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Bunduruș IA, Balta I, Ștef L, Ahmadi M, Peț I, McCleery D, Corcionivoschi N. Overview of Virulence and Antibiotic Resistance in Campylobacter spp. Livestock Isolates. Antibiotics (Basel) 2023; 12:antibiotics12020402. [PMID: 36830312 PMCID: PMC9952398 DOI: 10.3390/antibiotics12020402] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Abstract
Campylobacter remains the most prevalent foodborne pathogen bacterium responsible for causing gastroenteritis worldwide. Specifically, this pathogen colonises a ubiquitous range of environments, from poultry, companion pets and livestock animals to humans. The bacterium is uniquely adaptable to various niches, leading to complicated gastroenteritis and, in some cases, difficult to treat due to elevated resistance to certain antibiotics. This increased resistance is currently detected via genomic, clinical or epidemiological studies, with the results highlighting worrying multi-drug resistant (MDR) profiles in many food and clinical isolates. The Campylobacter genome encodes a rich inventory of virulence factors offering the bacterium the ability to influence host immune defences, survive antimicrobials, form biofilms and ultimately boost its infection-inducing potential. The virulence traits responsible for inducing clinical signs are not sufficiently defined because several populations have ample virulence genes with physiological functions that reflect their pathogenicity differences as well as a complement of antimicrobial resistance (AMR) systems. Therefore, exhaustive knowledge of the virulence factors associated with Campylobacter is crucial for collecting molecular insights into the infectivity processes, which could pave the way for new therapeutical targets to combat and control the infection and mitigate the spread of MDR bacteria. This review provides an overview of the spread and prevalence of genetic determinants associated with virulence and antibiotic resistance from studies performed on livestock animals. In addition, we have investigated the relevant coincidental associations between the prevalence of the genes responsible for pathogenic virulence, horizontal gene transfer (HGT) and transmissibility of highly pathogenic Campylobacter strains.
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Affiliation(s)
- Iulia Adelina Bunduruș
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Igori Balta
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Lavinia Ștef
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Mirela Ahmadi
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Ioan Peț
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - David McCleery
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT4 3SD, UK
- Correspondence: (D.M.); (N.C.)
| | - Nicolae Corcionivoschi
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT4 3SD, UK
- Correspondence: (D.M.); (N.C.)
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Subramanian D, Natarajan J. Leveraging big data bioinformatics approaches to extract knowledge from Staphylococcus aureus public omics data. Crit Rev Microbiol 2022; 49:391-413. [PMID: 35468027 DOI: 10.1080/1040841x.2022.2065905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Staphylococcus aureus is a notorious pathogen posing challenges in the medical industry due to drug resistance and biofilm formation. The horizon of knowledge on S. aureus pathogenesis has expanded with the advancement of data-driven bioinformatics techniques. Mining information from sequenced genomes and their expression data is an economic approach that alleviates wastage of resources and redundancy in experiments. The current review covers how big data bioinformatics has been used in the analysis of S. aureus from publicly available -omics data to uncover mechanisms of infection and inhibition. Particularly, advances in the past two decades in biomarker discovery, host responses, phenotype identification, consolidation of information, and drug development are discussed highlighting the challenges and shortcomings. Overall, the review summarizes the diverse aspects of scrupulous re-analysis of S. aureus proteomic and transcriptomic expression datasets retrieved from public repositories in terms of the efforts taken, benefits offered, and follow-up actions. The detailed review thus serves as a reference and aid for (i) Computational biologists by briefing the approaches utilized for bacterial omics re-analysis concerning S. aureus and (ii) Experimental biologists by elucidating the potential of bioinformatics in biological research to generate reliable postulates in a prompt and economical manner.
