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Bhuiya S, Kaushik S, Logheeswaran J, Karthika P, Prathiviraj R, Selvin J, Kiran GS. Emergence of Recurrent Urinary Tract Infection: Dissecting the mechanism of Antimicrobial Resistance, Host-Pathogen Interaction, and Hormonal Imbalance. Microb Pathog 2025:107698. [PMID: 40373943 DOI: 10.1016/j.micpath.2025.107698] [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: 12/16/2024] [Revised: 04/19/2025] [Accepted: 05/12/2025] [Indexed: 05/17/2025]
Abstract
Urinary tract infection is one of the most common infections worldwide, causing numerous deaths every year. The gut-bladder axis has been recently found to be a key factor in initiating UTI pathogenesis, along with the imbalance in the gut microbiome, which is associated with advanced susceptibility to rUTI. The patients who suffer from UTIs are, more often than not, the ones who have the lowest levels of butyrate-producing gut bacteria. Antibiotics cause dysbiosis in the gut and increase the growth of uropathogenic strains. Moreover, the gut-vagina and vagina-bladder axes are involved in UTIs by transferring microbial species, modulating the immune response, and developing intracellular bacterial reservoirs in the bladder. The rising usage of antibiotics has raised antimicrobial resistance (AMR) worldwide and recently worsened the treatment of UTIs. Resistance mechanisms include enzymatic hydrolysis of antibiotics, efflux systems, biofilm formation, horizontal gene transfer, and a weakened host's immune system, allowing bacteria to escape from the treatments. Besides, in pregnant women and adolescents, the alterations in sex hormone levels increase the risk of rUTIs. Knowledge of microbiota that harbor in the gut-vagina and vagina-bladder axes might lead to the invention of nonantibiotic preventive and therapeutic techniques in the future. In conclusion, this review emphasizes the need for a study to understand the host-microbe interactions, gut health, and AMR to effectively deal with and prevent recurrent UTIs. Also, the review explores a comprehensive analysis of the epigenetic network between host UTIs and marker genes in E. coli.
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Affiliation(s)
- Shraddha Bhuiya
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India
| | - Saumya Kaushik
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India
| | - Jwalaa Logheeswaran
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India
| | - P Karthika
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India
| | | | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry 605014, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India.
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Yarahmadi A, Najafiyan H, Yousefi MH, Khosravi E, Shabani E, Afkhami H, Aghaei SS. Beyond antibiotics: exploring multifaceted approaches to combat bacterial resistance in the modern era: a comprehensive review. Front Cell Infect Microbiol 2025; 15:1493915. [PMID: 40176987 PMCID: PMC11962305 DOI: 10.3389/fcimb.2025.1493915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 01/23/2025] [Indexed: 04/05/2025] Open
Abstract
Antibiotics represent one of the most significant medical breakthroughs of the twentieth century, playing a critical role in combating bacterial infections. However, the rapid emergence of antibiotic resistance has become a major global health crisis, significantly complicating treatment protocols. This paper provides a narrative review of the current state of antibiotic resistance, synthesizing findings from primary research and comprehensive review articles to examine the various mechanisms bacteria employ to counteract antibiotics. One of the primary sources of antibiotic resistance is the improper use of antibiotics in the livestock industry. The emergence of drug-resistant microorganisms from human activities and industrial livestock production has presented significant environmental and public health concerns. Today, resistant nosocomial infections occur following long-term hospitalization of patients, causing the death of many people, so there is an urgent need for alternative treatments. In response to this crisis, non-antibiotic therapeutic strategies have been proposed, including bacteriophages, probiotics, postbiotics, synbiotics, fecal microbiota transplantation (FMT), nanoparticles (NPs), antimicrobial peptides (AMPs), antibodies, traditional medicines, and the toxin-antitoxin (TA) system. While these approaches offer innovative solutions for addressing bacterial infections and preserving the efficacy of antimicrobial therapies, challenges such as safety, cost-effectiveness, regulatory hurdles, and large-scale implementation remain. This review examines the potential and limitations of these strategies, offering a balanced perspective on their role in managing bacterial infections and mitigating the broader impact of antibiotic resistance.
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Affiliation(s)
- Aref Yarahmadi
- Department of Biology, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Hamide Najafiyan
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Hasan Yousefi
- Department of Tissue Engineering and Applied Cell Sciences, School of Medicine, Qom University of Medical Sciences, Qom, Iran
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Elham Khosravi
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Shabani
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamed Afkhami
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Department of Medical Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran
| | - Seyed Soheil Aghaei
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
- Applied Physiology Research Center, Qom Medical Sciences, Islamic Azad University, Qom, Iran
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Prabhu D, Shankari G, Rajamanikandan S, Jeyakanthan J, Velusamy P, Gopinath SCB, Pattabi S. Designing potential lead compounds targeting aminoglycoside N (6')-acetyltransferase in Serratia marcescens: A drug discovery strategy. Int J Biol Macromol 2024; 281:136976. [PMID: 39490491 DOI: 10.1016/j.ijbiomac.2024.136976] [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: 04/14/2024] [Revised: 10/25/2024] [Accepted: 10/25/2024] [Indexed: 11/05/2024]
Abstract
Serratia marcescens is an opportunistic human pathogen that causes urinary tract infections, ocular lens infections, and respiratory tract infections. S. marcescens employs various defense mechanisms to evade antibiotics, one of which is mediated by aminoglycoside N-acetyltransferase (AAC). In this mechanism, the enzyme AAC facilitates the transfer and linkage of the acetyl moiety from the donor substrate acetyl-coenzyme A to specific positions on antibiotics. This modification alters the antibiotic's structure, leading to the inactivation of aminoglycoside antibiotics. In the current scenario, antibiotic resistance has become a global threat, and targeting the enzymes that mediate resistance is considered crucial to combat this issue. The study aimed to address the increasing global threat of antibiotic resistance in Serratia marcescens by targeting the aminoglycoside N-acetyltransferase (AAC (6')) enzyme, which inactivates aminoglycoside antibiotics through acetylation. Due to the absence of experimental structure, we constructed a homology model of aminoglycoside N (6')-acetyltransferase (AAC (6')) of S. marcescens using the atomic structure of aminoglycoside N-acetyltransferase AAC (6')-Ib (PDB ID: 1V0C) as a template. The stable architecture and integrity of the modelled AAC (6') structure were analyzed through a 100 ns simulation. Structure-guided high-throughput screening of four small molecule databases (Binding, Life Chemicals, Zinc, and Toslab) resulted in the identification of potent inhibitors against AAC (6'). The hits obtained from screening were manually clustered, and the five hit molecules were shortlisted based on the docking score, which are observed in the range of -17.09 kcal/mol to -11.95 kcal/mol. These selected five molecules displayed acceptable pharmacological properties in ADME predictions. The binding free energy calculations, and molecular dynamics simulations of ligand bound AAC (6') complexes represented higher affinity and stable binding. The selected molecules demonstrated stable binding with AAC (6'), indicating their strong potential to hamper the binding of aminoglycoside in the respective site. and thereby inhibit. This process mitigates enzyme mediated AAC (6') activity on aminoglycosides and reverse the bactericidal function of aminoglycosides, and also this method could serve as a platform for the development of potential antimicrobials.
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Affiliation(s)
- Dhamodharan Prabhu
- Centre for Bioinformatics, Karpagam Academy of Higher Education, Coimbatore 641021, India; Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore 641021, India.
| | - Gopalakrishnan Shankari
- Centre for Bioinformatics, Karpagam Academy of Higher Education, Coimbatore 641021, India; Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore 641021, India
| | - Sundararaj Rajamanikandan
- Centre for Bioinformatics, Karpagam Academy of Higher Education, Coimbatore 641021, India; Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore 641021, India; School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, PR China
| | | | - Palaniyandi Velusamy
- Innovation and Incubation Centre for Health Sciences (IICHS), Sree Balaji Medical College and Hospital (SBMCH), Bharath Institute of Higher Education and Research (BIHER), Chromepet 600 044, Tamil Nadu, India.
| | - Subash C B Gopinath
- Center for Global Health Research, Saveetha Medical College & Hospital, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai 602 105, Tamil Nadu, India; Faculty of Chemical Engineering & Technology and Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), 02600 Arau, Perlis, Malaysia; Department of Computer Science and Engineering, Faculty of Science and Information Technology, Daffodil International University, Daffodil Smart City, Birulia, Savar, Dhaka 1216, Bangladesh
| | - Sasikumar Pattabi
- Department of General Surgery, Sree Balaji Medical College and Hospital (SBMCH), Bharath Institute of Higher Education and Research (BIHER), Chromepet, 600 044 Chennai, Tamil Nadu, India
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Belay WY, Getachew M, Tegegne BA, Teffera ZH, Dagne A, Zeleke TK, Abebe RB, Gedif AA, Fenta A, Yirdaw G, Tilahun A, Aschale Y. Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review. Front Pharmacol 2024; 15:1444781. [PMID: 39221153 PMCID: PMC11362070 DOI: 10.3389/fphar.2024.1444781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.
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Affiliation(s)
- Wubetu Yihunie Belay
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Melese Getachew
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Bantayehu Addis Tegegne
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Zigale Hibstu Teffera
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abebe Dagne
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Tirsit Ketsela Zeleke
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Rahel Belete Abebe
- Department of clinical pharmacy, College of medicine and health sciences, University of Gondar, Gondar, Ethiopia
| | - Abebaw Abie Gedif
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abebe Fenta
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Getasew Yirdaw
- Department of environmental health science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Adane Tilahun
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Yibeltal Aschale
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
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Zhao Y, Ding WJ, Xu L, Sun JQ. A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas. Front Microbiol 2024; 15:1395477. [PMID: 38817968 PMCID: PMC11138164 DOI: 10.3389/fmicb.2024.1395477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.
