were identified in the genome of Campylobacter coli isolates, and the genomes of isolates sampled at week 11 harbored fewer AMR genes and insertion sequences (IS) than the isolates from other weeks. Consistent with this, pangenome-wide association analysis demonstrated that gene acquisition and loss could happen at week 11 and week 13. These genes were mainly associated with cell membrane biogenesis, ion metabolism, and DNA replication, suggesting that genomic change may be related to Campylobacter adaptive response. This is a novel study focused on the genetic changes occurring in Campylobacter spp. isolates in a particular space and time; it highlights that accessory genes and AMR genes were overall stable at chicken farm, which will help us understand the survival and the transmission route of Campylobacter spp. better, and have the potential to inform the strategy on the safety control of market-ready chickens.
Collapse
Affiliation(s)
- Xiaoqi Zang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hongyue Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Pingyu Huang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zhichu Sun
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Chen Gu
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Wei Ding
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Jinlin Huang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| |
Collapse
|
24
|
Pilati GVT, Cadamuro RD, Filho VB, Dahmer M, Elois MA, Savi BP, Salles GBC, Muniz EC, Fongaro G. Bacteriophage-Associated Antimicrobial Resistance Genes in Avian Pathogenic Escherichia coli Isolated from Brazilian Poultry. Viruses 2023; 15:1485. [PMID: 37515172 PMCID: PMC10386125 DOI: 10.3390/v15071485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Colibacillosis is a disease caused by Escherichia coli and remains a major concern in poultry production, as it leads to significant economic losses due to carcass condemnation and clinical symptoms. The development of antimicrobial resistance is a growing problem of worldwide concern. Lysogenic bacteriophages are effective vectors for acquiring and disseminating antibiotic resistance genes (ARGs). The aim of this study was to investigate the complete genome of Escherichia coli isolates from the femurs of Brazilian broiler chickens in order to investigate the presence of antimicrobial resistance genes associated with bacteriophages. Samples were collected between August and November 2021 from broiler batches from six Brazilian states. Through whole genome sequencing (WGS), data obtained were analyzed for the presence of antimicrobial resistance genes. Antimicrobial resistance genes against the aminoglycosides class were detected in 79.36% of the isolates; 74.6% had predicted sulfonamides resistance genes, 63.49% had predicted resistance genes against β-lactams, and 49.2% of the isolates had at least one of the tetracycline resistance genes. Among the detected genes, 27 have been described in previous studies and associated with bacteriophages. The findings of this study highlight the role of bacteriophages in the dissemination of ARGs in the poultry industry.
Collapse
Affiliation(s)
- Giulia Von Tönnemann Pilati
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Rafael Dorighello Cadamuro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Vilmar Benetti Filho
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Mariane Dahmer
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Mariana Alves Elois
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Beatriz Pereira Savi
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Gleidson Biasi Carvalho Salles
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
- Zoetis Industry of Veterinary Products LTDA, São Paulo 04709-111, Brazil
| | | | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| |
Collapse
|
25
|
Meyer L, Guyot S, Chalot M, Capelli N. The potential of microorganisms as biomonitoring and bioremediation tools for mercury-contaminated soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115185. [PMID: 37385017 DOI: 10.1016/j.ecoenv.2023.115185] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/20/2023] [Accepted: 06/24/2023] [Indexed: 07/01/2023]
Abstract
Mercury (Hg) pollution is a global issue due to the high toxicity and wide dispersion of Hg around the world. Whether due to anthropogenic activities or natural processes, Hg emissions are steadily increasing, with very high levels in some regions, directly threatening human and ecosystem health. However, bacteria and fungi have evolved and adapted in response to Hg-induced stress and have developed tolerance mechanisms, notably based on the mer operon system that is involved in Hg uptake and biovolatilization via Hg reduction reactions. Other processes, such as bioaccumulation or extracellular sequestration, are involved in Hg resistance, and the study of contaminated soils has allowed the isolation of a number of microorganisms capable of these mechanisms, with strong potential for the implementation of bioremediation approaches. In addition to playing an important role in determining the fate of Hg in the biogeochemical cycle, these microorganisms can indeed be applied to reduce Hg concentrations or at least stabilize Hg for the remediation of polluted soils. Moreover, thanks to the development of biotechnological tools, bioremediation based on Hg-tolerant microorganisms can be optimized. Finally, these microorganisms are relevant candidates for biomonitoring, for example, through the engineering of biosensors, because the detection of Hg is a major issue in preserving the health of living beings.
Collapse
Affiliation(s)
- Lorraine Meyer
- Chrono-environnement UMR 6249, Université de Franche-Comté CNRS, F-25000 Besançon, France
| | - Stéphane Guyot
- Université de Bourgogne, Institut Agro, PAM UMR A 02.102, F-21000 Dijon, France
| | - Michel Chalot
- Chrono-environnement UMR 6249, Université de Franche-Comté CNRS, F-25000 Besançon, France; Université de Lorraine, F-54000 Nancy, France
| | - Nicolas Capelli
- Chrono-environnement UMR 6249, Université de Franche-Comté CNRS, F-25000 Besançon, France.
| |
Collapse
|
26
|
Ashy RA, Jalal RS, Sonbol HS, Alqahtani MD, Sefrji FO, Alshareef SA, Alshehrei FM, Abuauf HW, Baz L, Tashkandi MA, Hakeem IJ, Refai MY, Abulfaraj AA. Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera. Front Microbiol 2023; 14:1166148. [PMID: 37260683 PMCID: PMC10227523 DOI: 10.3389/fmicb.2023.1166148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/10/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes. Methods Genes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil. Results Abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H2O2 and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include "antibiotic efflux pump" for ARGs soxR, OleC, and MuxB, "antibiotic target alteration" for parY mutant, and "antibiotic inactivation" for arr-1. Discussion These ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.
