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Hiller NL, Orihuela CJ. Biological puzzles solved by using Streptococcus pneumoniae: a historical review of the pneumococcal studies that have impacted medicine and shaped molecular bacteriology. J Bacteriol 2024; 206:e0005924. [PMID: 38809015 DOI: 10.1128/jb.00059-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024] Open
Abstract
The major human pathogen Streptococcus pneumoniae has been the subject of intensive clinical and basic scientific study for over 140 years. In multiple instances, these efforts have resulted in major breakthroughs in our understanding of basic biological principles as well as fundamental tenets of bacterial pathogenesis, immunology, vaccinology, and genetics. Discoveries made with S. pneumoniae have led to multiple major public health victories that have saved the lives of millions. Studies on S. pneumoniae continue today, where this bacterium is being used to dissect the impact of the host on disease processes, as a powerful cell biology model, and to better understand the consequence of human actions on commensal bacteria at the population level. Herein we review the major findings, i.e., puzzle pieces, made with S. pneumoniae and how, over the years, they have come together to shape our understanding of this bacterium's biology and the practice of medicine and modern molecular biology.
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Affiliation(s)
- N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Carlos J Orihuela
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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2
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Dorrazehi GM, Winkle M, Desmet M, Stroobant V, Tanriver G, Degand H, Evrard D, Desguin B, Morsomme P, Biboy J, Gray J, Mitusińska K, Góra A, Vollmer W, Soumillion P. PBP-A, a cyanobacterial DD-peptidase with high specificity for amidated muropeptides, exhibits pH-dependent promiscuous activity harmful to Escherichia coli. Sci Rep 2024; 14:13999. [PMID: 38890528 DOI: 10.1038/s41598-024-64806-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Penicillin binding proteins (PBPs) are involved in biosynthesis, remodeling and recycling of peptidoglycan (PG) in bacteria. PBP-A from Thermosynechococcus elongatus belongs to a cyanobacterial family of enzymes sharing close structural and phylogenetic proximity to class A β-lactamases. With the long-term aim of converting PBP-A into a β-lactamase by directed evolution, we simulated what may happen when an organism like Escherichia coli acquires such a new PBP and observed growth defect associated with the enzyme activity. To further explore the molecular origins of this harmful effect, we decided to characterize deeper the activity of PBP-A both in vitro and in vivo. We found that PBP-A is an enzyme endowed with DD-carboxypeptidase and DD-endopeptidase activities, featuring high specificity towards muropeptides amidated on the D-iso-glutamyl residue. We also show that a low promiscuous activity on non-amidated peptidoglycan deteriorates E. coli's envelope, which is much higher under acidic conditions where substrate discrimination is mitigated. Besides expanding our knowledge of the biochemical activity of PBP-A, this work also highlights that promiscuity may depend on environmental conditions and how it may hinder rather than promote enzyme evolution in nature or in the laboratory.
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Affiliation(s)
- Gol Mohammad Dorrazehi
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Matthias Winkle
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
- Benchmark Animal Health Ltd, 1 Pioneer Building, Edinburgh Technopole, Milton Bridge, Penicuik, EH26 0GB, UK
| | - Martin Desmet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Vincent Stroobant
- Ludwig Institute for Cancer Research, Brussels, Belgium
- de Duve Institute, UCLouvain, Brussels, Belgium
| | - Gamze Tanriver
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100, Gliwice, Poland
| | - Hervé Degand
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Damien Evrard
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Benoît Desguin
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Joe Gray
- Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100, Gliwice, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100, Gliwice, Poland
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium.
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3
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Li D, Ge Y, Wang N, Shi Y, Guo G, Zhang J, Zou Q, Liu Q. A novel member of drug/metabolite transporter (DMT) family efflux pump, SA00565, contributes to tetracycline antibiotics resistance in Staphylococcus aureus USA300. Microbiol Spectr 2024; 12:e0011124. [PMID: 38651886 DOI: 10.1128/spectrum.00111-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Abstract
Drug efflux systems have recently been recognized as a significant mechanism responsible for multidrug resistance in bacteria. In this study, we described the identification and characterization of a new chromosomally encoded efflux pump (SA00565) in Staphylococcus aureus. SA00565, which belongs to the drug/metabolite transporter (DMT) superfamily, was predicted to be a 10-transmembrane segment transporter. To evaluate the role of sa00565 in resistance, we generated sa00565 gene deletion mutant (Δsa00565) and assessed its susceptibility to 35 different antibiotic treatments. Our results demonstrated that the Δsa00565 mutant exhibited reduced resistance to tetracycline and doxycycline, with 64-fold and 12-fold decreased MICs, respectively. The mechanism of SA00565-mediated tetracycline resistance was demonstrated that SA00565 possesses the capability to efficiently extrud intracellular tetracycline into the environment. The efflux activity of SA00565 was further validated using EtBr accumulation and efflux assays. In summary, our study uncovered a previously unknown function of a DMT family transporter, which serves as a tetracycline efflux pump, thereby contributing to tetracycline resistance in S. aureus.IMPORTANCEIn this study, we addressed the significance of drug efflux systems in multidrug resistance of Staphylococcus aureus, focusing on the unexplored efflux pump SA00565 in the drug/metabolite transporter (DMT) superfamily. Through phylogenetic analysis, gene knockout, and overexpression experiments, we identified the role of SA00565 in antibiotic resistance. The Δsa00565 mutant showed increased susceptibility to tetracycline and doxycycline in disk diffusion assays, with significantly lower MICs compared to the WT. Remarkably, intracellular tetracycline concentration in the mutant was two- to threefold higher, indicating SA00565 actively eliminates intracellular tetracycline. Our findings emphasize the pivotal contribution of SA00565 to tetracycline antibiotic resistance in S. aureus, shedding light on its functional attributes within the DMT superfamily and providing valuable insights for combating multidrug resistance.
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Affiliation(s)
- Daiyu Li
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Ge
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Ning Wang
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Yun Shi
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Gang Guo
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Zhang
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Quanming Zou
- Department of Microbiology and Biochemical Pharmacy, National Engineering Research Center of Immunological Products, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Qiang Liu
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
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Bon CG, Grigg JC, Lee J, Robb CS, Caveney NA, Eltis LD, Strynadka NCJ. Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1. J Struct Biol 2024; 216:108086. [PMID: 38527711 DOI: 10.1016/j.jsb.2024.108086] [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: 02/02/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/27/2024]
Abstract
Staphylococcus aureus, an ESKAPE pathogen, is a major clinical concern due to its pathogenicity and manifold antimicrobial resistance mechanisms. The commonly used β-lactam antibiotics target bacterial penicillin-binding proteins (PBPs) and inhibit crosslinking of peptidoglycan strands that comprise the bacterial cell wall mesh, initiating a cascade of effects leading to bacterial cell death. S. aureus PBP1 is involved in synthesis of the bacterial cell wall during division and its presence is essential for survival of both antibiotic susceptible and resistant S. aureus strains. Here, we present X-ray crystallographic data for S. aureus PBP1 in its apo form as well as acyl-enzyme structures with distinct classes of β-lactam antibiotics representing the penicillins, carbapenems, and cephalosporins, respectively: oxacillin, ertapenem and cephalexin. Our structural data suggest that the PBP1 active site is readily accessible for substrate, with little conformational change in key structural elements required for its covalent acylation of β-lactam inhibitors. Stopped-flow kinetic analysis and gel-based competition assays support the structural observations, with even the weakest performing β-lactams still having comparatively high acylation rates and affinities for PBP1. Our structural and kinetic analysis sheds insight into the ligand-PBP interactions that drive antibiotic efficacy against these historically useful antimicrobial targets and expands on current knowledge for future drug design and treatment of S. aureus infections.
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Affiliation(s)
- Christopher G Bon
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jason C Grigg
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Craig S Robb
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nathanael A Caveney
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Benin BM, Hillyer T, Aguirre N, Sham YY, Willard B, Shin WS. Carbapenem-induced β-lactamase-isoform expression trends in Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596663. [PMID: 38853951 PMCID: PMC11160735 DOI: 10.1101/2024.05.30.596663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAb) is an urgent bacterial threat to public health, with only a few treatment options and a >50% fatality rate. Although several resistance mechanisms are understood, the appearance of these mutations is generally considered stochastic. Recent reports have, however, begun to challenge this assumption. Here, we demonstrate that independent samples of Ab, exposed to different carbapenems with escalating concentrations, show concentration- and carbapenem-dependent trends in β-lactamase-isoform expression. This result, based on the isoforms identified through label-free-quantification LC-MS/MS measurements of cell-free, gel-separated β-lactamases, suggests that the appearance of antibiotic resistance may be somewhat non-stochastic. Specifically, several minor AmpC/ADC β-lactamase-isoforms were found to exhibit both dose- and carbapenem-dependent expression, suggesting the possibility of non-stochastic mutations. Additionally, these also have high sequence similarity to major expressed isoforms, indicating a potential path over which resistance occurred in independent samples. Antibiotic resistance maybe somewhat antibiotic-directed by a hitherto unknown mechanism and further investigation may lead to new strategies for mitigating antibiotic resistance. Teaser The emergence of antibiotic-resistant β-lactamase proteins from mutations may exhibit patterns based on specific antibiotics.
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Berida TI, Adekunle YA, Dada-Adegbola H, Kdimy A, Roy S, Sarker SD. Plant antibacterials: The challenges and opportunities. Heliyon 2024; 10:e31145. [PMID: 38803958 PMCID: PMC11128932 DOI: 10.1016/j.heliyon.2024.e31145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Nature possesses an inexhaustible reservoir of agents that could serve as alternatives to combat the growing threat of antimicrobial resistance (AMR). While some of the most effective drugs for treating bacterial infections originate from natural sources, they have predominantly been derived from fungal and bacterial species. However, a substantial body of literature is available on the promising antibacterial properties of plant-derived compounds. In this comprehensive review, we address the major challenges associated with the discovery and development of plant-derived antimicrobial compounds, which have acted as obstacles preventing their clinical use. These challenges encompass limited sourcing, the risk of agent rediscovery, suboptimal drug metabolism, and pharmacokinetics (DMPK) properties, as well as a lack of knowledge regarding molecular targets and mechanisms of action, among other pertinent issues. Our review underscores the significance of these challenges and their implications in the quest for the discovery and development of effective plant-derived antimicrobial agents. Through a critical examination of the current state of research, we give valuable insights that will advance our understanding of these classes of compounds, offering potential solutions to the global crisis of AMR. © 2017 Elsevier Inc. All rights reserved.
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Affiliation(s)
- Tomayo I. Berida
- Department of BioMolecular Sciences, Division of Pharmacognosy, University of Mississippi, University, MS, 38677, USA
| | - Yemi A. Adekunle
- Department of Pharmaceutical and Medicinal Chemistry, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, United Kingdom
| | - Hannah Dada-Adegbola
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ayoub Kdimy
- LS3MN2E, CERNE2D, Faculty of Science, Mohammed V University in Rabat, Rabat, 10056, Morocco
| | - Sudeshna Roy
- Department of BioMolecular Sciences, Division of Pharmacognosy, University of Mississippi, University, MS, 38677, USA
| | - Satyajit D. Sarker
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, United Kingdom
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7
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Singh G, Rana A, Smriti. Decoding antimicrobial resistance: unraveling molecular mechanisms and targeted strategies. Arch Microbiol 2024; 206:280. [PMID: 38805035 DOI: 10.1007/s00203-024-03998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Antimicrobial resistance poses a significant global health threat, necessitating innovative approaches for combatting it. This review explores various mechanisms of antimicrobial resistance observed in various strains of bacteria. We examine various strategies, including antimicrobial peptides (AMPs), novel antimicrobial materials, drug delivery systems, vaccines, antibody therapies, and non-traditional antibiotic treatments. Through a comprehensive literature review, the efficacy and challenges of these strategies are evaluated. Findings reveal the potential of AMPs in combating resistance due to their unique mechanisms and lower propensity for resistance development. Additionally, novel drug delivery systems, such as nanoparticles, show promise in enhancing antibiotic efficacy and overcoming resistance mechanisms. Vaccines and antibody therapies offer preventive measures, although challenges exist in their development. Non-traditional antibiotic treatments, including CRISPR-Cas systems, present alternative approaches to combat resistance. Overall, this review underscores the importance of multifaceted strategies and coordinated global efforts to address antimicrobial resistance effectively.