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Affiliation(s)
- Devika Subramanian
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, India
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Integrated meta-analysis and machine learning approach identifies acyl-CoA thioesterase with other novel genes responsible for biofilm development in Staphylococcus aureus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 88:104702. [PMID: 33388440 DOI: 10.1016/j.meegid.2020.104702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 02/08/2023]
Abstract
Biofilm forming Staphylococcus aureus is a major threat to the health-care industry. It is important to understand the differences between planktonic and biofilm growth forms in the pathogen since conventional treatments targeting the planktonic forms are not effective against biofilms. The current study conducts a meta-analysis of three public transcriptomic profiles to examine the differences in gene expression between the planktonic and biofilm states of S. aureus using random-effects modeling. Mean effect sizes were calculated for 2847 genes among which 726 differentially expressed genes were taken for further analysis. Major genes that are discriminatory between the two conditions were mined using supervised learning techniques and validated by high-accuracy classifiers. Ten different feature selection algorithms were applied and used to rank the most important genes in S. aureus biofilms. Finally, an optimal set of 36 genes are presented as candidate genes in biofilm formation or development while throwing light on the novel roles of an acyl-CoA thioesterase enzyme and 10 hypothetical proteins in biofilms. The relevance of the identified gene set was further validated by building five different classification models using SVM, RF, kNN, NB and DT algorithms that were compared with models built from other relevant gene sets and by reviewing the functional role of 25 previously known genes in biofilm development. The study combines meta-analysis of differential expression with supervised machine learning strategies and feature selection for the first time to identify and validate a discriminatory set of genes important in biofilms of S. aureus. The functional roles of the identified genes predicted to be important in biofilms are further scrutinized and can be considered as a signature target list to develop anti-biofilm therapeutics in S. aureus.
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Pérez VKC, Costa GMD, Guimarães AS, Heinemann MB, Lage AP, Dorneles EMS. Relationship between virulence factors and antimicrobial resistance in Staphylococcus aureus from bovine mastitis. J Glob Antimicrob Resist 2020; 22:792-802. [PMID: 32603906 DOI: 10.1016/j.jgar.2020.06.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 05/10/2020] [Accepted: 06/09/2020] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES This review summarizes the literature on the role of virulence and antimicrobial resistance genes of Staphylococcus aureus in bovine mastitis, focusing on the association between these characteristics and their implications for public and animal health. CONCLUSIONS There is the possibility of antimicrobial resistance gene exchange among different bacteria, which is of serious concern in livestock husbandry, as well as in the treatment of human staphylococcal infections.
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Affiliation(s)
- Verónica Karen Castro Pérez
- Departamento de Medicina Veterinária, Universidade Federal de Lavras, Lavras 37200-000, Minas Gerais, Brazil
| | - Geraldo Márcio da Costa
- Departamento de Medicina Veterinária, Universidade Federal de Lavras, Lavras 37200-000, Minas Gerais, Brazil
| | - Alessandro Sá Guimarães
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Gado de Leite, Juiz de Fora 36038-330, Minas Gerais, Brazil
| | - Marcos Bryan Heinemann
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo 05508-900, São Paulo, Brazil
| | - Andrey Pereira Lage
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Elaine Maria Seles Dorneles
- Departamento de Medicina Veterinária, Universidade Federal de Lavras, Lavras 37200-000, Minas Gerais, Brazil.
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Tham EH, Koh E, Common JEA, Hwang IY. Biotherapeutic Approaches in Atopic Dermatitis. Biotechnol J 2020; 15:e1900322. [PMID: 32176834 DOI: 10.1002/biot.201900322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/24/2020] [Indexed: 12/15/2022]
Abstract
The skin microbiome plays a central role in inflammatory skin disorders such as atopic dermatitis (AD). In AD patients, an imbalance between pathogenic Staphylococcus aureus (S. aureus) and resident skin symbionts creates a state of dysbiosis which induces immune dysregulation and impairs skin barrier function. There are now exciting new prospects for microbiome-based interventions for AD prevention. In the hopes of achieving sustained control and management of disease in AD patients, current emerging biotherapeutic strategies aim to harness the skin microbiome associated with health by restoring a more diverse symbiotic skin microbiome, while selectively removing pathogenic S. aureus. Examples of such strategies are demonstrated in skin microbiome transplants, phage-derived anti-S. aureus endolysins, monoclonal antibodies, and quorum sensing (QS) inhibitors. However, further understanding of the skin microbiome and its role in AD pathogenesis is still needed to understand how these biotherapeutics alter the dynamics of the microbiome community; to optimize patient selection, drug delivery, and treatment duration; overcome rapid recolonization upon treatment cessation; and improve efficacy to allow these therapeutic options to eventually reach routine clinical practice.
