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George NL, Bennett EC, Orlando BJ. Guarding the walls: the multifaceted roles of Bce modules in cell envelope stress sensing and antimicrobial resistance. J Bacteriol 2024:e0012324. [PMID: 38869304 DOI: 10.1128/jb.00123-24] [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: 06/14/2024] Open
Abstract
Bacteria have developed diverse strategies for defending their cell envelopes from external threats. In Firmicutes, one widespread strategy is to use Bce modules-membrane protein complexes that unite a peptide-detoxifying ABC transporter with a stress response coordinating two-component system. These modules provide specific, front-line defense for a wide variety of antimicrobial peptides and small molecule antibiotics as well as coordinate responses for heat, acid, and oxidative stress. Because of these abilities, Bce modules play important roles in virulence and the development of antibiotic resistance in a variety of pathogens, including Staphylococcus, Streptococcus, and Enterococcus species. Despite their importance, Bce modules are still poorly understood, with scattered functional data in only a small number of species. In this review, we will discuss Bce module structure in light of recent cryo-electron microscopy structures of the B. subtilis BceABRS module and explore the common threads and variations-on-a-theme in Bce module mechanisms across species. We also highlight the many remaining questions about Bce module function. Understanding these multifunctional membrane complexes will enhance our understanding of bacterial stress sensing and may point toward new therapeutic targets for highly resistant pathogens.
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Affiliation(s)
- Natasha L George
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Ellen C Bennett
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Benjamin J Orlando
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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Cao R, Su H, Wei Z, He Z, Pan T, Li Y, Sun B. An induced mutation of ABC-transporter component VraF(K84E) contributes to vancomycin resistance and virulence in Staphylococcus aureus strain MW2. Int J Med Microbiol 2024; 315:151624. [PMID: 38838390 DOI: 10.1016/j.ijmm.2024.151624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024] Open
Abstract
Staphylococcus aureus is a notorious pathogen responsible for various severe diseases. Due to the emergence of drug-resistant strains, the prevention and treatment of S. aureus infections have become increasingly challenging. Vancomycin is considered to be one of the last-resort drugs for treating most methicillin-resistant S. aureus (MRSA), so it is of great significance to further reveal the mechanism of vancomycin resistance. VraFG is one of the few important ABC (ATP-binding cassette) transporters in S. aureus that can form TCS (two-component systems)/ABC transporter modules. ABC transporters can couple the energy released from ATP hydrolysis to translocate solutes across the cell membrane. In this study, we obtained a strain with decreased vancomycin susceptibility after serial passaging and selection. Subsequently, whole-genome sequencing was performed on this laboratory-derived strain MWA2 and a novel single point mutation was discovered in vraF gene, leading to decreased sensitivity to vancomycin and daptomycin. Furthermore, the mutation reduces autolysis of S. aureus and downregulates the expression of lytM, isaA, and atlA. Additionally, we observed that the mutant has a less net negative surface charge than wild-type strain. We also noted an increase in the expression of the dlt operon and mprF gene, which are associated with cell surface charge and serve to hinder the binding of cationic peptides by promoting electrostatic repulsion. Moreover, this mutation has been shown to enhance hemolytic activity, expand subcutaneous abscesses, reflecting an increased virulence. This study confirms the impact of a point mutation of VraF on S. aureus antibiotic resistance and virulence, contributing to a broader understanding of ABC transporter function and providing new targets for treating S. aureus infections.
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Affiliation(s)
- Ruobing Cao
- Institute of Advanced Technology, University of Science and Technology of China, Hefei, China
| | - Huimin Su
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Zichun Wei
- Institute of Advanced Technology, University of Science and Technology of China, Hefei, China
| | - Zhien He
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ting Pan
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yujie Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Baolin Sun
- Institute of Advanced Technology, University of Science and Technology of China, Hefei, China; Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
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3
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Liu X, Wang Y, Chang W, Dai Y, Ma X. AgrA directly binds to the promoter of vraSR and downregulates its expression in Staphylococcus aureus. Antimicrob Agents Chemother 2024; 68:e0089323. [PMID: 38259090 PMCID: PMC10916378 DOI: 10.1128/aac.00893-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Staphylococcus aureus is an important human pathogen and vancomycin is widely used for the treatment of S. aureus infections. The global regulator agr is known as a well-described virulence regulator. Previous studies have found that agr-dysfunction strains are more likely to develop into vancomycin-resistant strains, but the mechanism for this phenomenon remains unknown. VraSR is a two-component regulatory system related to vancomycin resistance. In this study, we found that the expression levels of vraR were higher in agr-dysfunction clinical strains than in the agr-functional strains. We knocked out agr in a clinical strain, and quantitative reverse transcription PCR and β-galactosidase activity assays revealed that agr repressed transcription of vraR. After vancomycin exposures, population analysis revealed larger subpopulations displaying reduced susceptibility in agr knockout strain compared with wild-type strain, and this pattern was also observed in agr-dysfunction clinical strains compared with the agr-functional strains. Electrophoretic mobility experiment demonstrated binding of purified AgrA to the promoter region of vraR. In conclusion, our results indicated that the loss of agr function in S. aureus may contribute to the evolution of reduced vancomycin susceptibility through the downregulation of vraSR.