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Affiliation(s)
- Gagandeep Singh
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India
| | - Anita Rana
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India.
| | - Smriti
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India
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Choi HJ, Ki DU, Yoon SI. Structural and biochemical analysis of penicillin-binding protein 2 from Campylobacter jejuni. Biochem Biophys Res Commun 2024; 710:149859. [PMID: 38581948 DOI: 10.1016/j.bbrc.2024.149859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 03/27/2024] [Indexed: 04/08/2024]
Abstract
Penicillin-binding protein 2 (PBP2) plays a key role in the formation of peptidoglycans in bacterial cell walls by crosslinking glycan chains through transpeptidase activity. PBP2 is also found in Campylobacter jejuni, a pathogenic bacterium that causes food-borne enteritis in humans. To elucidate the essential structural features of C. jejuni PBP2 (cjPBP2) that mediate its biological function, we determined the crystal structure of cjPBP2 and assessed its protein stability under various conditions. cjPBP2 adopts an elongated two-domain structure, consisting of a transpeptidase domain and a pedestal domain, and contains typical active site residues necessary for transpeptidase activity, as observed in other PBP2 proteins. Moreover, cjPBP2 responds to β-lactam antibiotics, including ampicillin, cefaclor, and cefmetazole, suggesting that β-lactam antibiotics inactivate cjPBP2. In contrast to typical PBP2 proteins, cjPBP2 is a rare example of a Zn2+-binding PBP2 protein, as the terminal structure of its transpeptidase domain accommodates a Zn2+ ion via three cysteine residues and one histidine residue. Zn2+ binding helps improve the protein stability of cjPBP2, providing opportunities to develop new C. jejuni-specific antibacterial drugs that counteract the Zn2+-binding ability of cjPBP2.
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Affiliation(s)
- Hong Joon Choi
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Dong Uk Ki
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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de Souza J, Vieira AZ, Dos Santos HG, Faoro H. Potential involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group. BMC Genomics 2024; 25:508. [PMID: 38778284 PMCID: PMC11112869 DOI: 10.1186/s12864-024-10410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Enzymatic degradation mediated by beta-lactamases constitutes one of the primary mechanisms of resistance to beta-lactam antibiotics in gram-negative bacteria. This enzyme family comprises four molecular classes, categorized into serine beta-lactamases (Classes A, C, and D) and zinc-dependent metallo-beta-lactamases (Class B). Gram-negative bacteria producing beta-lactamase are of significant concern, particularly due to their prevalence in nosocomial infections. A comprehensive understanding of the evolution and dissemination of this enzyme family is essential for effective control of these pathogens. In this study, we conducted the prospecting, phylogenetic analysis, and in silico analysis of beta-lactamases and homologous proteins identified in 1827 bacterial genomes with phenotypic data on beta-lactam resistance. These genomes were distributed among Klebsiella pneumoniae (45%), Acinetobacter baumannii (31%), Pseudomonas aeruginosa (14%), Escherichia coli (6%), and Enterobacter spp. (4%). Using an HMM profile and searching for conserved domains, we mined 2514, 8733, 5424, and 2957 proteins for molecular classes A, B, C, and D, respectively. This set of proteins encompasses canonical subfamilies of beta-lactamases as well as hypothetical proteins and other functional groups. Canonical beta-lactamases were found to be phylogenetically distant from hypothetical proteins, which, in turn, are closer to other representatives of the penicillin-binding-protein (PBP-like) and metallo-beta-lactamase (MBL) families. The catalytic amino acid residues characteristic of beta-lactamases were identified from the sequence alignment and revealed that motifs are less conserved in homologous groups than in beta-lactamases. After comparing the frequency of protein groups in genomes of resistant strains with those of sensitive ones applying Fisher's exact test and relative risk, it was observed that some groups of homologous proteins to classes B and C are more common in the genomes of resistant strains, particularly to carbapenems. We identified the beta-lactamase-like domain widely distributed in gram-negative species of the ESKAPEE group, which highlights its importance in the context of beta-lactam resistance. Some hypothetical homologous proteins have been shown to potentially possess promiscuous activity against beta-lactam antibiotics, however, they do not appear to expressly determine the resistance phenotype. The selective pressure due to the widespread use of antibiotics may favor the optimization of these functions for specialized resistance enzymes.
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Affiliation(s)
- Joyce de Souza
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil
| | - Alexandre Zanatta Vieira
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil
| | | | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil.
- Department of Microbiology, Infectious Disease and Immunology, CHU de Quebec Research Center, University Laval, Quebec, QC, G1V 0A6, Canada.
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Gayatri, Brewitz L, Ibbotson L, Salah E, Basak S, Choudhry H, Schofield CJ. Thiophene-fused γ-lactams inhibit the SARS-CoV-2 main protease via reversible covalent acylation. Chem Sci 2024; 15:7667-7678. [PMID: 38784729 PMCID: PMC11110133 DOI: 10.1039/d4sc01027b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Enzyme inhibitors working by O-acylation of nucleophilic serine residues are of immense medicinal importance, as exemplified by the β-lactam antibiotics. By contrast, inhibition of nucleophilic cysteine enzymes by S-acylation has not been widely exploited for medicinal applications. The SARS-CoV-2 main protease (Mpro) is a nucleophilic cysteine protease and a validated therapeutic target for COVID-19 treatment using small-molecule inhibitors. The clinically used Mpro inhibitors nirmatrelvir and simnotrelvir work via reversible covalent reaction of their electrophilic nitrile with the Mpro nucleophilic cysteine (Cys145). We report combined structure activity relationship and mass spectrometric studies revealing that appropriately functionalized γ-lactams can potently inhibit Mpro by reversible covalent reaction with Cys145 of Mpro. The results suggest that γ-lactams have potential as electrophilic warheads for development of covalently reacting small-molecule inhibitors of Mpro and, by implication, other nucleophilic cysteine enzymes.
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Affiliation(s)
- Gayatri
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Lewis Ibbotson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Shyam Basak
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Hani Choudhry
- Department of Biochemistry, Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University Jeddah Saudi Arabia
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
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Shirley JD, Nauta KM, Gillingham JR, Diwakar S, Carlson EE. kinact / KI Value Determination for Penicillin-Binding Proteins in Live Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592586. [PMID: 38746240 PMCID: PMC11092749 DOI: 10.1101/2024.05.05.592586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Penicillin-binding proteins (PBPs) are an essential family of bacterial enzymes that are inhibited by the β-lactam class of antibiotics. PBP inhibition disrupts cell wall biosynthesis, which results in deficient growth and proliferation, and ultimately leads to lysis. IC 50 values are often employed as descriptors of enzyme inhibition and inhibitor selectivity but can be misleading in the study of time-dependent, irreversible inhibitors. Due to this disconnect, the second order rate constant k inact / K I is a more appropriate metric of covalent inhibitor potency. Despite being the gold standard measurement of potency, k inact / K I values are typically obtained from in vitro assays, which limits assay throughput if investigating an enzyme family with multiple homologs (such as the PBPs). Therefore, we developed a whole-cell k inact / K I assay to define inhibitor potency for the PBPs in Streptococcus pneumoniae using the fluorescent activity-based probe Bocillin-FL. Our results align with in vitro k inact / K I data and show a comparable relationship to previously established IC 50 values. These results support the validity of our in vivo k inact / K I method as a means of obtaining a full picture of β-lactam potency for a suite of PBPs. Abstract Figure
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12
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Anglemyer A, Ren X, Gilkison C, Kumbaroff Z, Morgan J, DuBray K, Tiong A, Reingold A, Walls T. The impact of pneumococcal serotype replacement on the effectiveness of a national immunization program: a population-based active surveillance cohort study in New Zealand. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 46:101082. [PMID: 38745973 PMCID: PMC11091704 DOI: 10.1016/j.lanwpc.2024.101082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024]
Abstract
Background In Aotearoa New Zealand (NZ) PCV7 was introduced in 2008, then PCV10 in 2011 and PCV13 in 2014. In 2017 PCV10 was re-introduced, replacing PCV13. In the present study, we investigate the resultant rapidly changing invasive pneumococcal disease (IPD) epidemiology. Methods We compare the IPD incidence rate ratio (IRR) in NZ (2022 versus 2020) with other countries, and describe the IPD epidemiology (including trends in overall IPD and serotype 19A, and antimicrobial resistance) within NZ. Additionally, we performed a genomic-epidemiology investigation identifying the most common 19A sequence types and associated risk factors. Findings Though IPD incidence rates have increased in the US and Australia (2021-22) after declines in 2020, in NZ the incidence rate is the highest since 2011 with a significantly higher IRR than US (p < 0.01). Incidence rates among children <2 and adults 65 or over in 2022 are the highest since 2009, driven by significant increases of serotype 19A (p = 0.01). Māori and Pacific peoples are experiencing the highest rates since 2009. Further, penicillin resistance among 19A isolates has increased from 39% (2012) to 84% (2021) (p = 0.02). Genomic sequencing identified the more virulent ST-2062 as most common among 19A isolates sequenced, increasing from 5% (2010) to 55% (2022). Interpretation With very high incidence rates of IPD in NZ, inadequate protection against 19A, increasing resistance, and a more virulent 19A clade, targeted public health campaigns and increased PCV13 availability are needed. Funding The NZ Ministry of Health funds IPD surveillance and typing in NZ.
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Affiliation(s)
- Andrew Anglemyer
- Health Intelligence Team, Institute of Environmental Science and Research, Porirua, New Zealand
- Department of Preventive and Social Medicine, University of Otago, Dunedin, New Zealand
| | - Xiaoyun Ren
- Invasive Pathogens Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Charlotte Gilkison
- Health Intelligence Team, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Zoe Kumbaroff
- Health Intelligence Team, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Julie Morgan
- Invasive Pathogens Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Kara DuBray
- Department of Paediatrics, Dunedin Hospital, Dunedin, New Zealand
| | - Audrey Tiong
- Invasive Pathogens Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Arthur Reingold
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Tony Walls
- Department of Paediatrics, University of Otago, Christchurch, New Zealand
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13
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Rout AK, Gautam S, Kumar Mishra V, Bopardikar M, Dehury B, Singh H. NMR insights into β-Lactamase activity of UVI31+ Protein from Chlamydomonas reinhardtii. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 362:107689. [PMID: 38677224 DOI: 10.1016/j.jmr.2024.107689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/12/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
β-Lactamases (EC 3.5.2.6) confer resistance against β-lactam group-containing antibiotics in bacteria and higher eukaryotes, including humans. Pathogenic bacterial resistance against β-lactam antibiotics is a primary concern for potential therapeutic developments and drug targets. Here, we report putative β-lactamase activity, sulbactam binding (a β-lactam analogue) in the low μM affinity range, and site-specific interaction studies of a 14 kDa UV- and dark-inducible protein (abbreviated as UVI31+, a BolA homologue) from Chlamydomonas reinhartii. Intriguingly, the solution NMR structure of UVI31 + bears no resemblance to other known β-lactamases; however, the sulbactam binding is found at two sites rich in positively charged residues, mainly at the L2 loop regions and the N-terminus. Using NMR spectroscopy, ITC and MD simulations, we map the ligand binding sites in UVI31 + providing atomic-level insights into its β-lactamase activity. Current study is the first report on β-lactamase activity of UVI31+, a BolA analogue, from C. reinhartii. Furthermore, our mutation studies reveal that the active site serine-55 is crucial for β-lactamase activity.
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Affiliation(s)
- Ashok K Rout
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India; Institute of Chemistry and Metabolomics, University of Luebeck, 23562 Luebeck, Germany
| | - Saurabh Gautam
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | | | - Mandar Bopardikar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Berhampur, 760010 Odisha, India
| | - Budheswar Dehury
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Himanshu Singh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; Department of Chemical Sciences, Indian Institute of Science Education and Research, Berhampur, 760010 Odisha, India.
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14
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Nasser Binjawhar D, Abu Ali OA, Alqahtani AS, Fayad E, Abo-Bakr AM, Mekhael AM, Sadek FM. Powerful Approach for New Drugs as Antibacterial Agents via Molecular Docking and In Vitro Studies of Some New Cyclic Imides and Quinazoline-2,5-diones. ACS OMEGA 2024; 9:18566-18575. [PMID: 38680340 PMCID: PMC11044208 DOI: 10.1021/acsomega.4c01176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 05/01/2024]
Abstract
We generated novel elven 1,2,3,6-tetrahydrophthalimides and tetrahydroquinazoline derivatives from 1,2,3,6-tetrahydrophthalic anhydride (1) in response to our interest in using the anhydrides to produce heterocyclic nitrogen compounds. The elemental and spectral analyses of the produced compounds validated the recommended configurations and MOE 2014.09 (Molecular Operating Environment) computations were used to perform their in silico analysis. The synthesized compounds have been analyzed and put through various experiments, including in vitro and in silico methods to assess their biological activity against Escherichia coli Penicillin-Binding Protein 3 (PBP3) and Staphylococcus aureus Penicillin-Binding Protein 2 (PBP2), among these compounds showing promising data as antibacterial drugs.
