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Yu P, Guo X, Wang W, Wang L, Zhang H, Deng L, Yang H, He T, Wu P, Zhang Y. Distribution and driving mechanisms of antibiotic resistance genes in urbanized watersheds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176387. [PMID: 39317254 DOI: 10.1016/j.scitotenv.2024.176387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/12/2024] [Accepted: 09/17/2024] [Indexed: 09/26/2024]
Abstract
Antibiotic resistance genes (ARGs) have emerged as a global concern, posing significant threats to human health and safety. Understanding the contamination levels and driving mechanisms behind ARG proliferation is urgently needed. Urban watersheds, influenced by human activities, serve as critical reservoirs for ARGs; however, the impact of urbanization on ARG spread of and the underlying driving mechanisms remain unclear. This study evaluates the diversity and abundance of ARGs in water and sediment samples from the Jialing River watershed in Chongqing City, China. The obtained results indicate that aminoglycoside and multidrug ARGs are the primary contributors to ARG presence in both sediments and water. Additionally, the diversity and abundance of ARGs are higher in water than in sediments. ARGs in watershed show a significant positive correlation with mobile genetic elements (MGEs). While environmental factors in urbanized watersheds affect ARG abundance and distribution to some extent, they are not the primary drivers. Urbanization itself emerges as a prominent factor influencing ARG diversity and abundance in river basins. Specifically, livestock, healthcare, and agriculture are identified as the main social factors influencing ARG proliferation in the highly urbanized areas of the Jialing River watershed. Further investigation into other contributing social factors, such as industrial development, is warranted. This study reveals the factors driving ARG distribution in urbanized watersheds, providing a foundation for future efforts to maintain ecological health in these environments.
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Affiliation(s)
- Ping Yu
- College of Resources and Environment, Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, Chengdu 610225, PR China; Biogas Institute of Ministry of Agriculture and Rural Affairs, No. 13, Section 4, Renmin South Road, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Xujing Guo
- College of Resources and Environment, Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, Chengdu 610225, PR China
| | - Wenguo Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, No. 13, Section 4, Renmin South Road, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Lan Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, No. 13, Section 4, Renmin South Road, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Hongwei Zhang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, No. 13, Section 4, Renmin South Road, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Liangwei Deng
- Biogas Institute of Ministry of Agriculture and Rural Affairs, No. 13, Section 4, Renmin South Road, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Hongnan Yang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, No. 13, Section 4, Renmin South Road, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Ting He
- Biogas Institute of Ministry of Agriculture and Rural Affairs, No. 13, Section 4, Renmin South Road, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Peike Wu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, No. 13, Section 4, Renmin South Road, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Yunhong Zhang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, No. 13, Section 4, Renmin South Road, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.
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Deng T, He H, Chen H, Peng X, Li H, Yan X, Lei Y, Luo L. Dual-ligand lanthanide metal-organic framework based ratiometric fluorescent platform for visual monitoring of aminoglycoside residues in food samples. Talanta 2024; 276:126200. [PMID: 38735243 DOI: 10.1016/j.talanta.2024.126200] [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: 01/24/2024] [Revised: 04/02/2024] [Accepted: 05/02/2024] [Indexed: 05/14/2024]
Abstract
Herein, a dual-emission Eu metal-organic framework (Eu-MOF) is prepared and used as the ratiometric fluorescence probe for ultrasensitive detection of aminoglycoside antibiotics (AGs). Due to the strong hydrogen bond interactions between AGs and Eu-MOF, the blue emission is enhanced while the red emission has little fluctuation in Eu-MOF with the addition of AGs, thus a good linear relationship with the logarithm of AGs concentrations from 0.001 to 100 μg/mL can be established for quantitative analysis. Good sensitivity with the detection limit of 0.33 ng/mL for apramycin, 0.32 ng/mL for amikacin and 0.30 ng/mL for kanamycin is achieved. The proposed assay demonstrates good selectivity and applicability for determination of AGs in real milk and honey samples. The Eu-MOF materials are further fabricated as fluorescent test papers for facile visual detection. The as-established ratio fluorescence platform offers a portable and economical way for rapid monitoring AGs residues in complex food samples.