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Affiliation(s)
- Xueer Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yangyan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Wenjiao Chang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuanyuan Dai
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaoling Ma
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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4
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Marcos-Fernández R, Sánchez B, Ruiz L, Margolles A. Convergence of flow cytometry and bacteriology. Current and future applications: a focus on food and clinical microbiology. Crit Rev Microbiol 2023; 49:556-577. [PMID: 35749433 DOI: 10.1080/1040841x.2022.2086035] [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: 07/19/2021] [Revised: 05/12/2022] [Accepted: 05/31/2022] [Indexed: 11/03/2022]
Abstract
Since its development in the 1960s, flow cytometry (FCM) was quickly revealed a powerful tool to analyse cell populations in medical studies, yet, for many years, was almost exclusively used to analyse eukaryotic cells. Instrument and methodological limitations to distinguish genuine bacterial signals from the background, among other limitations, have hampered FCM applications in bacteriology. In recent years, thanks to the continuous development of FCM instruments and methods with a higher discriminatory capacity to detect low-size particles, FCM has emerged as an appealing technique to advance the study of microbes, with important applications in research, clinical and industrial settings. The capacity to rapidly enumerate and classify individual bacterial cells based on viability facilitates the monitoring of bacterial presence in foodstuffs or clinical samples, reducing the time needed to detect contamination or infectious processes. Besides, FCM has stood out as a valuable tool to advance the study of complex microbial communities, or microbiomes, that are very relevant in the context of human health, as well as to understand the interaction of bacterial and host cells. This review highlights current developments in, and future applications of, FCM in bacteriology, with a focus on those related to food and clinical microbiology.
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Affiliation(s)
- Raquel Marcos-Fernández
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
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5
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De Gaetano GV, Lentini G, Famà A, Coppolino F, Beninati C. Antimicrobial Resistance: Two-Component Regulatory Systems and Multidrug Efflux Pumps. Antibiotics (Basel) 2023; 12:965. [PMID: 37370284 DOI: 10.3390/antibiotics12060965] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The number of multidrug-resistant bacteria is rapidly spreading worldwide. Among the various mechanisms determining resistance to antimicrobial agents, multidrug efflux pumps play a noteworthy role because they export extraneous and noxious substrates from the inside to the outside environment of the bacterial cell contributing to multidrug resistance (MDR) and, consequently, to the failure of anti-infective therapies. The expression of multidrug efflux pumps can be under the control of transcriptional regulators and two-component systems (TCS). TCS are a major mechanism by which microorganisms sense and reply to external and/or intramembrane stimuli by coordinating the expression of genes involved not only in pathogenic pathways but also in antibiotic resistance. In this review, we describe the influence of TCS on multidrug efflux pump expression and activity in some Gram-negative and Gram-positive bacteria. Taking into account the strict correlation between TCS and multidrug efflux pumps, the development of drugs targeting TCS, alone or together with already discovered efflux pump inhibitors, may represent a beneficial strategy to contribute to the fight against growing antibiotic resistance.
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Affiliation(s)
| | - Germana Lentini
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
| | - Agata Famà
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
| | - Francesco Coppolino
- Department of Biomedical, Dental and Imaging Sciences, University of Messina, 98124 Messina, Italy
| | - Concetta Beninati
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
- Scylla Biotech Srl, 98124 Messina, Italy
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Thomas P, Deming MA, Sarkar A. β-Lactamase Suppression as a Strategy to Target Methicillin-Resistant Staphylococcus aureus: Proof of Concept. ACS OMEGA 2022; 7:46213-46221. [PMID: 36570253 PMCID: PMC9773349 DOI: 10.1021/acsomega.2c04381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
β-Lactamase (penicillinase) renders early, natural β-lactams like penicillin G useless against methicillin-resistant Staphylococcus aureus (MRSA), which also expresses PBP2a, responsible for resistance to semisynthetic, penicillinase-insensitive β-lactams like oxacillin. Antimicrobial discovery is difficult, and resistance exists against most treatment options. Enhancing β-lactams against MRSA would revive its clinical utility. Most research on antimicrobial enhancement against MRSA focuses on oxacillin due to β-lactamase expression. Yet, Moreillon and others have demonstrated that penicillin G is as potent against a β-lactamase gene knockout strain, as vancomycin is against wild-type MRSA. Penicillin G overcame PBP2a because β-lactamase activity was blocked. Additionally, animals treated with a combination of direct β-lactamase inhibitors like sulbactam and clavulanate with penicillin G developed resistant infections, clearly demonstrating that direct inhibition of β-lactamase is not a good strategy. Here, we show that 50 μM pyrimidine-2-amines (P2As) reduce the minimum inhibitory concentration (MIC) of penicillin G against MRSA strains by up to 16-fold by reducing β-lactamase activity but not by direct inhibition of the enzyme. Oxacillin was not enhanced due to PBP2a expression, demonstrating the advantage of penicillin G over penicillinase-insensitive β-lactams. P2As modulate an unknown global regulator but not established antimicrobial-enhancement targets Stk1 and VraS. P2As are a practical implementation of Moreillon's principle of suppressing β-lactamase activity to make penicillin G useful against MRSA, without employing direct enzyme inhibitors.
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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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8
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Hare PJ, LaGree TJ, Byrd BA, DeMarco AM, Mok WWK. Single-Cell Technologies to Study Phenotypic Heterogeneity and Bacterial Persisters. Microorganisms 2021; 9:2277. [PMID: 34835403 PMCID: PMC8620850 DOI: 10.3390/microorganisms9112277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic persistence is a phenomenon in which rare cells of a clonal bacterial population can survive antibiotic doses that kill their kin, even though the entire population is genetically susceptible. With antibiotic treatment failure on the rise, there is growing interest in understanding the molecular mechanisms underlying bacterial phenotypic heterogeneity and antibiotic persistence. However, elucidating these rare cell states can be technically challenging. The advent of single-cell techniques has enabled us to observe and quantitatively investigate individual cells in complex, phenotypically heterogeneous populations. In this review, we will discuss current technologies for studying persister phenotypes, including fluorescent tags and biosensors used to elucidate cellular processes; advances in flow cytometry, mass spectrometry, Raman spectroscopy, and microfluidics that contribute high-throughput and high-content information; and next-generation sequencing for powerful insights into genetic and transcriptomic programs. We will further discuss existing knowledge gaps, cutting-edge technologies that can address them, and how advances in single-cell microbiology can potentially improve infectious disease treatment outcomes.