Collapse
Affiliation(s)
- Ruba A. Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rewaa S. Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Hana S. Sonbol
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mashael D. Alqahtani
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatmah O. Sefrji
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatimah M. Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Haneen W. Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Manal A. Tashkandi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Aala A. Abulfaraj
- Biological Sciences Department, College of Science & Arts, King AbdulAziz University, Rabigh, Saudi Arabia
| |
Collapse
|
27
|
Ho SFS, Wheeler NE, Millard AD, van Schaik W. Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data. MICROBIOME 2023; 11:84. [PMID: 37085924 PMCID: PMC10120246 DOI: 10.1186/s40168-023-01533-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND The prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A comparative analysis of ten state-of-the-art phage identification tools was performed to inform their usage in microbiome research. METHODS Artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage species, were used to evaluate the precision, recall, and F1 scores of the tools. We also generated a dataset of randomly shuffled sequences to quantify false-positive calls. In addition, a set of previously simulated viromes was used to assess diversity bias in each tool's output. RESULTS VIBRANT and VirSorter2 achieved the highest F1 scores (0.93) in the RefSeq artificial contigs dataset, with several other tools also performing well. Kraken2 had the highest F1 score (0.86) in the mock community benchmark by a large margin (0.3 higher than DeepVirFinder in second place), mainly due to its high precision (0.96). Generally, k-mer-based tools performed better than reference similarity tools and gene-based methods. Several tools, most notably PPR-Meta, called a high number of false positives in the randomly shuffled sequences. When analysing the diversity of the genomes that each tool predicted from a virome set, most tools produced a viral genome set that had similar alpha- and beta-diversity patterns to the original population, with Seeker being a notable exception. CONCLUSIONS This study provides key metrics used to assess performance of phage detection tools, offers a framework for further comparison of additional viral discovery tools, and discusses optimal strategies for using these tools. We highlight that the choice of tool for identification of phages in metagenomic datasets, as well as their parameters, can bias the results and provide pointers for different use case scenarios. We have also made our benchmarking dataset available for download in order to facilitate future comparisons of phage identification tools. Video Abstract.
Collapse
Affiliation(s)
- Siu Fung Stanley Ho
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nicole E. Wheeler
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Andrew D. Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
28
|
Wang L, Yao H, Morgan DC, Lau KS, Leung SY, Ho JWK, Leung WK. Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori. Nat Commun 2023; 14:2196. [PMID: 37069161 PMCID: PMC10110541 DOI: 10.1038/s41467-023-37975-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
Transient gut microbiota alterations have been reported after antibiotic therapy for Helicobacter pylori. However, alteration in the gut virome after H. pylori eradication remains uncertain. Here, we apply metagenomic sequencing to fecal samples of 44 H. pylori-infected patients at baseline, 6-week (N = 44), and 6-month (N = 33) after treatment. Following H. pylori eradication, we discover contraction of the gut virome diversity, separation of virome community with increased community difference, and shifting towards a higher proportion of core virus. While the gut microbiota is altered at 6-week and restored at 6-month, the virome community shows contraction till 6-month after the treatment with enhanced phage-bacteria interactions at 6-week. Multiple courses of antibiotic treatments further lead to lower virus community diversity when compared with treatment naive patients. Our results demonstrate that H. pylori eradication therapies not only result in transient alteration in gut microbiota but also significantly alter the previously less known gut virome community.
Collapse
Affiliation(s)
- Lingling Wang
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Haobin Yao
- School of Biomedical Science, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science Park, Hong Kong, China
| | - Daniel C Morgan
- School of Biomedical Science, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science Park, Hong Kong, China
| | - Kam Shing Lau
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Suet Yi Leung
- Centre for PanorOmic Sciences (CPOS), The University of Hong Kong, Pokfulam, Hong Kong, China
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Joshua W K Ho
- School of Biomedical Science, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science Park, Hong Kong, China
- Centre for PanorOmic Sciences (CPOS), The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Wai K Leung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
29
|
Qi Q, Ghaly TM, Penesyan A, Rajabal V, Stacey JA, Tetu SG, Gillings MR. Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4870-4879. [PMID: 36912846 DOI: 10.1021/acs.est.2c09739] [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: 06/18/2023]
Abstract
Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.
Collapse
Affiliation(s)
- Qin Qi
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Jeremy Ac Stacey
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
30
|
Yang J, Shan G, Yu G, Wei J, Zhang Q, Su W, Lin Q, Zheng Z, Wu G, Li G, Chang Q, Yuan H, He Y, Chen Y, Zhang Y, Huang H, Hu W, Song R, Weng Y, Li X, Liu S. Whole genome sequencing of multidrug-resistant Proteus mirabilis strain PM1162 recovered from a urinary tract infection in China. J Glob Antimicrob Resist 2023; 33:44-50. [PMID: 36870531 DOI: 10.1016/j.jgar.2023.02.014] [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: 10/20/2022] [Revised: 01/26/2023] [Accepted: 02/19/2023] [Indexed: 03/06/2023] Open
Abstract
OBJECTIVES Proteus mirabilis is an important opportunistic Gram-negative pathogen. This study reports the whole genome sequence of multidrug-resistant (MDR) P. mirabilis PM1162 and explores its antibiotic resistance genes (ARGs) and their genetic environments. METHODS P. mirabilis PM1162 was isolated from a urinary tract infection in China. Antimicrobial susceptibility was determined, and whole genome sequencing (WGS) was performed. ARGs, insertion sequence (IS) elements, and prophages were identified using ResFinder, ISfinder, and PHASTER software, respectively. Sequence comparisons and map generation were performed using BLAST and Easyfig, respectively. RESULTS On its chromosome, P. mirabilis PM1162 harboured 15 ARGs, including cat, tet(J), blaCTX-M-14 (three copies), aph(3')-Ia, qnrB4, blaDHA-1, qacE, sul1, armA, msr(E), mph(E), aadA1, and dfrA1. We focused our analysis on the four related MDR regions: (1) genetic contexts associated with blaCTX-M-14; (2) the prophage containing blaDHA-1, qnrB4, and aph(3')-Ia; (3) genetic environments associated with mph(E), msr(E), armA, sul, and qacE; and (4) the class II integron harbouring dfrA1, sat2, and aadA1. CONCLUSION This study reported the whole genome sequence of MDR P. mirabilis PM1162 and the genetic context of its ARGs. This comprehensive genomic analysis of MDR P. mirabilis PM1162 provides a deeper understanding of its MDR mechanism and elucidates the horizontal spread of its ARGs, thus providing a basis for the containment and treatment of the bacteria.
Collapse
Affiliation(s)
- Jing Yang
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Ge Shan
- Department of Urology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Guangchao Yu
- Department of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jie Wei
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Qinghuan Zhang
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wen Su
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Qiuping Lin
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Zhixiong Zheng
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Guangliang Wu
- Department of Pharmacy, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Guangtian Li
- Department of Anesthesiology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Qing Chang
- Medical Department, Hengqin Branch of Zhuhai People's Hospital, Zhuhai, China
| | - Hong Yuan
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yanju He
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yanling Chen
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yi Zhang
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Haile Huang
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Wan Hu
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Rongqing Song
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yuqing Weng
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China.