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Affiliation(s)
- Tingting Deng
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Haibo He
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, 200444, PR China.
| | - Huinan Chen
- Department of Physics, College of Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Xitian Peng
- Institute of Agricultural Quality Standards and Testing Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Hongbo Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng, 224051, PR China
| | - Xiaoxia Yan
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Yunyi Lei
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Liqiang Luo
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, 200444, PR China
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Harbaoui S, Ferjani S, Abbassi MS, Guzmán-Puche J, Causse M, Elías-López C, Martínez-Martínez L, Boubaker IBB. Genetic background of aminoglycoside-modifying enzymes in various genetic lineages of clinical aminoglycosides-resistant E. coli and K. pneumoniae isolates in Tunisia. J Appl Microbiol 2024; 135:lxae164. [PMID: 38955378 DOI: 10.1093/jambio/lxae164] [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: 11/05/2023] [Revised: 06/10/2024] [Accepted: 07/01/2024] [Indexed: 07/04/2024]
Abstract
AIMS This study was conducted to evaluate the in vitro activity of clinically relevant aminoglycosides and to determine the prevalence of genes encoding aminoglycoside modifying enzymes (AMEs) and 16S ribosomal RNA (rRNA) methyltransferases among aminoglycoside-resistant E. coli (n = 61) and K. pneumoniae (n = 44) clinical isolates. Associated resistances to beta-lactams and their bla genes as well as the genetic relatedness of isolates were also investigated. MATERIALS AND METHODS A total of 105 aminoglycoside-resistant E. coli (n = 61) and K. pneumoniae (n = 44) isolates recovered between March and May 2017 from 100 patients hospitalized in different wards of Charles Nicolle Hospital of Tunis, Tunisia, were studied. Minimal inhibitory concentrations of aminoglycoside compounds were determined by broth microdilution method. Aminoglycosides resistance encoding genes [aph(3´)-Ia, aph(3') IIa, aph(3´)-VIa, ant(2″)-Ia, aac(3)-IIa, aac(3)-IVa, aac(6')-Ib, rmtA, rmtB, rmtC, armA, and npmA] and bla genes were investigated by PCR and sequencing. Genetic relatedness was examined by multilocus sequence typing (MLST) for representative isolates. RESULTS High rates of aminoglycoside resistance were found: gentamicin (85.7%), tobramycin (87.6%), kanamycin (78.0%), netilmincin (74.3%), and amikcin (18.0%). Most common AME gene was aac(3)-IIa (42%), followed by aac(6')-Ib (36.2%) and aph(3')-VIa (32.4%). The majority of isolates were resistant to beta-lactams and blaCTX-M-15 was the most common ESBL. The blaNDM-1 and blaOXA-48 were also produced by 1 and 23 isolates, respectively. Novel sequence types have been reported among our isolates and high-risk clonal lineages have been detected, such as E. coli ST43 (ST131 in Achtman MLST scheme) and K. pneumoniae (ST11/ST13). CONCLUSIONS The high prevalence of aminoglycoside resistance rates and the diversity of corresponding genes, with diverse β-lactamase enzymes among genetically heterogeneous clinical isolates present a matter of concern.