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Affiliation(s)
- Patricia J. Hare
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
- School of Dental Medicine, University of Connecticut, Farmington, CT 06032, USA
| | - Travis J. LaGree
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
| | - Brandon A. Byrd
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
- School of Medicine, University of Connecticut, Farmington, CT 06032, USA
| | - Angela M. DeMarco
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
| | - Wendy W. K. Mok
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
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Within-Host Adaptation of Staphylococcus aureus in a Bovine Mastitis Infection Is Associated with Increased Cytotoxicity. Int J Mol Sci 2021; 22:ijms22168840. [PMID: 34445550 PMCID: PMC8396210 DOI: 10.3390/ijms22168840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
Within-host adaptation is a typical feature of chronic, persistent Staphylococcus aureus infections. Research projects addressing adaptive changes due to bacterial in-host evolution increase our understanding of the pathogen’s strategies to survive and persist for a long time in various hosts such as human and bovine. In this study, we investigated the adaptive processes of S. aureus during chronic, persistent bovine mastitis using a previously isolated isogenic strain pair from a dairy cow with chronic, subclinical mastitis, in which the last variant (host-adapted, Sigma factor SigB-deficient) quickly replaced the initial, dominant variant. The strain pair was cultivated under specific in vitro infection-relevant growth-limiting conditions (iron-depleted RPMI under oxygen limitation). We used a combinatory approach of surfaceomics, molecular spectroscopic fingerprinting and in vitro phenotypic assays. Cellular cytotoxicity assays using red blood cells and bovine mammary epithelial cells (MAC-T) revealed changes towards a more cytotoxic phenotype in the host-adapted isolate with an increased alpha-hemolysin (α-toxin) secretion, suggesting an improved capacity to penetrate and disseminate the udder tissue. Our results foster the hypothesis that within-host evolved SigB-deficiency favours extracellular persistence in S. aureus infections. Here, we provide new insights into one possible adaptive strategy employed by S. aureus during chronic, bovine mastitis, and we emphasise the need to analyse genotype–phenotype associations under different infection-relevant growth conditions.
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Five major two components systems of Staphylococcus aureus for adaptation in diverse hostile environment. Microb Pathog 2021; 159:105119. [PMID: 34339796 DOI: 10.1016/j.micpath.2021.105119] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/21/2021] [Accepted: 07/28/2021] [Indexed: 11/21/2022]
Abstract
Staphylococcus aureus is an eminent and opportunistic human pathogen that can colonize in the intestines, skin tissue and perineal regions of the host and cause severe infectious diseases. The presence of complex regulatory network and existence of virulent gene expression along with tuning metabolism enables the S. aureus to adopt the diversity of environments. Two component system (TCS) is a widely distributed mechanism in S. aureus that permit it for changing gene expression profile in response of environment stimuli. TCS usually consist of transmembrane histidine kinase (HK) and cytosolic response regulator. S. aureus contains totally 16 conserved pairs of two component systems, involving in different signaling mechanisms. There is a connection among these regulatory circuits and they can easily have effect on each other's expression. This review has discussed five major types of TCS in S. aureus and covers the recent knowledge of their virulence gene expression. We can get more understanding towards staphylococcal pathogenicity by getting insights about gene regulatory pathways via TCS, which can further provide implications in vaccine formation and new ways for drug design to combat serious infections caused by S. aureus in humans.
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Wang W, Sun B. VraCP regulates cell wall metabolism and antibiotic resistance in vancomycin-intermediate Staphylococcus aureus strain Mu50. J Antimicrob Chemother 2021; 76:1712-1723. [PMID: 33948657 PMCID: PMC8212773 DOI: 10.1093/jac/dkab113] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/13/2021] [Indexed: 01/29/2023] Open
Abstract
Objectives Vancomycin-intermediate Staphylococcus aureus (VISA) is increasingly being reported. Previous studies have shown that vraC and vraP may be involved in vancomycin resistance, although the molecular mechanism remains elusive. Methods The vraC (SAV0577), vraP (SAV0578) and vraCP mutants were constructed in Mu50 by allelic replacement. Some common VISA phenotypes were assessed in mutants, such as, susceptibility to the cell wall-associated antibiotics, cell wall thickness, autolysis activity and growth rate. RT-qPCR was performed to reveal the differential genes associated with these phenotypes. The binding abilities of VraC and VraCP to the promoters of target genes were determined by electrophoretic mobility shift assay (EMSA). Results VraP forms a stable complex with VraC to preserve their own stability. The vraC, vraP and vraCP mutants exhibited increased susceptibility to the cell wall-associated antibiotics and thinner cell walls compared with the WT strain. Consistent with these phenotypes, RT-qPCR revealed downregulated transcription of glyS, sgtB, ddl and alr2, which are involved in cell wall biosynthesis. Moreover, the transcription of cell wall hydrolysis genes, including sceD, lytM and isaA, was significantly downregulated, supporting the finding that mutants exhibited reduced autolysis rates. EMSA confirmed that both VraC and VraCP can directly bind to the sceD, lytM and isaA promoter regions containing the consensus sequence (5′-TTGTAAN2AN3TGTAA-3′), which is crucial for the binding of VraCP with target genes. GFP-reporter assays further revealed VraC and VraCP can enhance promoter activity of sceD to positively regulate its expression. Conclusions vraCP plays a significant role in cell wall metabolism and antibiotic resistance in Mu50.