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Affiliation(s)
- Yang Zhao
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wen-Jing Ding
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ji-Quan Sun
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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6
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Xiao G, Li J, Sun Z. The Combination of Antibiotic and Non-Antibiotic Compounds Improves Antibiotic Efficacy against Multidrug-Resistant Bacteria. Int J Mol Sci 2023; 24:15493. [PMID: 37895172 PMCID: PMC10607837 DOI: 10.3390/ijms242015493] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Bacterial antibiotic resistance, especially the emergence of multidrug-resistant (MDR) strains, urgently requires the development of effective treatment strategies. It is always of interest to delve into the mechanisms of resistance to current antibiotics and target them to promote the efficacy of existing antibiotics. In recent years, non-antibiotic compounds have played an important auxiliary role in improving the efficacy of antibiotics and promoting the treatment of drug-resistant bacteria. The combination of non-antibiotic compounds with antibiotics is considered a promising strategy against MDR bacteria. In this review, we first briefly summarize the main resistance mechanisms of current antibiotics. In addition, we propose several strategies to enhance antibiotic action based on resistance mechanisms. Then, the research progress of non-antibiotic compounds that can promote antibiotic-resistant bacteria through different mechanisms in recent years is also summarized. Finally, the development prospects and challenges of these non-antibiotic compounds in combination with antibiotics are discussed.
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Affiliation(s)
| | | | - Zhiliang Sun
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (G.X.); (J.L.)
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Reys V, Kowalewski J, Gelin M, Lionne C. w TSA-CRAFT: an open-access web server for rapid analysis of thermal shift assay experiments. BIOINFORMATICS ADVANCES 2023; 3:vbad136. [PMID: 37822724 PMCID: PMC10562953 DOI: 10.1093/bioadv/vbad136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023]
Abstract
Motivation The automated data processing provided by the TSA-CRAFT tool enables now to reach high throughput speed analysis of thermal shift assays. While the software is powerful and freely available, it still requires installation process and command line efforts that could be discouraging. Results To simplify the procedure, we decided to make it available and easy to use by implementing it with a graphical interface via a web server, enabling a cross-platform usage from any web browsers. We developed a web server embedded version of the TSA-CRAFT tool, enabling a user-friendly graphical interface for formatting and submission of the input file and visualization of the selected thermal denaturation profiles. We describe a typical case study of buffer condition optimization of the biologically relevant APH(3')-IIb bacterial protein in a 96 deep-well thermal shift analysis screening. Availability and implementation wTSA-CRAFT is freely accessible for noncommercial usage at https://bioserv.cbs.cnrs.fr/TSA_CRAFT.
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Affiliation(s)
- Victor Reys
- Centre de Biologie Structurale (CBS), CNRS UMR 5048, Université de Montpellier, INSERM U 1054, 34090 Montpellier, France
| | - Julien Kowalewski
- Centre de Biologie Structurale (CBS), CNRS UMR 5048, Université de Montpellier, INSERM U 1054, 34090 Montpellier, France
| | - Muriel Gelin
- Centre de Biologie Structurale (CBS), CNRS UMR 5048, Université de Montpellier, INSERM U 1054, 34090 Montpellier, France
| | - Corinne Lionne
- Centre de Biologie Structurale (CBS), CNRS UMR 5048, Université de Montpellier, INSERM U 1054, 34090 Montpellier, France
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Magaña AJ, Sklenicka J, Pinilla C, Giulianotti M, Chapagain P, Santos R, Ramirez MS, Tolmasky ME. Restoring susceptibility to aminoglycosides: identifying small molecule inhibitors of enzymatic inactivation. RSC Med Chem 2023; 14:1591-1602. [PMID: 37731693 PMCID: PMC10507813 DOI: 10.1039/d3md00226h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Growing resistance to antimicrobial medicines is a critical health problem that must be urgently addressed. Adding to the increasing number of patients that succumb to infections, there are other consequences to the rise in resistance like the compromise of several medical procedures and dental work that are heavily dependent on infection prevention. Since their introduction in the clinics, aminoglycoside antibiotics have been a critical component of the armamentarium to treat infections. Still, the increase in resistance and their side effects led to a decline in their utilization. However, numerous current factors, like the urgent need for antimicrobials and their favorable properties, led to renewed interest in these drugs. While efforts to design new classes of aminoglycosides refractory to resistance mechanisms and with fewer toxic effects are starting to yield new promising molecules, extending the useful life of those already in use is essential. For this, numerous research projects are underway to counter resistance from different angles, like inhibition of expression or activity of resistance components. This review focuses on selected examples of one aspect of this quest, the design or identification of small molecule inhibitors of resistance caused by enzymatic modification of the aminoglycoside. These compounds could be developed as aminoglycoside adjuvants to overcome resistant infections.
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Affiliation(s)
- Angel J Magaña
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Jan Sklenicka
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Clemencia Pinilla
- Center for Translational Science, Florida International University Port St. Lucie FL 34987 USA
| | - Marc Giulianotti
- Center for Translational Science, Florida International University Port St. Lucie FL 34987 USA
| | - Prem Chapagain
- Department of Physics, Florida International University Miami FL 33199 USA
- Biomolecular Sciences Institute, Florida International University Miami FL 33199 USA
| | - Radleigh Santos
- Department of Mathematics, Nova Southeastern University Fort Lauderdale FL 33314 USA
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
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Jeremia L, Deprez BE, Dey D, Conn GL, Wuest WM. Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation. RSC Med Chem 2023; 14:624-643. [PMID: 37122541 PMCID: PMC10131624 DOI: 10.1039/d2md00459c] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.
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Affiliation(s)
- Learnmore Jeremia
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Benjamin E Deprez
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - William M Wuest
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
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Shi W, Lu J, Feng C, Gao M, Li A, Liu S, Zhang L, Zhang X, Li Q, Lin H, Lin X, Li K, Zhang H, Hu Y, Wang G, Bao Q, Jiang W. Functional characterization of a novel aminoglycoside phosphotransferase, APH(9)-Ic, and its variant from Stenotrophomonas maltophilia. Front Cell Infect Microbiol 2023; 12:1097561. [PMID: 36699730 PMCID: PMC9868417 DOI: 10.3389/fcimb.2022.1097561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
Background The intrinsic resistance mechanism plays an essential role in the bacterial resistance to a variety of the antimicrobials. The aim of this study is to find the chromosome-encoded novel antimicrobial resistance gene in the clinical isolate. Methods The function of the predicted resistance gene was verified by gene cloning and antibiotic susceptibility test. Recombinant protein expression and enzyme kinetic studies were performed to explore the in vivo activity of the enzyme. Expression of the resistance gene exposed to antimicrobial was determined by RT-qPCR. Whole genome sequencing and bioinformatic analysis were applied to analyze the genetic context of the resistance gene. Results The novel aminoglycoside (AG) resistance genes designated aph(9)-Ic and aph(9)-Ic1 confer resistance to spectinomycin, and a recombinant strain harboring aph(9)-Ic (pMD19-T-aph(9)-Ic/DH5α) showed a significantly increased minimum inhibitory concentration (MIC) level against spectinomycin compared with the control strains (DH5α and pMD19-T/DH5α). The result of the kinetic analysis of APH(9)-Ic was consistent with the MIC result for the recombinant pMD19-T-aph(9)-Ic/DH5α, showing the efficient catalytic activity for spectinomycin [kcat/Km ratio = (5.58 ± 0.31) × 104 M-1·s-1]. Whole-genome sequencing demonstrated that the aph(9)-Ic gene was located on the chromosome with a relatively conserved genetic environment, and no mobile genetic element was found in its surrounding region. Among all the function-characterized resistance genes, APH(9)-Ic shares the highest amino acid sequence identity of 33.75% with APH(9)-Ia. Conclusion We characterized a novel AG resistance gene aph(9)-Ic and its variant aph(9)-Ic1 that mediated spectinomycin resistance from S. maltophilia. The identification of the novel AG resistance genes will assist us in elucidating the complexity of resistance mechanisms in microbial populations.
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Affiliation(s)
- Weina Shi
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Anqi Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shuang Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hailong Lin
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yunliang Hu
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Guangli Wang
- School of Medicine and Health, Lishui University, Lishui, China,*Correspondence: Guangli Wang, ; Qiyu Bao, ; Weiyan Jiang,
| | - Qiyu Bao
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China,Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China,*Correspondence: Guangli Wang, ; Qiyu Bao, ; Weiyan Jiang,
| | - Weiyan Jiang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China,*Correspondence: Guangli Wang, ; Qiyu Bao, ; Weiyan Jiang,
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11
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Prabhu D, Rajamanikandan S, Amala M, Saritha P, Jeyakanthan J, Ramasamy P. Functional Characterization, Mechanism, and Mode of Action of Putative Streptomycin Adenylyltransferase from Serratia marcescens. Antibiotics (Basel) 2022; 11:antibiotics11121722. [PMID: 36551379 PMCID: PMC9774460 DOI: 10.3390/antibiotics11121722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Nosocomial infections are serious threats to the entire world in healthcare settings. The major causative agents of nosocomial infections are bacterial pathogens, among which Enterobacteriaceae family member Serratia marcescens plays a crucial role. It is a gram-negative opportunistic pathogen, predominantly affecting patients in intensive-care units. The presence of intrinsic genes in S. marcescens led to the development of resistance to antibiotics for survival. Complete scanning of the proteome, including hypothetical and partially annotated proteins, paves the way for a better understanding of potential drug targets. The targeted protein expressed in E. coli BL21 (DE3) pLysS cells has shown complete resistance to aminoglycoside antibiotic streptomycin (>256 MCG). The recombinant protein was purified using affinity and size-exclusion chromatography and characterized using SDS-PAGE, western blotting, and MALDI-TOF analysis. Free phosphate bound to malachite green was detected at 620 nm, evident of the conversion of adenosine triphosphate to adenosine monophosphate during the adenylation process. Similarly, in the chromatographic assay, adenylated streptomycin absorbed at 260 nm in AKTA (FPLC), confirming the enzyme-catalyzed adenylation of streptomycin. Further, the adenylated product of streptomycin was confirmed through HPLC and mass spectrometry analysis. In conclusion, our characterization studies identified the partially annotated hypothetical protein as streptomycin adenylyltransferase.