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China.
| | - Shengming Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| |
Collapse
|
31
|
Ji Y, Xi H, Zhao Z, Jiang Q, Chen C, Wang X, Li F, Li N, Sun C, Feng X, Lei L, Han W, Gu J. Metagenomics analysis reveals potential pathways and drivers of piglet gut phage-mediated transfer of ARGs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160304. [PMID: 36427721 DOI: 10.1016/j.scitotenv.2022.160304] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
The growing prevalence of antibiotic-resistant pathogens has led to a better understanding of the underlying processes that lead to this expansion. Intensive pig farms are considered one of the hotspots for antibiotic resistance gene (ARG) transmission. Phages, as important mobile carriers of ARGs, are widespread in the animal intestine. However, our understanding of phage-associated ARGs in the pig intestine and their underlying drivers is limited. Here, metagenomic sequencing and analysis of viral DNA and total DNA of different intestinal (ileum, cecum and feces) contents in healthy piglets and piglets with diarrhea were separately conducted. We found that phages in piglet ceca are the main repository for ARGs and mobile genetic element (MGE) genes. Phage-associated MGEs are important factors affecting the maintenance and transfer of ARGs. Interestingly, the colocalization of ARGs and MGE genes in piglet gut phages does not appear to be randomly selected but rather related to a specific phage host (Streptococcus). In addition, in the feces of piglets with diarrhea, the abundance of phages carrying ARGs and MGE genes was significantly increased, as was the diversity of polyvalent phages (phages with broad host ranges), which would facilitate the transfection and wider distribution of ARGs in the bacterial community. Moreover, the predicted host spectrum of polyvalent phages in diarrheal feces tended to be potential enteropathogenic genera, which greatly increased the risk of enteropathogens acquiring ARGs. Notably, we also found ARG-homologous genes in the sequences of piglet intestinal mimiviruses, suggesting that the piglet intestinal mimiviruses are a potential repository of ARGs. In conclusion, this study greatly expands our knowledge of the piglet gut microbiome, revealing the underlying mechanisms of maintenance and dissemination of piglet gut ARGs and providing a reference for the prevention and control of ARG pollution in animal husbandry.
Collapse
Affiliation(s)
- Yalu Ji
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Hengyu Xi
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Zhen Zhao
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Qiujie Jiang
- Jilin Animal Disease Control Center, Changchun 130062, People's Republic of China
| | - Chong Chen
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Xinwu Wang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Fengyang Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Na Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Changjiang Sun
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Xin Feng
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Liancheng Lei
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Wenyu Han
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, People's Republic of China.
| | - Jingmin Gu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, People's Republic of China.
| |
Collapse
|
32
|
Zhang F, Wu S, Dai J, Huang J, Zhang J, Zhao M, Rong D, Li Y, Wang J, Chen M, Xue L, Ding Y, Wu Q. The emergence of novel macrolide resistance island in Macrococcus caseolyticus and Staphylococcus aureus of food origin. Int J Food Microbiol 2023; 386:110020. [PMID: 36427466 DOI: 10.1016/j.ijfoodmicro.2022.110020] [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: 07/10/2022] [Revised: 10/11/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
Abstract
Food-derived Staphylococcaceae species with severe antimicrobial resistance, especially Staphylococcus aureus, is a major threat to public health. Macrococcus caseolyticus (M. caseolyticus) is a member of the Staphylococcaceae family which plays a vital role in fermented products and disease causation in animals. In our previous study, several Staphylococcus aureus antibiotic-resistant island msr (SaRImsr) were found in multidrug-resistant S. aureus. In this study, novel SaRImsr, SaRImsr-III emerged from S. aureus. Another novel SaRImsr-like further emerged in M. caseolyticus from food. These isolates' prevalence and genetic environment were investigated and characterized to understand the distribution and transmission of these novel SaRImsr strains. All SaRImsr-positive S. aureus isolates exhibited a multidrug resistance (MDR) phenotype, within which a series of antimicrobial resistance genes (ARGs) and virulence factor genes (VFs) were identified. In addition, three SaRImsr types, SaRImsr-I (15.1 kb), SaRImsr-II (16-17 kb), and SaRImsr-III (18 kb) carrying mef(D)-msr(F), were identified in these isolates' chromosomes. SaRImsr-(I-III) contains a site-specific integrase gene int and operon mef(D)-msr(F). SaRImsr-III has an additional orf3-orf4-IS30 arrangement downstream of mef(D) and msr(F). Moreover, the SaRImsr-like and macrolide-resistant transposon Tn6776 forming a novel mosaic structure coexisted in one M. caseolyticus isolate. Within this mosaic structure, the macrolide-resistant genes mef(D)-msr(F) were absent in SaRImsr-like, whereas an operon, mef(F)-msr(G), was identified in Tn6776. The SaRImsr-(I-III) and SaRImsr-like structure were inserted into the rpsI gene encoding the 30S ribosomal protein S9 in the chromosome. Excision and cyclisation of SaRImsr-III, SaRImsr-like, operon mef(D)-msr(F), and orf3-orf4-IS30 arrangements were confirmed using two-step PCR. This study is the first to report MDR S. aureus harbouring novel SaRImsr-III and M. caseolyticus containing novel mosaic structures isolated from retail foods. Similar SaRImsr-type resistant islands' occurrence and propagation in Staphylococcaceae species require continuous monitoring and investigation.
Collapse
Affiliation(s)
- Feng Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China; School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Shi Wu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Jingsha Dai
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Jiahui Huang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Jumei Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Miao Zhao
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Dongli Rong
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Yuanyu Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou 510432, China
| | - Moutong Chen
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Liang Xue
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Yu Ding
- Department of Food Science & Technology, Jinan University, Guangzhou 510632, China.
| | - Qingping Wu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China.