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Affiliation(s)
- Elizabeth Huiwen Tham
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, 119074, Singapore
| | - Elvin Koh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, Singapore, 119228, Singapore
| | - John E A Common
- Skin Research Institute of Singapore, A*STAR, Singapore, 308232, Singapore
| | - In Young Hwang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, Singapore, 119228, Singapore
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Subramanian D, Bhasuran B, Natarajan J. Genomic analysis of RNA-Seq and sRNA-Seq data identifies potential regulatory sRNAs and their functional roles in Staphylococcus aureus. Genomics 2019; 111:1431-1446. [DOI: 10.1016/j.ygeno.2018.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/21/2018] [Accepted: 09/26/2018] [Indexed: 12/17/2022]
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Opoku-Temeng C, Onyedibe KI, Aryal UK, Sintim HO. Proteomic analysis of bacterial response to a 4-hydroxybenzylidene indolinone compound, which re-sensitizes bacteria to traditional antibiotics. J Proteomics 2019; 202:103368. [PMID: 31028946 DOI: 10.1016/j.jprot.2019.04.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/21/2019] [Accepted: 04/23/2019] [Indexed: 02/07/2023]
Abstract
Halogenated 4-hydroxybenzylidene indolinones have been shown to re-sensitize methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE) to methicillin and vancomycin respectively. The mechanism of antibiotic re-sensitization was however not previously studied. Here, we probe the scope of antibiotic re-sensitization and present the global proteomics analysis of S. aureus treated with GW5074, a 4-hydroxybenzylidene indolinone compound. With a minimum inhibitory concentration (MIC) of 8 μg/mL against S. aureus, GW5074 synergized with beta-lactam antibiotics like ampicillin, carbenicillin and cloxacillin, the DNA synthesis inhibitor, ciprofloxacin, the protein synthesis inhibitor, gentamicin and the folate acid synthesis inhibitor, trimethoprim. Global proteomics analysis revealed that GW5074 treatment resulted in significant downregulation of enzymes involved in the purine biosynthesis. S. aureus proteins involved in amino acid metabolism and peptide transport were also observed to be downregulated. Interestingly, anti-virulence targets such as AgrC (a quorum sensing-related histidine kinase), AgrA (a quorum sensing-related response regulator) as well as downstream targets, such as hemolysins, lipases and proteases in S. aureus were also downregulated by GW5074. We observed that the peptidoglycan hydrolase, SceD was significantly upregulated. The activity of GW5074 on S. aureus suggests that the compound primes bacteria for the antibacterial action of ineffective antibiotics. SIGNIFICANCE: Antibiotic resistance continues to present significant challenges to the treatment of bacterial infections. Given that antibiotic resistance is a natural phenomenon and that it has become increasingly difficult to discover novel antibiotics, efforts to improve the activity of existing agents are worth pursuing. A few small molecules that re-sensitize resistant bacteria to traditional antibiotics have been described but the molecular details that underpin how these compounds work to re-sensitize bacteria remain largely unknown. In this report, global label-free quantitative proteomics was used to identify changes in the proteome that occurs when GW5074, a compound that re-sensitize MRSA to methicillin, is administered to S. aureus. The identification of pathways that are impacted by GW5074 could help identify novel targets for antibiotic re-sensitization.
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Affiliation(s)
- Clement Opoku-Temeng
- Graduate Program in Biochemistry, University of Maryland, College Park, MD 20742, USA; Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Kenneth Ikenna Onyedibe
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Herman O Sintim
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA.
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Subramanian D, Natarajan J. RNA-seq analysis reveals resistome genes and signalling pathway associated with vancomycin-intermediate Staphylococcus aureus. Indian J Med Microbiol 2019; 37:173-185. [PMID: 31745016 DOI: 10.4103/ijmm.ijmm_18_311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Context Vancomycin-intermediate Staphylococcus aureus remains one of the most prevalent multidrug-resistant pathogens causing healthcare infections that are difficult to treat. Aims This study uses a comprehensive computational analysis to systematically investigate various gene expression profiles of resistant and sensitive S. aureus strains on exposure to antibiotics. Settings and Design The transcriptional changes leading to the development of multiple antibiotic resistance were examined by an integrative analysis of nine differential expression experiments under selected conditions of vancomycin-intermediate and -sensitive strains for four different antibiotics using publicly available RNA-Seq datasets. Materials and Methods For each antibiotic, three experimental conditions for expression analysis were selected to identify those genes that are particularly involved in the development of resistance. The results were further scrutinised to generate a resistome that can be analysed for their role in the development or adaptation to antibiotic resistance. Results The 99 genes in the resistome are then compiled to create a multiple drug resistome of 25 known and novel genes identified to play a part in antibiotic resistance. The inclusion of agr genes and associated virulence factors in the identified resistome supports the role of agr quorum sensing system in multiple drug resistance. In addition, enrichment analysis also identified the kyoto encyclopedia of genes and genomes (KEGG) pathways - quorum sensing and two-component system pathways - in the resistome gene set. Conclusion Further studies on understanding the role of the identified molecular targets such as SAA6008_00181, SAA6008_01127, agrA, agrC and coa in adapting to the pressure of antibiotics at sub-inhibitory concentrations can help in learning the molecular mechanisms causing resistance to the pathogens as well as finding other potential therapeutics.