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Affiliation(s)
- Dalal Nasser Binjawhar
- Department
of Chemistry, College of Science, Princess
Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Ola A. Abu Ali
- Department
of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Arwa Sultan Alqahtani
- Department
of Chemistry, College of Science, Imam Mohammad
Ibn Saud Islamic University (IMSIU), P.O. Box 90950, Riyadh 11623, Saudi Arabia
| | - Eman Fayad
- Department
of Biotechnology, College of Sciences, Taif
University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed M. Abo-Bakr
- Chemistry
Department, Faculty of Science, South Valley
University, P.O. Box 83523, Qena 83523, Egypt
| | - Antonous. M. Mekhael
- Cotton Leaf
Worm Department, Plant Protection Research Institute, Agriculture Research Center, P.O. Box 12619, Giza 12611, Egypt
| | - Fayza M. Sadek
- Radiation
Sciences Department, Medical Research Institution, Alexandria University, P.O. Box 21500, Alexandria 5424041, Egypt
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15
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Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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16
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Zhang S, Liao X, Ding T, Ahn J. Role of β-Lactamase Inhibitors as Potentiators in Antimicrobial Chemotherapy Targeting Gram-Negative Bacteria. Antibiotics (Basel) 2024; 13:260. [PMID: 38534695 DOI: 10.3390/antibiotics13030260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
Since the discovery of penicillin, β-lactam antibiotics have commonly been used to treat bacterial infections. Unfortunately, at the same time, pathogens can develop resistance to β-lactam antibiotics such as penicillins, cephalosporins, monobactams, and carbapenems by producing β-lactamases. Therefore, a combination of β-lactam antibiotics with β-lactamase inhibitors has been a promising approach to controlling β-lactam-resistant bacteria. The discovery of novel β-lactamase inhibitors (BLIs) is essential for effectively treating antibiotic-resistant bacterial infections. Therefore, this review discusses the development of innovative inhibitors meant to enhance the activity of β-lactam antibiotics. Specifically, this review describes the classification and characteristics of different classes of β-lactamases and the synergistic mechanisms of β-lactams and BLIs. In addition, we introduce potential sources of compounds for use as novel BLIs. This provides insights into overcoming current challenges in β-lactamase-producing bacteria and designing effective treatment options in combination with BLIs.
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Affiliation(s)
- Song Zhang
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Xinyu Liao
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
| | - Tian Ding
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
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17
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Djorić D, Atkinson SN, Kristich CJ. Reciprocal regulation of enterococcal cephalosporin resistance by products of the autoregulated yvcJ-glmR-yvcL operon enhances fitness during cephalosporin exposure. PLoS Genet 2024; 20:e1011215. [PMID: 38512984 PMCID: PMC10986989 DOI: 10.1371/journal.pgen.1011215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/02/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Enterococci are commensal members of the gastrointestinal tract and also major nosocomial pathogens. They possess both intrinsic and acquired resistance to many antibiotics, including intrinsic resistance to cephalosporins that target bacterial cell wall synthesis. These antimicrobial resistance traits make enterococcal infections challenging to treat. Moreover, prior therapy with antibiotics, including broad-spectrum cephalosporins, promotes enterococcal proliferation in the gut, resulting in dissemination to other sites of the body and subsequent infection. As a result, a better understanding of mechanisms of cephalosporin resistance is needed to enable development of new therapies to treat or prevent enterococcal infections. We previously reported that flow of metabolites through the peptidoglycan biosynthesis pathway is one determinant of enterococcal cephalosporin resistance. One factor that has been implicated in regulating flow of metabolites into cell wall biosynthesis pathways of other Gram-positive bacteria is GlmR. In enterococci, GlmR is encoded as the middle gene of a predicted 3-gene operon along with YvcJ and YvcL, whose functions are poorly understood. Here we use genetics and biochemistry to investigate the function of the enterococcal yvcJ-glmR-yvcL gene cluster. Our results reveal that YvcL is a DNA-binding protein that regulates expression of the yvcJ-glmR-yvcL operon in response to cell wall stress. YvcJ and GlmR bind UDP-GlcNAc and reciprocally regulate cephalosporin resistance in E. faecalis, and binding of UDP-GlcNAc by YvcJ appears essential for its activity. Reciprocal regulation by YvcJ/GlmR is essential for fitness during exposure to cephalosporin stress. Additionally, our results indicate that enterococcal GlmR likely acts by a different mechanism than the previously studied GlmR of Bacillus subtilis, suggesting that the YvcJ/GlmR regulatory module has evolved unique targets in different species of bacteria.
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Affiliation(s)
- Dušanka Djorić
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Samantha N. Atkinson
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Center for Microbiome Research, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Christopher J. Kristich
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
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18
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Ding L, Yang Z, Sun B. Understanding blaNDM-1 gene regulation in CRKP infections: toward novel antimicrobial strategies for hospital-acquired pneumonia. Mol Med 2024; 30:29. [PMID: 38395744 PMCID: PMC10893750 DOI: 10.1186/s10020-024-00794-y] [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: 11/24/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND The escalating challenge of Carbapenem-resistant Klebsiella pneumoniae (CRKP) in hospital-acquired pneumonia (HAP) is closely linked to the blaNDM-1 gene. This study explores the regulatory mechanisms of blaNDM-1 expression and aims to enhance antibacterial tactics to counteract the spread and infection of resistant bacteria. METHODS KP and CRKP strains were isolated from HAP patients' blood samples. Transcriptomic sequencing (RNA-seq) identified significant upregulation of blaNDM-1 gene expression in CRKP strains. Bioinformatics analysis revealed blaNDM-1 gene involvement in beta-lactam resistance pathways. CRISPR-Cas9 was used to delete the blaNDM-1 gene, restoring sensitivity. In vitro and in vivo experiments demonstrated enhanced efficacy with Imipenem and Thanatin or Subatan combination therapy. RESULTS KP and CRKP strains were isolated with significant upregulation of blaNDM-1 in CRKP strains identified by RNA-seq. The Beta-lactam resistance pathway was implicated in bioinformatics analysis. Knockout of blaNDM-1 reinstated sensitivity in CRKP strains. Further, co-treatment with Imipenem, Thanatin, or Subactam markedly improved antimicrobial effectiveness. CONCLUSION Silencing blaNDM-1 in CRKP strains from HAP patients weakens their Carbapenem resistance and optimizes antibacterial strategies. These results provide new theoretical insights and practical methods for treating resistant bacterial infections.
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Affiliation(s)
- Liang Ding
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China
| | - Zheng Yang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China
| | - Baier Sun
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China.
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19
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Padhi AK, Maurya S. Uncovering the secrets of resistance: An introduction to computational methods in infectious disease research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:173-220. [PMID: 38448135 DOI: 10.1016/bs.apcsb.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Antimicrobial resistance (AMR) is a growing global concern with significant implications for infectious disease control and therapeutics development. This chapter presents a comprehensive overview of computational methods in the study of AMR. We explore the prevalence and statistics of AMR, underscoring its alarming impact on public health. The role of AMR in infectious disease outbreaks and its impact on therapeutics development are discussed, emphasizing the need for novel strategies. Resistance mutations are pivotal in AMR, enabling pathogens to evade antimicrobial treatments. We delve into their importance and contribution to the spread of AMR. Experimental methods for quantitatively evaluating resistance mutations are described, along with their limitations. To address these challenges, computational methods provide promising solutions. We highlight the advantages of computational approaches, including rapid analysis of large datasets and prediction of resistance profiles. A comprehensive overview of computational methods for studying AMR is presented, encompassing genomics, proteomics, structural bioinformatics, network analysis, and machine learning algorithms. The strengths and limitations of each method are briefly outlined. Additionally, we introduce ResScan-design, our own computational method, which employs a protein (re)design protocol to identify potential resistance mutations and adaptation signatures in pathogens. Case studies are discussed to showcase the application of ResScan in elucidating hotspot residues, understanding underlying mechanisms, and guiding the design of effective therapies. In conclusion, we emphasize the value of computational methods in understanding and combating AMR. Integration of experimental and computational approaches can expedite the discovery of innovative antimicrobial treatments and mitigate the threat posed by AMR.
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Affiliation(s)
- Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India.
| | - Shweata Maurya
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
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20
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Massacci FR, Cucco L, Panicciá M, Luppi A, Albini E, Peruzzo A, Ferroni L, Ustulin M, Orsini M, Magistrali CF. Streptococcus suis serotype 9 in Italy: genomic insights into high-risk clones with emerging resistance to penicillin. J Antimicrob Chemother 2024; 79:403-411. [PMID: 38153239 PMCID: PMC10832592 DOI: 10.1093/jac/dkad395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Streptococcus suis is an important pig pathogen and an emerging zoonotic agent. In a previous study, we described a high proportion of penicillin-resistant serotype 9 S. suis (SS9) isolates on pig farms in Italy. OBJECTIVES We hypothesized that resistance to penicillin emerged in some SS9 lineages characterized by substitutions at the PBPs, contributing to the successful spread of these lineages in the last 20 years. METHODS Sixty-six SS9 isolates from cases of streptococcosis in pigs were investigated for susceptibility to penicillin, ceftiofur and ampicillin. The isolates were characterized for ST, virulence profile, and antimicrobial resistance genes through WGS. Multiple linear regression models were employed to investigate the associations between STs, year of isolation, substitutions at the PBPs and an increase in MIC values to β-lactams. RESULTS MIC values to penicillin increased by 4% each year in the study period. Higher MIC values for penicillin were also positively associated with ST123, ST1540 and ST1953 compared with ST16. The PBP sequences presented a mosaic organization of blocks. Within the same ST, substitutions at the PBPs were generally more frequent in recent isolates. Resistance to penicillin was driven by substitutions at PBP2b, including K479T, D512E and K513E, and PBP2x, including T551S, while reduced susceptibility to ceftiofur and ampicillin were largely dependent on substitutions at PBP2x. CONCLUSIONS Here, we identify the STs and substitutions at the PBPs responsible for increased resistance of SS9 to penicillin on Italian pig farms. Our data highlight the need for monitoring the evolution of S. suis in the coming years.
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Affiliation(s)
| | - Lucilla Cucco
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Marta Panicciá
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Andrea Luppi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Parma, Italy
| | - Elisa Albini
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Arianna Peruzzo
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Laura Ferroni
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Martina Ustulin
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
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21
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Wu XY, Zhao ZY, Osman EEA, Wang XJ, Choo YM, Benjamin MM, Xiong J, Hamann MT, Luo C, Hu JF. Platanosides from Platanus × acerifolia: New molecules, SAR, and target validation of a strong lead for drug-resistant bacterial infections and the associated sepsis. Bioorg Chem 2024; 143:107103. [PMID: 38211549 DOI: 10.1016/j.bioorg.2024.107103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024]
Abstract
Three undescribed (1-3) and nine known (4-12) platanosides were isolated and characterized from a bioactive extract of the May leaves of Platanus × acerifolia that initially showed inhibition against Staphylococcus aureus. Targeted compound mining was guided by an LC-MS/MS-based molecular ion networking (MoIN) strategy combined with conventional isolation procedures from a unique geographic location. The novel structures were mainly determined by 2D NMR and computational (NMR/ECD calculations) methods. Compound 1 is a rare acylated kaempferol rhamnoside possessing a truxinate unit. 6 (Z,E-platanoside) and 7 (E,E-platanoside) were confirmed to have remarkable inhibitory effects against both methicillin-resistant S. aureus (MIC: ≤ 16 μg/mL) and glycopeptide-resistant Enterococcus faecium (MIC: ≤ 1 μg/mL). These platanosides were subjected to docking analyses against FabI (enoyl-ACP reductase) and PBP1/2 (penicillin binding protein), both of which are pivotal enzymes governing bacterial growth but not found in the human host. The results showed that 6 and 7 displayed superior binding affinities towards FabI and PBP2. Moreover, surface plasmon resonance studies on the interaction of 1/7 and FabI revealed that 7 has a higher affinity (KD = 1.72 μM), which further supports the above in vitro data and is thus expected to be a novel anti-antibacterial drug lead.
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Affiliation(s)
- Xi-Ying Wu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China; Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, PR China
| | - Ze-Yu Zhao
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Ezzat E A Osman
- Department of Medicinal Chemistry, Theodor Bilharz Research Institute, Kornaish El-Nile St., Giza 12411, Egypt
| | - Xiao-Juan Wang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, Gansu, PR China; Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA
| | - Yeun-Mun Choo
- Chemistry Department, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Menny M Benjamin
- Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA
| | - Juan Xiong
- School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Mark T Hamann
- Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA.
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, PR China
| | - Jin-Feng Hu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China; Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA.
