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Gatpatan IGT, Cabulong RB, Sadaba RB. Diversity and Screening of Cellulolytic Microorganisms from Mangrove Forests, Natural Parks, Paddy Field, and Sugarcane Plantation in Panay Island, Philippines. Int J Microbiol 2024; 2024:5573158. [PMID: 39081934 PMCID: PMC11288694 DOI: 10.1155/2024/5573158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 05/12/2024] [Accepted: 06/10/2024] [Indexed: 08/02/2024] Open
Abstract
Cellulolytic microorganisms secrete cellulase, which plays a crucial role in the conversion of lignocellulosic biomass into value-added products with diverse applications in industries, such as biofuel, healthcare, and agriculture. As the world transitions to a bioenergy future, cellulase demand is likely to expand. However, the high cost and low catalytic activity of cellulase hinder the commercialization of biorefineries. Searching for cellulase-producing microorganisms in different environments through bioprospecting can aid in broadening the range of cellulases that are currently available. Meanwhile, the cellulolytic activity of marine microorganisms remains largely unexplored, making it difficult to compare the cellulolytic activity of terrestrial and marine environments. Thus, this study aimed to investigate the diversity and activity of culturable cellulolytic microorganisms in four terrestrial and three marine sites within Panay Island, Philippines. The results showed that the cellulolytic microbial load was tenfold higher in the terrestrial sites than in the marine sites, possibly due to the dynamic mangrove environment. Out of the 42 isolates with a high cellulolytic index (CI) of ≥3.0, 36 were from terrestrial and 6 from marine habitats. The CMCase, Avicelase, and FPase activities were then tested on the 18 isolates with the highest CI. It was observed that many isolates had a high CI, but few exhibited high enzyme activities. Marine isolates showed higher CMCase and Avicelase activities, with comparable FPase activity to their terrestrial counterparts. Isolates S1ACP6B from a sugarcane field and MS1OMP2A from a mangrove site exhibited the highest cellulase activities at 0.41 and 0.29 U/mg, respectively, and were identified as Enterobacter roggenkampii and Rhodococcus erythropolis, respectively. Among the 18 identified isolates, three are resistant to chloramphenicol and three isolates are potentially new species of Halomonas sp. MS1ACP1B, Albirhodobacter sp. MP2ACP3B, and Saccharomycetaceae sp. B1CZP10A. Overall, this study provides an insight on the composition of cellulolytic microbial load and their activities among various habitats.
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Affiliation(s)
- Isabel Grace T. Gatpatan
- Division of Biological SciencesCollege of Arts and SciencesUniversity of the Philippines Visayas, Miagao, Iloilo 5023, Philippines
| | - Rhudith B. Cabulong
- Division of Biological SciencesCollege of Arts and SciencesUniversity of the Philippines Visayas, Miagao, Iloilo 5023, Philippines
| | - Resurreccion B. Sadaba
- Division of Biological SciencesCollege of Arts and SciencesUniversity of the Philippines Visayas, Miagao, Iloilo 5023, Philippines
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Ludwig J, Mrázek J. OrthoRefine: automated enhancement of prior ortholog identification via synteny. BMC Bioinformatics 2024; 25:163. [PMID: 38664637 PMCID: PMC11044567 DOI: 10.1186/s12859-024-05786-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Identifying orthologs continues to be an early and imperative step in genome analysis but remains a challenging problem. While synteny (conservation of gene order) has previously been used independently and in combination with other methods to identify orthologs, applying synteny in ortholog identification has yet to be automated in a user-friendly manner. This desire for automation and ease-of-use led us to develop OrthoRefine, a standalone program that uses synteny to refine ortholog identification. RESULTS We developed OrthoRefine to improve the detection of orthologous genes by implementing a look-around window approach to detect synteny. We tested OrthoRefine in tandem with OrthoFinder, one of the most used software for identification of orthologs in recent years. We evaluated improvements provided by OrthoRefine in several bacterial and a eukaryotic dataset. OrthoRefine efficiently eliminates paralogs from orthologous groups detected by OrthoFinder. Using synteny increased specificity and functional ortholog identification; additionally, analysis of BLAST e-value, phylogenetics, and operon occurrence further supported using synteny for ortholog identification. A comparison of several window sizes suggested that smaller window sizes (eight genes) were generally the most suitable for identifying orthologs via synteny. However, larger windows (30 genes) performed better in datasets containing less closely related genomes. A typical run of OrthoRefine with ~ 10 bacterial genomes can be completed in a few minutes on a regular desktop PC. CONCLUSION OrthoRefine is a simple-to-use, standalone tool that automates the application of synteny to improve ortholog detection. OrthoRefine is particularly efficient in eliminating paralogs from orthologous groups delineated by standard methods.
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Affiliation(s)
- J Ludwig
- Institute of Bioinformatics, The University of Georgia, Athens, GA, 30602, USA.