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Affiliation(s)
- Dhamodharan Prabhu
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai 600 044, Tamil Nadu, India
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
- Correspondence: (D.P.); (J.J.); (P.R.)
| | - Sundararaj Rajamanikandan
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai 600 044, Tamil Nadu, India
| | - Mathimaran Amala
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Poopandi Saritha
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
- Correspondence: (D.P.); (J.J.); (P.R.)
| | - Palaniappan Ramasamy
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai 600 044, Tamil Nadu, India
- Correspondence: (D.P.); (J.J.); (P.R.)
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12
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Gao M, Feng C, Ji Y, Shi Y, Shi W, Zhang L, Liu S, Li A, Zhang X, Li Q, Lu J, Bao Q, Zhang H. AadA36, a novel chromosomal aminoglycoside nucleotidyltransferase from a clinical isolate of Providencia stuartii. Front Microbiol 2022; 13:1035651. [PMID: 36386671 PMCID: PMC9663854 DOI: 10.3389/fmicb.2022.1035651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/06/2022] [Indexed: 01/25/2023] Open
Abstract
In this study, we characterized a novel chromosome-encoded aminoglycoside nucleotidyltransferase (ANT), AadA36, from the Providencia stuartii strain P14 isolated from the sputum specimen of a burn patient at a hospital in Wenzhou, China. Among the functionally characterized ANTs, AadA36 shared the highest amino acid sequence identity of 51.91% with AadA14. The whole genome of P. stuartii P14 consisted of one chromosome and two plasmids (designated pP14-166 and pP14-114). A total of 19 genes with ≥80% similarity with functionally characterized antimicrobial resistance genes (ARGs) were identified in the whole genome, including aminoglycosides [aac(2')-Ia, aph(6)-Id, aph(3″)-Ib, aac(6')-Ib, ant(3″)-IIa, aph(3')-Ia], β-lactams (bla CMY-2 and bla OXA-10) and so on. Antimicrobial susceptibility testing showed that the aadA36 gene conferred specific resistance to spectinomycin and streptomycin, and the minimum inhibitory concentration (MIC) of these antimicrobials increased 128- and 64-fold compared with the control strain. The kinetic parameters of AadA36 were consistent with the MIC data of spectinomycin and streptomycin, with kcat /Km ratios of (1.07 ± 2.23) × 104 M-1 s-1 and (8.96 ± 1.01) × 103 M-1 s-1, respectively. The identification of a novel aminoglycoside resistance gene will help us further understand the complexity of the resistance mechanisms and provide deep insights into the dissemination of resistance genes in the microbial population.
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Affiliation(s)
- Mengdi Gao
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yongan Ji
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yaokai Shi
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shuang Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Anqi Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Qiyu Bao
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China,Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China,*Correspondence: Qiyu Bao,
| | - Hailin Zhang
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Hailin Zhang,
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13
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Wang N, Chen X, Luo J, Deng F, Shi F, Wu Q, Huang Y, Ouyang Q, Qin R, Zhou H. Artemisinin derivative DHA27 enhances the antibacterial effect of aminoglycosides against Pseudomonas aeruginosa by inhibiting mRNA expression of aminoglycoside-modifying enzymes. Front Pharmacol 2022; 13:970400. [PMID: 36353502 PMCID: PMC9637796 DOI: 10.3389/fphar.2022.970400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/10/2022] [Indexed: 09/08/2024] Open
Abstract
Bacterial resistance is becoming increasingly serious, the present study aimed to investigate the mechanism of antibacterial sensitization effect of DHA27 combined with tobramycin in tobramycin-resistant Pseudomonas aeruginosa (PA). We found that DHA27 combined with aminoglycosides had an antibacterial sensitization effect on PA. Tobramycin, owing to its lower toxic and side effects, was selected to further study the molecular mechanism of drug combination. A sublethal-dose bacterial challenge/sepsis mouse model was established to study the protective effect of DHA27 plus tobramycin. Scanning electron microscopy was used to investigate whether DHA27 exerts the antibacterial sensitization effect by directly affecting bacterial morphology. The effect of DHA27 on daunorubicin accumulation in bacteria was studied, and quantitative reverse transcription PCR was used to study the effect of DHA27 plus tobramycin on 16S rRNA methyltransferase and aminoglycoside-modifying enzyme mRNA expression. Twenty clinical isolates of PA were found to be tobramycin resistant; DHA27 plus tobramycin had a significant antibacterial sensitization effect on many of these resistant strains. DHA27 plus tobramycin reduced the bacterial load in the spleen and lungs of sepsis model mice and levels of proinflammatory cytokines interleukin-1β (IL-1β) and interferon-γ (IFN-γ). DHA27 plus tobramycin significantly inhibited the mRNA expression of aminoglycoside-modifying enzymes in bacteria. DHA27 combined with AGs had an antibacterial sensitization effect on PA; the molecular mechanism underlying this effect is closely related to the inhibition of the mRNA expression of aminoglycoside-modifying enzymes, especially aac(3)-II.
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Affiliation(s)
- Nuoyan Wang
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, College of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Xuemin Chen
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, College of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Jing Luo
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, College of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Fei Deng
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, College of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Fuguo Shi
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, College of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Qin Wu
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, College of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Yasi Huang
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, College of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Qin Ouyang
- Department of Pharmaceutical Chemistry, College of Pharmacy, Army Medical University (The Third Military Medical University), Chongqing, China
| | - Rongxin Qin
- Department of Pharmacology, College of Pharmacy, Army Medical University (The Third Military Medical University), Chongqing, China
| | - Hong Zhou
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, College of Pharmacy, Zunyi Medical University, Zunyi, China
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14
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Samtiya M, Matthews KR, Dhewa T, Puniya AK. Antimicrobial Resistance in the Food Chain: Trends, Mechanisms, Pathways, and Possible Regulation Strategies. Foods 2022; 11:2966. [PMID: 36230040 PMCID: PMC9614604 DOI: 10.3390/foods11192966] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/09/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) remains of major interest for different types of food stakeholders since it can negatively impact human health on a global scale. Antimicrobial-resistant bacteria and/or antimicrobial resistance genes (transfer in pathogenic bacteria) may contaminate food at any stage, from the field to retail. Research demonstrates that antimicrobial-resistant bacterial infection(s) occur more frequently in low- and middle-income countries (LMICs) than in developed countries. Worldwide, foodborne pathogens are a primary cause of morbidity and mortality. The spread of pathogenic bacteria from food to consumers may occur by direct or indirect routes. Therefore, an array of approaches both at the national and international level to control the spread of foodborne pathogens and promote food safety and security are essential. Zoonotic microbes can spread through the environment, animals, humans, and the food chain. Antimicrobial drugs are used globally to treat infections in humans and animals and prophylactically in production agriculture. Research highlights that foods may become contaminated with AMR bacteria (AMRB) during the continuum from the farm to processing to retail to the consumer. To mitigate the risk of AMRB in humans, it is crucial to control antibiotic use throughout food production, both for animal and crop agriculture. The main inferences of this review are (1) routes by which AMRB enters the food chain during crop and animal production and other modes, (2) prevention and control steps for AMRB, and (3) impact on human health if AMR is not addressed globally. A thorough perspective is presented on the gaps in current systems for surveillance of antimicrobial use in food production and/ or AMR in the food chain.
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Affiliation(s)
- Mrinal Samtiya
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh 123029, India
| | - Karl R. Matthews
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA
| | - Tejpal Dhewa
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh 123029, India
| | - Anil Kumar Puniya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal 132001, India
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15
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Akunuri R, Unnissa T, Vadakattu M, Bujji S, Mahammad Ghouse S, Madhavi Yaddanapudi V, Chopra S, Nanduri S. Bacterial Pyruvate Kinase: A New Potential Target to Combat Drug‐Resistant
Staphylococcus aureus
Infections. ChemistrySelect 2022. [DOI: 10.1002/slct.202201403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ravikumar Akunuri
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Tanveer Unnissa
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Manasa Vadakattu
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Sushmitha Bujji
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Shaik Mahammad Ghouse
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Venkata Madhavi Yaddanapudi
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Sidharth Chopra
- Division of Molecular Microbiology and Immunology CSIR-Central Drug Research Institute (CDRI) Sitapur Road, Sector 10, Janakipuram Extension Lucknow 226 031, Uttar Pradesh India
| | - Srinivas Nanduri
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
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16
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Tuon FF, Dantas LR, Suss PH, Tasca Ribeiro VS. Pathogenesis of the Pseudomonas aeruginosa Biofilm: A Review. Pathogens 2022; 11:pathogens11030300. [PMID: 35335624 PMCID: PMC8950561 DOI: 10.3390/pathogens11030300] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/08/2022] [Accepted: 02/24/2022] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa is associated with several human infections, mainly related to healthcare services. In the hospital, it is associated with resistance to several antibiotics, which poses a great challenge to therapy. However, one of the biggest challenges in treating P. aeruginosa infections is that related to biofilms. The complex structure of the P. aeruginosa biofilm contributes an additional factor to the pathogenicity of this microorganism, leading to therapeutic failure, in addition to escape from the immune system, and generating chronic infections that are difficult to eradicate. In this review, we address several molecular aspects of the pathogenicity of P. aeruginosa biofilms.
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17
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Privalsky TM, Soohoo AM, Wang J, Walsh CT, Wright GD, Gordon EM, Gray NS, Khosla C. Prospects for Antibacterial Discovery and Development. J Am Chem Soc 2021; 143:21127-21142. [PMID: 34860516 PMCID: PMC8855840 DOI: 10.1021/jacs.1c10200] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The rising prevalence of multidrug-resistant bacteria is an urgent health crisis that can only be countered through renewed investment in the discovery and development of antibiotics. There is no panacea for the antibacterial resistance crisis; instead, a multifaceted approach is called for. In this Perspective we make the case that, in the face of evolving clinical needs and enabling technologies, numerous validated antibacterial targets and associated lead molecules deserve a second look. At the same time, many worthy targets lack good leads despite harboring druggable active sites. Creative and inspired techniques buoy discovery efforts; while soil screening efforts frequently lead to antibiotic rediscovery, researchers have found success searching for new antibiotic leads by studying underexplored ecological niches or by leveraging the abundance of available data from genome mining efforts. The judicious use of "polypharmacology" (i.e., the ability of a drug to alter the activities of multiple targets) can also provide new opportunities, as can the continued search for inhibitors of resistance enzymes with the capacity to breathe new life into old antibiotics. We conclude by highlighting available pharmacoeconomic models for antibacterial discovery and development while making the case for new ones.