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Panchal J, Patel A, Patel S, Goswami D. Understanding mastitis: Microbiome, control strategies, and prevalence - A comprehensive review. Microb Pathog 2024; 187:106533. [PMID: 38171428 DOI: 10.1016/j.micpath.2023.106533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/12/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024]
Abstract
Mastitis significantly affects the udder tissue in dairy cattle, leading to inflammation, discomfort, and a decline in both milk yield and quality. The condition can be attributed to an array of microbial agents that access the mammary gland through multiple pathways. The ramifications of this ailment are not merely confined to animal welfare but extend to the financial viability of the livestock industry. This review offers a historical lens on mastitis, tracing its documentation back to 1851, and examines its global distribution with a focus on regional differences in prevalence and antimicrobial resistance (AMR) patterns. Specific microbial genes and communities implicated in both mastitis and AMR are explored, including Staphylococcus aureus, Streptococcus agalactiae,Streptococcus dysagalactiae, Streptococcus uberis Escherichia coli, Klebsiella pneumoniae, Mycoplasma bovis, Corynebacterium bovis, among others. These microorganisms have evolved diverse strategies to elude host immune responses and neutralize commonly administered antibiotics, complicating management efforts. The review aims a comprehensive overview of the current knowledge and research gaps on mastitis and AMR, and to highlight the need for a One Health approach to address this global health issue. Such an approach entails multi-disciplinary cooperation to foster judicious antibiotic use, enhance preventive measures against mastitis, and bolster surveillance and monitoring of AMR in pathogens responsible for mastitis.
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Affiliation(s)
- Janki Panchal
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Arun Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Sardarkrushinagar, 385505, Kamdhenu University, Gujarat, India
| | - Sandip Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Sardarkrushinagar, 385505, Kamdhenu University, Gujarat, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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23
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Abdolvahab MH, Safari M, Hasannejad F, Asefi N, Salimi A, Nazari M. Optimization of a recombinant BlaR-CTD protein formulation using the response surface methodology. J Biol Eng 2024; 18:4. [PMID: 38212764 PMCID: PMC10785353 DOI: 10.1186/s13036-023-00399-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024] Open
Abstract
The sequence of a carboxy-terminal of the β-lactam sensor-transducer protein (BlaR-CTD) from Bacillus licheniformis ATCC14580 was extracted from US7745193B2 patent and expressed in E. coli using pColdI vector as a soluble His-tag recombinant protein. In this study, several excipients were used to improve the stability of recombinant BlaR-CTD and obtain the optimal formulation for this protein using response surface methodology (RSM)/ Central Composite Design (CCD). Total protein concentration was measured by UV spectroscopy and the Bradford test. A total of 7 various factors were designed using four different excipients including Glycerol, Sucrose, Triton x-100, and Tween-20, and three different buffers like Tris, Borate, and PBS. By obtaining suitable excipients and buffer i.e. glycerol and sucrose, pH ranging from 7 to 9 were evaluated. The pH 7.62, glycerol 15.35%, and sucrose 152.52 mM were determined as the most suitable for improving the thermal stability of recombinant BlaR-CTD.
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Affiliation(s)
- Mohadeseh Haji Abdolvahab
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
| | - Mojdeh Safari
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farkhonde Hasannejad
- Genetic Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Nika Asefi
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Genetic Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Alireza Salimi
- Department of Advanced Technologies, School of Medicine, North Khorasan University of Medical Science, Bojnurd, Iran
| | - Mahboobeh Nazari
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
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Conti P, Lazzaro LM, Longo F, Lenzo F, Giardina A, Fortuna SA, Stefani S, Campanile F. Unveiling the Relationship between Ceftobiprole and High-Molecular-Mass (HMM) Penicillin-Binding Proteins (PBPs) in Enterococcus faecalis. Antibiotics (Basel) 2024; 13:65. [PMID: 38247624 PMCID: PMC10812503 DOI: 10.3390/antibiotics13010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/30/2023] [Accepted: 01/06/2024] [Indexed: 01/23/2024] Open
Abstract
Low-affinity PBP4, historically linked to penicillin resistance in Enterococcus faecalis, may still have affinity for novel cephalosporins. Ceftobiprole (BPR) is a common therapeutic choice, even with PBP4-related overexpression and amino acid substitution due to mutations. Our study aims to explore the interaction between BPR and High-Molecular-Mass (HMM) low-reactive PBPs in Penicillin-Resistant-Ampicillin-Susceptible/Ceftobiprole Non-Susceptible (PRAS/BPR-NS) E. faecalis clinical isolates. We conducted competition assays examining class A and B HMM PBPs from four PRAS/BPR-NS E. faecalis strains using purified membrane proteins and fluorescent penicillin (Bocillin FL), in treated and untreated conditions. Interaction strength was assessed calculating the 50% inhibitory concentration (IC50) values for ceftobiprole, by analyzing fluorescence intensity trends. Due to its low affinity, PBP4 did not display significant acylation among all strains. Moreover, both PBP1a and PBP1b showed a similar insensitivity trend. Conversely, other PBPs showed IC50 values ranging from 1/2-fold to 4-fold MICs. Upon higher BPR concentrations, increased percentages of PBP4 inhibition were observed in all strains. Our results support the hypothesis that PBP4 is necessary but not sufficient for BPR resistance, changing the paradigm for enterococcal cephalosporin resistance. We hypothesize that cooperation between class B PBP4 and at least one bifunctional class A PBP could be required to synthesize peptidoglycan and promote growth.
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Affiliation(s)
- Paola Conti
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Lorenzo Mattia Lazzaro
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
| | - Fabio Longo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
- Department of Public Health and Pediatrics, University of Torino, 10126 Turin, Italy
| | - Federica Lenzo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
| | - Alessandra Giardina
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
| | - Sebastiano Alberto Fortuna
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
| | - Floriana Campanile
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
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25
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Huang LD, Gou XY, Yang MJ, Li MJ, Chen SN, Yan J, Liu XX, Sun AH. Peptidoglycan biosynthesis-associated enzymatic kinetic characteristics and β-lactam antibiotic inhibitory effects of different Streptococcus pneumoniae penicillin-binding proteins. Int J Biol Macromol 2024; 254:127784. [PMID: 37949278 DOI: 10.1016/j.ijbiomac.2023.127784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/15/2023] [Accepted: 10/28/2023] [Indexed: 11/12/2023]
Abstract
Penicillin-binding proteins (PBPs) include transpeptidases, carboxypeptidases, and endopeptidases for biosynthesis of peptidoglycans in the cell wall to maintain bacterial morphology and survival in the environment. Streptococcus pneumoniae expresses six PBPs, but their enzymatic kinetic characteristics and inhibitory effects on different β-lactam antibiotics remain poorly understood. In this study, all the six recombinant PBPs of S. pneumoniae displayed transpeptidase activity with different substrate affinities (Km = 1.56-9.11 mM) in a concentration-dependent manner, and rPBP3 showed a greater catalytic efficiency (Kcat = 2.38 s-1) than the other rPBPs (Kcat = 3.20-7.49 × 10-2 s-1). However, only rPBP3 was identified as a carboxypeptidase (Km = 8.57 mM and Kcat = 2.57 s-1). None of the rPBPs exhibited endopeptidase activity. Penicillin and cefotaxime inhibited the transpeptidase and carboxypeptidase activity of all the rPBPs but imipenem did not inhibited the enzymatic activities of rPBP3. Except for the lack of binding of imipenem to rPBP3, penicillin, cefotaxime, and imipenem bound to all the other rPBPs (KD = 3.71-9.35 × 10-4 M). Sublethal concentrations of penicillin, cefotaxime, and imipenem induced a decrease of pneumococcal pbps-mRNA levels (p < 0.05). These results indicated that all six PBPs of S. pneumoniae are transpeptidases, while only PBP3 is a carboxypeptidase. Imipenem has no inhibitory effect on pneumococcal PBP3. The pneumococcal genes for encoding endopeptidases remain to be determined.
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Affiliation(s)
- Li-Dan Huang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China; Yiwu Central Blood Station, Yiwu, Zhejiang 322000, PR China
| | - Xiao-Yu Gou
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China
| | - Mei-Juan Yang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China; The First Hospital of Putian City, Putian, Fujian 351100, PR China
| | - Meng-Jie Li
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China
| | - Sui-Ning Chen
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China
| | - Jie Yan
- Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, PR China
| | - Xiao-Xiang Liu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China.
| | - Ai-Hua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China.
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Wattam AR, Bowers N, Brettin T, Conrad N, Cucinell C, Davis JJ, Dickerman AW, Dietrich EM, Kenyon RW, Machi D, Mao C, Nguyen M, Olson RD, Overbeek R, Parrello B, Pusch GD, Shukla M, Stevens RL, Vonstein V, Warren AS. Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance. Methods Mol Biol 2024; 2802:547-571. [PMID: 38819571 DOI: 10.1007/978-1-0716-3838-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
As genomic and related data continue to expand, research biologists are often hampered by the computational hurdles required to analyze their data. The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Centers (BRC) to assist researchers with their analysis of genome sequence and other omics-related data. Recently, the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD), and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs merged to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) at https://www.bv-brc.org/ . The combined BV-BRC leverages the functionality of the original resources for bacterial and viral research communities with a unified data model, enhanced web-based visualization and analysis tools, and bioinformatics services. Here we demonstrate how antimicrobial resistance data can be analyzed in the new resource.
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Affiliation(s)
- Alice R Wattam
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA.
| | - Nicole Bowers
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Thomas Brettin
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, USA
| | - Neal Conrad
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Clark Cucinell
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Allan W Dickerman
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
| | - Emily M Dietrich
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Ronald W Kenyon
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
| | - Dustin Machi
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
| | - Chunhong Mao
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Robert D Olson
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Ross Overbeek
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA
| | - Bruce Parrello
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA
| | - Gordon D Pusch
- Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Rick L Stevens
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | | | - Andrew S Warren
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
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27
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Aribisala JO, Sabiu S. Cheminformatics identification of phenolics as modulators of penicillin-binding protein-3 of Pseudomonas aeruginosa towards interventive antibacterial therapy. J Biomol Struct Dyn 2024; 42:298-313. [PMID: 36974951 DOI: 10.1080/07391102.2023.2192808] [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: 11/29/2022] [Accepted: 03/11/2023] [Indexed: 03/29/2023]
Abstract
Antibacterial resistance to β-lactams in microorganisms has been attributed majorly to alterations in penicillin-binding proteins (PBPs) coupled with β-lactams' inactivation by β-lactamase. Consequently, the identification of a novel class of therapeutics with improved modulatory action on the PBPs is imperative and plant secondary metabolites, including phenolics, have found relevance in this regard. For the first time in this study, the over 10,000 phenolics currently known were computationally evaluated against PBP3 of Pseudomonas aeruginosa, a superbug implicated in several nosocomial infections. In doing this, a library of phenolics with an affinity for PBP3 of P. aeruginosa was screened using structure-activity relationship-based pharmacophore and molecular docking approaches. Subsequent thermodynamic screening of the top five phenolics with higher docking scores, more drug-likeness attributes, and feasible synthetic accessibility was achieved through a 120 ns molecular dynamic (MD) simulation. Four of the top five hits had higher binding free energy than cefotaxime (-18.72 kcal/mol), with catechin-3-rhamside having the highest affinity (-28.99 kcal/mol). All the hits were stable at the active site of the PBP3, with catechin-3-rhamside being the most stable (2.14 Å), and established important interactions with Ser294, implicated in the catalytic activity of PBP3. Also, PBP3 became more compact with less fluctuation of the active site amino acid residues following the binding of the hits. These observations are indicative of the potential of the test compounds as PBP3 inhibitors, with catechin-3-rhamside being the most prominent of the compounds that could be further improved for enhanced druggability against PBP3 in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jamiu Olaseni Aribisala
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
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28
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Sarkar S, Moitra P, Bhattacharya S. Structure-activity relationship of drug conjugated polymeric materials against uropathogenic bacteria colonization under in vitro and in vivo settings. J Mater Chem B 2023; 12:187-201. [PMID: 38059523 DOI: 10.1039/d3tb01841e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The human world has been plagued with different kinds of bacterial infections from time immemorial. The increased development of resistance towards commercial antibiotics has made these bacterial infections an even more critical challenge. Bacteria have modified their mode of interactions with different types of commercial drugs by bringing changes to the receptor proteins or by other resisting mechanisms like drug efflux. Various chemical approaches have been made to date to fight against these smart adapting species. Towards this, we hypothesize chemically modifying the commercial antibacterial drugs in order to deceive the bacteria and destroy the bacterial biomass. In this study, different molecular weight polyethyleneimines are taken and conjugated with some well-known commercial drugs like penicillin and chloramphenicol to explore their antibacterial properties against some of the laboratory and uro-pathogenic strains of Gram-positive and Gram-negative bacteria. A detailed structure-activity relationship of these polymeric prodrug-like materials has been evaluated to determine the optimum formulation. The standardized system not only shows significant ∼90% bacterial killing in liquid broth culture, but also demonstrates promising bacterial inhibition towards biofilm formation for the pathogenic strains on inanimate surfaces like urinary catheters and on an in vivo mouse skin abrasion model. The reported bioactive polymeric materials can be successfully used for widespread therapeutic applications with promising medical relevance.