| | - J Mrázek
- Department of Microbiology and Institute of Bioinformatics, The University of Georgia, Athens, GA, 30602, USA
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Allemailem KS. Recent Advances in Understanding the Molecular Mechanisms of Multidrug Resistance and Novel Approaches of CRISPR/Cas9-Based Genome-Editing to Combat This Health Emergency. Int J Nanomedicine 2024; 19:1125-1143. [PMID: 38344439 PMCID: PMC10859101 DOI: 10.2147/ijn.s453566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The rapid spread of multidrug resistance (MDR), due to abusive use of antibiotics has led to global health emergency, causing substantial morbidity and mortality. Bacteria attain MDR by different means such as antibiotic modification/degradation, target protection/modification/bypass, and enhanced efflux mechanisms. The classical approaches of counteracting MDR bacteria are expensive and time-consuming, thus, it is highly significant to understand the molecular mechanisms of this resistance to curb the problem from core level. The revolutionary approach of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated sequence 9 (CRISPR/Cas9), considered as a next-generation genome-editing tool presents an innovative opportunity to precisely target and edit bacterial genome to alter their MDR strategy. Different bacteria possessing antibiotic resistance genes such as mecA, ermB, ramR, tetA, mqrB and blaKPC that have been targeted by CRISPR/Cas9 to re-sensitize these pathogens against antibiotics, such as methicillin, erythromycin, tigecycline, colistin and carbapenem, respectively. The CRISPR/Cas9 from S. pyogenes is the most widely studied genome-editing tool, consisting of a Cas9 DNA endonuclease associated with tracrRNA and crRNA, which can be systematically coupled as sgRNA. The targeting strategies of CRISPR/Cas9 to bacterial cells is mediated through phage, plasmids, vesicles and nanoparticles. However, the targeting approaches of this genome-editing tool to specific bacteria is a challenging task and still remains at a very preliminary stage due to numerous obstacles awaiting to be solved. This review elaborates some recent updates about the molecular mechanisms of antibiotic resistance and the innovative role of CRISPR/Cas9 system in modulating these resistance mechanisms. Furthermore, the delivery approaches of this genome-editing system in bacterial cells are discussed. In addition, some challenges and future prospects are also described.
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Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah51452, Saudi Arabia
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Ji S, An F, Zhang T, Lou M, Guo J, Liu K, Zhu Y, Wu J, Wu R. Antimicrobial peptides: An alternative to traditional antibiotics. Eur J Med Chem 2024; 265:116072. [PMID: 38147812 DOI: 10.1016/j.ejmech.2023.116072] [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: 10/16/2023] [Revised: 12/04/2023] [Accepted: 12/17/2023] [Indexed: 12/28/2023]
Abstract
As antibiotic-resistant bacteria and genes continue to emerge, the identification of effective alternatives to traditional antibiotics has become a pressing issue. Antimicrobial peptides are favored for their safety, low residue, and low resistance properties, and their unique antimicrobial mechanisms show significant potential in combating antibiotic resistance. However, the high production cost and weak activity of antimicrobial peptides limit their application. Moreover, traditional laboratory methods for identifying and designing new antimicrobial peptides are time-consuming and labor-intensive, hindering their development. Currently, novel technologies, such as artificial intelligence (AI) are being employed to develop and design new antimicrobial peptide resources, offering new opportunities for the advancement of antimicrobial peptides. This article summarizes the basic characteristics and antimicrobial mechanisms of antimicrobial peptides, as well as their advantages and limitations, and explores the application of AI in antimicrobial peptides prediction amd design. This highlights the crucial role of AI in enhancing the efficiency of antimicrobial peptide research and provides a reference for antimicrobial drug development.
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Affiliation(s)
- Shuaiqi Ji
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China
| | - Feiyu An
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang, 110866, PR China
| | - Taowei Zhang
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China
| | - Mengxue Lou
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang, 110866, PR China
| | - Jiawei Guo
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China
| | - Kexin Liu
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China
| | - Yi Zhu
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang, 110866, PR China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China.
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China; Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang, 110866, PR China; Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, 110866, PR China.
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Cheema HS, Maurya A, Kumar S, Pandey VK, Singh RM. Antibiotic Potentiation Through Phytochemical-Based Efflux Pump Inhibitors to Combat Multidrug Resistance Bacteria. Med Chem 2024; 20:557-575. [PMID: 37907487 DOI: 10.2174/0115734064263586231022135644] [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: 06/28/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND Antimicrobial resistance development poses a significant danger to the efficacy of antibiotics, which were once believed to be the most efficient method for treating infections caused by bacteria. Antimicrobial resistance typically involves various mechanisms, such as drug inactivation or modification, drug target modification, drug uptake restriction, and drug efflux, resulting in decreased antibiotic concentrations within the cell. Antimicrobial resistance has been associated with efflux Pumps, known for their capacity to expel different antibiotics from the cell non-specifically. This makes EPs fascinating targets for creating drugs to combat antimicrobial resistance (AMR). The varied structures of secondary metabolites (phytomolecules) found in plants have positioned them as a promising reservoir of efflux pump inhibitors. These inhibitors act as modifiers of bacterial resistance and facilitate the reintroduction of antibiotics that have lost clinical effectiveness. Additionally, they may play a role in preventing the emergence of multidrug resistant strains. OBJECTIVE The objective of this review article is to discuss the latest studies on plant-based efflux pump inhibitors such as terpenoids, alkaloids, flavonoids, glycosides, and tetralones. It highlighted their potential in enhancing the effectiveness of antibiotics and combating the development of multidrug resistance. RESULTS Efflux pump inhibitors (EPIs) derived from botanical sources, including compounds like lysergol, chanaoclavine, niazrin, 4-hydroxy-α-tetralone, ursolic acid, phytol, etc., as well as their partially synthesized forms, have shown significant potential as practical therapeutic approaches in addressing antimicrobial resistance caused by efflux pumps. Further, several phyto-molecules and their analogs demonstrated superior potential for reversing drug resistance, surpassing established agents like reserpine, niaziridin, etc. Conclusion: This review found that while the phyto-molecules and their derivatives did not possess notable antimicrobial activity, their combination with established antibiotics significantly reduced their minimum inhibitory concentration (MIC). Specific molecules, such as chanaoclavine and niaziridin, exhibited noteworthy potential in reversing the effectiveness of drugs, resulting in a reduction of the MIC of tetracycline by up to 16 times against the tested strain of bacteria. These molecules inhibited the efflux pumps responsible for drug resistance and displayed a stronger affinity for membrane proteins. By employing powerful EPIs, these molecules can selectively target and obstruct drug efflux pumps. This targeted approach can significantly augment the strength and efficacy of older antibiotics against various drug resistant bacteria, given that active drug efflux poses a susceptibility for nearly all antibiotics.