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Affiliation(s)
- Wanying Wang
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, People's Republic of China
| | - Baolin Sun
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, People's Republic of China
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Dekio I, Sugiura Y, Hamada-Tsutsumi S, Murakami Y, Tamura H, Suematsu M. What Do We See in Spectra?: Assignment of High-Intensity Peaks of Cutibacterium and Staphylococcus Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics. Microorganisms 2021; 9:microorganisms9061243. [PMID: 34201063 PMCID: PMC8227259 DOI: 10.3390/microorganisms9061243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
Matrix-assisted laser-desorption/ionization time-of-flight (MALDI–TOF) mass spectrometry is a widely used and reliable technology to identify microbial species and subspecies. The current methodology is based on spectral fingerprinting, analyzing protein peaks, most of which are yet to be characterized. In order to deepen the understanding of these peaks and to develop a more reasonable identification workflow, we applied proteogenomic approaches to assign the high-intensity peaks of MALDI–TOF spectra of two bacterial genera. First, the 3–22 kD proteomes of 5 Cutibacterium strains were profiled by UPLC–MS/MS, and the amino acid sequences were refined by referring to their genome in the public database. Then, the sequences were converted to m/z (x-axis) values based on their molecular masses. When the interspecies comparison of calculated m/z values was well-fitted to the observed peaks, the peak assignments for the five Cutibacterium species were confirmed. Second, the peak assignments for six Staphylococcus species were performed by using the above result for Cutibacterium and referring to ribosomal subunit proteins coded on the S10-spc-alpha operon (the S10-GERMS method), a previous proteomics report by Becher et al., and comprehensive genome analysis. We successfully assigned 13 out of 15 peaks for the Cutibacterium species and 11 out of 13 peaks for the Staphylococcus species. DNA-binding protein HU, the CsbD-like protein, and 50S ribosomal protein L7/L12 were observed in common. The commonality suggests they consist of high-intensity peaks in the MALDI spectra of other bacterial species. Our workflow may lead to the development of a more accurate species identification database of MALDI–TOF mass spectrometry based on genome data.
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Affiliation(s)
- Itaru Dekio
- Department of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (Y.S.); (M.S.)
- Correspondence: ; Tel.: +81-3-3433-1111 (ext. 3341); Fax: +81-3-5401-0125
| | - Yuki Sugiura
- Department of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (Y.S.); (M.S.)
| | - Susumu Hamada-Tsutsumi
- Department of Environmental Bioscience, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan; (S.H.-T.); (H.T.)
| | - Yoshiyuki Murakami
- Seikakai Mildix Skin Clinic, 3rd Floor, 3-98 Senju, Adachi-ku, Tokyo 120-0034, Japan;
| | - Hiroto Tamura
- Department of Environmental Bioscience, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan; (S.H.-T.); (H.T.)
| | - Makoto Suematsu
- Department of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (Y.S.); (M.S.)
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13
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Baseri N, Najar-Peerayeh S, Bakhshi B. The effect of subinhibitory concentration of chlorhexidine on the evolution of vancomycin-intermediate Staphylococcus aureus and the induction of mutations in walKR and vraTSR systems. INFECTION GENETICS AND EVOLUTION 2020; 87:104628. [PMID: 33171303 DOI: 10.1016/j.meegid.2020.104628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/08/2023]
Abstract
The molecular mechanism underlying the development of vancomycin-intermediate Staphylococcus aureus (VISA) remains unclear. The abuses of antibacterial compounds lead to a change in the bacterial susceptibility patterns. Therefore, we examined the effect of Chlorhexidine (CHX) on in vitro development of VISA and reported CHX-selected VISA mutant Tm1 with phenotypic features similar to the clinical VISA isolates. WalKR, VraTSR, and GraSR are the most common regulatory systems involved in VISA evaluation. The expression of these systems, as well as walKR-regulated autolysins and VraTSR-regulated cell wall stimulon, were compared, by RT-qPCR, between the mutant and parental strains. The results revealed the downregulation of walKR, vraTSR, atlA, sle1, lytM, and pbpB genes in Tm1. The complete sequences of walKR and vraTSR genes was compared using the Sanger sequencing method. We detected Walk.R55C, WalR.A38T, and VraS·N340-D347del novel mutations in Tm1. These mutations were classified as deleterious mutations and predicted to affect protein function using the SIFT prediction algorithm. Novel mutations in Tm1 confirm the genetic diversity of VISA isolates. We suggest that WalKR and VraTSR may be involved in sense and response to CHX. In this regard, CHX may have a role in cell wall degradation of S. aureus and the emergence of VISA due to mutations in the CA domain of the Walk and VraS and the REC domain of WalR. Therefore, CHX should be used with caution.