| |
Collapse
|
33
|
Blanco-Picazo P, Morales-Cortes S, Ramos-Barbero MD, García-Aljaro C, Rodríguez-Rubio L, Muniesa M. Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources. THE ISME JOURNAL 2023; 17:195-203. [PMID: 36289309 PMCID: PMC9860054 DOI: 10.1038/s41396-022-01338-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
The growth of antibiotic resistance has stimulated interest in understanding the mechanisms by which antibiotic resistance genes (ARG) are mobilized. Among them, studies analyzing the presence of ARGs in the viral fraction of environmental, food and human samples, and reporting bacteriophages as vehicles of ARG transmission, have been the focus of increasing research. However, it has been argued that in these studies the abundance of phages carrying ARGs has been overestimated due to experimental contamination with non-packaged bacterial DNA or other elements such as outer membrane vesicles (OMVs). This study aims to shed light on the extent to which phages, OMVs or contaminating non-packaged DNA contribute as carriers of ARGs in the viromes. The viral fractions of three types of food (chicken, fish, and mussels) were selected as sources of ARG-carrying phage particles, whose ability to infect and propagate in an Escherichia coli host was confirmed after isolation. The ARG-containing fraction was further purified by CsCl density gradient centrifugation and, after removal of DNA outside the capsids, ARGs inside the particles were confirmed. The purified fraction was stained with SYBR Gold, which allowed the visualization of phage capsids attached to and infecting E. coli cells. Phages with Myoviridae and Siphoviridae morphology were observed by electron microscopy. The proteins in the purified fraction belonged predominantly to phages (71.8% in fish, 52.9% in mussels, 78.7% in chicken sample 1, and 64.1% in chicken sample 2), mainly corresponding to tail, capsid, and other structural proteins, whereas membrane proteins, expected to be abundant if OMVs were present, accounted for only 3.8-21.4% of the protein content. The predominance of phage particles in the viromes supports the reliability of the protocols used in this study and in recent findings on the abundance of ARG-carrying phage particles.
Collapse
Affiliation(s)
- Pedro Blanco-Picazo
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain
| | - Sara Morales-Cortes
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain
| | - María Dolores Ramos-Barbero
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain ,grid.5268.90000 0001 2168 1800Departmento de Fisiologia, Genética y Microbiología, Universidad de Alicante (UA), 03080 Alicante, Spain
| | - Cristina García-Aljaro
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain
| | - Maite Muniesa
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain
| |
Collapse
|
34
|
Silva V, Araújo S, Monteiro A, Eira J, Pereira JE, Maltez L, Igrejas G, Lemsaddek TS, Poeta P. Staphylococcus aureus and MRSA in Livestock: Antimicrobial Resistance and Genetic Lineages. Microorganisms 2023; 11:microorganisms11010124. [PMID: 36677414 PMCID: PMC9865216 DOI: 10.3390/microorganisms11010124] [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: 12/21/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Animal production is associated with the frequent use of antimicrobial agents for growth promotion and for the prevention, treatment, and control of animal diseases, thus maintaining animal health and productivity. Staphylococcus aureus, in particular methicillin-resistant S. aureus (MRSA), can cause a variety of infections from superficial skin and soft tissue infections to life-threatening septicaemia. S. aureus represents a serious public health problem in hospital and community settings, as well as an economic and animal welfare problem. Livestock-associated MRSA (LA-MRSA) was first described associated with the sequence (ST) 398 that was grouped within the clonal complex (CC) 398. Initially, LA-MRSA strains were restricted to CC398, but over the years it has become clear that its diversity is much greater and that it is constantly changing, a trend increasingly associated with multidrug resistance. Therefore, in this review, we aimed to describe the main clonal lineages associated with different production animals, such as swine, cattle, rabbits, and poultry, as well as verify the multidrug resistance associated with each animal species and clonal lineage. Overall, S. aureus ST398 still remains the most common clone among livestock and was reported in rabbits, goats, cattle, pigs, and birds, often together with spa-type t011. Nevertheless, a wide diversity of clonal lineages was reported worldwide in livestock.
Collapse
Affiliation(s)
- Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisbon, Portugal
| | - Sara Araújo
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Andreia Monteiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - José Eira
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - José Eduardo Pereira
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Luís Maltez
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisbon, Portugal
| | - Teresa Semedo Lemsaddek
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Av. Universidade Técnica de Lisboa, 1300-477 Lisboa, Portugal
- Correspondence: (T.S.L.); (P.P.)
| | - Patricia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Correspondence: (T.S.L.); (P.P.)
| |
Collapse
|
35
|
Li S, Wu Y, Zheng H, Li H, Zheng Y, Nan J, Ma J, Nagarajan D, Chang JS. Antibiotics degradation by advanced oxidation process (AOPs): Recent advances in ecotoxicity and antibiotic-resistance genes induction of degradation products. CHEMOSPHERE 2023; 311:136977. [PMID: 36309060 DOI: 10.1016/j.chemosphere.2022.136977] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/09/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic contamination could cause serious risks of ecotoxicity and resistance gene induction. Advanced oxidation processes (AOPs) such as Fenton, photocatalysis, activated persulfate, electrochemistry and other AOPs technologies have been proven effective in the degradation of high-risk, refractory organic pollutants such as antibiotics. However, due to the limited mineralization ability, a large number of degradation intermediates will be produced in the oxidation process. The residual or undiscovered ecological risks of degradation products are potential safety hazards and problems necessitating comprehensive studies. In-depth investigations especially on the full assessments of ecotoxicity and resistance genes induction capability of antibiotic degradation products are important issues in reducing the environmental problems of antibiotics. Therefore, this review presents an overview of the current knowledge on the efficiency of different AOPs systems in reducing antibiotics toxicity and antibiotic resistance.
Collapse
Affiliation(s)
- Shuo Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China; Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Yanan Wu
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Heshan Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China.
| | - Hongbin Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Yongjie Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Jun Nan
- Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jun Ma
- Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Dillirani Nagarajan
- Department of Chemical Engineering, National Cheng-Kung University, Tainan, Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng-Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung, 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, 407, Taiwan; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, Taiwan.
| |
Collapse
|
36
|
Zhu Y, Shang J, Peng C, Sun Y. Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework. Front Microbiol 2022; 13:1032186. [PMID: 36590402 PMCID: PMC9800612 DOI: 10.3389/fmicb.2022.1032186] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to (viral) metagenomic sequencing, a large number of new bacteriophages have been discovered. However, lacking a standard and automatic virus classification pipeline, the taxonomic characterization of new viruses seriously lag behind the sequencing efforts. In particular, according to the latest version of ICTV, several large phage families in the previous classification system are removed. Therefore, a comprehensive review and comparison of taxonomic classification tools under the new standard are needed to establish the state-of-the-art. In this work, we retrained and tested four recently published tools on newly labeled databases. We demonstrated their utilities and tested them on multiple datasets, including the RefSeq, short contigs, simulated metagenomic datasets, and low-similarity datasets. This study provides a comprehensive review of phage family classification in different scenarios and a practical guidance for choosing appropriate taxonomic classification pipelines. To our best knowledge, this is the first review conducted under the new ICTV classification framework. The results show that the new family classification framework overall leads to better conserved groups and thus makes family-level classification more feasible.