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Affiliation(s)
| | - Anupam Maurya
- Chemistry Section, Pharmacopoeia Commission for Indian Medicine, and Homoeopathy (PCIM&H), Ministry of Ayush, Ghaziabad, 201002, (U.P.), India
| | - Sandeep Kumar
- Department of Botany, Meerut College, Meerut, 250003 (U.P.), India
| | - Vineet Kumar Pandey
- Chemistry Section, Pharmacopoeia Commission for Indian Medicine, and Homoeopathy (PCIM&H), Ministry of Ayush, Ghaziabad, 201002, (U.P.), India
| | - Raman Mohan Singh
- Chemistry Section, Pharmacopoeia Commission for Indian Medicine, and Homoeopathy (PCIM&H), Ministry of Ayush, Ghaziabad, 201002, (U.P.), India
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Yadav S, Mehta P, Soni J, Chattopadhyay P, Devi P, Habyarimana T, Tardalkar K, Joshi M, Pandey R. Single-cell RNA-Seq reveals intracellular microbial diversity within immune cells during SARS-CoV-2 infection and recovery. iScience 2023; 26:108357. [PMID: 38026191 PMCID: PMC10663746 DOI: 10.1016/j.isci.2023.108357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/05/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Intracellular microorganisms, like viruses, bacteria, and fungi, pose challenges in detection due to their non-culturable forms. Transcriptomic analysis at cellular level enables exploration of distributions and the impact of these microorganisms on host cells, a domain that remains underexplored because of methodological limitations. Single-cell technology shows promise in addressing this by capturing polyadenine-tailed transcripts, because recent studies confirmed polyadenylation in microbial transcriptomes. We utilized single-cell RNA-seq from PBMCs to probe intracellular microbes in healthy, SARS-CoV-2-positive, and recovered individuals. Among 76 bacterial species detected, 16 showed significant abundance differences. Buchnera aphidicola, Streptomyces clavuligerus, and Ehrlichia canis emerged significantly in memory-B, Naïve-T, and Treg cells. Staphylococcus aureus, Mycoplasma mycoides, Leptospira interrogans, and others displayed elevated levels in SARS-CoV-2-positive patients, suggesting possible disease association. This highlights the strength of single-cell technology in revealing potential microorganism's cell-specific functions. Further research is essential for functional understanding of their cell-specific abundance across physiological states.
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Affiliation(s)
- Sunita Yadav
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Priti Devi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Thierry Habyarimana
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Department of Biomedical Laboratory Sciences, INES-Ruhengeri, Ruhengeri, Rwanda
| | - Kishore Tardalkar
- Dr. D. Y. Patil Medical College, Hospital and Research Institute, Kolhapur, Maharashtra 416003, India
| | - Meghnad Joshi
- Dr. D. Y. Patil Medical College, Hospital and Research Institute, Kolhapur, Maharashtra 416003, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Delbari Y, Mohassel Y, Kakaei E, Bahrami Y. Identification and anti-bacterial property of endophytic actinobacteria from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa. Sci Rep 2023; 13:13145. [PMID: 37573468 PMCID: PMC10423286 DOI: 10.1038/s41598-023-40478-x] [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: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 08/14/2023] Open
Abstract
The arbitrary and overuses of antibiotics have resulted in the emergence of multidrug resistance bacteria which encounters human to a serious public health problem. Thus, there is an ever-increasing demand for discovery of novel effective antibiotics with new modes of function against resistant pathogens. Endophytic actinobacteria (EA) have currently been considered as one of the most prospective group of microorganisms for discovery of therapeutic agents. This study aimed to isolate EA from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa plants and to evaluate their antibacterial properties. The healthy samples were collected, dissected and surface-sterilized before cultured on four different selection media at 28 °C. Nine EA were isolated and identified based on morphological and molecular properties, and scanning electron micrograph analyses. Based on phylogenetic analysis, they were taxonomically grouped into four families Streptomycetaceae, Nocardiaceae, Micromonosporaceae, and Pseudonocardiaceae. Their branched aerial mycelia produced chains of cylindrical or cube or oval shaped spores with smooth or rough surfaces. Four strains; IKBG03, IKBG05, IKBG13, and IKBG17 had less than 98.65% sequence similarity to their closely related strains, which constitute them as novel species/strains. Besides, three strains; IKBG05, IKBG13, and IKBG18 were reported as endophytes for the first time. Preliminary antibacterial activity conducted on the all isolates revealed potent antibacterial effects against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. All isolates strongly inhibited the growth of at least one of the tested pathogens. Our results reveals that the test plants are novel sources for isolating a diverse group of rare and common actinobacteria that could produce a wide range of novel biologically active natural products with antibacterial activity which have a great potential in pharmaceutical and biotechnological applications.