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Affiliation(s)
- Sarra Harbaoui
- Research Laboratory «Antimicrobial resistance» LR99ES09, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia
| | - Sana Ferjani
- Research Laboratory «Antimicrobial resistance» LR99ES09, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Mohamed Salah Abbassi
- Research Laboratory «Antimicrobial resistance» LR99ES09, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia
- Laboratory of Bacteriological Research, Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis 1006, Tunisia
| | - Julia Guzmán-Puche
- Unidad de Gestión Clínica de Microbiologia, Hospital Universitario Reina Sofía de Córdoba, Córdoba 14004, Spain
| | - Manuel Causse
- Unidad de Gestión Clínica de Microbiologia, Hospital Universitario Reina Sofía de Córdoba, Córdoba 14004, Spain
| | - Cristina Elías-López
- Instituto Maimónides de Investigación Biomédica de Córdoba, Córdoba 14004, Spain
| | - Luis Martínez-Martínez
- Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, Córdoba 14004, Spain
| | - Ilhem Boutiba-Ben Boubaker
- Research Laboratory «Antimicrobial resistance» LR99ES09, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Boulevard 9 Avril, Tunis 1006, Tunisia
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Otun SO, Graca R, Achilonu I. Combating Aminoglycoside Resistance: From Structural and Functional Characterisation to Therapeutic Challenges with RKAAT. Curr Protein Pept Sci 2024; 25:454-468. [PMID: 38314602 DOI: 10.2174/0113892037278814231226104509] [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: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 02/06/2024]
Abstract
A comprehensive knowledge of aminoglycoside-modifying enzymes (AMEs) and their role in bacterial resistance mechanisms is urgently required due to the rising incidence of antibiotic resistance, particularly in Klebsiella pneumoniae infections. This study explores the essential features of AMEs, including their structural and functional properties, the processes by which they contribute to antibiotic resistance, and the therapeutic importance of aminoglycosides. The study primarily examines the Recombinant Klebsiella pneumoniae Aminoglycoside Adenylyl Transferase (RKAAT), particularly emphasizing its biophysical characteristics and the sorts of resistance it imparts. Furthermore, this study examines the challenges presented by RKAAT-mediated resistance, an evaluation of treatment methods and constraints, and options for controlling infection. The analysis provides a prospective outlook on strategies to address and reduce antibiotic resistance. This extensive investigation seeks to provide vital insights into the continuing fight against bacterial resistance, directing future research efforts and medicinal approaches.
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Affiliation(s)
- Sarah Oluwatobi Otun
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Richard Graca
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
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Zhang S, Shu Y, Wang Y, Zhong Z, Wang M, Jia R, Chen S, Liu M, Zhu D, Zhao X, Wu Y, Yang Q, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A. High rate of multidrug resistance and integrons in Escherichia coli isolates from diseased ducks in select regions of China. Poult Sci 2023; 102:102956. [PMID: 37586192 PMCID: PMC10450990 DOI: 10.1016/j.psj.2023.102956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/18/2023] Open
Abstract
With the increasing number of ducks being raised and consumed, it is crucial to monitor the presence of multidrug resistant (MDR) bacteria in duck farming. Waterfowl, such as ducks, can contribute to the rapid dissemination of antibiotic resistance genes (ARGs). The objective of this study was to investigate the antimicrobial resistance (AMR), ARGs, and mobile genetic elements (MGEs), such as IS26, tbrC, ISEcp1 in Escherichia coli(E. coli) isolated from the intestinal contents of diseased ducks between 2021 and 2022 in Sichuan, Chongqing and Anhui, China. The AMR phenotypes of 201 isolated E. coli strains were determined using the minimum inhibitory concentrations (MICs) method. Subsequently, polymerase chain reaction and sequencing techniques were employed to screen for integron-integrase genes (intI1, intI2, intI3 genes), gene cassettes (GCs), MGEs, and ARGs. The results demonstrated that 96.5% of the E. coli isolates were resistant to at least 1 antibiotic, with 88.1% of the strains displaying MDR phenotype. The highest AMR phenotype observed was for trimethoprim-sulfamethoxazole (88.1%). Furthermore, class 1 and class 2 integrons were detected in 68.2% and 3.0% of all the isolates, respectively, whereas no class 3 integrons were found. Ten types of GCs were identified in the variable regions of class 1 and class 2 integrons. Moreover, 10 MGEs were observed in 46 combinations, with IS26 exhibiting the highest detection rate (89.6%). Among the 22 types of ARGs, tetA (77.1%) was the most frequently detected. In the conjugational transfer experiment, transconjugants were found to carry specific ARGs and MGEs, with their MIC values were significantly higher than those of recipient E. coli J53, indicating their status as MDR bacteria. This study emphasizes the necessity of monitoring MGEs, ARGs, and integrons in duck farms. It provides valuable insights into the complex formation mechanisms of AMR and may aid in preventing and controlling the spread of MDR bacteria in waterfowl breeding farm.
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Affiliation(s)
- Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Yanxi Shu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Yuwei Wang
- Mianyang Academy of Agricultural Sciences, Mianyang, Sichuan 621023, P.R. China
| | - Zhijun Zhong
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Ying Wu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Qiao Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Juan Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Xumin Ou
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Sai Mao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Qun Gao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Di Sun
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China.