Collapse
|
37
|
Yang Y, Li L, Huang F, Hu X, Cao X, Mi J, Liao X, Xing S. The fate of antibiotic resistance genes and their association with bacterial and archaeal communities during advanced treatment of pig farm wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158364. [PMID: 36041618 DOI: 10.1016/j.scitotenv.2022.158364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Advanced wastewater treatment plants are widely used in most large-scale pig farms in southern China. However, the fate of antibiotic resistance genes (ARGs) and their association with bacterial and archaeal communities during advanced wastewater treatment remain unclear. In this study, the profiles of ARGs in typical advanced wastewater treatment plants were surveyed using metagenomic analysis. The results showed that 279- 326 different subtypes of ARGs were detected in raw wastewater, with a total abundance of 5.98 ± 0.48 copies per bacterial cell. During the advanced wastewater treatment, the abundance and number of ARGs were significantly reduced. Microbial communities (bacteria and archaea) contributed the most to the variation in ARG abundance and composition (PCA axis_1), accounting for 10.8 % and 15.7 %, respectively, followed by mobile genetic elements (MGEs) and physicochemical factors. Special attention should be given to potential pathogenic bacteria such as Escherichia, Streptococcus, Enterococcus and Staphylococcus and archaea such as Methanocorpusculum, Candidatus Methanoplasma and Candidatus Methanomethylophilus, which were important potential ARG hosts. Bacterial communities may indirectly affect ARG variation by affecting archaeal communities. These findings indicated that ARG levels in pig farm wastewater can be effectively reduced during advanced treatment and highlighted the important role played by archaea, which should not be ignored.
Collapse
Affiliation(s)
- Yiwen Yang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Linfei Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Feng Huang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Xinwen Hu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Xinwei Cao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Jiandui Mi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xindi Liao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Sicheng Xing
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
38
|
Abstract
Antibiotic resistance is rapidly spreading via the horizontal transfer of resistance genes in mobile genetic elements. While plasmids are key drivers of this process, few integrative phages encode antibiotic resistance genes. Here, we find that phage-plasmids, elements that are both phages and plasmids, often carry antibiotic resistance genes. We found 60 phage-plasmids with 184 antibiotic resistance genes, providing resistance for broad-spectrum-cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, and colistin. These genes are in a few hot spots, seem to have been cotranslocated with transposable elements, and are often in class I integrons, which had not been previously found in phages. We tried to induce six phage-plasmids with resistance genes (including four with resistance integrons) and succeeded in five cases. Other phage-plasmids and integrative prophages were coinduced in these experiments. As a proof of concept, we focused on a P1-like element encoding an extended spectrum β-lactamase, blaCTX-M-55. After induction, we confirmed that it is capable of infecting and converting four other E. coli strains. Its reinduction led to the further conversion of a sensitive strain, confirming that it is a fully functional phage. This study shows that phage-plasmids carry a large diversity of clinically relevant antibiotic resistance genes that they can transfer across bacteria. As plasmids, these elements seem plastic and capable of acquiring genes from other plasmids. As phages, they may provide novel paths of transfer for resistance genes because they can infect bacteria that are distant in time and space from the original host. As a matter of alarm, they may also mediate transfer to other types of phages.
Collapse
|
39
|
Zhang Y, Guo Y, Qiu T, Gao M, Wang X. Bacteriophages: Underestimated vehicles of antibiotic resistance genes in the soil. Front Microbiol 2022; 13:936267. [PMID: 35992716 PMCID: PMC9386270 DOI: 10.3389/fmicb.2022.936267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteriophages (phages), the most abundant biological entities on Earth, have a significant effect on the composition and dynamics of microbial communities, biogeochemical cycles of global ecosystems, and bacterial evolution. A variety of antibiotic resistance genes (ARGs) have been identified in phage genomes in different soil samples. Phages can mediate the transfer of ARGs between bacteria via transduction. Recent studies have suggested that anthropogenic activities promote phage-mediated horizontal gene transfer events. Therefore, the role of phages in the dissemination of ARGs, which are a potential threat to human health, may be underestimated. However, the contribution of phages to the transfer of ARGs is still poorly understood. Considering the growing and wide concerns of antibiotic resistance, phages should be considered a research focus in the mobile resistome. This review aimed to provide an overview of phages as vehicles of ARGs in soil. Here, we summarized the current knowledge on the diversity and abundance of ARGs in soilborne phages and analyzed the contribution of phages to the horizontal transfer of ARGs. Finally, research deficiencies and future perspectives were discussed. This study provides a reference for preventing and controlling ARG pollution in agricultural systems.
Collapse
|
40
|
Proteome Exploration of
Legionella pneumophila
To Identify Novel Therapeutics: a Hierarchical Subtractive Genomics and Reverse Vaccinology Approach. Microbiol Spectr 2022; 10:e0037322. [PMID: 35863001 PMCID: PMC9430848 DOI: 10.1128/spectrum.00373-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Legionella pneumophila
is a human pathogen distributed worldwide, causing Legionnaires’ disease (LD), a severe form of pneumonia and respiratory tract infection.
L. pneumophila
is emerging as an antibiotic-resistant strain, and controlling LD is now difficult. Hence, developing novel drugs and vaccines against
L. pneumophila
is a major research priority.
Collapse
|
41
|
Cao Y, Zhao J, Wang Q, Bai S, Yang Q, Wei Y, Wang R. Industrial aerobic composting and the addition of microbial agents largely reduce the risks of heavy metal and ARG transfer through livestock manure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 239:113694. [PMID: 35644095 DOI: 10.1016/j.ecoenv.2022.113694] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/08/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Composting is an effective and necessary modality in the recycling of agricultural wastes such as livestock manure, furfural, and straw. However, the risks of heavy metals (HMs) and antibiotic resistance genes (ARGs) during industrial-scale composting process have not been adequately assessed, especially with the addition of bacterial agents. In this study, changes in HMs toxicity, ARGs propagation and microbial community structure during industrial-scale aerobic composting of livestock manure were firstly investigated with various substrates addition. Moreover, the effect of the addition of bacterial agents (Bacillus strains) was evaluated. The results showed that industrial aerobic composting process could immobilize various HMs with different extents and significantly reduce the levels of ARGs such as intl1 and oqxB genes. The addition of Bacillus strains could further reduce the levels of most detected ARGs and the bioavailability of Cu and Cr, and the relative abundance of ereA and tetA was undetectable in some materials. After composting, the main bacterial community structures were similar among different substrates irrespective of bacterial agents and indicated that the composting process was the main driver for their change. This study provides a scientific reference for the safe reuse of livestock manure.