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Affiliation(s)
- Yaser Delbari
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yaser Mohassel
- Department of Clinical Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Elham Kakaei
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yadollah Bahrami
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Department of Medical Biotechnology, School of Medicine, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
- Advanced Marine Biomanufacturing Laboratory, Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
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Berger H, Bacher M, Labuda R, Eppel IM, Bayer F, Sulyok M, Gasparotto E, Zehetbauer F, Doppler M, Gratzl H, Strauss J. Polaramycin B, and not physical interaction, is the signal that rewires fungal metabolism in the Streptomyces-Aspergillus interaction. Environ Microbiol 2022; 24:4899-4914. [PMID: 35848075 PMCID: PMC9796313 DOI: 10.1111/1462-2920.16118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/26/2022] [Indexed: 01/01/2023]
Abstract
Co-culturing the bacterium Streptomyces rapamycinicus and the ascomycete Aspergillus nidulans has previously been shown to trigger the production of orsellinic acid (ORS) and its derivates in the fungal cells. Based on these studies it was assumed that direct physical contact is a prerequisite for the metabolic reaction that involves a fungal amino acid starvation response and activating chromatin modifications at the biosynthetic gene cluster (BGC). Here we show that not physical contact, but a guanidine containing macrolide, named polaramycin B, triggers the response. The substance is produced constitutively by the bacterium and above a certain concentration, provokes the production of ORS. In addition, several other secondary metabolites were induced by polaramycin B. Our genome-wide transcriptome analysis showed that polaramycin B treatment causes downregulation of fungal genes necessary for membrane stability, general metabolism and growth. A compensatory genetic response can be observed in the fungus that included upregulation of BGCs and genes necessary for ribosome biogenesis, translation and membrane stability. Our work discovered a novel chemical communication, in which the antifungal bacterial metabolite polaramycin B leads to the production of antibacterial defence chemicals and to the upregulation of genes necessary to compensate for the cellular damage caused by polaramycin B.
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Affiliation(s)
- Harald Berger
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Markus Bacher
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
- Department of Chemistry, Institute of Chemistry of Renewable ResourcesUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Roman Labuda
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food ScienceUniversity of Veterinary Medicine, ViennaViennaAustria
| | - Isabel Maria Eppel
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Florentina Bayer
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Michael Sulyok
- Department of Agro‐BiotechnologyInstitute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Erika Gasparotto
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
| | - Franz Zehetbauer
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Maria Doppler
- Department of Agro‐BiotechnologyInstitute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Hannes Gratzl
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
- Department of Agro‐BiotechnologyInstitute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
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Gambushe SM, Zishiri OT, El Zowalaty ME. Review of Escherichia coli O157:H7 Prevalence, Pathogenicity, Heavy Metal and Antimicrobial Resistance, African Perspective. Infect Drug Resist 2022; 15:4645-4673. [PMID: 36039321 PMCID: PMC9420067 DOI: 10.2147/idr.s365269] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/23/2022] [Indexed: 12/02/2022] Open
Abstract
Escherichia coli O157:H7 is an important food-borne and water-borne pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome in humans and may cause serious morbidity and large outbreaks worldwide. People with bloody diarrhea have an increased risk of developing serious complications such as acute renal failure and neurological damage. The hemolytic-uremic syndrome (HUS) is a serious condition, and up to 50% of HUS patients can develop long-term renal dysfunction or blood pressure-related complications. Children aged two to six years have an increased risk of developing HUS. Clinical enteropathogenic Escherichia coli (EPEC) infections show fever, vomiting, and diarrhea. The EPEC reservoir is unknown but is suggested to be an asymptomatic or symptomatic child or an asymptomatic adult carrier. Spreading is often through the fecal-oral route. The prevalence of EPEC in infants is low, and EPEC is highly contagious in children. EPEC disease in children tends to be clinically more severe than other diarrheal infections. Some children experience persistent diarrhea that lasts for more than 14 days. Enterotoxigenic Escherichia coli (ETEC) strains are a compelling cause of the problem of diarrheal disease. ETEC strains are a global concern as the bacteria are the leading cause of acute watery diarrhea in children and the leading cause of traveler’s diarrhea. It is contagious to children and can cause chronic diarrhea that can affect the development and well-being of children. Infections with diarrheagenic E. coli are more common in African countries. Antimicrobial agents should be avoided in the acute phase of the disease since studies showed that antimicrobial agents may increase the risk of HUS in children. The South African National Veterinary Surveillance and Monitoring Programme for Resistance to Antimicrobial Drugs has reported increased antimicrobial resistance in E. coli. Pathogenic bacterial strains have developed resistance to a variety of antimicrobial agents due to antimicrobial misuse. The induced heavy metal tolerance may also enhance antimicrobial resistance. The prevalence of antimicrobial resistance depends on the type of the antimicrobial agent, bacterial strain, dose, time, and mode of administration. Developing countries are severely affected by increased resistance to antimicrobial agents due to poverty, lack of proper hygiene, and clean water, which can lead to bacterial infections with limited treatment options due to resistance.
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Affiliation(s)
- Sydney M Gambushe
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Oliver T Zishiri
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Mohamed E El Zowalaty
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE 75 123, Sweden
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Kotrbová L, Lara AC, Corretto E, Scharfen J, Ulmann V, Petříčková K, Chroňáková A. Evaluation and comparison of antibiotic susceptibility profiles of Streptomyces spp. from clinical specimens revealed common and region-dependent resistance patterns. Sci Rep 2022; 12:9353. [PMID: 35672429 PMCID: PMC9174267 DOI: 10.1038/s41598-022-13094-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022] Open
Abstract
Notwithstanding the fact that streptomycetes are overlooked in clinical laboratories, studies describing their occurrence in disease and potential pathogenicity are emerging. Information on their species diversity in clinical specimens, aetiology and appropriate therapeutic treatment is scarce. We identified and evaluated the antibiotic susceptibility profile of 84 Streptomyces clinical isolates from the Czech Republic. In the absence of appropriate disk diffusion (DD) breakpoints for antibiotic susceptibility testing (AST) of Streptomyces spp., we determined DD breakpoints by correlation with the broth microdilution method and by the distribution of zone diameters among isolates. Correlation accuracy was high for 9 antibiotics, leading to the establishment of the most valid DD breakpoints for Streptomyces antibiotic susceptibility evaluation so far. Clinical strains belonged to 17 different phylotypes dominated by a cluster of strains sharing the same percentage of 16S rRNA gene sequence identity with more than one species (S. albidoflavus group, S. hydrogenans, S. resistomycificus, S. griseochromogenes; 70% of isolates). AST results showed that Streptomyces exhibited intrinsic resistance to penicillin, general susceptibility to amikacin, gentamycin, vancomycin and linezolid, and high percentage of susceptibility to tetracyclines and clarithromycin. For the remaining antibiotics, AST showed inter- and intra-species variations when compared to available literature (erythromycin, trimethoprim-sulfamethoxazole), indicating a region-dependent rather than species-specific patterns.