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Affiliation(s)
- Devika Subramanian
- Department of Bioinformatics, Data Mining and Text Mining Laboratory, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Jeyakumar Natarajan
- Department of Bioinformatics, Data Mining and Text Mining Laboratory, Bharathiar University, Coimbatore, Tamil Nadu, India
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Sun L, Zhang L, Wang T, Jiao W, Li Q, Yin Q, Li J, Qi H, Xu F, Shen C, Xiao J, Liu S, Mokrousov I, Huang H, Shen A. Mutations of Mycobacterium tuberculosis induced by anti-tuberculosis treatment result in metabolism changes and elevation of ethambutol resistance. INFECTION GENETICS AND EVOLUTION 2018; 72:151-158. [PMID: 30292007 DOI: 10.1016/j.meegid.2018.09.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/12/2018] [Accepted: 09/30/2018] [Indexed: 10/28/2022]
Abstract
Selective pressure from antibiotic use is one of the most important risk factors associated with the development of drug resistance in Mycobacterium tuberculosis (MTB). However, the mechanisms underlying drug resistance at the molecular level remain partly unclear. Therefore, the purpose of this study was to investigate the potential functional effect of novel mutations arising from anti-tuberculosis treatment. We analyzed two multidrug-resistant TB (MDR-TB) isolates from the same patient; one collected before and one almost a year after commencing MDR-TB treatment. The post-treatment isolate exhibited elevated ethambutol resistance. We sequenced the whole genomes of the two clinical isolates and detected six novel polymorphisms affecting the genes Rv1026, nc0021, Rv2155c, Rv2437, and Rv3696c, and the intergenic region between Rv2764c and Rv2765. Metabolomics approach was used to reveal the effect of the found variation on the metabolic pathways of MTB. Partial least squares-discriminant analysis showed a clear differentiation between the two isolates, involving a total of 175 metabolites. Pathway analysis showed that these metabolites are mainly involved in amino sugar and nucleotide sugar metabolism, β-alanine metabolism, sulfur metabolism, and galactose metabolism. The increased ethambutol resistance exhibited by the post-treatment MDR-TB strain could speculatively be linked to the identified genetic variations, which affected the synthesis of a number of metabolites associated with sources of carbon and energy. This may have been the main factor underlying the increased ethambutol resistance of this isolate.
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Affiliation(s)
- Lin Sun
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Liqun Zhang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Ting Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Weiwei Jiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Qinjing Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Qingqin Yin
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Jieqiong Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Hui Qi
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Fang Xu
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Chen Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Jing Xiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Shuping Liu
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St Petersburg Pasteur Institute, St Petersburg, Russia.
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China.
| | - Adong Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China.
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Fei Q, Gao EB, Liu B, Wei Y, Ning D. A Toxin-Antitoxin System VapBC15 from Synechocystis sp. PCC 6803 Shows Distinct Regulatory Features. Genes (Basel) 2018; 9:E173. [PMID: 29561797 PMCID: PMC5924515 DOI: 10.3390/genes9040173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/26/2022] Open
Abstract
Type II toxin-antitoxin (TA) systems play important roles in bacterial stress survival by regulating cell growth or death. They are highly abundant in cyanobacteria yet remain poorly characterized. Here, we report the identification and regulation of a putative type II TA system from Synechocystis PCC6803, VapBC15. The VapBC15 system is encoded by the chromosomal operon vapBC15. Exogenous expression of VapC15 dramatically arrested cell growth of Escherichia coli and reduced the numbers of colony-forming units (CFU). The VapC15 toxicity could be which was counteracted neutralized by simultaneous or delayed production of VapB15. Biochemical analysis demonstrated the formation of VapB15-VapC15 complexes by the physical interaction between VapB15 and VapC15. Notably, the VapB15 antitoxin up-regulated the transcription of the vapBC15 operon by directly binding to the promoter region, and the VapC15 toxin abolished the up-regulatory effect by destabilizing the binding. Moreover, VapB15 can be degraded by the proteases Lons and ClpXP2s from Synechocystis PCC6803, thus activating the latent toxicity of VapBC15. These findings suggest that VapBC15 represents a genuine TA system that utilizes a distinct mechanism to regulate toxin activity.