Collapse
Affiliation(s)
- Yu Cao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Jihong Zhao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qianqian Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Shuang Bai
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China.
| | - Yixuan Wei
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Ruifei Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
| |
Collapse
|
42
|
Cao Z, Sugimura N, Burgermeister E, Ebert MP, Zuo T, Lan P. The gut virome: A new microbiome component in health and disease. EBioMedicine 2022; 81:104113. [PMID: 35753153 PMCID: PMC9240800 DOI: 10.1016/j.ebiom.2022.104113] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/14/2022] [Accepted: 05/30/2022] [Indexed: 12/19/2022] Open
Abstract
The human gastrointestinal tract harbours an abundance of viruses, collectively known as the gut virome. The gut virome is highly heterogeneous across populations and is linked to geography, ethnicity, diet, lifestyle, and urbanisation. The currently known function of the gut virome varies greatly across human populations, and much remains unknown. We review current literature on the human gut virome, and the intricate trans-kingdom interplay among gut viruses, bacteria, and the mammalian host underlying health and diseases. We summarise evidence on the use of the gut virome as diagnostic markers and a therapeutic target. We shed light on novel avenues of microbiome-inspired diagnosis and therapies. We also review pre-clinical and clinical studies on gut virome-rectification-based therapies, including faecal microbiota transplantation, faecal virome transplantation, and refined phage therapy. Our review suggests that future research effort should focus on unravelling the mechanisms exerted by gut viruses/phages in human pathophysiology, and on developing phage-prompted precision therapies.
Collapse
Affiliation(s)
- Zhirui Cao
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China; Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Naoki Sugimura
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Elke Burgermeister
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; DKFZ-Hector Cancer Institute, Mannheim, Germany; Mannheim Cancer Centre (MCC), University Medical Centre Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tao Zuo
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China; Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Ping Lan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China; Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
43
|
The Notable Achievements and the Prospects of Bacterial Pathogen Genomics. Microorganisms 2022; 10:microorganisms10051040. [PMID: 35630482 PMCID: PMC9148168 DOI: 10.3390/microorganisms10051040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 05/16/2022] [Indexed: 02/04/2023] Open
Abstract
Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and evolution of these pathogens. In this review, we discuss how the short- (Illumina) and long-read (PacBio, Oxford Nanopore) sequencing technologies have shaped the discipline of bacterial pathogen genomics, in terms of fundamental research (i.e., evolution of pathogenicity), forensics, food safety, and routine clinical microbiology. We have mined and discuss some of the most prominent data/bioinformatics resources such as NCBI pathogens, PATRIC, and Pathogenwatch. Based on this mining, we present some of the most popular sequencing technologies, hybrid approaches, assemblers, and annotation pipelines. A small number of bacterial pathogens are of very high importance, and we also present the wealth of the genomic data for these species (i.e., which ones they are, the number of antimicrobial resistance genes per genome, the number of virulence factors). Finally, we discuss how this discipline will probably be transformed in the near future, especially by transitioning into metagenome-assembled genomes (MAGs), thanks to long-read sequencing.
Collapse
|
44
|
Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection. Nat Ecol Evol 2022; 6:555-564. [PMID: 35347261 DOI: 10.1038/s41559-022-01705-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/17/2022] [Indexed: 12/30/2022]
Abstract
The spread of genes encoding antibiotic resistance is often mediated by horizontal gene transfer (HGT). Many of these genes are associated with transposons, a type of mobile genetic element that can translocate between the chromosome and plasmids. It is widely accepted that the translocation of antibiotic resistance genes onto plasmids potentiates their spread by HGT. However, it is unclear how this process is modulated by environmental factors, especially antibiotic treatment. To address this issue, we asked whether antibiotic exposure would select for the transposition of resistance genes from chromosomes onto plasmids and, if so, whether antibiotic concentration could tune the distribution of resistance genes between chromosomes and plasmids. We addressed these questions by analysing the transposition dynamics of synthetic and natural transposons that encode resistance to different antibiotics. We found that stronger antibiotic selection leads to a higher fraction of cells carrying the resistance on plasmids because the increased copy number of resistance genes on multicopy plasmids leads to higher expression of those genes and thus higher cell survival when facing antibiotic selection. Once they have transposed to plasmids, antibiotic resistance genes are primed for rapid spread by HGT. Our results provide quantitative evidence for a mechanism by which antibiotic selection accelerates the spread of antibiotic resistance in microbial communities.
Collapse
|
45
|
Blanco-Picazo P, Gómez-Gómez C, Aguiló-Castillo S, Fernández-Orth D, Cerdà-Cuéllar M, Muniesa M, Rodríguez-Rubio L. Chicken liver is a potential reservoir of bacteriophages and phage-derived particles containing antibiotic resistance genes. Microb Biotechnol 2022; 15:2464-2475. [PMID: 35485188 PMCID: PMC9437878 DOI: 10.1111/1751-7915.14056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/15/2022] [Indexed: 11/30/2022] Open
Abstract
Poultry meat production is one of the most important agri‐food industries in the world. The selective pressure exerted by widespread prophylactic or therapeutic use of antibiotics in intensive chicken farming favours the development of drug resistance in bacterial populations. Chicken liver, closely connected with the intestinal tract, has been directly involved in food‐borne infections and found to be contaminated with pathogenic bacteria, including Campylobacter and Salmonella. In this study, 74 chicken livers, divided into sterile and non‐sterile groups, were analysed, not only for microbial indicators but also for the presence of phages and phage particles containing antibiotic resistance genes (ARGs). Both bacteria and phages were detected in liver tissues, including those dissected under sterile conditions. The phages were able to infect Escherichia coli and showed a Siphovirus morphology. The chicken livers contained from 103 to 106 phage particles per g, which carried a range of ARGs (blaTEM, blaCTx‐M‐1, sul1, qnrA, armA and tetW) detected by qPCR. The presence of phages in chicken liver, mostly infecting E. coli, was confirmed by metagenomic analysis, although this technique was not sufficiently sensitive to identify ARGs. In addition, ARG‐carrying phages were detected in chicken faeces by qPCR in a previous study of the group. Comparison of the viromes of faeces and liver showed a strong coincidence of species, which suggests that the phages found in the liver originate in faeces. These findings suggests that phages, like bacteria, can translocate from the gut to the liver, which may therefore constitute a potential reservoir of antibiotic resistance genes.