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11
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Martin JF, Alvarez-Alvarez R, Liras P. Penicillin-Binding Proteins, β-Lactamases, and β-Lactamase Inhibitors in β-Lactam-Producing Actinobacteria: Self-Resistance Mechanisms. Int J Mol Sci 2022; 23:5662. [PMID: 35628478 PMCID: PMC9146315 DOI: 10.3390/ijms23105662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 01/27/2023] Open
Abstract
The human society faces a serious problem due to the widespread resistance to antibiotics in clinical practice. Most antibiotic biosynthesis gene clusters in actinobacteria contain genes for intrinsic self-resistance to the produced antibiotics, and it has been proposed that the antibiotic resistance genes in pathogenic bacteria originated in antibiotic-producing microorganisms. The model actinobacteria Streptomyces clavuligerus produces the β-lactam antibiotic cephamycin C, a class A β-lactamase, and the β lactamases inhibitor clavulanic acid, all of which are encoded in a gene supercluster; in addition, it synthesizes the β-lactamase inhibitory protein BLIP. The secreted clavulanic acid has a synergistic effect with the cephamycin produced by the same strain in the fight against competing microorganisms in its natural habitat. High levels of resistance to cephamycin/cephalosporin in actinobacteria are due to the presence (in their β-lactam clusters) of genes encoding PBPs which bind penicillins but not cephalosporins. We have revised the previously reported cephamycin C and clavulanic acid gene clusters and, in addition, we have searched for novel β-lactam gene clusters in protein databases. Notably, in S. clavuligerus and Nocardia lactamdurans, the β-lactamases are retained in the cell wall and do not affect the intracellular formation of isopenicillin N/penicillin N. The activity of the β-lactamase in S. clavuligerus may be modulated by the β-lactamase inhibitory protein BLIP at the cell-wall level. Analysis of the β-lactam cluster in actinobacteria suggests that these clusters have been moved by horizontal gene transfer between different actinobacteria and have culminated in S. clavuligerus with the organization of an elaborated set of genes designed for fine tuning of antibiotic resistance and cell wall remodeling for the survival of this Streptomyces species. This article is focused specifically on the enigmatic connection between β-lactam biosynthesis and β-lactam resistance mechanisms in the producer actinobacteria.
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Affiliation(s)
| | | | - Paloma Liras
- Departamento de Biología Molecular, Universidad de León, 24071 León, Spain; (J.F.M.); (R.A.-A.)
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12
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Koch N, Islam NF, Sonowal S, Prasad R, Sarma H. Environmental antibiotics and resistance genes as emerging contaminants: Methods of detection and bioremediation. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100027. [PMID: 34841318 PMCID: PMC8610363 DOI: 10.1016/j.crmicr.2021.100027] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/02/2021] [Accepted: 03/07/2021] [Indexed: 12/13/2022] Open
Abstract
In developing countries, the use of antibiotics has helped to reduce the mortality rate by minimizing the deaths caused by pathogenic infections, but the costs of antibiotic contamination remain a major concern. Antibiotics are released into the environment, creating a complicated environmental problem. Antibiotics are used in human, livestock and agriculture, contributing to its escalation in the environment. Environmental antibiotics pose a range of risks and have significant effects on human and animal health. Nevertheless, this is the result of the development of antibiotic-resistant and multi-drug-resistant bacteria. In the area of health care, animal husbandry and crop processing, the imprudent use of antibiotic drugs produces antibiotic-resistant bacteria. This threat is the deepest in the developing world, with an estimated 700,000 people suffering from antibiotic-resistant infections each year. The study explores how bacteria use a wide variety of antibiotic resistance mechanism and how these approaches have an impact on the environment and on our health. The paper focuses on the processes by which antibiotics degrade, the health effects of these emerging contaminants, and the tolerance of bacteria to antibiotics.
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Affiliation(s)
- Niharika Koch
- Department of Botany, Mahatma Gandhi Central University, Motihari 845401, Bihar, India
| | - Nazim F. Islam
- Department of Botany, Nanda Nath Saikia College, Titabar, Assam 785630, India
| | - Songita Sonowal
- Department of Botany, Mahatma Gandhi Central University, Motihari 845401, Bihar, India
| | - Ram Prasad
- Department of Botany, Mahatma Gandhi Central University, Motihari 845401, Bihar, India
| | - Hemen Sarma
- Department of Botany, Nanda Nath Saikia College, Titabar, Assam 785630, India
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13
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Christensen SB. Drugs That Changed Society: History and Current Status of the Early Antibiotics: Salvarsan, Sulfonamides, and β-Lactams. Molecules 2021; 26:6057. [PMID: 34641601 PMCID: PMC8512414 DOI: 10.3390/molecules26196057] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/13/2021] [Accepted: 09/29/2021] [Indexed: 01/25/2023] Open
Abstract
The appearance of antibiotic drugs revolutionized the possibilities for treatment of diseases with high mortality such as pneumonia, sepsis, plaque, diphtheria, tetanus, typhoid fever, and tuberculosis. Today fewer than 1% of mortalities in high income countries are caused by diseases caused by bacteria. However, it should be recalled that the antibiotics were introduced in parallel with sanitation including sewerage, piped drinking water, high standard of living and improved understanding of the connection between food and health. Development of salvarsan, sulfonamides, and β-lactams into efficient drugs is described. The effects on life expectancy and life quality of these new drugs are indicated.