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Affiliation(s)
- Qian Fei
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - E-Bin Gao
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Biao Liu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Yao Wei
- Huai'an Research Center, Institute of Hydrobiology, Chinese Academy of Sciences, Huai'an 223005, China.
| | - Degang Ning
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Huai'an Research Center, Institute of Hydrobiology, Chinese Academy of Sciences, Huai'an 223005, China.
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Identification of Staphylococcus aureus Cellular Pathways Affected by the Stilbenoid Lead Drug SK-03-92 Using a Microarray. Antibiotics (Basel) 2017; 6:antibiotics6030017. [PMID: 28892020 PMCID: PMC5617981 DOI: 10.3390/antibiotics6030017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/25/2017] [Accepted: 09/07/2017] [Indexed: 12/16/2022] Open
Abstract
The mechanism of action for a new lead stilbene compound coded SK-03-92 with bactericidal activity against methicillin-resistant Staphylococcus aureus (MRSA) is unknown. To gain insight into the killing process, transcriptional profiling was performed on SK-03-92 treated vs. untreated S. aureus. Fourteen genes were upregulated and 38 genes downregulated by SK-03-92 treatment. Genes involved in sortase A production, protein metabolism, and transcriptional regulation were upregulated, whereas genes encoding transporters, purine synthesis proteins, and a putative two-component system (SACOL2360 (MW2284) and SACOL2361 (MW2285)) were downregulated by SK-03-92 treatment. Quantitative real-time polymerase chain reaction analyses validated upregulation of srtA and tdk as well as downregulation of the MW2284/MW2285 and purine biosynthesis genes in the drug-treated population. A quantitative real-time polymerase chain reaction analysis of MW2284 and MW2285 mutants compared to wild-type cells demonstrated that the srtA gene was upregulated by both putative two-component regulatory gene mutants compared to the wild-type strain. Using a transcription profiling technique, we have identified several cellular pathways regulated by SK-03-92 treatment, including a putative two-component system that may regulate srtA and other genes that could be tied to the SK-03-92 mechanism of action, biofilm formation, and drug persisters.
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Domínguez Á, Muñoz E, López MC, Cordero M, Martínez JP, Viñas M. Transcriptomics as a tool to discover new antibacterial targets. Biotechnol Lett 2017; 39:819-828. [PMID: 28289911 DOI: 10.1007/s10529-017-2319-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/07/2017] [Indexed: 12/20/2022]
Abstract
The emergence of antibiotic-resistant pathogens, multiple drug-resistance, and extremely drug-resistant strains demonstrates the need for improved strategies to discover new drug-based compounds. The development of transcriptomics, proteomics, and metabolomics has provided new tools for global studies of living organisms. However, the compendium of expression profiles produced by these methods has introduced new scientific challenges into antimicrobial research. In this review, we discuss the practical value of transcriptomic techniques as well as their difficulties and pitfalls. We advocate the construction of new databases of transcriptomic data, using standardized formats in addition to standardized models of bacterial and yeast similar to those used in systems biology. The inclusion of proteomic and metabolomic data is also essential, as the resulting networks can provide a landscape to rationally predict and exploit new drug targets and to understand drug synergies.
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Affiliation(s)
- Ángel Domínguez
- Department of Microbiology and Genetics, Universidad de Salamanca, Plaza de los Drs. de la Reina s/n, 37007, Salamanca, Spain.