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Chang Y, Sun W, Murchie AIH, Chen D. Genome-wide identification of Kanamycin B binding RNA in Escherichia coli. BMC Genomics 2023; 24:120. [PMID: 36927548 PMCID: PMC10018874 DOI: 10.1186/s12864-023-09234-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND The aminoglycosides are established antibiotics that inhibit bacterial protein synthesis by binding to ribosomal RNA. Additional non-antibiotic aminoglycoside cellular functions have also been identified through aminoglycoside interactions with cellular RNAs. The full extent, however, of genome-wide aminoglycoside RNA interactions in Escherichia coli has not been determined. Here, we report genome-wide identification and verification of the aminoglycoside Kanamycin B binding to Escherichia coli RNAs. Immobilized Kanamycin B beads in pull-down assays were used for transcriptome-profiling analysis (RNA-seq). RESULTS Over two hundred Kanamycin B binding RNAs were identified. Functional classification analysis of the RNA sequence related genes revealed a wide range of cellular functions. Small RNA fragments (ncRNA, tRNA and rRNA) or small mRNA was used to verify the binding with Kanamycin B in vitro. Kanamycin B and ibsC mRNA was analysed by chemical probing. CONCLUSIONS The results will provide biochemical evidence and understanding of potential extra-antibiotic cellular functions of aminoglycosides in Escherichia coli.
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Affiliation(s)
- Yaowen Chang
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wenxia Sun
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Alastair I H Murchie
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China. .,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Dongrong Chen
- Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China. .,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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7
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Chang Y, Zhang X, Murchie AIH, Chen D. Transcriptome profiling in response to Kanamycin B reveals its wider non-antibiotic cellular function in Escherichia coli. Front Microbiol 2022; 13:937827. [DOI: 10.3389/fmicb.2022.937827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/10/2022] [Indexed: 12/03/2022] Open
Abstract
Aminoglycosides are not only antibiotics but also have wider and diverse non-antibiotic cellular functions. To elucidate the understanding of non-antibiotic cellular functions, here we report transcriptome-profiling analysis of Escherichia coli in the absence or presence of 0.5 and 1 μM of Kanamycin B, concentrations that are neither lethal nor inhibit growth, and identified the differentially expressed genes (DEGs) at two given concentrations of Kanamycin B. Functional classification of the DEGs revealed that they were mainly related to microbial metabolism including two-component systems, biofilm formation, oxidative phosphorylation and nitrogen metabolism in diverse environments. We further showed that Kanamycin B and other aminoglycosides can induce reporter gene expression through the 5′ UTR of napF gene or narK gene (both identified as DEG) and Kanamycin B can directly bind to the RNA. The results provide new insights into a better understanding of the wider aminoglycosides cellular function in E. coli rather than its known antibiotics function.
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Miotto P, Sorrentino R, De Giorgi S, Provvedi R, Cirillo DM, Manganelli R. Transcriptional regulation and drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:990312. [PMID: 36118045 PMCID: PMC9480834 DOI: 10.3389/fcimb.2022.990312] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial drug resistance is one of the major challenges to present and future human health, as the continuous selection of multidrug resistant bacteria poses at serious risk the possibility to treat infectious diseases in the near future. One of the infection at higher risk to become incurable is tuberculosis, due to the few drugs available in the market against Mycobacterium tuberculosis. Drug resistance in this species is usually due to point mutations in the drug target or in proteins required to activate prodrugs. However, another interesting and underexplored aspect of bacterial physiology with important impact on drug susceptibility is represented by the changes in transcriptional regulation following drug exposure. The main regulators involved in this phenomenon in M. tuberculosis are the sigma factors, and regulators belonging to the WhiB, GntR, XRE, Mar and TetR families. Better understanding the impact of these regulators in survival to drug treatment might contribute to identify new drug targets and/or to design new strategies of intervention.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Rita Sorrentino
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano De Giorgi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
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Hipólito A, García-Pastor L, Blanco P, Trigo da Roza F, Kieffer N, Vergara E, Jové T, Álvarez J, Escudero J. The expression of aminoglycoside resistance genes in integron cassettes is not controlled by riboswitches. Nucleic Acids Res 2022; 50:8566-8579. [PMID: 35947699 PMCID: PMC9410878 DOI: 10.1093/nar/gkac662] [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: 06/02/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022] Open
Abstract
Regulation of gene expression is a key factor influencing the success of antimicrobial resistance determinants. A variety of determinants conferring resistance against aminoglycosides (Ag) are commonly found in clinically relevant bacteria, but whether their expression is regulated or not is controversial. The expression of several Ag resistance genes has been reported to be controlled by a riboswitch mechanism encoded in a conserved sequence. Yet this sequence corresponds to the integration site of an integron, a genetic platform that recruits genes of different functions, making the presence of such a riboswitch counterintuitive. We provide, for the first time, experimental evidence against the existence of such Ag-sensing riboswitch. We first tried to reproduce the induction of the well characterized aacA5 gene using its native genetic environment, but were unsuccessful. We then broadened our approach and analyzed the inducibility of all AgR genes encoded in integrons against a variety of antibiotics. We could not observe biologically relevant induction rates for any gene in the presence of several aminoglycosides. Instead, unrelated antibiotics produced mild but consistently higher increases in expression, that were the result of pleiotropic effects. Our findings rule out the riboswitch control of aminoglycoside resistance genes in integrons.