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Affiliation(s)
- Sourav Sarkar
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
| | - Parikshit Moitra
- Department of Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Technical Research Centre, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Santanu Bhattacharya
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
- Technical Research Centre, Indian Association for the Cultivation of Science, Kolkata 700032, India
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Srinivasapuram, Yerpedu Mandal, Tirupati District, Andhra Pradesh 517619, India
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29
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Gwynne PJ, Stocks KLK, Karozichian ES, Pandit A, Hu LT. Metabolic modeling predicts unique drug targets in Borrelia burgdorferi. mSystems 2023; 8:e0083523. [PMID: 37855615 PMCID: PMC10734484 DOI: 10.1128/msystems.00835-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Lyme disease is often treated using long courses of antibiotics, which can cause side effects for patients and risks the evolution of antimicrobial resistance. Narrow-spectrum antimicrobials would reduce these risks, but their development has been slow because the Lyme disease bacterium, Borrelia burgdorferi, is difficult to work with in the laboratory. To accelerate the drug discovery pipeline, we developed a computational model of B. burgdorferi's metabolism and used it to predict essential enzymatic reactions whose inhibition prevented growth in silico. These predictions were validated using small-molecule enzyme inhibitors, several of which were shown to have specific activity against B. burgdorferi. Although the specific compounds used are not suitable for clinical use, we aim to use them as lead compounds to develop optimized drugs targeting the pathways discovered here.
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Affiliation(s)
- Peter J. Gwynne
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Tufts Lyme Disease Initiative, Tufts University, Boston, Massachusetts, USA
| | - Kee-Lee K. Stocks
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Tufts Lyme Disease Initiative, Tufts University, Boston, Massachusetts, USA
| | - Elysse S. Karozichian
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Tufts Lyme Disease Initiative, Tufts University, Boston, Massachusetts, USA
| | - Aarya Pandit
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Tufts Lyme Disease Initiative, Tufts University, Boston, Massachusetts, USA
| | - Linden T. Hu
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Tufts Lyme Disease Initiative, Tufts University, Boston, Massachusetts, USA
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30
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Xiong X, Chen R, Lai J. Comparative genomics analysis of Streptococcus iniae isolated from Trachinotus ovatus: novel insight into antimicrobial resistance and virulence differentiation. BMC Genomics 2023; 24:775. [PMID: 38097934 PMCID: PMC10720119 DOI: 10.1186/s12864-023-09882-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Streptococcus iniae is an important fish pathogen that cause significant economic losses to the global aquaculture industry every year. Although there have some reports on the genotype of S.iniae and its relationship with virulence, no genome-scale comparative analysis has been performed so far. In our previous work, we characterized 17 isolates of S.iniae from Trachinotus ovatus and divided them into two genotypes using RAPD and rep-PCR methods. Among them, BH15-2 was classified as designated genotype A (in RAPD) and genotype 1 (in rep-PCR), while BH16-24 was classified as genotype B and genotype 2. Herein, we compared the differences in growth, drug resistance, virulence, and genome between BH15-2 and BH16-24. RESULTS The results showed that the growth ability of BH16-24 was significantly faster than that of BH15-2 at the exponential stage. Antimicrobial tests revealed that BH15-2 was susceptible to most of the tested antibiotics except neomycin and gentamycin. In contrast, BH16-24 was resistant to 7 antibiotics including penicillin, sulfasomizole, compound sulfamethoxazole tablets, polymyxin B, spectinomycin, rifampin and ceftazidime. Intraperitoneal challenge of T.ovatus, showed that the LD50 value of BH15-2 was 4.0 × 102 CFU/g, while that of BH16-24 was 1.2 × 105 CFU/g. The genome of S.iniae BH15-2 was 2,175,659 bp with a GC content of 36.80%. Meanwhile, the genome of BH16-24 was 2,153,918 bp with a GC content of 36.83%. Comparative genome analysis indicated that compared with BH15-2, BH16-24 genome had a large-scale genomic inversion fragment, at the location from 502,513 bp to 1,788,813 bp, resulting in many of virulence and resistance genes differentially expression. In addition, there was a 46 kb length, intact phage sequence in BH15-2 genome, which was absent in BH16-24. CONCLUSION Comparative genomic studies of BH15-2 and BH16-24 showed that the main difference is a 1.28 Mbp inversion fragment. The inversion fragment may lead to abnormal expression of drug resistant and virulence genes, which is believed to be the main reason for the multiple resistance and weakened virulence of BH16-24. Our study revealed the potential mechanisms in underlying the differences of multidrug resistance and virulence among different genotypes of S.iniae.
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Affiliation(s)
- Xiangying Xiong
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
- Guangxi Institute of Oceanology Limited Liability Company, Beihai, 536000, Guangxi, China.
- Beibu Gulf Marine Industry Research Institute, Fangchenggang, 538000, Guangxi, China.
| | - Ruifang Chen
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
- Guangxi Institute of Oceanology Limited Liability Company, Beihai, 536000, Guangxi, China
- Beibu Gulf Marine Industry Research Institute, Fangchenggang, 538000, Guangxi, China
| | - Junxiang Lai
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
- Beibu Gulf Marine Industry Research Institute, Fangchenggang, 538000, Guangxi, China
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31
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Chen XW, Wu JH, Liu YL, Munang’andu HM, Peng B. Fructose promotes ampicillin killing of antibiotic-resistant Streptococcus agalactiae. Virulence 2023; 14:2180938. [PMID: 36803528 PMCID: PMC9980678 DOI: 10.1080/21505594.2023.2180938] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
Streptococcus agalactiae (GBS) is an important pathogenic bacteria that infected both aquatic animals and human beings, causing huge economic loss. The increasing cases of antibiotic-resistant GBS impose challenges to treat such infection by antibiotics. Thus, it is highly demanded for the approach to tackle antibiotic resistance in GBS. In this study, we adopt a metabolomic approach to identify the metabolic signature of ampicillin-resistant GBS (AR-GBS) that ampicillin is the routine choice to treat infection by GBS. We find glycolysis is significantly repressed in AR-GBS, and fructose is the crucial biomarker. Exogenous fructose not only reverses ampicillin resistance in AR-GBS but also in clinic isolates including methicillin-resistant Staphylococcus aureus (MRSA) and NDM-1 expressing Escherichia coli. The synergistic effect is confirmed in a zebrafish infection model. Furthermore, we demonstrate that the potentiation by fructose is dependent on glycolysis that enhances ampicillin uptake and the expression of penicillin-binding proteins, the ampicillin target. Our study demonstrates a novel approach to combat antibiotic resistance in GBS.
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Affiliation(s)
- Xuan-Wei Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Higher Education Mega Center, Guangzhou, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jia-Han Wu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Higher Education Mega Center, Guangzhou, China
| | - Ying-Li Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Higher Education Mega Center, Guangzhou, China
| | | | - Bo Peng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Higher Education Mega Center, Guangzhou, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,CONTACT Bo Peng
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El-Telbany M, Lin CY, Abdelaziz MN, Maung AT, El-Shibiny A, Mohammadi TN, Zayda M, Wang C, Zar Chi Lwin S, Zhao J, Masuda Y, Honjoh KI, Miyamoto T, El M. Potential application of phage vB_EfKS5 to control Enterococcus faecalis and its biofilm in food. AMB Express 2023; 13:130. [PMID: 37985524 PMCID: PMC10661674 DOI: 10.1186/s13568-023-01628-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 11/22/2023] Open
Abstract
Contaminated food with antibiotic-resistant Enterococcus spp. could be the vehicle for transmitting Enterococcus to humans and accordingly cause a public health problem. The accumulation of biogenic amines produced by Enterococcus faecalis (E. faecalis) in food may have cytological effects. Bacteriophages (phage in short) are natural antimicrobial agents and can be used alone or in combination with other food preservatives to reduce food microbial contaminants. The aim of this study was to isolate a novel phage against E. faecalis and determine its host range to evaluate its potential application. Bacteriophage, vB_EfKS5, with a broad host range, was isolated to control the growth of E. faecalis. The vB_EfKS5 genome is 59,246 bp in length and has a GC content of 39.7%. The computational analysis of phage vB_EfKS5 genome confirmed that it does not contain any lysogenic, toxic, or virulent genes. Phage vB_EfKS5 exhibited lytic activity against most E. faecalis isolates with different multiplicities of infections and it infected 75.5% (22/29) of E. faecalis isolates and 42.3% (3/7) of E. faecium isolates. It was also able to destroy the biofilm formed by E. faecalis with different MOIs. Phage vB_EfKS5 alone or in combination with nisin could control the growth of E. faecalis in broth and milk. Based on its high productivity, stability, short latent period, and large burst size, phage vB_EfKS5 has a high potential for applications both in food and medical applications.
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Affiliation(s)
- Mohamed El-Telbany
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, 44519, Zagazig, Egypt
| | - Chen-Yu Lin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Marwa Nabil Abdelaziz
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Aye Thida Maung
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, 12578, Giza, Egypt
| | - Tahir Noor Mohammadi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
- Teagasc Food Research Center, Moorepark, Fermoy, Cork, Ireland
| | - Mahmoud Zayda
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Monofiya Governorate, Egypt
| | - Chen Wang
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Su Zar Chi Lwin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Junxin Zhao
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshimitsu Masuda
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395, Fukuoka, Japan
| | - Ken-Ichi Honjoh
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395, Fukuoka, Japan.
| | - Takahisa Miyamoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, 819-0395, Fukuoka, Japan
| | - Mohamed El
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
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Gong J, Yi JS, Cho HS, Shin CH, Won HJ, Cho BK, Noh M, Yoon YJ. Transcriptome profiles of Streptomyces clavuligerus strains producing different titers of clavulanic acid. Sci Data 2023; 10:804. [PMID: 37973966 PMCID: PMC10654394 DOI: 10.1038/s41597-023-02727-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Streptomyces clavuligerus NRRL 3585 is a native producer of clavulanic acid (CA), a clinically used β-lactamase inhibitor, and is widely used as an industrial strain for the production of antibiotics. Selective random mutagenesis has successfully generated the improved CA-producing S. clavuligerus mutant strains as well as the strain with the loss of CA biosynthesis. To understand the molecular mechanisms associated with the improved CA-production potential, genome-scale RNA-sequencing-based transcriptional data were obtained for the wild-type S. clavuligerus strain and its three mutant strains. Total RNA samples for each strain were collected across four different growth stages, and all 32 sequencing data points exhibited an average Phred score of 36. The high-quality genome-scale transcriptional profile of S. clavuligerus strains with varied CA biosynthetic potential provides valuable insights and new opportunities for discovering efficient metabolic engineering strategies for the development of improved industrial strains.
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Affiliation(s)
- Junpyo Gong
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jeong Sang Yi
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hang Su Cho
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang Hun Shin
- Research Institute of CKD BiO, Ansan, 15604, Republic of Korea
| | - Hyung-Jin Won
- Research Institute of CKD BiO, Ansan, 15604, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Minsoo Noh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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Raza S, Wdowiak M, Grotek M, Adamkiewicz W, Nikiforow K, Mente P, Paczesny J. Enhancing the antimicrobial activity of silver nanoparticles against ESKAPE bacteria and emerging fungal pathogens by using tea extracts. NANOSCALE ADVANCES 2023; 5:5786-5798. [PMID: 37881701 PMCID: PMC10597549 DOI: 10.1039/d3na00220a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/12/2023] [Indexed: 10/27/2023]
Abstract
The sale of antibiotics and antifungals has skyrocketed since 2020. The increasing threat of pathogens like ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), which are effective in evading existing antibiotics, and yeasts like Candida auris or Cryptococcus neoformans is pressing to develop efficient antimicrobial alternatives. Nanoparticles, especially silver nanoparticles (AgNPs), are believed to be promising candidates to supplement or even replace antibiotics in some applications. Here, we propose a way to increase the antimicrobial efficiency of silver nanoparticles by using tea extracts (black, green, or red) for their synthesis. This allows for using lower concentrations of nanoparticles and obtaining the antimicrobial effect in a short time. We found that AgNPs synthesized using green tea extract (G-TeaNPs) are the most effective, causing approximately 80% bacterial cell death in Gram-negative bacteria within only 3 hours at a concentration of 0.1 mg mL-1, which is better than antibiotics. Ampicillin at the same concentration (0.1 mg mL-1) and within the same duration (3 h) causes only up to 40% decrease in the number of S. aureus and E. cloacae cells (non-resistant strains). The tested silver nanoparticles also have antifungal properties and are effective against C. auris and C. neoformans, which are difficult to eradicate using other means. We established that silver nanoparticles synthesized with tea extracts have higher antibacterial properties than silver nanoparticles alone. Such formulations using inexpensive tea extracts and lower concentrations of silver nanoparticles show a promising solution to fight various pathogens.