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Affiliation(s)
- Neda Baseri
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shahin Najar-Peerayeh
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Bita Bakhshi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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14
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Abstract
Bacteria are able to sense environmental conditions and respond accordingly. Their sensorial system relies on pairs of sensory and regulatory proteins, known as two-component systems (TCSs). The majority of bacteria contain dozens of TCSs, each of them responsible for sensing and responding to a different range of signals. Traditionally, the function of each TCS has been determined by analyzing the changes in gene expression caused by the absence of individual TCSs. Here, we used a bacterial strain deprived of the complete TC sensorial system to introduce, one by one, the active form of every TCS. This gain-of-function strategy allowed us to identify the changes in gene expression conferred by each TCS without interference of other members of the family. In bacteria, adaptation to changes in the environment is mainly controlled through two-component signal transduction systems (TCSs). Most bacteria contain dozens of TCSs, each of them responsible for sensing a different range of signals and controlling the expression of a repertoire of target genes (regulon). Over the years, identification of the regulon controlled by each individual TCS in different bacteria has been a recurrent question. However, limitations associated with the classical approaches used have left our knowledge far from complete. In this report, using a pioneering approach in which a strain devoid of the complete nonessential TCS network was systematically complemented with the constitutively active form of each response regulator, we have reconstituted the regulon of each TCS of S. aureus in the absence of interference between members of the family. Transcriptome sequencing (RNA-Seq) and proteomics allowed us to determine the size, complexity, and insulation of each regulon and to identify the genes regulated exclusively by one or many TCSs. This gain-of-function strategy provides the first description of the complete TCS regulon in a living cell, which we expect will be useful to understand the pathobiology of this important pathogen. IMPORTANCE Bacteria are able to sense environmental conditions and respond accordingly. Their sensorial system relies on pairs of sensory and regulatory proteins, known as two-component systems (TCSs). The majority of bacteria contain dozens of TCSs, each of them responsible for sensing and responding to a different range of signals. Traditionally, the function of each TCS has been determined by analyzing the changes in gene expression caused by the absence of individual TCSs. Here, we used a bacterial strain deprived of the complete TC sensorial system to introduce, one by one, the active form of every TCS. This gain-of-function strategy allowed us to identify the changes in gene expression conferred by each TCS without interference of other members of the family.
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15
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Baindara P, Ghosh AK, Mandal SM. Coevolution of Resistance Against Antimicrobial Peptides. Microb Drug Resist 2020; 26:880-899. [PMID: 32119634 DOI: 10.1089/mdr.2019.0291] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antimicrobial peptides (AMPs) are produced by all forms of life, ranging from eukaryotes to prokaryotes, and they are a crucial component of innate immunity, involved in clearing infection by inhibiting pathogen colonization. In the recent past, AMPs received high attention due to the increase of extensive antibiotic resistance by these pathogens. AMPs exhibit a diverse spectrum of activity against bacteria, fungi, parasites, and various types of cancer. AMPs are active against various bacterial pathogens that cause disease in animals and plants. However, because of the coevolution of host and pathogen interaction, bacteria have developed the mechanisms to sense and exhibit an adaptive response against AMPs. These resistance mechanisms are playing an important role in bacterial virulence within the host. Here, we have discussed the different resistance mechanisms used by gram-positive and gram-negative bacteria to sense and combat AMP actions. Understanding the mechanism of AMP resistance may provide directions toward the development of novel therapeutic strategies to control multidrug-resistant pathogens.
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Affiliation(s)
- Piyush Baindara
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Ananta K Ghosh
- Department of Biotechnology, Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Santi M Mandal
- Department of Biotechnology, Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, India
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16
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Ahmad A, Majaz S, Nouroz F. Two-component systems regulate ABC transporters in antimicrobial peptide production, immunity and resistance. Microbiology (Reading) 2020; 166:4-20. [DOI: 10.1099/mic.0.000823] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacteria offer resistance to a broad range of antibiotics by activating their export channels of ATP-binding cassette transporters. These transporters perform a central role in vital processes of self-immunity, antibiotic transport and resistance. The majority of ATP-binding cassette transporters are capable of detecting the presence of antibiotics in an external vicinity and are tightly regulated by two-component systems. The presence of an extracellular loop and an adjacent location of both the transporter and two-component system offers serious assistance to induce a quick and specific response against antibiotics. Both systems have demonstrated their ability of sensing such agents, however, the exact mechanism is not yet fully established. This review highlighted the three key functions of antibiotic resistance, transport and self-immunity of ATP-binding cassette transporters and an adjacent two-component regulatory system.
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Affiliation(s)
- Ashfaq Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Sidra Majaz
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Faisal Nouroz
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
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17
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Coe KA, Lee W, Stone MC, Komazin-Meredith G, Meredith TC, Grad YH, Walker S. Multi-strain Tn-Seq reveals common daptomycin resistance determinants in Staphylococcus aureus. PLoS Pathog 2019; 15:e1007862. [PMID: 31738809 PMCID: PMC6934316 DOI: 10.1371/journal.ppat.1007862] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 12/27/2019] [Accepted: 09/24/2019] [Indexed: 01/30/2023] Open
Abstract
Antibiotic-resistant Staphylococcus aureus remains a leading cause of antibiotic resistance-associated mortality in the United States. Given the reality of multi-drug resistant infections, it is imperative that we establish and maintain a pipeline of new compounds to replace or supplement our current antibiotics. A first step towards this goal is to prioritize targets by identifying the genes most consistently required for survival across the S. aureus phylogeny. Here we report the first direct comparison of multiple strains of S. aureus via transposon sequencing. We show that mutant fitness varies by strain in key pathways, underscoring the importance of using more than one strain to differentiate between core and strain-dependent essential genes. We treated the libraries with daptomycin to assess whether the strain-dependent differences impact pathways important for survival. Despite baseline differences in gene importance, several pathways, including the lipoteichoic acid pathway, consistently promote survival under daptomycin exposure, suggesting core vulnerabilities that can be exploited to resensitize daptomycin-nonsusceptible isolates. We also demonstrate the merit of using transposons with outward-facing promoters capable of overexpressing nearby genes for identifying clinically-relevant gain-of-function resistance mechanisms. Together, the daptomycin vulnerabilities and resistance mechanisms support a mode of action with wide-ranging effects on the cell envelope and cell division. This work adds to a growing body of literature demonstrating the nuanced insights gained by comparing Tn-Seq results across multiple bacterial strains. Antibiotic-resistant Staphylococcus aureus kills thousands of people every year in the United States alone. To stay ahead of the looming threat of multidrug-resistant infections, we must continue to develop new antibiotics and find ways to make our current repertoire of antibiotics more effective, including by finding pairs of compounds that perform best when administered together. In the age of next-generation sequencing, we can now use transposon sequencing to find potential targets for new antibiotics on a genome-wide scale, identified as either essential genes or genes that positively influence survival in the presence of an antibiotic. In this work, we created a compendium of genes that are essential across a range of S. aureus strains, as well as those that are important for growth in the presence of the antibiotic daptomycin. The results will be a resource for researchers working to develop the next generation of antibiotic therapies.