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Affiliation(s)
- Alberto Hipólito
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Lucía García-Pastor
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | | | | | - Nicolas Kieffer
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Ester Vergara
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, University of Limoges, Limoges, France
| | - Julio Álvarez
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
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Fonseca ÉL, Vicente AC. Integron Functionality and Genome Innovation: An Update on the Subtle and Smart Strategy of Integrase and Gene Cassette Expression Regulation. Microorganisms 2022; 10:microorganisms10020224. [PMID: 35208680 PMCID: PMC8876359 DOI: 10.3390/microorganisms10020224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022] Open
Abstract
Integrons are considered hot spots for bacterial evolution, since these platforms allow one-step genomic innovation by capturing and expressing genes that provide advantageous novelties, such as antibiotic resistance. The acquisition and shuffling of gene cassettes featured by integrons enable the population to rapidly respond to changing selective pressures. However, in order to avoid deleterious effects and fitness burden, the integron activity must be tightly controlled, which happens in an elegant and elaborate fashion, as discussed in detail in the present review. Here, we aimed to provide an up-to-date overview of the complex regulatory networks that permeate the expression and functionality of integrons at both transcriptional and translational levels. It was possible to compile strong shreds of evidence clearly proving that these versatile platforms include functions other than acquiring and expressing gene cassettes. The well-balanced mechanism of integron expression is intricately related with environmental signals, host cell physiology, fitness, and survival, ultimately leading to adaptation on the demand.
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Kim M, Park J, Kang M, Yang J, Park W. Gain and loss of antibiotic resistant genes in multidrug resistant bacteria: One Health perspective. J Microbiol 2021; 59:535-545. [PMID: 33877574 DOI: 10.1007/s12275-021-1085-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/17/2022]
Abstract
The emergence of multidrug resistance (MDR) has become a global health threat due to the increasing unnecessary use of antibiotics. Multidrug resistant bacteria occur mainly by accumulating resistance genes on mobile genetic elements (MGEs), made possible by horizontal gene transfer (HGT). Humans and animal guts along with natural and engineered environments such as wastewater treatment plants and manured soils have proven to be the major reservoirs and hotspots of spreading antibiotic resistance genes (ARGs). As those environments support the dissemination of MGEs through the complex interactions that take place at the human-animal-environment interfaces, a growing One Health challenge is for multiple sectors to communicate and work together to prevent the emergence and spread of MDR bacteria. However, maintenance of ARGs in a bacterial chromosome and/or plasmids in the environments might place energy burdens on bacterial fitness in the absence of antibiotics, and those unnecessary ARGs could eventually be lost. This review highlights and summarizes the current investigations into the gain and loss of ARG genes in MDR bacteria among human-animal-environment interfaces. We also suggest alternative treatments such as combinatory therapies or sequential use of different classes of antibiotics/adjuvants, treatment with enzyme-inhibitors, and phage therapy with antibiotics to solve the MDR problem from the perspective of One Health issues.
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Affiliation(s)
- Misung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jaeeun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Mingyeong Kang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jihye Yang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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