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Affiliation(s)
- Thomas M. Privalsky
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Alexander M. Soohoo
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 United States
| | - Christopher T. Walsh
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Eric M. Gordon
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States
- Department of Medicine, Stanford University, Stanford, CA 94305, United States
| | - Nathanael S. Gray
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, United States
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States
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18
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Zhou K, Liang J, Dong X, Zhang P, Feng C, Shi W, Gao M, Li Q, Zhang X, Lu J, Lin X, Li K, Zhang H, Zhu M, Bao Q. Identification and Characterization of a Novel Chromosomal Aminoglycoside 2'- N-Acetyltransferase, AAC(2')-If, From an Isolate of a Novel Providencia Species, Providencia wenzhouensis R33. Front Microbiol 2021; 12:711037. [PMID: 34867838 PMCID: PMC8640171 DOI: 10.3389/fmicb.2021.711037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/08/2021] [Indexed: 11/15/2022] Open
Abstract
Multidrug-resistant bacteria from different sources have been steadily emerging, and an increasing number of resistance mechanisms are being uncovered. In this work, we characterized a novel resistance gene named aac(2′)-If from an isolate of a novel Providencia species, Providencia wenzhouensis R33 (CCTCC AB 2021339). Susceptibility testing and enzyme kinetic parameter analysis were conducted to determine the function of the aminoglycoside 2′-N-acetyltransferase. Whole-genome sequencing and comparative genomic analysis were performed to elucidate the molecular characteristics of the genome and the genetic context of the resistance gene-related sequences. Among the functionally characterized resistance genes, AAC(2′)-If shares the highest amino acid sequence identity of 70.79% with AAC(2′)-Ia. AAC(2′)-If confers resistance to several aminoglycoside antibiotics, showing the highest resistance activity against ribostamycin and neomycin. The recombinant strain harboring aac(2′)-If (pUCP20-aac(2′)-If/DH5α) showed 256- and 128-fold increases in the minimum inhibitory concentration (MIC) levels to ribostamycin and neomycin, respectively, compared with those of the control strains (DH5α and pUCP20/DH5α). The results of the kinetic analysis of AAC(2′)-If were consistent with the MIC results of the cloned aac(2′)-If with the highest catalytic efficiency for ribostamycin (kcat/Km ratio = [3.72 ± 0.52] × 104 M–1⋅s–1). Whole-genome sequencing demonstrated that the aac(2′)-If gene was located on the chromosome with a relatively unique genetic environment. Identification of a novel aminoglycoside resistance gene in a strain of a novel Providencia species will help us find ways to elucidate the complexity of resistance mechanisms in the microbial population.
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Affiliation(s)
- Kexin Zhou
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jialei Liang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xu Dong
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Peiyao Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Mei Zhu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Qiyu Bao
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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19
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Boy C, Lesage J, Alfenore S, Guillouet SE, Gorret N. Investigation of the robustness of Cupriavidus necator engineered strains during fed-batch cultures. AMB Express 2021; 11:151. [PMID: 34783891 PMCID: PMC8595445 DOI: 10.1186/s13568-021-01307-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 11/10/2022] Open
Abstract
It is of major interest to ensure stable and performant microbial bioprocesses, therefore maintaining high strain robustness is one of the major future challenges in industrial microbiology. Strain robustness can be defined as the persistence of genotypic and/or phenotypic traits in a system. In this work, robustness of an engineered strain is defined as plasmid expression stability, cultivability, membrane integrity and macroscopic cell behavior and was assessed in response to implementations of sugar feeding strategies (pulses and continuous) and two plasmid stabilization systems (kanamycin resistance and Post-Segregational Killing hok/sok). Fed-batch bioreactor cultures, relevant mode to reach high cell densities and higher cell generation number, were implemented to investigate the robustness of C. necator engineered strains. Host cells bore a recombinant plasmid encoding for a plasmid expression level monitoring system, based on eGFP fluorescence quantified by flow cytometry. We first showed that well-controlled continuous feeding in comparison to a pulse-based feeding allowed a better carbon use for protein synthesis (avoiding organic acid excretion), a lower heterogeneity of the plasmid expression and a lower cell permeabilization. Moreover, the plasmid stabilization system Post-Segregational Killing hok/sok, an autonomous system independent on external addition of compounds, showed the best ability to maintain plasmid expression level stability insuring a greater population homogeneity in the culture. Therefore, in the case of engineered C. necator, the PSK system hok/sok appears to be a relevant and an efficient alternative to antibiotic resistance system for selection pressure, especially, in the case of bioprocess development for economic and environmental reasons.
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20
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Long F, Cheung CY, Whitman WB, Cook GM, Ronimus RS. Using genome comparisons of wild-type and resistant mutants of Methanococcus maripaludis to help understand mechanisms of resistance to methane inhibitors. Access Microbiol 2021; 3:000244. [PMID: 34595395 PMCID: PMC8479958 DOI: 10.1099/acmi.0.000244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 06/08/2021] [Indexed: 11/24/2022] Open
Abstract
Methane emissions from enteric fermentation in the ruminant digestive system generated by methanogenic archaea are a significant contributor to anthropogenic greenhouse gas emissions. Additionally, methane produced as an end-product of enteric fermentation is an energy loss from digested feed. To control the methane emissions from ruminants, extensive research in the last decades has been focused on developing viable enteric methane mitigation practices, particularly, using methanogen-specific inhibitors. We report here the utilization of two known inhibitors of methanogenic archaea, neomycin and chloroform, together with a recently identified inhibitor, echinomycin, to produce resistant mutants of Methanococcus maripaludis S2 and S0001. Whole-genome sequencing at high coverage (> 100-fold) was performed subsequently to investigate the potential targets of these inhibitors at the genomic level. Upon analysis of the whole-genome sequencing data, we identified mutations in a number of genetic loci pointing to potential mechanisms of inhibitor action and their underlying mechanisms of resistance.
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Affiliation(s)
- Feng Long
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Present address: Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH, USA
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ron S Ronimus
- Rumen Microbiology, AgResearch Ltd., Palmerston North, New Zealand
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21
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Wang Y, Wang Y, Zhang Z, Turap Y, Wang Y, Wang I, Wang Z, Wang W. Combined hydrothermal treatment, pyrolysis, and anaerobic digestion for removal of antibiotic resistance genes and energy recovery from antibiotic fermentation residues. BIORESOURCE TECHNOLOGY 2021; 337:125413. [PMID: 34175766 DOI: 10.1016/j.biortech.2021.125413] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
A process combining hydrothermal treatment (HT), pyrolysis, and anaerobic digestion can efficiently treat antibiotic fermentation residues (AFR). The process characteristics and antibiotic resistance genes (ARGs) removal efficiencies of each unit have been investigated. HT of 180 °C improved the biodegradability and dewaterability of the AFR. Pyrolysis of 500 °C and upflow anaerobic sludge blanket (UASB) of 6.5 ± 0.5 kg COD•(m3•d)-1 recovered the organic matter in filter cake and filtrate of AFR. The biogas and pyrolysis gas can compensate the energy this system needs. HT of 180 °C could reduce 16S rRNA, ARGs, and mobile genetic elements (MGEs) by 2.3 to 7.4 logs. UASB increased the copy numbers of ARGs and MGEs, but the relative abundances of ARGs normalized against 16S rRNA were significantly declined. The ARGs and MGEs were enriched in suspended solids of digestate. The application of this process can promote the resources recycling of fermentation waste.
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Affiliation(s)
- Yidi Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yongya Wang
- School of Environment, Tsinghua University, Beijing 100084, China; Department of Material Chemistry, Huzhou University, Huzhou 313000, China
| | - Zhe Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yusan Turap
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yongkang Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Iwei Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhentong Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Wei Wang
- School of Environment, Tsinghua University, Beijing 100084, China.
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22
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Role of Aminoglycoside-Modifying Enzymes (AMEs) in Resistance to Aminoglycosides among Clinical Isolates of Pseudomonas aeruginosa in the North of Iran. BIOMED RESEARCH INTERNATIONAL 2021; 2021:7077344. [PMID: 34471641 PMCID: PMC8405309 DOI: 10.1155/2021/7077344] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 08/07/2021] [Indexed: 11/18/2022]
Abstract
In recent years, the prevalence of resistance to aminoglycosides among clinical isolates of Pseudomonas aeruginosa is increasing. The aim of this study was to investigate the role of aminoglycoside-modifying enzymes (AMEs) in resistance to aminoglycosides in clinical isolates of P. aeruginosa. The clinical isolates were collected from different hospitals. Disk agar diffusion test was used to determine the antimicrobial resistance pattern of the clinical isolates, and the minimum inhibitory concentration of aminoglycosides was detected by microbroth dilution method. The PCR was performed for discovery of aminoglycoside-modifying enzyme-encoding genes. Among 100 screened isolates, 43 (43%) isolates were resistant to at least one tested aminoglycosides. However, 13 (13%) isolates were resistant to all tested aminoglycosides and 37 isolates were detected as multidrug resistant (MDR). The resistance rates of P. aeruginosa isolates against tested antibiotics were as follows: ciprofloxacin (41%), piperacillin-tazobactam (12%), cefepime (32%), piperacillin (26%), and imipenem (31%). However, according to the MIC method, 13%, 32%, 33%, and 37% of the isolates were resistant to amikacin, gentamicin, tobramycin, and netilmicin, respectively. The PCR results showed that AAC(6')-Ib was the most commonly (26/43, 60.4%) identified AME-encoding gene followed by AAC(6')-IIa (41.86%), APH(3')-IIb (34.8%), ANT(3 ″ )-Ia (18.6), ANT(2 ″ )-Ia (13.95%), and APH(3 ″ )-Ib (2.32%). However, APH(3')-Ib was not found in any of the studied isolates. The high prevalence of AME-encoding genes among aminoglycoside-resistant P. aeruginosa isolates in this area indicated the important role of AMEs in resistance to these antibiotics similar to most studies worldwide. Due to the transmission possibility of these genes between the Gram-negative bacteria, we need to control the prescription of aminoglycosides in hospitals.