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Affiliation(s)
- Kathryn A. Coe
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Wonsik Lee
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Madeleine C. Stone
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gloria Komazin-Meredith
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
| | - Timothy C. Meredith
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- * E-mail: (TCM); (YHG); (SW)
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (TCM); (YHG); (SW)
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (TCM); (YHG); (SW)
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18
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Dall GF, Tsang STJ, Gwynne PJ, MacKenzie SP, Simpson AHRW, Breusch SJ, Gallagher MP. Unexpected synergistic and antagonistic antibiotic activity against Staphylococcus biofilms. J Antimicrob Chemother 2019; 73:1830-1840. [PMID: 29554250 DOI: 10.1093/jac/dky087] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/15/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives To evaluate putative anti-staphylococcal biofilm antibiotic combinations used in the management of periprosthetic joint infections (PJIs). Methods Using the dissolvable bead biofilm assay, the minimum biofilm eradication concentration (MBEC) was determined for the most commonly used antimicrobial agents and combination regimens against staphylococcal PJIs. The established fractional inhibitory concentration (FIC) index was modified to create the fractional biofilm eradication concentration (FBEC) index to evaluate synergism or antagonism between antibiotics. Results Only gentamicin (MBEC 64 mg/L) and daptomycin (MBEC 64 mg/L) were observed to be effective antistaphylococcal agents at clinically achievable concentrations. Supplementation of gentamicin with daptomycin, vancomycin or ciprofloxacin resulted in a similar or lower MBEC than gentamicin alone (FBEC index 0.25-2). Conversely, when rifampicin, clindamycin or linezolid was added to gentamicin, there was an increase in the MBEC of gentamicin relative to its use as a monotherapy (FBEC index 8-32). Conclusions This study found that gentamicin and daptomycin were the only effective single-agent antibiotics against established Staphylococcus biofilms. Interestingly the addition of a bacteriostatic antibiotic was found to antagonize the ability of gentamicin to eradicate Staphylococcus biofilms.
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Affiliation(s)
- G F Dall
- Department of Orthopaedic Surgery, Borders General Hospital, Huntlyburn, Melrose TD6 9BS, UK.,School of Biological Sciences, University of Edinburgh, Darwin Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK.,Department of Orthopaedic Surgery, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Old Dalkeith Road, Edinburgh EH16 4SB, UK
| | - S-T J Tsang
- School of Biological Sciences, University of Edinburgh, Darwin Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK.,Department of Orthopaedic Surgery, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Old Dalkeith Road, Edinburgh EH16 4SB, UK.,Department of Orthopaedic Surgery, Royal Infirmary of Edinburgh, 51 Little France Crescent, Old Dalkeith Road, Edinburgh EH16 4SA, UK
| | - P J Gwynne
- School of Biological Sciences, University of Edinburgh, Darwin Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - S P MacKenzie
- Department of Orthopaedic Surgery, Royal Infirmary of Edinburgh, 51 Little France Crescent, Old Dalkeith Road, Edinburgh EH16 4SA, UK
| | - A H R W Simpson
- Department of Orthopaedic Surgery, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Old Dalkeith Road, Edinburgh EH16 4SB, UK
| | - S J Breusch
- Department of Orthopaedic Surgery, Royal Infirmary of Edinburgh, 51 Little France Crescent, Old Dalkeith Road, Edinburgh EH16 4SA, UK
| | - M P Gallagher
- School of Biological Sciences, University of Edinburgh, Darwin Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
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19
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Role of the msaABCR Operon in Cell Wall Biosynthesis, Autolysis, Integrity, and Antibiotic Resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2019; 63:AAC.00680-19. [PMID: 31307991 DOI: 10.1128/aac.00680-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/10/2019] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is an important human pathogen in both community and health care settings. One of the challenges with S. aureus as a pathogen is its acquisition of antibiotic resistance. Previously, we showed that deletion of the msaABCR operon reduces cell wall thickness, resulting in decreased resistance to vancomycin in vancomycin-intermediate S. aureus (VISA). In this study, we investigated the nature of the cell wall defect in the msaABCR operon mutant in the Mu50 (VISA) and USA300 LAC methicillin-resistant Staphylococcus aureus (MRSA) strains. Results showed that msaABCR mutant cells had decreased cross-linking in both strains. This defect is typically due to increased murein hydrolase activity and/or nonspecific processing of murein hydrolases mediated by increased protease activity in mutant cells. The defect was enhanced by a decrease in teichoic acid content in the msaABCR mutant. Therefore, we propose that deletion of the msaABCR operon results in decreased peptidoglycan cross-linking, leading to increased susceptibility toward cell wall-targeting antibiotics, such as β-lactams and vancomycin. Moreover, we also observed significantly downregulated transcription of early cell wall-synthesizing genes, supporting the finding that msaABCR mutant cells have decreased peptidoglycan synthesis. More specifically, the msaABCR mutant in the USA300 LAC strain (MRSA) showed significantly reduced expression of the murA gene, whereas the msaABCR mutant in the Mu50 strain (VISA) showed significantly reduced expression of glmU, murA, and murD Thus, we conclude that the msaABCR operon controls the balance between cell wall synthesis and cell wall hydrolysis, which is required for maintaining a robust cell wall and acquiring resistance to cell wall-targeting antibiotics, such as vancomycin and the β-lactams.