Collapse
Affiliation(s)
- Pedro Blanco-Picazo
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Planta 0, Barcelona, 08028, Spain
| | - Clara Gómez-Gómez
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Planta 0, Barcelona, 08028, Spain
| | - Sergi Aguiló-Castillo
- Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Barcelona Supercomputing Center, Barcelona, Spain
| | - Dietmar Fernández-Orth
- Department of Bioinformatics and Molecular Biology, Cerba Internacional Pl. Ramon Llull, 7-10, Sabadell, Barcelona, 08203, Spain
| | - Marta Cerdà-Cuéllar
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Maite Muniesa
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Planta 0, Barcelona, 08028, Spain
| | - Lorena Rodríguez-Rubio
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Planta 0, Barcelona, 08028, Spain
| |
Collapse
|
46
|
Chang MX, Zhang J, Zhang JF, Ding XM, Lu Y, Zhang J, Li R, Jiang HX. Formation, Transmission, and Dynamic Evolution of a Multidrug-Resistant Chromosomally Integrated Plasmid in Salmonella Spp. Front Microbiol 2022; 13:846954. [PMID: 35464949 PMCID: PMC9019673 DOI: 10.3389/fmicb.2022.846954] [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: 12/31/2021] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
IncHI2 plasmids, possessing high flexibility and genetic plasticity, play a vital role in the acquisition and transmission of resistance determinants. Polymorphic mobile genetic elements (MGEs) generated by a chromosomally integrated IncHI2 plasmid in an individual Salmonella isolate have not yet been detected, and the mechanisms of the formation, excision, and dynamic evolution of a multidrug-resistant chromosomally integrated plasmid (MRCP) have remained obscure. Herein, we identified a 260-kb blaCTX–M–55-qnrS1-bearing IncHI2 plasmid within a Salmonella Muenster strain. Plenty of heterogeneous MGEs (new Escherichia coli chromosomally integrated plasmid or circular plasmids with different profiles) were yielded when this MRCP was conjugated into E. coli J53 with a transfer frequency of 10–4–10–5 transconjugants per donor. A bioinformatic analysis indicated that replicative transposition and homologous recombination of IS26 elements were particularly active, and the truncated Tn1721 also played a vital role in the formation of MRCP offspring. More importantly, when released from the chromosome, MRCP could capture and co-transfer adjacent chromosomal segments to form larger plasmid progeny than itself. Stability and growth kinetics assays showed that the biological characteristics of MRCP progeny were differentiated. This study provides an insight into a flexible existence of MRCP. The conversion between vertical and horizontal transmission endowed MRCP with genetic stability as a chromosomal coding structure and transferability as extra-chromosomal elements. This alternation may accelerate the acquisition and persistence of antibiotic resistance of clinical pathogens and enhance their ability to respond to adverse environments, which poses a great challenge to the traditional antibiotic treatment.
Collapse
Affiliation(s)
- Man-Xia Chang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jing Zhang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jin-Fei Zhang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao-Min Ding
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yang Lu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jie Zhang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| |
Collapse
|
47
|
Lu J, Zhang Y, Wu J, Wang J. Intervention of antimicrobial peptide usage on antimicrobial resistance in aquaculture. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:128154. [PMID: 34979393 DOI: 10.1016/j.jhazmat.2021.128154] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/08/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance genes (ARGs) widely exist in diverse matrices to pose potential risks and attract global attention. This study performed tilapia-cultivation experiment to discuss the intervention of antimicrobial peptide usage on antimicrobial resistance in aquaculture by analyzing 29 target ARGs in water, residue, and fish muscle samples. The sul1 gene was the dominant ARG in most of samples while absolute abundances of total ARGs were in the range of 1.5 × 102-2.3 × 107 copies/mL in water samples and 2.1 × 108-3.9 × 109 copies/g in the residue and fish muscle samples. Compared with antibiotic treatment, the cecropin treatment could significantly reduce the absolute abundance of ARGs and intI1 in all samples. Proteobacteria were the dominant phylum for most of samples while Aeromonas/Cetobacterium served as the dominant genus for samples with antibiotic/cecropin treatment. Network analysis showed that cecropin treatment could significantly reduce occurrence of multi-drug resistant bacteria and the correlation between genera and ARGs. Results of partial least squares structural equation modeling which was used to discuss the influential factors of ARGs exhibited that antibiotics could increase ARGs, further proving that cecropin peptide could effectively reduce ARGs in aquaculture. This study will provide important information on controlling ARGs in aquaculture in terms of antimicrobial peptide application.
Collapse
Affiliation(s)
- Jian Lu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, People's Republic of China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, People's Republic of China
| | - Yuxuan Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, People's Republic of China
| | - Jun Wu
- Yantai Research Institute, Harbin Engineering University, Yantai 264006, People's Republic of China.
| | - Jianhua Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, People's Republic of China
| |
Collapse
|
48
|
Vázquez R, Díez-Martínez R, Domingo-Calap P, García P, Gutiérrez D, Muniesa M, Ruiz-Ruigómez M, Sanjuán R, Tomás M, Tormo-Mas MÁ, García P. Essential Topics for the Regulatory Consideration of Phages as Clinically Valuable Therapeutic Agents: A Perspective from Spain. Microorganisms 2022; 10:microorganisms10040717. [PMID: 35456768 PMCID: PMC9025261 DOI: 10.3390/microorganisms10040717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 01/08/2023] Open
Abstract
Antibiotic resistance is one of the major challenges that humankind shall face in the short term. (Bacterio)phage therapy is a valuable therapeutic alternative to antibiotics and, although the concept is almost as old as the discovery of phages, its wide application was hindered in the West by the discovery and development of antibiotics in the mid-twentieth century. However, research on phage therapy is currently experiencing a renaissance due to the antimicrobial resistance problem. Some countries are already adopting new ad hoc regulations to favor the short-term implantation of phage therapy in clinical practice. In this regard, the Phage Therapy Work Group from FAGOMA (Spanish Network of Bacteriophages and Transducing Elements) recently contacted the Spanish Drugs and Medical Devices Agency (AEMPS) to promote the regulation of phage therapy in Spain. As a result, FAGOMA was asked to provide a general view on key issues regarding phage therapy legislation. This review comes as the culmination of the FAGOMA initiative and aims at appropriately informing the regulatory debate on phage therapy.
Collapse
Affiliation(s)
- Roberto Vázquez
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium;
| | | | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain; (P.D.-C.); (R.S.)
| | - Pedro García
- Center for Biological Research Margarita Salas (CIB-CSIC) and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 28040 Madrid, Spain;
| | - Diana Gutiérrez
- Telum Therapeutics SL, 31110 Noáin, Spain; (R.D.-M.); (D.G.)