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Affiliation(s)
- Søren Brøgger Christensen
- The Museum of Natural Medicine & The Pharmacognostic Collection, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
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14
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Environmental antimicrobial resistance and its drivers: a potential threat to public health. J Glob Antimicrob Resist 2021; 27:101-111. [PMID: 34454098 DOI: 10.1016/j.jgar.2021.08.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/21/2023] Open
Abstract
Imprudent and overuse of clinically relevant antibiotics in agriculture, veterinary and medical sectors contribute to the global epidemic increase in antimicrobial resistance (AMR). There is a growing concern among researchers and stakeholders that the environment acts as an AMR reservoir and plays a key role in the dissemination of antimicrobial resistance genes (ARGs). Various drivers are contributing factors to the spread of antibiotic-resistant bacteria and their ARGs either directly through antimicrobial drug use in health care, agriculture/livestock and the environment or antibiotic residues released from various domestic settings. Resistant micro-organisms and their resistance genes enter the soil, air, water and sediments through various routes or hotspots such as hospital wastewater, agricultural waste or wastewater treatment plants. Global mitigation strategies primarily involve the identification of high-risk environments that are responsible for the evolution and spread of resistance. Subsequently, AMR transmission is affected by the standards of infection control, sanitation, access to clean water, access to assured quality antimicrobials and diagnostics, travel and migration. This review provides a brief description of AMR as a global concern and the possible contribution of different environmental drivers to the transmission of antibiotic-resistant bacteria or ARGs through various mechanisms. We also aim to highlight the key knowledge gaps that hinder environmental regulators and mitigation strategies in delivering environmental protection against AMR.
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15
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Králová S, Sandoval-Powers M, Fawwal DV, Degnes KF, Lewin AS, Klinkenberg G, Nguyen GS, Liles MR, Wentzel A. Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord. Front Microbiol 2021; 12:714233. [PMID: 34421874 PMCID: PMC8371330 DOI: 10.3389/fmicb.2021.714233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
Marine environments are home to an extensive number of microorganisms, many of which remain unexplored for taxonomic novelty and functional capabilities. In this study, a slow-growing Streptomyces strain expressing unique genomic and phenotypic characteristics, P38-E01 T , was described using a polyphasic taxonomic approach. This strain is part of a collection of over 8,000 marine Actinobacteria isolates collected in the Trondheim fjord of Norway by SINTEF Industry (Trondheim, Norway) and the Norwegian University of Science and Technology (NTNU, Trondheim, Norway). Strain P38-E01 T was isolated from the sediments of the Trondheim fjord, and phylogenetic analyses affiliated this strain with the genus Streptomyces, but it was not closely affiliated with other described species. The closest related type strains were Streptomyces daliensis YIM 31724 T (98.6%), Streptomyces rimosus subsp. rimosus ATCC 10970 T (98.4%), and Streptomyces sclerotialus NRRL ISP-5269 T (98.3%). Predominant fatty acids were C16:0 iso, C16:0, and Summed Feature 3, and the predominant respiratory quinones were MK-10(H6), MK-10(H4), and MK9(H4). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphoglycolipid. The whole-cell sugars were glucose, ribose, and in minor amounts, mannose. The cell wall peptidoglycan contained LL-diaminopimelic acid. The draft genome has a size of 6.16 Mb, with a %G + C content of 71.4% and is predicted to contain at least 19 biosynthetic gene clusters encoding diverse secondary metabolites. Strain P38-E01 T was found to inhibit the growth of the pathogenic yeast Candida albicans ATCC 90028 and a number of Gram-positive bacterial human and plant pathogens. Metabolites extracted from cultures of P38-E01 T were analyzed by mass spectrometry, and it was found that the isolate produced the antifungal compound candicidin. Phenotypic and chemotaxonomic signatures, along with phylogenetic analyses, distinguished isolate P38-E01 T from its closest neighbors; thus, this isolate represents a novel species of the genus Streptomyces for which the name Streptomyces tardus sp. nov. (P38-E01 T = CCM 9049 T = DSM 111582 T ) is proposed.
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Affiliation(s)
- Stanislava Králová
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Dorelle V. Fawwal
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Kristin F. Degnes
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Anna Sofia Lewin
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Geir Klinkenberg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Giang-Son Nguyen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Mark R. Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
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16
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Jiang W, Yang W, Zhao X, Wang N, Ren H. Klebsiella pneumoniae presents antimicrobial drug resistance for β-lactam through the ESBL/PBP signaling pathway. Exp Ther Med 2020; 19:2449-2456. [PMID: 32256721 PMCID: PMC7086219 DOI: 10.3892/etm.2020.8498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
Overuse and misuse of antibiotics leads to antibiotic resistance which has become a significant public health concern. Klebsiella pneumoniae is the most common pathogenic bacteria underlying nosocomial infections due to the expression of virulence factors and occurrence of antibiotic resistance. Evidence indicates that β-lactamase is involved in the antibiotic resistance of Klebsiella pneumoniae to β-lactam antibiotics. The aim of the present study was to investigate the association between the molecular biological mechanisms of antibiotic resistance of Klebsiella pneumoniae and extended-spectrum β-lactamase (ESBL). In order to assess temporal trends in prevalence and antimicrobial susceptibility, Klebsiella pneumoniae bacteria were isolated and the ESBL expression level was analyzed. Susceptibility tests were performed using automated systems. The β-lactam-resistance in Klebsiella pneumoniae was assessed by the β-lactam agar screen plate and respective MIC values were evaluated using E-test strips. The confirmatory disk diffusion methods were applied for phenotypic identification of the ESBL production of Klebsiella pneumoniae. The results showed that Klebsiella pneumoniae bacteria exhibited higher ESBL production after treatment with β-lactam compared to the control. The ESBL gene expression was upregulated in Klebsiella pneumoniae after treatment with β-lactam. Results identified that penicillin-binding proteins (PBPs) were associated with the growth and resistance to β-lactams. Zinc finger nuclease markedly inhibited the antibiotic resistance of Klebsiella pneumoniae to β-lactam. PBP knockdown abolished the inhibitory effects of zinc finger nuclease on the growth of Klebsiella pneumoniae induced by β-lactam antibiotic treatment. In conclusion, these results suggest that the resistance of Klebsiella pneumoniae bacteria to antimicrobial drugs is through the ESBL signaling pathway, which indicates that ESBL may be a potential target for abolishing resistance to β-lactam.