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20
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Gao C, Dai Y, Chang W, Fang C, Wang Z, Ma X. VraSR has an important role in immune evasion of Staphylococcus aureus with low level vancomycin resistance. Microbes Infect 2019; 21:361-367. [PMID: 31009806 DOI: 10.1016/j.micinf.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 01/13/2023]
Abstract
Vancomycin-intermediate Staphylococcus aureus (VISA) and heterogeneous VISA (hVISA) are increasingly being reported as associated with treatment failure. Previous studies indicated that VISA/hVISA resists clearance by the host immune system, thereby allowing persistence within the host. VraSR is a vancomycin-resistance-associated sensor/regulator that is highly expressed in VISA/hVISA strains. Whether VraSR plays an important role in immune escape by VISA/hVISA strains is unclear. Here, we constructed a vraSR deletion mutant strain (ΔvraSR) and complementary strain (CΔvraSR) in Mu3 to investigate the effect of VraSR on S. aureus viability in polymorphonuclear leukocytes (PMNs). The ΔvraSR strain was more susceptible to phagocytosis by PMNs and reduced the ability of S. aureus to survive within PMNs. ΔvraSR showed phenotypic changes, including a thinner cell wall, reduced adhesion, and decreased biofilm-forming ability. Real-time quantitative PCR revealed that the transcript levels of cell wall synthesis-related genes (cap5K, cap5N, nanA, tagA, murD) and adhesion-associated genes (fnbA, fnbB, clfA, ebps, sbi) were significantly decreased in the ΔvraSR strain compared with Mu3. In summary, VraSR promotes the survival of S. aureus in the host, which may be associated with an increase in the thickness of the cell wall, adhesion, and biofilm formation.
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Affiliation(s)
- Caihong Gao
- Department of Laboratory Medicine, Affiliated Provincial Hospital of Anhui Medical University, Hefei 230001, Anhui, PR China
| | - Yuanyuan Dai
- Department of Laboratory Medicine, Affiliated Provincial Hospital of Anhui Medical University, Hefei 230001, Anhui, PR China
| | - Wenjiao Chang
- Department of Laboratory Medicine, Affiliated Provincial Hospital of Anhui Medical University, Hefei 230001, Anhui, PR China
| | - Chao Fang
- Department of Laboratory Medicine, Affiliated Provincial Hospital of Anhui Medical University, Hefei 230001, Anhui, PR China
| | - Ziran Wang
- Department of Laboratory Medicine, Affiliated Provincial Hospital of Anhui Medical University, Hefei 230001, Anhui, PR China
| | - Xiaoling Ma
- Department of Laboratory Medicine, Affiliated Provincial Hospital of Anhui Medical University, Hefei 230001, Anhui, PR China.
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21
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Yang Y, Luo M, Zhou H, Li C, Luk A, Zhao G, Fung K, Ip M. Role of Two-Component System Response Regulator bceR in the Antimicrobial Resistance, Virulence, Biofilm Formation, and Stress Response of Group B Streptococcus. Front Microbiol 2019; 10:10. [PMID: 30728810 PMCID: PMC6351488 DOI: 10.3389/fmicb.2019.00010] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/07/2019] [Indexed: 01/31/2023] Open
Abstract
Group B Streptococcus (GBS; Streptococcus agalactiae) is a leading cause of sepsis in neonates and pregnant mothers worldwide. Whereas the hyper-virulent serogroup III clonal cluster 17 has been associated with neonatal disease and meningitis, serogroup III ST283 was recently implicated in invasive disease among non-pregnant adults in Asia. Here, through comparative genome analyses of invasive and non-invasive ST283 strains, we identified a truncated DNA-binding regulator of a two-component system in a non-invasive strain that was homologous to Bacillus subtilis bceR, encoding the bceRSAB response regulator, which was conserved among GBS strains. Using isogenic knockout and complementation mutants of the ST283 strain, we demonstrated that resistance to bacitracin and the human antimicrobial peptide cathelicidin LL-37 was reduced in the ΔbceR strain with MICs changing from 64 and 256 μg/ml to 0.25 and 64 μg/ml, respectively. Further, the ATP-binding cassette transporter was upregulated by sub-inhibitory concentrations of bacitracin in the wild-type strain. Upregulation of dltA in the wild-type strain was also observed and thought to explain the increased resistance to antimicrobial peptides. DltA, an enzyme involved in D-alanylation during the synthesis of wall teichoic acids, which mediates reduced antimicrobial susceptibility, was previously shown to be regulated by the bceR-type regulator in Staphylococcus aureus. In a murine infection model, we found that the ΔbceR mutation significantly reduced the mortality rate compared to that with the wild-type strain (p < 0.01). Moreover, this mutant was more susceptible to oxidative stress compared to the wild-type strain (p < 0.001) and was associated with reduced biofilm formation (p < 0.0001). Based on 2-DGE and mass spectrometry, we showed that downregulation of alkyl hydroperoxide reductase (AhpC), a Gls24 family stress protein, and alcohol dehydrogenase (Adh) in the ΔbceR strain might explain the attenuated virulence and compromised stress response. Together, we showed for the first time that the bceR regulator in GBS plays an important role in bacitracin and antimicrobial peptide resistance, virulence, survival under oxidative stress, and biofilm formation.