| | - Elisa Muñoz
- Department of Cell Biology & Pathology, Universidad de Salamanca, Salamanca, Spain
| | - M Carmen López
- Department of Microbiology and Genetics, Universidad de Salamanca, Plaza de los Drs. de la Reina s/n, 37007, Salamanca, Spain
| | - Miguel Cordero
- Department of Medicine, Universidad de Salamanca, Salamanca, Spain
| | - José Pedro Martínez
- Department of Microbiology & Ecology, Universitat de Valencia/Estudi General (UVEG), Valencia, Spain
| | - Miguel Viñas
- Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain
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Schroeder M, Brooks BD, Brooks AE. The Complex Relationship between Virulence and Antibiotic Resistance. Genes (Basel) 2017; 8:E39. [PMID: 28106797 PMCID: PMC5295033 DOI: 10.3390/genes8010039] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/21/2016] [Accepted: 01/07/2017] [Indexed: 12/17/2022] Open
Abstract
Antibiotic resistance, prompted by the overuse of antimicrobial agents, may arise from a variety of mechanisms, particularly horizontal gene transfer of virulence and antibiotic resistance genes, which is often facilitated by biofilm formation. The importance of phenotypic changes seen in a biofilm, which lead to genotypic alterations, cannot be overstated. Irrespective of if the biofilm is single microbe or polymicrobial, bacteria, protected within a biofilm from the external environment, communicate through signal transduction pathways (e.g., quorum sensing or two-component systems), leading to global changes in gene expression, enhancing virulence, and expediting the acquisition of antibiotic resistance. Thus, one must examine a genetic change in virulence and resistance not only in the context of the biofilm but also as inextricably linked pathologies. Observationally, it is clear that increased virulence and the advent of antibiotic resistance often arise almost simultaneously; however, their genetic connection has been relatively ignored. Although the complexities of genetic regulation in a multispecies community may obscure a causative relationship, uncovering key genetic interactions between virulence and resistance in biofilm bacteria is essential to identifying new druggable targets, ultimately providing a drug discovery and development pathway to improve treatment options for chronic and recurring infection.
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Affiliation(s)
- Meredith Schroeder
- Department of Microbiological Sciences; North Dakota State University, Fargo, ND 58105, USA.
| | - Benjamin D Brooks
- Department of Electrical and Computer Engineering; North Dakota State University, Fargo, ND 58105, USA.
| | - Amanda E Brooks
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105, USA.
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Coussens NP, Daines DA. Wake me when it's over - Bacterial toxin-antitoxin proteins and induced dormancy. Exp Biol Med (Maywood) 2016; 241:1332-42. [PMID: 27216598 DOI: 10.1177/1535370216651938] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Toxin-antitoxin systems are encoded by bacteria and archaea to enable an immediate response to environmental stresses, including antibiotics and the host immune response. During normal conditions, the antitoxin components prevent toxins from interfering with metabolism and arresting growth; however, toxin activation enables microbes to remain dormant through unfavorable conditions that might continue over millions of years. Intense investigations have revealed a multitude of mechanisms for both regulation and activation of toxin-antitoxin systems, which are abundant in pathogenic microorganisms. This minireview provides an overview of the current knowledge regarding type II toxin-antitoxin systems along with their clinical and environmental implications.
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Affiliation(s)
- Nathan P Coussens
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Dayle A Daines
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA
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15
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Schuster CF, Bertram R. Toxin-Antitoxin Systems of Staphylococcus aureus. Toxins (Basel) 2016; 8:E140. [PMID: 27164142 PMCID: PMC4885055 DOI: 10.3390/toxins8050140] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 01/02/2023] Open
Abstract
Toxin-antitoxin (TA) systems are small genetic elements found in the majority of prokaryotes. They encode toxin proteins that interfere with vital cellular functions and are counteracted by antitoxins. Dependent on the chemical nature of the antitoxins (protein or RNA) and how they control the activity of the toxin, TA systems are currently divided into six different types. Genes comprising the TA types I, II and III have been identified in Staphylococcus aureus. MazF, the toxin of the mazEF locus is a sequence-specific RNase that cleaves a number of transcripts, including those encoding pathogenicity factors. Two yefM-yoeB paralogs represent two independent, but auto-regulated TA systems that give rise to ribosome-dependent RNases. In addition, omega/epsilon/zeta constitutes a tripartite TA system that supposedly plays a role in the stabilization of resistance factors. The SprA1/SprA1AS and SprF1/SprG1 systems are post-transcriptionally regulated by RNA antitoxins and encode small membrane damaging proteins. TA systems controlled by interaction between toxin protein and antitoxin RNA have been identified in S. aureus in silico, but not yet experimentally proven. A closer inspection of possible links between TA systems and S. aureus pathophysiology will reveal, if these genetic loci may represent druggable targets. The modification of a staphylococcal TA toxin to a cyclopeptide antibiotic highlights the potential of TA systems as rather untapped sources of drug discovery.
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Affiliation(s)
- Christopher F Schuster
- Section of Microbiology & MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
| | - Ralph Bertram
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Lehrbereich Mikrobielle Genetik, University of Tübingen, 72076 Tübingen, Germany.
- Klinikum Nürnberg Medical School GmbH, Research Department, Paracelsus Medical University, 90419 Nuremberg, Germany.
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