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23
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Yeh YC, Kim HJ, Liu HW. Mechanistic Investigation of 1,2-Diol Dehydration of Paromamine Catalyzed by the Radical S-Adenosyl-l-methionine Enzyme AprD4. J Am Chem Soc 2021; 143:5038-5043. [PMID: 33784078 DOI: 10.1021/jacs.1c00076] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AprD4 is a radical S-adenosyl-l-methionine (SAM) enzyme catalyzing C3'-deoxygenation of paromamine to form 4'-oxo-lividamine. It is the only 1,2-diol dehydratase in the radical SAM enzyme superfamily that has been identified and characterized in vitro. The AprD4 catalyzed 1,2-diol dehydration is a key step in the biosynthesis of several C3'-deoxy-aminoglycosides. While the regiochemistry of the hydrogen atom abstraction catalyzed by AprD4 has been established, the mechanism of the subsequent chemical transformation remains not fully understood. To investigate the mechanism, several substrate analogues were synthesized and their fates upon incubation with AprD4 were analyzed. The results support a mechanism involving formation of a ketyl radical intermediate followed by direct elimination of the C3'-hydroxyl group rather than that of a gem-diol intermediate generated via 1,2-migration of the C3'-hydroxyl group to C4'. The stereochemistry of hydrogen atom incorporation after radical-mediated dehydration was also established.
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Affiliation(s)
- Yu-Cheng Yeh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hak Joong Kim
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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24
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Liu Y, Tong Z, Shi J, Li R, Upton M, Wang Z. Drug repurposing for next-generation combination therapies against multidrug-resistant bacteria. Theranostics 2021; 11:4910-4928. [PMID: 33754035 PMCID: PMC7978324 DOI: 10.7150/thno.56205] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance has been a global health challenge that threatens our ability to control and treat life-threatening bacterial infections. Despite ongoing efforts to identify new drugs or alternatives to antibiotics, no new classes of antibiotic or their alternatives have been clinically approved in the last three decades. A combination of antibiotics and non-antibiotic compounds that could inhibit bacterial resistance determinants or enhance antibiotic activity offers a sustainable and effective strategy to confront multidrug-resistant bacteria. In this review, we provide a brief overview of the co-evolution of antibiotic discovery and the development of bacterial resistance. We summarize drug-drug interactions and uncover the art of repurposing non-antibiotic drugs as potential antibiotic adjuvants, including discussing classification and mechanisms of action, as well as reporting novel screening platforms. A pathogen-by-pathogen approach is then proposed to highlight the critical value of drug repurposing and its therapeutic potential. Finally, general advantages, challenges and development trends of drug combination strategy are discussed.
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Affiliation(s)
- Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ziwen Tong
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jingru Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Mathew Upton
- School of Biomedical Sciences, University of Plymouth, Drake Circus, Plymouth, UK
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
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25
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Abstract
Apramycin is an aminoglycoside antibiotic with the potential to be developed to combat multidrug-resistant pathogens. Its unique structure evades the clinically widespread mechanisms of aminoglycoside resistance that currently compromise the efficacy of other members in this drug class. Of the aminoglycoside-modifying enzymes that chemically alter these antibiotics, only AAC(3)-IVa has been demonstrated to confer resistance to apramycin through N-acetylation. Knowledge of other modification mechanisms is important to successfully develop apramycin for clinical use. Here, we show that ApmA is structurally unique among the previously described aminoglycoside-modifying enzymes and capable of conferring a high level of resistance to apramycin. In vitro experiments indicated ApmA to be an N-acetyltransferase, but in contrast to AAC(3)-IVa, ApmA has a unique regiospecificity of the acetyl transfer to the N2' position of apramycin. Crystallographic analysis of ApmA conclusively showed that this enzyme is an acetyltransferase from the left-handed β-helix protein superfamily (LβH) with a conserved active site architecture. The success of apramycin will be dependent on consideration of the impact of this potential form of clinical resistance.IMPORTANCE Apramycin is an aminoglycoside antibiotic that has been traditionally used in veterinary medicine. Recently, it has become an attractive candidate to repurpose in the fight against multidrug-resistant pathogens prioritized by the World Health Organization. Its atypical structure circumvents most of the clinically relevant mechanisms of resistance that impact this class of antibiotics. Prior to repurposing apramycin, it is important to understand the resistance mechanisms that could be a liability. Our study characterizes the most recently identified apramycin resistance element, apmA We show ApmA does not belong to the protein families typically associated with aminoglycoside resistance and is responsible for modifying a different site on the molecule. The data presented will be critical in the development of apramycin derivatives that will evade apmA in the event it becomes prevalent in the clinic.
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26
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Jeong CS, Hwang J, Do H, Cha SS, Oh TJ, Kim HJ, Park HH, Lee JH. Structural and biochemical analyses of an aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis. Sci Rep 2020; 10:21503. [PMID: 33299080 PMCID: PMC7725843 DOI: 10.1038/s41598-020-78699-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/27/2020] [Indexed: 11/22/2022] Open
Abstract
The expression of aminoglycoside-modifying enzymes represents a survival strategy of antibiotic-resistant bacteria. Aminoglycoside 2′-N-acetyltransferase [AAC(2′)] neutralizes aminoglycoside drugs by acetylation of their 2′ amino groups in an acetyl coenzyme A (CoA)-dependent manner. To understand the structural features and molecular mechanism underlying AAC(2′) activity, we overexpressed, purified, and crystallized AAC(2′) from Mycolicibacterium smegmatis [AAC(2′)-Id] and determined the crystal structures of its apo-form and ternary complexes with CoA and four different aminoglycosides (gentamicin, sisomicin, neomycin, and paromomycin). These AAC(2′)-Id structures unraveled the binding modes of different aminoglycosides, explaining the broad substrate specificity of the enzyme. Comparative structural analysis showed that the α4-helix and β8–β9 loop region undergo major conformational changes upon CoA and substrate binding. Additionally, structural comparison between the present paromomycin-bound AAC(2′)-Id structure and the previously reported paromomycin-bound AAC(6′)-Ib and 30S ribosome structures revealed the structural features of paromomycin that are responsible for its antibiotic activity and AAC binding. Taken together, these results provide useful information for designing AAC(2′) inhibitors and for the chemical modification of aminoglycosides.
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Affiliation(s)
- Chang-Sook Jeong
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Jisub Hwang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Republic of Korea.,Genome-Based BioIT Convergence Institute, Asan, 31460, Republic of Korea.,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, 31460, Republic of Korea
| | - Hak Jun Kim
- Department of Chemistry, Pukyong National University, 45 Yongso-ro, Busan, 48513, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul, 06974, Republic of Korea.
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea. .,Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
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27
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Jang H, Kwon S, Jeong CS, Lee CW, Hwang J, Jung KH, Lee JH, Park HH. Structural analysis of a novel substrate-free form of the aminoglycoside 6'-N-acetyltransferase from Enterococcus faecium. Acta Crystallogr F Struct Biol Commun 2020; 76:364-371. [PMID: 32744248 PMCID: PMC7397467 DOI: 10.1107/s2053230x20009735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022] Open
Abstract
Aminoglycoside acetyltransferases (AACs) catalyze the transfer of an acetyl group between acetyl-CoA and an aminoglycoside, producing CoA and an acetylated aminoglycoside. AAC(6')-Ii enzymes target the amino group linked to the 6' C atom in an aminoglycoside. Several structures of the AAC(6')-Ii from Enterococcus faecium [Ef-AAC(6')-Ii] have been reported to date. However, the detailed mechanism of its enzymatic function remains elusive. In this study, the crystal structure of Ef-AAC(6')-Ii was determined in a novel substrate-free form. Based on structural analysis, it is proposed that Ef-AAC(6')-Ii sequentially undergoes conformational selection and induced fit for substrate binding. These results therefore provide a novel viewpoint on the mechanism of action of Ef-AAC(6')-Ii.
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Affiliation(s)
- Hyunseok Jang
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Sunghark Kwon
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chang-Sook Jeong
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Chang Woo Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jisub Hwang
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Kyoung Ho Jung
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea
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28
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Selvaraj B, Kocaman S, Trifas M, Serpersu EH, Cuneo MJ. "Catch and Release": A Variation of the Archetypal Nucleotidyl Transfer Reaction. ACS Catal 2020; 10:3548-3555. [PMID: 38250052 PMCID: PMC10797667 DOI: 10.1021/acscatal.9b05201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nucleotidyl transfer is an archetypal enzyme reaction central to DNA replication and repair. Here we describe a variation of the nucleotidylation reaction termed "catch and release" that is used by an antibiotic modifying enzyme. The aminoglycoside nucleotidyl transferase 4' (ANT4') inactivates antibiotics such as kanamycin and neomycin through nucleotidylation within an active site that shares significant structural, and inferred underlying catalytic similarity, with human DNA polymerase beta. Here we follow the entire nucleotidyl transfer reaction coordinate of ANT4' covalently inactivating neomycin using X-ray crystallography. These studies show that although the underlying reaction mechanism is conserved with polymerases, a short 2.35 A hydrogen bond is initially formed to facilitate tight binding of the aminoglycoside substrate and is subsequently disrupted by the assembly of the catalytically active ternary complex. This enables the release of products post catalysis due to a lower free energy of the product state compared to the starting substrate complex. We propose that this "catch and release" mechanism of antibiotic turnover observed in ANT4' is a variation of nucleotidyl transfer that has been adapted for the inactivation of antibiotics.