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Affiliation(s)
- Wei Jiang
- Department of Infectious Disease, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Wenjie Yang
- Department of Transplantation, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Xuequn Zhao
- Department of Transplantation, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Na Wang
- Department of Infectious Disease, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Haixia Ren
- Department of Pharmaceutical Preparation, Tianjin First Central Hospital, Tianjin 300000, P.R. China
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17
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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18
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Unsleber S, Wohlleben W, Stegmann E. Diversity of peptidoglycan structure—Modifications and their physiological role in resistance in antibiotic producers. Int J Med Microbiol 2019; 309:151332. [DOI: 10.1016/j.ijmm.2019.151332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 11/29/2022] Open
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19
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Alekseeva MG, Boyko KM, Nikolaeva AY, Mavletova DA, Rudakova NN, Zakharevich NV, Korzhenevskiy DA, Ziganshin RH, Popov VO, Danilenko VN. Identification, functional and structural characterization of novel aminoglycoside phosphotransferase APH(3″)-Id from Streptomyces rimosus subsp. rimosus ATCC 10970. Arch Biochem Biophys 2019; 671:111-122. [DOI: 10.1016/j.abb.2019.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/21/2019] [Accepted: 06/22/2019] [Indexed: 01/03/2023]
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20
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Antibiotic resistance genes in the Actinobacteria phylum. Eur J Clin Microbiol Infect Dis 2019; 38:1599-1624. [PMID: 31250336 DOI: 10.1007/s10096-019-03580-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.
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21
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Srivastava SK, King KS, AbuSara NF, Malayny CJ, Piercey BM, Wilson JA, Tahlan K. In vivo functional analysis of a class A β-lactamase-related protein essential for clavulanic acid biosynthesis in Streptomyces clavuligerus. PLoS One 2019; 14:e0215960. [PMID: 31013337 PMCID: PMC6478378 DOI: 10.1371/journal.pone.0215960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/12/2019] [Indexed: 11/23/2022] Open
Abstract
In Streptomyces clavuligerus, the gene cluster involved in the biosynthesis of the clinically used β-lactamase inhibitor clavulanic acid contains a gene (orf12 or cpe) encoding a protein with a C-terminal class A β-lactamase-like domain. The cpe gene is essential for clavulanic acid production, and the recent crystal structure of its product (Cpe) was shown to also contain an N-terminal isomerase/cyclase-like domain, but the function of the protein remains unknown. In the current study, we show that Cpe is a cytoplasmic protein and that both its N- and C-terminal domains are required for in vivo clavulanic acid production in S. clavuligerus. Our results along with those from previous studies allude towards a biosynthetic role for Cpe during the later stages of clavulanic acid production in S. clavuligerus. Amino acids from Cpe essential for biosynthesis were also identified, including one (Lys89) from the recently described N-terminal isomerase-like domain of unknown function. Homologues of Cpe from other clavulanic acid-producing Streptomyces spp. were shown to be functionally equivalent to the S. clavuligerus protein, whereas those from non-producers containing clavulanic acid-like gene clusters were not. The suggested in vivo involvement of an isomerase-like domain recruited by an ancestral β-lactamase related protein, supports a previous hypothesis that Cpe could be involved in a step requiring the opening and modification of the clavulanic acid core during its biosynthesis from 5S precursors.
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Affiliation(s)
| | - Kelcey S. King
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Nader F. AbuSara
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Chelsea J. Malayny
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Brandon M. Piercey
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Jaime A. Wilson
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
- * E-mail:
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22
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 PMCID: PMC6283892 DOI: 10.3389/fmicb.2018.02928] [Citation(s) in RCA: 424] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 11/13/2022] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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23
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Viana Marques DDA, Machado SEF, Ebinuma VCS, Duarte CDAL, Converti A, Porto ALF. Production of β-Lactamase Inhibitors by Streptomyces Species. Antibiotics (Basel) 2018; 7:E61. [PMID: 30018235 PMCID: PMC6163296 DOI: 10.3390/antibiotics7030061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/07/2018] [Accepted: 07/12/2018] [Indexed: 12/11/2022] Open
Abstract
β-Lactamase inhibitors have emerged as an effective alternative to reduce the effects of resistance against β-lactam antibiotics. The Streptomyces genus is known for being an exceptional natural source of antimicrobials and β-lactamase inhibitors such as clavulanic acid, which is largely applied in clinical practice. To protect against the increasing prevalence of multidrug-resistant bacterial strains, new antibiotics and β-lactamase inhibitors need to be discovered and developed. This review will cover an update about the main β-lactamase inhibitors producers belonging to the Streptomyces genus; advanced methods, such as genetic and metabolic engineering, to enhance inhibitor production compared with wild-type strains; and fermentation and purification processes. Moreover, clinical practice and commercial issues are discussed. The commitment of companies and governments to develop innovative strategies and methods to improve the access to new, efficient, and potentially cost-effective microbial products to combat the antimicrobial resistance is also highlighted.