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Affiliation(s)
- Sada Raza
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| | - Mateusz Wdowiak
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| | - Mateusz Grotek
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
- Military University of Technology gen. Sylwestra Kaliskiego 2 00-908 Warsaw Poland
| | - Witold Adamkiewicz
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| | - Kostiantyn Nikiforow
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| | - Pumza Mente
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| | - Jan Paczesny
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
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Ambade SS, Gupta VK, Bhole RP, Khedekar PB, Chikhale RV. A Review on Five and Six-Membered Heterocyclic Compounds Targeting the Penicillin-Binding Protein 2 (PBP2A) of Methicillin-Resistant Staphylococcus aureus (MRSA). Molecules 2023; 28:7008. [PMID: 37894491 PMCID: PMC10609489 DOI: 10.3390/molecules28207008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a common human pathogen. Methicillin-resistant Staphylococcus aureus (MRSA) infections pose significant and challenging therapeutic difficulties. MRSA often acquires the non-native gene PBP2a, which results in reduced susceptibility to β-lactam antibiotics, thus conferring resistance. PBP2a has a lower affinity for methicillin, allowing bacteria to maintain peptidoglycan biosynthesis, a core component of the bacterial cell wall. Consequently, even in the presence of methicillin or other antibiotics, bacteria can develop resistance. Due to genes responsible for resistance, S. aureus becomes MRSA. The fundamental premise of this resistance mechanism is well-understood. Given the therapeutic concerns posed by resistant microorganisms, there is a legitimate demand for novel antibiotics. This review primarily focuses on PBP2a scaffolds and the various screening approaches used to identify PBP2a inhibitors. The following classes of compounds and their biological activities are discussed: Penicillin, Cephalosporins, Pyrazole-Benzimidazole-based derivatives, Oxadiazole-containing derivatives, non-β-lactam allosteric inhibitors, 4-(3H)-Quinazolinones, Pyrrolylated chalcone, Bis-2-Oxoazetidinyl macrocycles (β-lactam antibiotics with 1,3-Bridges), Macrocycle-embedded β-lactams as novel inhibitors, Pyridine-Coupled Pyrimidinones, novel Naphthalimide corbelled aminothiazoximes, non-covalent inhibitors, Investigational-β-lactam antibiotics, Carbapenem, novel Benzoxazole derivatives, Pyrazolylpyridine analogues, and other miscellaneous classes of scaffolds for PBP2a. Additionally, we discuss the penicillin-binding protein, a crucial target in the MRSA cell wall. Various aspects of PBP2a, bacterial cell walls, peptidoglycans, different crystal structures of PBP2a, synthetic routes for PBP2a inhibitors, and future perspectives on MRSA inhibitors are also explored.
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Affiliation(s)
- Shraddha S. Ambade
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
| | - Vivek Kumar Gupta
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra 282004, UP, India
| | - Ritesh P. Bhole
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune 411018, MH, India
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, MH, India
| | - Pramod B. Khedekar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
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K S, Vasanthrao R, Chattopadhyay I. Impact of environment on transmission of antibiotic-resistant superbugs in humans and strategies to lower dissemination of antibiotic resistance. Folia Microbiol (Praha) 2023; 68:657-675. [PMID: 37589876 DOI: 10.1007/s12223-023-01083-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
Antibiotics are the most efficient type of therapy developed in the twentieth century. From the early 1960s to the present, the rate of discovery of new and therapeutically useful classes of antibiotics has significantly decreased. As a result of antibiotic use, novel strains emerge that limit the efficiency of therapies in patients, resulting in serious consequences such as morbidity or mortality, as well as clinical difficulties. Antibiotic resistance has created major concern and has a greater impact on global health. Horizontal and vertical gene transfers are two mechanisms involved in the spread of antibiotic resistance genes (ARGs) through environmental sources such as wastewater treatment plants, agriculture, soil, manure, and hospital-associated area discharges. Mobile genetic elements have an important part in microbe selection pressure and in spreading their genes into new microbial communities; additionally, it establishes a loop between the environment, animals, and humans. This review contains antibiotics and their resistance mechanisms, diffusion of ARGs, prevention of ARG transmission, tactics involved in microbiome identification, and therapies that aid to minimize infection, which are explored further below. The emergence of ARGs and antibiotic-resistant bacteria (ARB) is an unavoidable threat to global health. The discovery of novel antimicrobial agents derived from natural products shifts the focus from chemical modification of existing antibiotic chemical composition. In the future, metagenomic research could aid in the identification of antimicrobial resistance genes in the environment. Novel therapeutics may reduce infection and the transmission of ARGs.
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Affiliation(s)
- Suganya K
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India
| | - Ramavath Vasanthrao
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India
| | - Indranil Chattopadhyay
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India.
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Abdelsalam NA, Elhadidy M, Saif NA, Elsayed SW, Mouftah SF, Sayed AA, Ziko L. Biosynthetic gene cluster signature profiles of pathogenic Gram-negative bacteria isolated from Egyptian clinical settings. Microbiol Spectr 2023; 11:e0134423. [PMID: 37707241 PMCID: PMC10580877 DOI: 10.1128/spectrum.01344-23] [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: 03/28/2023] [Accepted: 07/03/2023] [Indexed: 09/15/2023] Open
Abstract
Biosynthetic gene clusters (BGCs) are a subset of consecutive genes present within a variety of organisms to produce specialized metabolites (SMs). These SMs are becoming a cornerstone to produce multiple medications including antibacterial and anticancer agents. Natural products (NPs) also play a pivotal role in enhancing the virulence of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), which represent a global health threat. We aimed to sequence and computationally analyze the BGCs present in 66 strains pertaining to three different ESKAPE pathogenic species: 21 A. baumannii, 28 K. pneumoniae, and 17 P. aeruginosa strains recovered from clinical settings in Egypt. DNA was extracted using QIAamp DNA Mini kit and Illumina NextSeq 550 was used for whole-genome sequencing. The sequences were quality-filtered by fastp and assembled by Unicycler. BGCs were detected by antiSMASH, BAGEL, GECCO, and PRISM, and aligned using Clinker. The highest abundance of BGCs was detected in P. aeruginosa (590), then K. pneumoniae (146) and the least in A. baumannii strains (133). P. aeruginosa isolates shared mostly the non-ribosomal peptide synthase (NRPS) type, K. pneumoniae isolates shared the ribosomally synthesized and post-translationally modified peptide-like (RiPP-like) type, while A. baumannii isolates shared the siderophore type. Most of the isolates harbored non-ribosomal peptide (NRP) BGCs with few K. pneumoniae isolates encoding polyketide BGCs. Sactipeptides and bottromycin BGCs were the most frequently detected RiPP clusters. We hypothesize that each species' BGC signature confers its virulence. Future experiments will link the detected clusters with their species and determine whether the encoded SMs are produced and cause their virulence. IMPORTANCE Our study analyzes the biosynthetic gene clusters (BGCs) present in 66 assemblies from clinical ESKAPE pathogen isolates pertaining to Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa strains. We report their sequencing and assembly followed by the analysis of their BGCs using several bioinformatics tools. We then focused on the most abundant BGC type in each species and we discussed their potential roles in the virulence of each species. This study is pivotal to further build on its experimental work that deciphers the role in virulence, possible antibacterial effects, and characterization of the encoded specialized metabolites (SMs). The study highlights the importance of studying the "harmful" BGCs and understanding the pathogenicity and virulence of those species, as well as possible benefits if the SMs were used as antibacterial agents. This could be the first study of its kind from Egypt and would shed light on BGCs from ESKAPE pathogens from Egypt.
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Affiliation(s)
- Nehal Adel Abdelsalam
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Nehal A. Saif
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Salma W. Elsayed
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Shaimaa F. Mouftah
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Ahmed A. Sayed
- Genomic research program, Basic research department, Children’s Cancer Hospital Egypt, Cairo, Egypt
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Laila Ziko
- School of Life and Medical Sciences, University of Hertfordshire, Hosted by Global Academic Foundation, Cairo, Egypt
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Hershko Y, Levytskyi K, Rannon E, Assous MV, Ken-Dror S, Amit S, Ben-Zvi H, Sagi O, Schwartz O, Sorek N, Szwarcwort M, Barkan D, Burstein D, Adler A. Phenotypic and genotypic analysis of antimicrobial resistance in Nocardia species. J Antimicrob Chemother 2023; 78:2306-2314. [PMID: 37527397 DOI: 10.1093/jac/dkad236] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Antimicrobial resistance is common in Nocardia species but data regarding the molecular mechanisms beyond their resistance traits are limited. Our study aimed to determine the species distribution, the antimicrobial susceptibility profiles, and investigate the associations between the resistance traits and their genotypic determinants. METHODS The study included 138 clinical strains of Nocardia from nine Israeli microbiology laboratories. MIC values of 12 antimicrobial agents were determined using broth microdilution. WGS was performed on 129 isolates of the eight predominant species. Bioinformatic analysis included phylogeny and determination of antimicrobial resistance genes and mutations. RESULTS Among the isolates, Nocardia cyriacigeorgica was the most common species (36%), followed by Nocardia farcinica (16%), Nocardia wallacei (13%), Nocardia abscessus (9%) and Nocardia brasiliensis (8%). Linezolid was active against all isolates, followed by trimethoprim/sulfamethoxazole (93%) and amikacin (91%). Resistance to other antibiotics was species-specific, often associated with the presence of resistance genes or mutations: (1) aph(2″) in N. farcinica and N. wallacei (resistance to tobramycin); (ii) blaAST-1 in N. cyriacigeorgica and Nocardia neocaledoniensis (resistance to amoxicillin/clavulanate); (iii) blaFAR-1 in N. farcinica (resistance to ceftriaxone); (iv) Ser83Ala substitution in the gyrA gene in four species (resistance to ciprofloxacin); and (v) the 16S rRNA m1A1408 methyltransferase in N. wallacei isolates (correlating with amikacin resistance). CONCLUSIONS Our study provides a comprehensive understanding of Nocardia species diversity, antibiotic resistance patterns, and the molecular basis of antimicrobial resistance. Resistance appears to follow species-related patterns, suggesting a lesser role for de novo evolution or transmission of antimicrobial resistance.
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Affiliation(s)
- Yizhak Hershko
- Koret School of Veterinary Medicine, Robert H. Smith Faculty for Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv University, Tel-Aviv, Israel
| | - Katia Levytskyi
- Koret School of Veterinary Medicine, Robert H. Smith Faculty for Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ella Rannon
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Marc V Assous
- Clinical Microbiology Laboratory, Shaare Zedek Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shifra Ken-Dror
- Clalit Health Services, Haifa and Western Galilee District, Israel
| | - Sharon Amit
- Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Haim Ben-Zvi
- Microbiology Laboratory, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Orli Sagi
- Clinical Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva 84105, Israel
| | | | - Nadav Sorek
- Assuta Ashdod University Hospital, Ashdod, Israel
| | - Moran Szwarcwort
- Clinical Microbiology Laboratories, Laboratories Division, Rambam Health Care Campus, Haifa, Israel
| | - Daniel Barkan
- Koret School of Veterinary Medicine, Robert H. Smith Faculty for Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Amos Adler
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv University, Tel-Aviv, Israel
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Handayani D, Aminah I, Pontana Putra P, Eka Putra A, Arbain D, Satriawan H, Efdi M, Celik I, Ekawati Tallei T. The depsidones from marine sponge-derived fungus Aspergillus unguis IB151 as an anti-MRSA agent: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies. Saudi Pharm J 2023; 31:101744. [PMID: 37649676 PMCID: PMC10462890 DOI: 10.1016/j.jsps.2023.101744] [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: 05/12/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an emerging nosocomial pathogen among hospitalized patients, with high morbidity and mortality rates. The discovery of a novel antibacterial is urgently needed to address this resistance problem. The present study aims to explore the antibacterial potential of three depsidone compounds: 2-clorounguinol (1), unguinol (2), and nidulin (3), isolated from the marine sponge-derived fungus Aspergillus unguis IB1, both in vitro and in silico. The antibacterial activity of all compounds was evaluated by calculating the Minimum inhibitory concentration (MIC) and Minimum bactericidal concentration (MBC) against MRSA using agar diffusion and total plate count methods, respectively. Bacterial cell morphology changes were studied for the first time using scanning electron microscopy (SEM). Molecular docking, pharmacokinetics analysis, and molecular dynamics simulation were performed to determine possible protein-ligand interactions and the stability of the targeting penicillin-binding protein 2a (PBP2a) against 2-clorounguinol (1). The research findings indicated that compounds 1 to 3 exhibited MIC and MBC values of 2 µg/mL and 16 µg/mL against MRSA, respectively. MRSA cells displayed a distinct shape after the addition of the depsidone compound, as observed in SEM. According to the in silico study, 2-chlorounguinol exhibited the highest binding-free energy (BFE) with PBP2a (-6.7 kcal/mol). For comparison, (E)-3-(2-(4-cyanostyryl)-4-oxoquinazolin-3(4H)-yl) benzoic acid inhibits PBP2a with a BFE less than -6.6 kcal/mol. Based on the Lipinski's rule of 5, depsidone compounds constitute a class of compounds with good pharmacokinetic properties, being easily absorbed and permeable. These findings suggest that 2-chlorounguinol possesses potential antibacterial activity and could be developed as an antibiotic adjuvant to reduce antimicrobial resistance.