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Affiliation(s)
- Brinda Selvaraj
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Seda Kocaman
- The Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, 1311 Cumberland Ave, Knoxville, Tennessee 37916, United States
| | - Maria Trifas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Engin H. Serpersu
- The Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, 1311 Cumberland Ave, Knoxville, Tennessee 37916, United States
- National Science Foundation, 2415 Eisenhower Avenue, Alexandria, Virginia 22314, United States
| | - Matthew J. Cuneo
- Department of Structural Biology, 262 Danny Thomas Pl, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
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29
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Functional and Structural Roles of the Major Facilitator Superfamily Bacterial Multidrug Efflux Pumps. Microorganisms 2020; 8:microorganisms8020266. [PMID: 32079127 PMCID: PMC7074785 DOI: 10.3390/microorganisms8020266] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/30/2020] [Accepted: 02/11/2020] [Indexed: 12/31/2022] Open
Abstract
Pathogenic microorganisms that are multidrug-resistant can pose severe clinical and public health concerns. In particular, bacterial multidrug efflux transporters of the major facilitator superfamily constitute a notable group of drug resistance mechanisms primarily because multidrug-resistant pathogens can become refractory to antimicrobial agents, thus resulting in potentially untreatable bacterial infections. The major facilitator superfamily is composed of thousands of solute transporters that are related in terms of their phylogenetic relationships, primary amino acid sequences, two- and three-dimensional structures, modes of energization (passive and secondary active), and in their mechanisms of solute and ion translocation across the membrane. The major facilitator superfamily is also composed of numerous families and sub-families of homologous transporters that are conserved across all living taxa, from bacteria to humans. Members of this superfamily share several classes of highly conserved amino acid sequence motifs that play essential mechanistic roles during transport. The structural and functional importance of multidrug efflux pumps that belong to the major facilitator family and that are harbored by Gram-negative and -positive bacterial pathogens are considered here.
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30
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Das B, Verma J, Kumar P, Ghosh A, Ramamurthy T. Antibiotic resistance in Vibrio cholerae: Understanding the ecology of resistance genes and mechanisms. Vaccine 2020; 38 Suppl 1:A83-A92. [DOI: 10.1016/j.vaccine.2019.06.031] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/11/2019] [Accepted: 06/04/2019] [Indexed: 11/29/2022]
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31
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Smith CA, Toth M, Stewart NK, Maltz L, Vakulenko SB. Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2''-phosphotransferases. Acta Crystallogr D Struct Biol 2019; 75:1129-1137. [PMID: 31793906 PMCID: PMC6889913 DOI: 10.1107/s2059798319015079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 11/10/2022] Open
Abstract
Aminoglycoside phosphotransferases (APHs) are one of three families of aminoglycoside-modifying enzymes that confer high-level resistance to the aminoglycoside antibiotics via enzymatic modification. This has now rendered many clinically important drugs almost obsolete. The APHs specifically phosphorylate hydroxyl groups on the aminoglycosides using a nucleotide triphosphate as the phosphate donor. The APH(2'') family comprises four distinct members, isolated primarily from Enterococcus sp., which vary in their substrate specificities and also in their preference for the phosphate donor (ATP or GTP). The structure of the ternary complex of APH(2'')-IIIa with GDP and kanamycin was solved at 1.34 Å resolution and was compared with substrate-bound structures of APH(2'')-Ia, APH(2'')-IIa and APH(2'')-IVa. In contrast to the case for APH(2'')-Ia, where it was proposed that the enzyme-mediated hydrolysis of GTP is regulated by conformational changes in its N-terminal domain upon GTP binding, APH(2'')-IIa, APH(2'')-IIIa and APH(2'')-IVa show no such regulatory mechanism, primarily owing to structural differences in the N-terminal domains of these enzymes.
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Affiliation(s)
- Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Nichole K. Stewart
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Lauren Maltz
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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Verma A, Nayek A, Kumar A, Singh R, Salotra P. Elucidation of role of an acetyltransferase like protein in paromomycin resistance in Leishmania donovani using in silico and in vitro approaches. J Biomol Struct Dyn 2019; 38:4449-4460. [PMID: 31625467 DOI: 10.1080/07391102.2019.1682674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Paromomycin, an aminoglycoside antibiotic, is an effective treatment for VL (visceral leishmaniasis) in India. The modification of aminoglycoside antibiotics by enzymes such as aminoglycoside acetyltransferases is the predominant mechanism of resistance to antibiotics in bacterial system. In the present study, we identified and characterized LdATLP (an acetyltransferase-like protein) and elucidated its role in paromomycin resistance in Leishmania donovani. Gene encoding LdATLP was consistently up-regulated (>2fold) in three distinct paromomycin resistant in comparison with sensitive parasites, although the gene sequence was identical in the two. In silico analysis revealed that LdATLP consisted of conserved GNAT (GCN5-related N-Acetyltransferase) domain which is characteristic of aminoglycoside N-acetyltransferases. Evolutionary relationship among LdATLP of Leishmania and aminoglycoside acetyltransferases of bacteria was established by phylogenetic analysis. The 3D structure of LdATLP, predicted by ab-initio modeling, constituted 6 α-helices and 6 β-sheets. A few residues, such as R175, R177, E196, R197, V198, V200, K202, R205, C206, D208, G210, R211, R215, A234, S237, S238, K239, D240, F241 and Y242 of GNAT domain were predicted to be present at active site. Molecular docking of LdATLP with paromomycin or indolicidin (broad spectrum inhibitor of aminoglycoside modifying enzymes), followed by molecular dynamics simulation of docked complex suggested that both paromomycin and indolicidin bind to LdATLP with comparable free energy of binding. In vitro studies revealed that in the presence of indolicidin, paromomycin resistant parasites exhibited reversion of phenotype into sensitive parasites with marked increase in paromomycin susceptibility, suggesting the role of LdATLP in paromomycin resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aditya Verma
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India.,Faculty of Health and Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Arnab Nayek
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Amit Kumar
- ICMR Computational Genomics Center, Division of ISRM, ICMR, New Delhi, India
| | - Ruchi Singh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Poonam Salotra
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
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Doddam SN, Peddireddy V, Yerra P, Sai Arun PP, Qaria MA, Baddam R, Sarker N, Ahmed N. Mycobacterium tuberculosis DosR regulon gene Rv2004c contributes to streptomycin resistance and intracellular survival. Int J Med Microbiol 2019; 309:151353. [PMID: 31521502 DOI: 10.1016/j.ijmm.2019.151353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/26/2019] [Accepted: 08/29/2019] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis (TB) is the deadly infectious disease challenging the public health globally and its impact is further aggravated by co-infection with HIV and the emergence of drug resistant strains of Mycobacterium tuberculosis. In this study, we attempted to characterise the Rv2004c encoded protein, a member of DosR regulon, for its role in drug resistance. In silico docking analysis revealed that Rv2004c binds with streptomycin (SM). Phosphotransferase assay demonstrated that Rv2004c possibly mediates SM resistance through the aminoglycoside phosphotransferase activity. Further, E. coli expressing Rv2004c conferred resistance to 100μM of SM in liquid broth cultures indicating a mild aminoglycoside phosphotransferase activity of Rv2004c. Moreover, we investigated the role of MSMEG_3942 (an orthologous gene of Rv2004c) encoded protein in intracellular survival, its effect on in-vitro growth and its expression in different stress conditions by over expressing it in Mycobacterium smegmatis (M. smegmatis). MSMEG_3942 overexpressing recombinant M. smegmatis strains grew faster in acidic medium and also showed higher bacillary counts in infected macrophages when compared to M. smegmatis transformed with vector alone. Our results are likely to contribute to the better understanding of the involvement of Rv2004c in partial drug resistance, intracellular survival and adaptation of bacilli to stress conditions.
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Affiliation(s)
- Sankara Narayana Doddam
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, 500046, India
| | - Vidyullatha Peddireddy
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, 500046, India; Department of Microbiology & FST, GITAM Institute of Science, GITAM Deemed University, Visakhapatnam, Andhra Pradesh, 530045, India.
| | - Priyadarshini Yerra
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, 500046, India
| | - Pv Parvati Sai Arun
- Department of Biotechnology, Chaitanya Bharathi Institute of Technology, Gandipet, Hyderabad, Telangana, 500075, India
| | - Majjid A Qaria
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, 500046, India
| | - Ramani Baddam
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nishat Sarker
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, 500046, India; Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.
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Molecules that Inhibit Bacterial Resistance Enzymes. Molecules 2018; 24:molecules24010043. [PMID: 30583527 PMCID: PMC6337270 DOI: 10.3390/molecules24010043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/14/2022] Open
Abstract
Antibiotic resistance mediated by bacterial enzymes constitutes an unmet clinical challenge for public health, particularly for those currently used antibiotics that are recognized as "last-resort" defense against multidrug-resistant (MDR) bacteria. Inhibitors of resistance enzymes offer an alternative strategy to counter this threat. The combination of inhibitors and antibiotics could effectively prolong the lifespan of clinically relevant antibiotics and minimize the impact and emergence of resistance. In this review, we first provide a brief overview of antibiotic resistance mechanism by bacterial secreted enzymes. Furthermore, we summarize the potential inhibitors that sabotage these resistance pathways and restore the bactericidal activity of inactive antibiotics. Finally, the faced challenges and an outlook for the development of more effective and safer resistance enzyme inhibitors are discussed.
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Serio AW, Keepers T, Andrews L, Krause KM. Aminoglycoside Revival: Review of a Historically Important Class of Antimicrobials Undergoing Rejuvenation. EcoSal Plus 2018; 8. [PMID: 30447062 PMCID: PMC11575671 DOI: 10.1128/ecosalplus.esp-0002-2018] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Indexed: 01/04/2023]
Abstract
Aminoglycosides are cidal inhibitors of bacterial protein synthesis that have been utilized for the treatment of serious bacterial infections for almost 80 years. There have been approximately 15 members of this class approved worldwide for the treatment of a variety of infections, many serious and life threatening. While aminoglycoside use declined due to the introduction of other antibiotic classes such as cephalosporins, fluoroquinolones, and carbapenems, there has been a resurgence of interest in the class as multidrug-resistant pathogens have spread globally. Furthermore, aminoglycosides are recommended as part of combination therapy for empiric treatment of certain difficult-to-treat infections. The development of semisynthetic aminoglycosides designed to overcome common aminoglycoside resistance mechanisms, and the shift to once-daily dosing, has spurred renewed interest in the class. Plazomicin is the first new aminoglycoside to be approved by the FDA in nearly 40 years, marking the successful start of a new campaign to rejuvenate the class.