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, 08028 Barcelona, Spain;
| | - María Ruiz-Ruigómez
- Internal Medicine, Infectious Diseases Unit, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain;
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain; (P.D.-C.); (R.S.)
| | - María Tomás
- Department of Microbiology, Hospital Universitario de A Coruña (INIBIC-CHUAC, SERGAS), 15006 A Coruña, Spain;
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María Ángeles Tormo-Mas
- Severe Infection Group, Hospital Universitari i Politècnic La Fe, Health Research Institute Hospital La Fe, IISLaFe, 46026 Valencia, Spain;
| | - Pilar García
- Dairy Research Institute of Asturias, IPLA-CSIC, 33300 Villaviciosa, Spain
- DairySafe Group, Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
- Correspondence:
| |
Collapse
|
49
|
Abdallah R, Kuete Yimagou E, Hadjadj L, Mediannikov O, Ibrahim A, Davoust B, Barciela A, Hernandez-Aguilar RA, Diatta G, Sokhna C, Raoult D, Rolain JM, Baron SA. Population Diversity of Antibiotic Resistant Enterobacterales in Samples From Wildlife Origin in Senegal: Identification of a Multidrug Resistance Transposon Carrying blaCTX–M–15 in Escherichia coli. Front Microbiol 2022; 13:838392. [PMID: 35369484 PMCID: PMC8971907 DOI: 10.3389/fmicb.2022.838392] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/18/2022] [Indexed: 01/08/2023] Open
Abstract
Introduction The role of wildlife in the transmission of antimicrobial resistant (AMR) is suspected but scarcely reported in current studies. Therefore, we studied the dynamics and prevalence of antibiotic-resistant Enterobacterales in antibiotic-limited areas of Senegal. Materials and Methods We collected fecal samples from monkeys and apes (N = 226) and non-fecal environmental samples (N = 113) from Senegal in 2015 and 2019. We grew the samples on selective media, subsequently isolated AMR Enterobacterales, and then sequenced their genomes. Results We isolated 72 different Enterobacterales among which we obtained a resistance rate of 65% for colistin (N = 47/72) and 29% for third generation-cephalosporin (C3G) (29%, N = 21/72). Interestingly, almost 46% of our isolates, among Enterobacter sp., Citrobacter cronae and Klebsiella aerogenes, belong to 34 new STs. Moreover, the genes blaCTX–M–15, blaTEM1B, sul2, dfrA14, qnrs, aph(3′′), aph(6), tetA, and tetR harbored within a transposon on the IncY plasmid of ST224 Escherichia coli were transferred and inserted into a ST10 E. coli phage coding region. Conclusion Wildlife constitutes a rich, unexplored reservoir of natural microbial diversity, AMR genes and international resistant clones pathogenic in humans. The presence of a transposon that carries AMR genes is intriguing since no antibiotics are used in the non-human primates we studied.
Collapse
Affiliation(s)
- Rim Abdallah
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Edmond Kuete Yimagou
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Linda Hadjadj
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Oleg Mediannikov
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ahmad Ibrahim
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard Davoust
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Amanda Barciela
- Dindefelo Biological Station, Jane Goodall Institute Spain and Senegal, Kedougou, Senegal
| | - R. Adriana Hernandez-Aguilar
- Dindefelo Biological Station, Jane Goodall Institute Spain and Senegal, Kedougou, Senegal
- Department of Social Psychology and Quantitative Psychology, Faculty of Psychology, Serra Hunter Programme, University of Barcelona, Barcelona, Spain
| | - Georges Diatta
- VITROME IRD 257, Campus International de Recherche IRD-UCAD de Hann, Dakar, Senegal
| | - Cheikh Sokhna
- IHU Méditerranée Infection, Marseille, France
- VITROME IRD 257, Campus International de Recherche IRD-UCAD de Hann, Dakar, Senegal
| | - Didier Raoult
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- *Correspondence: Sophie Alexandra Baron,
| |
Collapse
|
50
|
Mahdavi S, Sadeghi M, Shokri R, Sadegh B. The Role of Bacteriophages as Important Reservoirs of Extended-Spectrum Beta-Lactamase Genes in Azerbaijan Hospitals. Microb Drug Resist 2022; 28:436-443. [PMID: 35076323 DOI: 10.1089/mdr.2021.0163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aims: The aim of this study was to investigate the role of resident bacteriophages in hospital effluents, as a potential reservoir of extended-spectrum beta-lactamase (ESBL) genes. Methods: Effluent samples were collected from four major medical centers in Azerbaijan. Phage enrichments were prepared and purified using standard subculturing, amplification, and phage purification protocols. DNA materials from phage stocks and bacterial isolates were examined for the presence of ESBL genes using polymerase chain reaction. Restriction fragment length polymorphism (RFLP) profiles were used for the construction of a dendrogram and cluster analysis. Results: A total of 112 phage enrichments were obtained from 48 effluent samples against resident bacterial hosts. A total of 95 nonduplicate Gram-negative isolates were recovered from effluent samples. The most common isolate was Escherichia coli (n = 48), followed by Klebsiella pneumoniae (n = 18), Pseudomonas spp. (n = 9), and Enterobacter cloacae (n = 6). Thirty-two EcoRV-RFLP profiles consisting of ∼4 to 20 bands were obtained for the 40 E. coli phage enrichments. ESBL genes were detected in 23 of 40 (57.5%) E. coli phage enrichments, including blaCTX-M (n = 15), blaTEM (n = 14), and blaSHV (n = 6). Detected genes in phage enrichments against resident hosts other than E. coli include blaTEM (n = 4), blaCTX-M (n = 3), and blaSHV (n = 1). A total of 63 (66.3%) bacterial isolates were positive for tested genes, including blaCTX-M (n = 32), blaTEM (n = 61), and blaSHV (n = 12). The present research provides a strong evidence for the possible role of bacteriophages in antimicrobial resistance genes circulation in Azerbaijan clinical settings through generalized transduction. Conclusions: Our results showed a remarkable occurrence of ESBL genes in bacteriophage and bacterial population of effluent discharge, which clearly indicates that bacteriophages are an important factor in ESBL genes exchange among bacterial population through generalized transduction.
Collapse
Affiliation(s)
- Sahar Mahdavi
- Department of Microbiology, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Mohammadreza Sadeghi
- Department of Clinical Microbiology, Maku Branch, Islamic Azad University, Maku, Iran.,Department of Clinical Microbiology, Faculty of Medical Sciences, Urmia Branch, Islamic Azad University, Urmia, Iran
| | - Rasoul Shokri
- Department of Microbiology, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Babak Sadegh
- Department of Clinical Microbiology, Faculty of Medical Sciences, Urmia Branch, Islamic Azad University, Urmia, Iran
| |
Collapse
|