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Affiliation(s)
- Dian Handayani
- Faculty of Pharmacy/Sumatran Biota Laboratory, Andalas University, Padang 25163, Indonesia
| | - Ibtisamatul Aminah
- Faculty of Pharmacy/Sumatran Biota Laboratory, Andalas University, Padang 25163, Indonesia
- Department of Biomedical Science, Faculty of Medicine, Andalas University, Padang 25163, Indonesia
| | - Purnawan Pontana Putra
- Faculty of Pharmacy/Sumatran Biota Laboratory, Andalas University, Padang 25163, Indonesia
| | - Andani Eka Putra
- Department of Biomedical Science, Faculty of Medicine, Andalas University, Padang 25163, Indonesia
| | - Dayar Arbain
- Faculty of Pharmacy, 17 Agustus 1945 University, Sunter Permai Raya St, Jakarta 14350, Indonesia
| | - Herland Satriawan
- Institute of Ocean and Earth Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mai Efdi
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Andalas University, Padang 25163, Indonesia
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
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Lee Y, Kim N, Roh H, Ho DT, Park J, Lee JY, Kim YJ, Kang HY, Lee J, Song JY, Kim A, Kim MS, Cho M, Choi HS, Park CI, Kim DH. Serotype distribution and antibiogram of Streptococcus parauberis isolated from fish in South Korea. Microbiol Spectr 2023; 11:e0440022. [PMID: 37555676 PMCID: PMC10581249 DOI: 10.1128/spectrum.04400-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/27/2023] [Indexed: 08/10/2023] Open
Abstract
Streptococcus parauberis is the dominant etiological agent of streptococcosis, the most devastating bacterial disease in the olive flounder farming industry in South Korea. In this study, the distribution of serotypes, antimicrobial susceptibility, and presence of antimicrobial resistance genes (ARGs) in S. parauberis isolates obtained between 1999 and 2021 was thoroughly investigated to gain insight into the dynamics of their presence and the relationship between serotypes and antimicrobial resistance. Disk diffusion testing of 103 isolates against 10 antimicrobial agents was performed, and epidemiological cut-off values generated through normalized resistance interpretation analysis were used to classify wild-type (WT) and non-wild-type (NWT) populations. Principal component analysis and hierarchical clustering were implemented to achieve an understanding on the relationship between serotypes and antimicrobial resistance patterns. PCR-based serotyping showed that serotype Ia (67.1%) was the most prevalent in South Korea, followed by serotypes Ib/Ic (25.2%) and II (7.7%). The highest proportion of isolates was assigned to NWT against amoxicillin (80.6%), followed by oxytetracycline (77.7%) and erythromycin (48.5%). The time-scale data showed that recently obtained serotypes Ib/Ic and II isolates tended to be categorized as NWT populations resistant to more antibiotics, possibly due to microbial adaptation to antibiotic pressure. ARGs responsible for resistance to oxytetracycline and erythromycin were found only in NWT populations in serotype Ia [tet(S) and erm(B), respectively], and serotype II [tet(M) and mef(J)-msr(I), respectively]. We also found that the mef-msr gene pair in S. parauberis serotype II might be involved in low-level resistance to erythromycin. IMPORTANCE This study presents serotype distribution and antimicrobial susceptibility data along with the antimicrobial resistance genes (ARGs) of Streptococcus parauberis, which is an important bacterial fish pathogen worldwide. In particular, almost all oxytetracycline and erythromycin non-wild-type (NWT) populations harbored tet(S) or tet(M), and erm(B) or mef(J)-msr(I), respectively. Interestingly, these ARGs were distributed in a highly serotype-dependent manner, resulting in a clear correlation between the antibiogram and serotype distribution. Moreover, recent isolates belonging to serotypes Ib/Ic and II tended to be more frequently categorized as NWT against antimicrobials, including amoxicillin and cefalexin compared to old isolates, while a dramatic decrease in erythromycin and clindamycin NWT frequencies was observed in recent serotype Ia isolates, which lacked erm(B). These variations might be attributed to shifts in the antibiotics employed in South Korean aquaculture over time. The overall findings would provide important background knowledge for understanding the epidemiology of S. parauberis infection in aquaculture.
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Affiliation(s)
- Yoonhang Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Nameun Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - HeyongJin Roh
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Diem Tho Ho
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Jiyeon Park
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Ju Yeop Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Yoon-Jae Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Hyo-Young Kang
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Jungmin Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Jun-Young Song
- Pathology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Ahran Kim
- Pathology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Myoung Sug Kim
- Pathology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Miyoung Cho
- Pathology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Hye Sung Choi
- Pathology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Chan-Il Park
- Department of Marine Biology and Aquaculture, Gyeongsang National University, Tongyeong, South Korea
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
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Puzia W, Gawor J, Gromadka R, Żuchniewicz K, Wróbel-Pawelczyk I, Ronkiewicz P, Gołębiewska A, Hryniewicz W, Sadowy E, Skoczyńska A. Highly Resistant Serotype 19A Streptococcus pneumoniae of the GPSC1/CC320 Clone from Invasive Infections in Poland Prior to Antipneumococcal Vaccination of Children. Infect Dis Ther 2023; 12:2017-2037. [PMID: 37442903 PMCID: PMC10505132 DOI: 10.1007/s40121-023-00842-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
INTRODUCTION The introduction of pneumococcal conjugate vaccines (PCV) into the national immunization programs (NIPs) has significantly reduced the number of pneumococcal infections. However, infections caused by isolates of non-vaccine serotypes (NVT) started spreading shortly thereafter and strains of NVT 19A have become the main cause of invasive pneumococcal disease burden worldwide. The aim of the study was to characterize serotype 19A invasive pneumococci of GPSC1/CC320 circulating in Poland before the introduction of PCV into the Polish NIP in 2017 and to compare them to isolates from other countries where PCVs were implemented much earlier than in Poland. METHODS All the GPSC1/CC320 isolates were analyzed by serotyping, susceptibility testing, and whole genome sequencing followed by analyses of resistome, virulome, and core genome multilocus sequence typing (cgMLST), including comparative analysis with isolates with publicly accessible genomic sequences (PubMLST). RESULTS During continuous surveillance the NRCBM collected 4237 invasive Streptococcus pneumoniae isolates between 1997 and 2016, including 200 isolates (4.7%) of serotype 19A. The most prevalent among 19A pneumococci were highly resistant representatives of Global Pneumococcal Sequence Cluster 1/Clonal Complex 320, GPSC1/CC320 (n = 97, 48.5%). Isolates of GPSC1/CC320 belonged to three sequence types (STs): ST320 (75.2%) ST4768 (23.7%), and ST15047 (1.0%), which all represented the 19A-III cps subtype and had complete loci for both PI-1 and PI-2 pili types. On the basis of the cgMLST analysis the majority of Polish GPSC1/CC320 isolates formed a group clearly distinct from pneumococci of this clone observed in other countries. CONCLUSION Before introduction of PCV in the Polish NIP we noticed an unexpected increase of serotype 19A in invasive pneumococcal infections, with the most common being representatives of highly drug-resistant GPSC1/CC320 clone, rarely identified in Europe both before and even after PCV introduction.
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Affiliation(s)
- Weronika Puzia
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106, Warsaw, Poland
| | - Robert Gromadka
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106, Warsaw, Poland
| | - Karolina Żuchniewicz
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106, Warsaw, Poland
| | - Izabela Wróbel-Pawelczyk
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
| | - Patrycja Ronkiewicz
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
| | - Agnieszka Gołębiewska
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
| | - Anna Skoczyńska
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland.
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Neto NAS, Aguiar TKB, Costa RJP, Mesquita FP, Oliveira LLBD, Moraes MEAD, Montenegro RC, Carneiro RF, Nagano CS, Freitas CDT, Souza PFN. United we stand, divided we fall: in-depth proteomic evaluation of the synergistic effect of Mo-CBP 3-PepI and Ciprofloxacin against Staphylococcus aureus biofilms. BIOFOULING 2023; 39:838-852. [PMID: 37955278 DOI: 10.1080/08927014.2023.2279992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023]
Abstract
Staphylococcus aureus forms biofilms, a structure that protects bacterial cells, conferring more resistance to difficult treatment. Synthetic peptides surge as an alternative to overcome the biofilm of multidrug-resistant pathogens. Mo-CBP3-PepI, when combined with Ciprofloxacin, reduced preformed S. aureus biofilm by 50% at low concentrations (0.2 and 6.2 μg. mL-1, respectively). The goal of this study was to evaluate the proteomic profile of biofilms after treatment with the Mo-CBP3-PepI combined with ciprofloxacin. Here, proteomic analysis confirmed with more depth previously described mechanisms and revealed changes in the accumulation of proteins related to DNA and protein metabolism, cell wall biosynthesis, redox metabolism, quorum sensing, and biofilm formation. Some proteins related to DNA and protein metabolism were reduced, while other proteins, like redox system proteins, disappeared in Ciprofloxacin+Mo-CBP3-PepI treatment. Our results indicated a synergistic effect of these two molecules with several mechanisms against S. aureus biofilm and opened new doors for combined treatments with other drugs.
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Affiliation(s)
- Nilton A S Neto
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Tawanny K B Aguiar
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Rayara J P Costa
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Felipe P Mesquita
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Lais L B de Oliveira
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Maria E A de Moraes
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Raquel C Montenegro
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Rômulo F Carneiro
- Department of Fisheries Engineering, Federal University of Ceará (UFC), Fortaleza, CE, Brazil
| | - Celso S Nagano
- Department of Fisheries Engineering, Federal University of Ceará (UFC), Fortaleza, CE, Brazil
| | - Cleverson D T Freitas
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Pedro F N Souza
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
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Paschoalini BR, Nuñez KVM, Maffei JT, Langoni H, Guimarães FF, Gebara C, Freitas NE, dos Santos MV, Fidelis CE, Kappes R, Gonçalves MC, Silva NCC. The Emergence of Antimicrobial Resistance and Virulence Characteristics in Enterococcus Species Isolated from Bovine Milk. Antibiotics (Basel) 2023; 12:1243. [PMID: 37627663 PMCID: PMC10451337 DOI: 10.3390/antibiotics12081243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Enterococcus spp., including E. faecalis and E. faecium, pose risks to dairy farms as opportunistic pathogens. The study evaluates antimicrobial resistance (AMR) and virulence characteristics of Enterococcus spp. isolated from bovine milk. Bile esculin agar was used to assess 1471 milk samples, followed by colony identification, gram staining, catalase tests, and 45 °C incubation. PCR analysis targeted E. faecalis and E. faecium in characteristic Enterococcus spp. colonies, with MALDI-TOF used for negative samples. Multiple tests, including disk diffusion, chromogenic VRE agar for vancomycin resistance, Vancomycin Etest® for MIC determination, and PCR for virulence factors (cylA, esp, efaA, ace, asa1, gelE, and hyl genes), were performed. Out of 100 identified strains, E. durans (30.66%), E. faecium (26.28%), and E. faecalis (18.25%) were predominant. AMR in Enterococcus spp. varied, with the highest rates against rifampicin (27%), tetracycline (20%), and erythromycin (18%). Linezolid (5%), vancomycin, ciprofloxacin, and teicoplanin (3% each) had lower prevalence. E. faecium and E. faecalis showed high AMR to rifampicin, erythromycin, and tetracycline. Thirty-two strains (18.98%) grew on VRE Chromoselect agar, while 4 (2 E. faecalis and 2 E. faecium) showed vancomycin resistance by MIC values. E. faecalis carried gelE (45.5%) and asa1 (36%), and E. gallinarum had 9.1% with the asa1 gene. Detecting resistant Enterococcus in bovine milk supports control strategies for enterococci on dairy farms, highlighting AMR concerns in the food chain.
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Affiliation(s)
- Beatriz Rizzo Paschoalini
- Department of Food Science and Nutrition, School of Food Engineering, University of Campinas, Campinas 13083-862, SP, Brazil; (B.R.P.); (K.V.M.N.); (J.T.M.)
| | - Karen Vanessa Munive Nuñez
- Department of Food Science and Nutrition, School of Food Engineering, University of Campinas, Campinas 13083-862, SP, Brazil; (B.R.P.); (K.V.M.N.); (J.T.M.)
| | - Juliana Takahashi Maffei
- Department of Food Science and Nutrition, School of Food Engineering, University of Campinas, Campinas 13083-862, SP, Brazil; (B.R.P.); (K.V.M.N.); (J.T.M.)
| | - Hélio Langoni
- Department of Animal Production and Preventive Veterinary Medicine, Faculty of Veterinary Medicine and Animal Science, São Paulo State University, Botucatu 18618-681, SP, Brazil; (H.L.); (F.F.G.)
| | - Felipe Freitas Guimarães
- Department of Animal Production and Preventive Veterinary Medicine, Faculty of Veterinary Medicine and Animal Science, São Paulo State University, Botucatu 18618-681, SP, Brazil; (H.L.); (F.F.G.)
| | - Clarice Gebara
- Food Research Center, School of Veterinary Medicine and Animal Science, Federal University of Goiás, Campus Road, Goiânia 74690-900, GO, Brazil; (C.G.); (N.E.F.)
| | - Natylane Eufransino Freitas
- Food Research Center, School of Veterinary Medicine and Animal Science, Federal University of Goiás, Campus Road, Goiânia 74690-900, GO, Brazil; (C.G.); (N.E.F.)
| | - Marcos Veiga dos Santos
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Sciences, University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil; (M.V.d.S.); (C.E.F.)
| | - Carlos Eduardo Fidelis
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Sciences, University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil; (M.V.d.S.); (C.E.F.)
| | - Roberto Kappes
- Center for Agroveterinary Sciences, University of the State of Santa Catarina, Lages 88520-000, SC, Brazil;
| | - Mônica Correia Gonçalves
- Center for Agro-Food Science and Technology, Federal University of Campina Grande, Campina Grande 58840-000, PB, Brazil;
| | - Nathália Cristina Cirone Silva
- Department of Food Science and Nutrition, School of Food Engineering, University of Campinas, Campinas 13083-862, SP, Brazil; (B.R.P.); (K.V.M.N.); (J.T.M.)