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Antibiotic-Resistant Escherichia coli and Class 1 Integrons in Humans, Domestic Animals, and Wild Primates in Rural Uganda. Appl Environ Microbiol 2018; 84:AEM.01632-18. [PMID: 30171005 DOI: 10.1128/aem.01632-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/27/2018] [Indexed: 11/20/2022] Open
Abstract
Antibiotic resistance is a global concern, although it has been studied most extensively in developed countries. We studied Escherichia coli and class 1 integrons in western Uganda by analyzing 1,685 isolates from people, domestic animals, and wild nonhuman primates near two national parks. Overall, 499 isolates (29.6%) were resistant to at least one of 11 antibiotics tested. The frequency of resistance reached 20.3% of isolates for trimethoprim-sulfamethoxazole but was nearly zero for the less commonly available antibiotics ciprofloxacin (0.4%), gentamicin (0.2%), and ceftiofur (0.1%). The frequency of resistance was 57.4% in isolates from people, 19.5% in isolates from domestic animals, and 16.3% in isolates from wild nonhuman primates. Isolates of livestock and primate origin displayed multidrug resistance patterns identical to those of human-origin isolates. The percentage of resistant isolates in people was higher near Kibale National Park (64.3%) than near Bwindi Impenetrable National Park (34.6%), perhaps reflecting local socioeconomic or ecological conditions. Across antibiotics, resistance correlated negatively with the local price of the antibiotic, with the most expensive antibiotics (nalidixic acid and ciprofloxacin) showing near-zero resistance. Among phenotypically resistant isolates, 33.2% harbored class 1 integrons containing 11 common resistance genes arranged into nine distinct gene cassettes, five of which were present in isolates from multiple host species. Overall, these results show that phenotypic resistance and class 1 integrons are distributed broadly among E. coli isolates from different host species in this region, where local socioeconomic and ecological conditions may facilitate widespread diffusion of bacteria or resistance-conferring genetic elements.IMPORTANCE Antibiotic resistance is a global problem. This study, conducted in rural western Uganda, describes antibiotic resistance patterns in Escherichia coli bacteria near two forested national parks. Resistance was present not only in people, but also in their livestock and in nearby wild nonhuman primates. Multidrug resistance and class 1 integrons containing genes that confer resistance were common and were similar in people and animals. The percentage of resistant isolates decreased with increasing local price of the antibiotic. Antibiotic resistance in this setting likely reflects environmental diffusion of bacteria or their genes, perhaps facilitated by local ecological and socioeconomic conditions.
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Cox G, Ejim L, Stogios PJ, Koteva K, Bordeleau E, Evdokimova E, Sieron AO, Savchenko A, Serio AW, Krause KM, Wright GD. Plazomicin Retains Antibiotic Activity against Most Aminoglycoside Modifying Enzymes. ACS Infect Dis 2018; 4:980-987. [PMID: 29634241 DOI: 10.1021/acsinfecdis.8b00001] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Plazomicin is a next-generation, semisynthetic aminoglycoside antibiotic currently under development for the treatment of infections due to multidrug-resistant Enterobacteriaceae. The compound was designed by chemical modification of the natural product sisomicin to provide protection from common aminoglycoside modifying enzymes that chemically alter these drugs via N-acetylation, O-adenylylation, or O-phosphorylation. In this study, plazomicin was profiled against a panel of isogenic strains of Escherichia coli individually expressing twenty-one aminoglycoside resistance enzymes. Plazomicin retained antibacterial activity against 15 of the 17 modifying enzyme-expressing strains tested. Expression of only two of the modifying enzymes, aac(2')-Ia and aph(2″)-IVa, decreased plazomicin potency. On the other hand, expression of 16S rRNA ribosomal methyltransferases results in a complete lack of plazomicin potency. In vitro enzymatic assessment confirmed that AAC(2')-Ia and APH(2'')-IVa (aminoglycoside acetyltransferase, AAC; aminoglycoside phosphotransferase, APH) were able to utilize plazomicin as a substrate. AAC(2')-Ia and APH(2'')-IVa are limited in their distribution to Providencia stuartii and Enterococci, respectively. These data demonstrate that plazomicin is not modified by a broad spectrum of common aminoglycoside modifying enzymes including those commonly found in Enterobacteriaceae. However, plazomicin is inactive in the presence of 16S rRNA ribosomal methyltransferases, which should be monitored in future surveillance programs.
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Affiliation(s)
- Georgina Cox
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Linda Ejim
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Peter J. Stogios
- Center for Structural Genomics of Infectious Diseases (CSGID) and Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Kalinka Koteva
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Emily Bordeleau
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Elena Evdokimova
- Center for Structural Genomics of Infectious Diseases (CSGID) and Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Arthur O. Sieron
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID) and Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Health Research Innovation Centre, University of Calgary, 3330 Hospital Drive NW, HRIC-2C66, Calgary, Alberta T2N 4N1, Canada
| | - Alisa W. Serio
- Achaogen, One Tower Place, Suite 300, South San Francisco, California 94080, United States
| | - Kevin M. Krause
- Achaogen, One Tower Place, Suite 300, South San Francisco, California 94080, United States
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
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Subedi YP, AlFindee MN, Takemoto JY, Chang CWT. Antifungal amphiphilic kanamycins: new life for an old drug. MEDCHEMCOMM 2018; 9:909-919. [PMID: 30108980 PMCID: PMC6071784 DOI: 10.1039/c8md00155c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/15/2018] [Indexed: 11/21/2022]
Abstract
Classical aminoglycoside antibiotics are obsolete or hampered by the emergence of drug resistant bacteria. Recent discoveries of antifungal amphiphilic kanamycins offer new strategies for reviving and repurposing these old drugs. A simple structural modification turns the clinically obsolete antibacterial kanamycin into an antifungal agent. Structure-activity relationship studies have led to the production of K20, an antifungal kanamycin that can be mass-produced for uses in agriculture as well as in animals. This review delineates the path to the discovery of K20 and other related antifungal amphiphilic kanamycins, determination of its mode of action, and findings in greenhouse and field trials with K20 that could lead to crop disease protection strategies.
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Affiliation(s)
- Yagya Prasad Subedi
- Department of Chemistry and Biochemistry , Utah State University , 0300 Old Main Hill , Logan , Utah 84322-0300 , USA .
| | - Madher N AlFindee
- Department of Chemistry and Biochemistry , Utah State University , 0300 Old Main Hill , Logan , Utah 84322-0300 , USA .
| | - Jon Y Takemoto
- Department of Biology , Utah State University , 5305 Old Main Hill , Logan , Utah 84322-5305 , USA
| | - Cheng-Wei Tom Chang
- Department of Chemistry and Biochemistry , Utah State University , 0300 Old Main Hill , Logan , Utah 84322-0300 , USA .
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Ojdana D, Sieńko A, Sacha P, Majewski P, Wieczorek P, Wieczorek A, Tryniszewska E. Genetic basis of enzymatic resistance of E. coli to aminoglycosides. Adv Med Sci 2018; 63:9-13. [PMID: 28763677 DOI: 10.1016/j.advms.2017.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/10/2017] [Accepted: 05/21/2017] [Indexed: 11/30/2022]
Abstract
PURPOSE Over the past years, an increase in resistance to aminoglycosides has been observed among Enterobacteriaceae rods. This resistance development reduces therapeutic options for infections caused by multidrug-resistance organisms. Because of the changing epidemiology of extended-spectrum β-lactamases (ESBLs) and resistance to aminoglycosides, we investigated the prevalence of the aac(3)-Ia, aac(6')-Ib, ant(4')-IIa, ant(2")-Ia, and aph(3")-Ib genes encoding aminoglycoside-modifying enzymes (AMEs) in ESBL-producing Escherichia coli as well as ESBL-non-producing isolates. To understand bacterial resistance to aminoglycoside antibiotics, we estimated resistance phenotypes and the presence of genes responsible for this resistance. MATERIALS AND METHODS The study was conducted on 44 E.coli strains originated from patients hospitalized at University Hospital of Bialystok. MIC values were obtained for gentamicin, amikacin, netilmicin, and tobramycin. Isolates were tested for the presence of the aac(3)-Ia, aac(6')-Ib, ant(4')-IIa, ant(2")-Ia, and aph(3")-Ib genes with the use of the PCR technique. RESULTS Resistance to aminoglycosides was found in 79.5% of the isolates. The highest percentages of resistance were observed for tobramycin (70,5%) and gentamicin (59%), followed by netilmicin (43.2%) and amikacin (11.4%). PCR assays revealed the presence of aac(6')-Ib among 26 (59.2%) strains, aph(3")-Ib among 16 (36.2%), aac(3)-Ia among 7 (15.9%), and ant(2")-Ia among 2 (4.6%) strains. CONCLUSIONS The enzymatic resistance against aminoglycosides in northeastern Poland among clinical isolates of E. coli is predominantly caused by aac(6')-Ib and aph(3")-Ib. Amikacin may be used for therapy of infections caused by ESBL-producing E. coli, because of the low rates of resistance.
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Affiliation(s)
- Dominika Ojdana
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland.
| | - Anna Sieńko
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Paweł Sacha
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Piotr Majewski
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Piotr Wieczorek
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Wieczorek
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Elżbieta Tryniszewska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
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Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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Green KD, Biswas T, Pang AH, Willby MJ, Reed MS, Stuchlik O, Pohl J, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight. Biochemistry 2018; 57:781-790. [PMID: 29345920 DOI: 10.1021/acs.biochem.7b01089] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD+-dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics. We propose that activities of Eis and Rv1151c could regulate the acetylation status of HupB to remodel the mycobacterial chromosome in response to environmental changes.