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Affiliation(s)
- Daniela de Araújo Viana Marques
- Campus Serra Talhada, University of Pernambuco, Avenida Custódio Conrado, 600, AABB, Serra Talhada, Pernambuco 56912-550, Brazil.
| | - Suellen Emilliany Feitosa Machado
- Department of Antibiotics, Federal University of Pernambuco, Avenida da Engenharia, 2° andar, Cidade Universitária, Recife, Pernambuco 50740-600, Brazil.
| | - Valéria Carvalho Santos Ebinuma
- Department of Bioprocesses and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara-Jaú/Km 01, Araraquara 14800-903, Brazil.
| | | | - Attilio Converti
- Department of Civil, Chemical and Environmental Engineering, Chemical Pole, University of Genoa, Via Opera Pia 15, 16145 Genoa, Italy.
| | - Ana Lúcia Figueiredo Porto
- Department of Morphology and Animal Physiology, Federal Rural University of Pernambuco, Av. Dom Manoel de Medeiros, Recife, Pernambuco 52171-900, Brazil.
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24
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Ogawara H. Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms. Molecules 2018; 23:E1476. [PMID: 29912169 PMCID: PMC6100412 DOI: 10.3390/molecules23061476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Drug resistance, especially antibiotic resistance, is a growing threat to human health. To overcome this problem, it is significant to know precisely the mechanisms of drug resistance and/or self-resistance in various kingdoms, from bacteria through plants to animals, once more. This review compares the molecular mechanisms of the resistance against phycotoxins, toxins from marine and terrestrial animals, plants and fungi, and antibiotics. The results reveal that each kingdom possesses the characteristic features. The main mechanisms in each kingdom are transporters/efflux pumps in phycotoxins, mutation and modification of targets and sequestration in marine and terrestrial animal toxins, ABC transporters and sequestration in plant toxins, transporters in fungal toxins, and various or mixed mechanisms in antibiotics. Antibiotic producers in particular make tremendous efforts for avoiding suicide, and are more flexible and adaptable to the changes of environments. With these features in mind, potential alternative strategies to overcome these resistance problems are discussed. This paper will provide clues for solving the issues of drug resistance.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 DOI: 10.3389/fmicb.2018.02928/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 05/20/2023] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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Ünsaldı E, Kurt-Kızıldoğan A, Voigt B, Becher D, Özcengiz G. Proteome-wide alterations in an industrial clavulanic acid producing strain of Streptomyces clavuligerus. Synth Syst Biotechnol 2016; 2:39-48. [PMID: 29062960 PMCID: PMC5625738 DOI: 10.1016/j.synbio.2016.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/17/2016] [Accepted: 10/23/2016] [Indexed: 11/26/2022] Open
Abstract
The usefulness of genetic/metabolic engineering for further improvement of industrial strains is subject of discussion because of the general lack of knowledge on genetic alterations introduced by iterative cycles of random mutagenesis in such strains. An industrial clavulanic acid (CA)-overproducer Streptomyces clavuligerus DEPA was assessed to understand proteome-wide changes that have occurred in a local industrial CA overproducer developed through succesive mutagenesis programs. The proteins that could be identified corresponded to 33 distinct ORFs for underrepresented ones and 60 ORFs for overrepresented ones. Three CA biosynthetic enzymes were overrepresented in S. clavuligerus DEPA; carboxyethylarginine synthase (Ceas2), clavaldehyde dehydrogenase (Car) and carboxyethyl-arginine beta-lactam-synthase (Bls2) whereas the enzymes of two other secondary metabolites were underrepresented along with two important global regulators [two-component system (TCS) response regulator (SCLAV_2102) and TetR-family transcriptional regulator (SCLAV_3146)] that might be related with CA production and/or differentiation. γ-butyrolactone biosynthetic protein AvaA2 was 2.6 fold underrepresented in S. clavuligerus DEPA. The levels of two glycolytic enzymes, 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase and phosophoglycerate kinase were found decreased while those of dihydrolipoyl dehydrogenase (E3) and isocitrate dehydrogenase, with two isoforms were found as significantly increased. A decrease of amino acid metabolism, methionine biosynthesis in particular, as well as S-adenosylmethionine synthetase appeared as one of the prominent mechanisms of success of S. clavuligerus DEPA strain as a prolific producer of CA. The levels of two enzymes of shikimate pathway that leads to the production of aromatic amino acids and aromatic secondary metabolites were also underrepresented. Some of the overrepresented stress proteins in S. clavuligerus DEPA included polynucleotide phosphorylase/polyadenylase (PNPase), ATP-dependent DNA helicase, two isoforms of an anti-sigma factor and thioredoxin reductase. Downregulation of important proteins of cell wall synthesis and division was recorded and a protein with β-lactamase domain (SCLAV_p1007) appeared in 12 isoforms, 5 of which were drastically overrepresented in DEPA strain. These results described herein provide useful information for rational engineering to improve CA production in Streptomyces clavuligerus.
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Affiliation(s)
- Eser Ünsaldı
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Aslıhan Kurt-Kızıldoğan
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey.,Department of Agricultural Biotechnology, Ondokuz Mayıs University, 55139, Samsun, Turkey
| | - Birgit Voigt
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, D-17487, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, D-17487, Greifswald, Germany
| | - Gülay Özcengiz
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
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