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Okello E, ElAshmawy WR, Williams DR, Lehenbauer TW, Aly SS. Effect of dry cow therapy on antimicrobial resistance of mastitis pathogens post-calving. Front Vet Sci 2023; 10:1132810. [PMID: 37546337 PMCID: PMC10399697 DOI: 10.3389/fvets.2023.1132810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/26/2023] [Indexed: 08/08/2023] Open
Abstract
The aim of this study was to evaluate the effect of dry cow therapy (DCT) on the antimicrobial resistance (AMR) profile of mastitis pathogens post-calving. A repository of isolates based on a DCT trial was utilized for the current study. A stratified random survey sample of cows from the trial were identified within the strata of season, herd, and trial treatment resulting in 382 cows. All isolates from the 382 cows were selected for the current study, which identified 566 isolates from milk samples collected at dry off (S1), post-calving (S2), and at the first clinical mastitis event up to 150 days in milk (S3). The AMR profiles were determined using broth microdilution method. Less than 10% of the coagulase-negative Staphylococcus species (CNS) isolates (n = 421) were resistant to tetracycline, ceftiofur, penicillin/novobiocin or erythromycin, while higher proportions of resistance to sulfadimethoxine (72%) and penicillin (28%) were observed. All Staphylococcus aureus (S. aureus) isolates (n = 4) were susceptible to all tested AMD except sulfadimethoxine, to which all isolates were resistant. Similarly, all Streptococcus spp. (n = 37) were susceptible to penicillin, penicillin/novobiocin, and ampicillin while resistant to tetracycline (17%). All coliforms (n = 21) were susceptible to ceftiofur, but resistance was recorded for sulfadimethoxine (70%), cephalothin (56%), and tetracycline (43%). The increased resistance percent from S1 to S2 was observed in CNS isolates from AMD-treated cows, with the highest increase recorded for penicillin (12.2%). Parametric survival interval regression models were used to explore the association between antimicrobial drug (AMD) therapy at dry off and the AMR phenotype post-calving. The accelerated failure-time metric was adopted to minimum inhibitory concentration measurements to permit interpretation of model exponentiated coefficients. Models for cows with CNS isolated at both S1 and S2 showed increased resistance against cephalothin, oxacillin, and ceftiofur in cows that received DCT from the same drug class, or a class with a shared resistance mechanism. In contrast, resistance of CNS isolates to tetracycline were associated with any AMD therapy at dry off. Resistance of CNS isolates to Penicillin decreased in CNS isolates in cows that received any AMD therapy at dry off compared to those that didn't. The study provided evidence that dry-cow IMM AMD was associated with AMR post-calving.
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Affiliation(s)
- Emmanuel Okello
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Wagdy R. ElAshmawy
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
- Department of Internal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Deniece R. Williams
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
| | - Terry W. Lehenbauer
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Sharif S. Aly
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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Hunashal Y, Kumar GS, Choy MS, D'Andréa ÉD, Da Silva Santiago A, Schoenle MV, Desbonnet C, Arthur M, Rice LB, Page R, Peti W. Molecular basis of β-lactam antibiotic resistance of ESKAPE bacterium E. faecium Penicillin Binding Protein PBP5. Nat Commun 2023; 14:4268. [PMID: 37460557 DOI: 10.1038/s41467-023-39966-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
Penicillin-binding proteins (PBPs) are essential for the formation of the bacterial cell wall. They are also the targets of β-lactam antibiotics. In Enterococcus faecium, high levels of resistance to β-lactams are associated with the expression of PBP5, with higher levels of resistance associated with distinct PBP5 variants. To define the molecular mechanism of PBP5-mediated resistance we leveraged biomolecular NMR spectroscopy of PBP5 - due to its size (>70 kDa) a challenging NMR target. Our data show that resistant PBP5 variants show significantly increased dynamics either alone or upon formation of the acyl-enzyme inhibitor complex. Furthermore, these variants also exhibit increased acyl-enzyme hydrolysis. Thus, reducing sidechain bulkiness and expanding surface loops results in increased dynamics that facilitates acyl-enzyme hydrolysis and, via increased β-lactam antibiotic turnover, facilitates β-lactam resistance. Together, these data provide the molecular basis of resistance of clinical E. faecium PBP5 variants, results that are likely applicable to the PBP family.
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Affiliation(s)
- Yamanappa Hunashal
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Ganesan Senthil Kumar
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
- National Institute of Immunology, New Delhi, India
| | - Meng S Choy
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Éverton D D'Andréa
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | | | - Marta V Schoenle
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Charlene Desbonnet
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Michel Arthur
- INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Louis B Rice
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA.
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Farid N, Bux K, Ali K, Bashir A, Tahir R. Repurposing Amphotericin B: anti-microbial, molecular docking and molecular dynamics simulation studies suggest inhibition potential of Amphotericin B against MRSA. BMC Chem 2023; 17:67. [PMID: 37386581 DOI: 10.1186/s13065-023-00980-9] [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: 04/14/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023] Open
Abstract
Amphotericin B (AMPH) is an anti-fungal drug and this study, for the first time as best of our knowledge, reports the repurposing of the Amphotericin B. The drug was found to show significant antibacterial potential revealed by antimicrobial screening, molecular docking, and mode of action analysis targeting Penicillin Binding Protein 2a (PBP 2a protein) which is target of β-lactam drugs and is involved in cell wall synthesis. Mode of action analysis showed the drug to have hydrophobic and hydrophilic interactions with both C-terminal, trans-peptidase and non-penicillin binding domain of the protein. Additionally, to evaluate the impact of ligand binding on the protein's conformational dynamics, molecular dynamics (MD) simulations were used. Comparative Dynamical flexibility (RMSF) and Dynamics Cross Correlation (DCCM) followed by MD simulations revealed the complex formation significantly effecting structural dynamics of the enzyme significantly in the non-penicillin binding domain (327-668) and slightly in trans peptidase domain. Radius of gyration assessment further showed ligand binding also decreasing over all compactness of protein. Secondary structure analysis indicated the complex formation changing the conformational integrity in non-penicillin binding domain. Hydrogen bond analysis and MMPBSA, free energy of calculations followed by MD simulations, also complemented the antimicrobial and molecular docking revelations suggesting Amphotericin B to have substantial antibacterial potential.
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Affiliation(s)
- Neha Farid
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan.
| | - Khair Bux
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan.
| | - Kashif Ali
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan
| | - Asma Bashir
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan
| | - Rahima Tahir
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan
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Wielogorska E, Flynn PB, Meneely J, Thompson TP, Graham WG, Gilmore BF, Elliott CT. Assessment of Cold Atmospheric Pressure Plasma (CAPP) Treatment for Degradation of Antibiotic Residues in Water. Antibiotics (Basel) 2023; 12:1115. [PMID: 37508211 PMCID: PMC10376056 DOI: 10.3390/antibiotics12071115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
The presence of antibiotic residues in water is linked to the emergence of antibiotic resistance globally and necessitates novel decontamination strategies to minimize antibiotic residue exposure in both the environment and food. A holistic assessment of cold atmospheric pressure plasma technology (CAPP) for β-lactam antibiotic residue removal is described in this study. CAPP operating parameters including plasma jet voltage, gas composition and treatment time were optimized, with highest β-lactam degradation efficiencies obtained for a helium jet operated at 6 kV. Main by-products detected indicate pH-driven peroxidation as a main mechanism of CAPP-induced decomposition of β-lactams. No in vitro hepatocytotoxicity was observed in HepG2 cells following exposure to treated samples, and E. coli exposed to CAPP-degraded β-lactams did not exhibit resistance development. In surface water, over 50% decrease in antibiotic levels was achieved after only 5 min of treatment. However, high dependence of treatment efficiency on residue concentration, pH and presence of polar macromolecules was observed.
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Affiliation(s)
- Ewa Wielogorska
- Institute for Global Food Security, Queen's University Belfast, Belfast BT9 5DL, UK
- School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Padrig B Flynn
- School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Julie Meneely
- Institute for Global Food Security, Queen's University Belfast, Belfast BT9 5DL, UK
| | | | - William G Graham
- Centre for Plasma Physics, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, UK
| | - Brendan F Gilmore
- Institute for Global Food Security, Queen's University Belfast, Belfast BT9 5DL, UK
- School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, UK
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49
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Hayes KA, Dressler JM, Norris SJ, Edmondson DG, Jutras BL. A large screen identifies beta-lactam antibiotics which can be repurposed to target the syphilis agent. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:4. [PMID: 38686211 PMCID: PMC11057208 DOI: 10.1038/s44259-023-00006-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/09/2023] [Indexed: 05/02/2024]
Abstract
Syphilis, caused by the spirochete Treponema pallidum subsp. pallidum (hereafter called T. pallidum), is re-emerging as a worldwide sexually transmitted infection. A single intramuscular dose of benzathine penicillin G is the preferred syphilis treatment option. Both supply shortage concerns and the potential for acquired antibiotic resistance further the need to broaden the repertoire of syphilis therapeutics. We reasoned that other β-lactams may be equally or more effective at targeting the disease-causing agent, Treponema pallidum, but have yet to be discovered due to a previous lack of a continuous in vitro culture system. Recent technical advances with respect to in vitro T. pallidum propagation allowed us to conduct a high-throughput screen of almost 100 β-lactams. Using several molecular and cellular approaches that we developed or adapted, we identified and confirmed the efficacy of several β-lactams that were similar to or outperformed the current standard, benzathine penicillin G. These options are either currently used to treat bacterial infections or are synthetic derivatives of naturally occurring compounds. Our studies not only identified additional potential therapeutics in the resolution of syphilis, but provide techniques to study the complex biology of T. pallidum-a spirochete that has plagued human health for centuries.
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Affiliation(s)
- Kathryn A. Hayes
- Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061 USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061 USA
| | - Jules M. Dressler
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061 USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061 USA
| | - Steven J. Norris
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at Houston, Houston, TX USA
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Diane G. Edmondson
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Brandon L. Jutras
- Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061 USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061 USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061 USA
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA 24061 USA
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50
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Lucena ACR, Ferrarini MG, de Oliveira WK, Marcon BH, Morello LG, Alves LR, Faoro H. Modulation of Klebsiella pneumoniae Outer Membrane Vesicle Protein Cargo under Antibiotic Treatment. Biomedicines 2023; 11:1515. [PMID: 37371610 DOI: 10.3390/biomedicines11061515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/14/2023] [Accepted: 05/14/2023] [Indexed: 06/29/2023] Open
Abstract
Klebsiella pneumoniae is a nosocomial pathogen and an important propagator of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Like other Gram-negative bacteria, they secrete outer membrane vesicles (OMVs) that distribute virulence and resistance factors. Here, we subjected a K. pneumoniae-XDR to subinhibitory concentrations of meropenem, amikacin, polymyxin B, and a combination of these agents to evaluate changes in the protein cargo of OMVs through liquid chromatography-tandem mass spectrometry (LC-MS/MS). Genome sequencing of the clinical isolate K. pneumoniae strain HCD1 (KpHCD1) revealed the presence of 41 resistance genes and 159 virulence factors. We identified 64 proteins in KpHCD1-OMVs modulated with different antibiotic treatments involved in processing genetic information, environmental information, cell envelope formation, energy metabolism, and drug resistance. The OMV proteome expression profile suggests that OMVs may be associated with pathogenicity, survival, stress response, and resistance dissemination.
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Affiliation(s)
- Aline Castro Rodrigues Lucena
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Mariana Galvão Ferrarini
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon 1, 69622 Villeurbanne, France
| | - Willian Klassen de Oliveira
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Bruna Hilzendeger Marcon
- Laboratory for Basic Biology of Stem Cells, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Luis Gustavo Morello
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Lysangela Ronalte Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
| | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
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