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Affiliation(s)
- Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | | | | | | | | | | | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
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Foster TJ. Antibiotic resistance in Staphylococcus aureus. Current status and future prospects. FEMS Microbiol Rev 2018; 41:430-449. [PMID: 28419231 DOI: 10.1093/femsre/fux007] [Citation(s) in RCA: 456] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/12/2017] [Indexed: 12/11/2022] Open
Abstract
The major targets for antibiotics in staphylococci are (i) the cell envelope, (ii) the ribosome and (iii) nucleic acids. Several novel targets emerged from recent targeted drug discovery programmes including the ClpP protease and FtsZ from the cell division machinery. Resistance can either develop by horizontal transfer of resistance determinants encoded by mobile genetic elements viz plasmids, transposons and the staphylococcal cassette chromosome or by mutations in chromosomal genes. Horizontally acquired resistance can occur by one of the following mechanisms: (i) enzymatic drug modification and inactivation, (ii) enzymatic modification of the drug binding site, (iii) drug efflux, (iv) bypass mechanisms involving acquisition of a novel drug-resistant target, (v) displacement of the drug to protect the target. Acquisition of resistance by mutation can result from (i) alteration of the drug target that prevents the inhibitor from binding, (ii) derepression of chromosomally encoded multidrug resistance efflux pumps and (iii) multiple stepwise mutations that alter the structure and composition of the cell wall and/or membrane to reduce drug access to its target. This review focuses on development of resistance to currently used antibiotics and examines future prospects for new antibiotics and informed use of drug combinations.
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van Duijkeren E, Schink AK, Roberts MC, Wang Y, Schwarz S. Mechanisms of Bacterial Resistance to Antimicrobial Agents. Microbiol Spectr 2018; 6:10.1128/microbiolspec.arba-0019-2017. [PMID: 29327680 PMCID: PMC11633570 DOI: 10.1128/microbiolspec.arba-0019-2017] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Indexed: 12/31/2022] Open
Abstract
During the past decades resistance to virtually all antimicrobial agents has been observed in bacteria of animal origin. This chapter describes in detail the mechanisms so far encountered for the various classes of antimicrobial agents. The main mechanisms include enzymatic inactivation by either disintegration or chemical modification of antimicrobial agents, reduced intracellular accumulation by either decreased influx or increased efflux of antimicrobial agents, and modifications at the cellular target sites (i.e., mutational changes, chemical modification, protection, or even replacement of the target sites). Often several mechanisms interact to enhance bacterial resistance to antimicrobial agents. This is a completely revised version of the corresponding chapter in the book Antimicrobial Resistance in Bacteria of Animal Origin published in 2006. New sections have been added for oxazolidinones, polypeptides, mupirocin, ansamycins, fosfomycin, fusidic acid, and streptomycins, and the chapters for the remaining classes of antimicrobial agents have been completely updated to cover the advances in knowledge gained since 2006.
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Affiliation(s)
- Engeline van Duijkeren
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Anne-Kathrin Schink
- Institute of Microbiology and Epizootics, Centre of Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195-7234
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre of Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
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Ezeokonkwo MA, Ogbonna ON, Okafor SN, Godwin-Nwakwasi EU, Ibeanu FN, Okoro UC. Angular Phenozaxine Ethers as Potent Multi-microbial Targets Inhibitors: Design, Synthesis, and Molecular Docking Studies. Front Chem 2017; 5:107. [PMID: 29238706 PMCID: PMC5712349 DOI: 10.3389/fchem.2017.00107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/13/2017] [Indexed: 01/25/2023] Open
Abstract
The reaction of diaza-5H-benzo[a]phenoxazin-5-one and 5H-benzo[a]phenoxazin-5-one with various phenols catalyzed by Pd/t-BuXPhos/K3PO4 system gave previously unknown ether derivatives (7a-f and 8a-f) in good yields. UV-visible, FTIR, and 1H NMR data were used to confirm structures of the synthesized compounds. The parent compounds and the derivatives were screened in-silico for their drug-likeness and binding affinities to the microbial targets through molecular docking. Molinspiration software and AutoDock were used for the drug-likeness and docking studies, respectively. All the synthesized compounds showed strong drug-likeness. They also showed excellent binding affinities with glucosamine-6-phosphate synthase (2VF5), AmpC beta-lactamase (1KE4), and Lanosterol-14α-demethylase (3JUV), with compound 7e having the highest binding energies -9.5, -9.3, and -9.3 kcal/mol, respectively. These were found to be higher than the binding energies of the standard drugs. The binding energies of ciprofloxacin with 2VF5 and 1KE4 were -7.8 and -7.5 kcal/mol, respectively, while that of ketoconazole with 3JUV was -8.6 kcal/mol. The study showed that the synthesized compounds have multi-target inhibitory effects and can be very useful in multi-drug resistance cases. A 2D quantitative structural activity relationship (QSAR) model against target Glucosamine-6-phosphate synthase (2VF5) was developed using partial least squares regression (PLS) with good internal prediction (R2 = 0.7400) and external prediction (R2_ predicted = 0.5475) via Molecular Operating Environment (2014).
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Affiliation(s)
- Mercy A. Ezeokonkwo
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | | | - Sunday N. Okafor
- Department of Pharmaceutical and Medicinal Chemistry, University of Nigeria, Nsukka, Nigeria
| | | | | | - Uchechukwu C. Okoro
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
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Jin N, Paraskevaidi M, Semple KT, Martin FL, Zhang D. Infrared Spectroscopy Coupled with a Dispersion Model for Quantifying the Real-Time Dynamics of Kanamycin Resistance in Artificial Microbiota. Anal Chem 2017; 89:9814-9821. [DOI: 10.1021/acs.analchem.7b01765] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Naifu Jin
- Lancaster
Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
| | - Maria Paraskevaidi
- School
of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Kirk T. Semple
- Lancaster
Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
| | - Francis L. Martin
- School
of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Dayi Zhang
- Lancaster
Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
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Affiliation(s)
- Dmitrii V. Kalinin
- Institut für Organische Chemie, Universität Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
| | - Ralph Holl
- Institut für Organische Chemie, Universität Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems
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Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. J Bacteriol 2017; 199:JB.00245-17. [PMID: 28559295 PMCID: PMC5512222 DOI: 10.1128/jb.00245-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/17/2017] [Indexed: 12/29/2022] Open
Abstract
Intense biological conflicts between prokaryotic genomes and their genomic parasites have resulted in an arms race in terms of the molecular “weaponry” deployed on both sides. Using a recursive computational approach, we uncovered a remarkable class of multidomain proteins with 2 to 15 domains in the same polypeptide deployed by viruses and plasmids in such conflicts. Domain architectures and genomic contexts indicate that they are part of a widespread conflict strategy involving proteins injected into the host cell along with parasite DNA during the earliest phase of infection. Their unique feature is the combination of domains with highly disparate biochemical activities in the same polypeptide; accordingly, we term them polyvalent proteins. Of the 131 domains in polyvalent proteins, a large fraction are enzymatic domains predicted to modify proteins, target nucleic acids, alter nucleotide signaling/metabolism, and attack peptidoglycan or cytoskeletal components. They further contain nucleic acid-binding domains, virion structural domains, and 40 novel uncharacterized domains. Analysis of their architectural network reveals both pervasive common themes and specialized strategies for conjugative elements and plasmids or (pro)phages. The themes include likely processing of multidomain polypeptides by zincin-like metallopeptidases and mechanisms to counter restriction or CRISPR/Cas systems and jump-start transcription or replication. DNA-binding domains acquired by eukaryotes from such systems have been reused in XPC/RAD4-dependent DNA repair and mitochondrial genome replication in kinetoplastids. Characterization of the novel domains discovered here, such as RNases and peptidases, are likely to aid in the development of new reagents and elucidation of the spread of antibiotic resistance. IMPORTANCE This is the first report of the widespread presence of large proteins, termed polyvalent proteins, predicted to be transmitted by genomic parasites such as conjugative elements, plasmids, and phages during the initial phase of infection along with their DNA. They are typified by the presence of multiple domains with disparate activities combined in the same protein. While some of these domains are predicted to assist the invasive element in replication, transcription, or protection of their DNA, several are likely to target various host defense systems or modify the host to favor the parasite's life cycle. Notably, DNA-binding domains from these systems have been transferred to eukaryotes, where they have been incorporated into DNA repair and mitochondrial genome replication systems.
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Awasthi D, Freundlich JS. Antimycobacterial Metabolism: Illuminating Mycobacterium tuberculosis Biology and Drug Discovery. Trends Microbiol 2017. [PMID: 28622844 DOI: 10.1016/j.tim.2017.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Bacteria are capable of performing a number of biotransformations that may activate or deactivate xenobiotics. Recent efforts have utilized metabolomics techniques to study the fate of small-molecule antibacterials within the targeted organism. Examples involving Mycobacterium tuberculosis are reviewed and analyzed with regard to the insights they provide as to both activation and deactivation of the antibacterial. The studies, in particular, shed light on biosynthetic transformations performed by M. tuberculosis while suggesting avenues for the evolution of chemical tools, highlighting potential areas for drug discovery, and mechanisms of approved drugs. A two-pronged approach investigating the metabolism of antibacterials within both the host and bacterium is outlined and will be of value to both the chemical biology and drug discovery fields.
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Affiliation(s)
- Divya Awasthi
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University - New Jersey Medical School, Newark, NJ, USA
| | - Joel S Freundlich
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University - New Jersey Medical School, Newark, NJ, USA; Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, Rutgers University - New Jersey Medical School, Newark, NJ, USA.
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New aminoglycoside-modifying enzymes APH(3′)-VIII and APH(3′)-IX in Acinetobacter rudis and Acinetobacter gerneri. J Antibiot (Tokyo) 2016; 70:400-403. [DOI: 10.1038/ja.2016.144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/03/2016] [Accepted: 10/31/2016] [Indexed: 11/09/2022]
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