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Affiliation(s)
- Ying Yang
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Mingjing Luo
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Haokui Zhou
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Carmen Li
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Alison Luk
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - GuoPing Zhao
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kitty Fung
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
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22
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Chen FJ, Lauderdale TL, Lee CH, Hsu YC, Huang IW, Hsu PC, Yang CS. Effect of a Point Mutation in mprF on Susceptibility to Daptomycin, Vancomycin, and Oxacillin in an MRSA Clinical Strain. Front Microbiol 2018; 9:1086. [PMID: 29887848 PMCID: PMC5980971 DOI: 10.3389/fmicb.2018.01086] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/07/2018] [Indexed: 12/22/2022] Open
Abstract
We previously reported the sequential recovery of daptomycin-nonsusceptible MRSA clinical isolates with an L431F substitution in the MprF protein. The aim of the present study is to determine the effect of this mutation by replacing the mprF gene on the chromosome of a daptomycin-susceptible progenitor strain, CGK5, to obtain CGK5mut having the L431F MprF mutation. Compared to CGK5, the daptomycin and vancomycin MICs of CGK5mut increased from 0.5 to 3 μg/ml and from 1.5 to 3 μg/ml, respectively; however, its oxacillin MIC decreased from 128 to 1 μg/ml in medium without added 2% NaCl. The expression levels of vraSR and several other cell-wall synthesis-related genes were significantly increased in CGK5mut, and the mutant also had significantly reduced negative cell membrane charge, thicker cell wall, and longer doubling time. These features were abolished in the reverse mutant carrying F431L MprF, confirming the pleiotropic effects of the L431F MprF mutation. We believe that this is the first work that shows a single MprF missense mutation can lead to not only changes in the cell membrane but also increased expression of vraSR and subsequently increased resistance to daptomycin and vancomycin while simultaneously conferring increased susceptibility to oxacillin in an isogenic MRSA strain.
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Affiliation(s)
- Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Tsai-Ling Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Chen-Hsiang Lee
- Division of Infectious Diseases, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Yu-Chieh Hsu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - I-Wen Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Pei-Chi Hsu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Chung-Shi Yang
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Zhunan, Taiwan
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23
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Lin LC, Chang SC, Ge MC, Liu TP, Lu JJ. Novel single-nucleotide variations associated with vancomycin resistance in vancomycin-intermediate Staphylococcus aureus. Infect Drug Resist 2018; 11:113-123. [PMID: 29403293 PMCID: PMC5783010 DOI: 10.2147/idr.s148335] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Prolonged vancomycin usage may cause methicillin-resistant Staphylococcus aureus to become vancomycin-intermediate S. aureus (VISA) and heterogeneous VISA (hVISA). Mechanisms of vancomycin resistance of VISA and hVISA are still unclear. In this study, analyses of nucleotide sequence variations in 30 vancomycin-sensitive S. aureus (VSSA), 41 hVISA and 16 VISA isolates revealed 29 single-nucleotide variations in 12 genes (fmtC, graR, graS, htrA, mecA, pbp2, pbp4, srtA, tcaA, upps, vicK and vraR) that are related to cell wall synthesis or the two-component system. Six of these 29 single-nucleotide variations were novel and resulted in the following amino acid changes: Q692E in FmtC; T278I, P306L and I311T in HtrA; and I63V and K101E in Upps. Since P306L and I311T in HtrA and I63V in Upps were present in the majority (76.7%–86.7%) of VSSA isolates, these three amino acid variations may not be associated with vancomycin resistance. The other three amino acid variations (T278I in HtrA, K101E in Upps and Q692E in FmtC) were present in the majority (87.5%–93.8%) of hVISA and VISA isolates, but only in a small number (22.9%–25.7%) of VSSA isolates, suggesting that they are associated with vancomycin resistance.
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Affiliation(s)
- Lee-Chung Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Shih-Cheng Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Mao-Cheng Ge
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Tsui-Ping Liu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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24
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Young BC, Wu CH, Gordon NC, Cole K, Price JR, Liu E, Sheppard AE, Perera S, Charlesworth J, Golubchik T, Iqbal Z, Bowden R, Massey RC, Paul J, Crook DW, Peto TE, Walker AS, Llewelyn MJ, Wyllie DH, Wilson DJ. Severe infections emerge from commensal bacteria by adaptive evolution. eLife 2017; 6. [PMID: 29256859 PMCID: PMC5736351 DOI: 10.7554/elife.30637] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/02/2017] [Indexed: 12/23/2022] Open
Abstract
Bacteria responsible for the greatest global mortality colonize the human microbiota far more frequently than they cause severe infections. Whether mutation and selection among commensal bacteria are associated with infection is unknown. We investigated de novo mutation in 1163 Staphylococcus aureus genomes from 105 infected patients with nose colonization. We report that 72% of infections emerged from the nose, with infecting and nose-colonizing bacteria showing parallel adaptive differences. We found 2.8-to-3.6-fold adaptive enrichments of protein-altering variants in genes responding to rsp, which regulates surface antigens and toxin production; agr, which regulates quorum-sensing, toxin production and abscess formation; and host-derived antimicrobial peptides. Adaptive mutations in pathogenesis-associated genes were 3.1-fold enriched in infecting but not nose-colonizing bacteria. None of these signatures were observed in healthy carriers nor at the species-level, suggesting infection-associated, short-term, within-host selection pressures. Our results show that signatures of spontaneous adaptive evolution are specifically associated with infection, raising new possibilities for diagnosis and treatment.
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Affiliation(s)
- Bernadette C Young
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Chieh-Hsi Wu
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom
| | - N Claire Gordon
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom
| | - Kevin Cole
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, United Kingdom
| | - James R Price
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, United Kingdom.,Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Elian Liu
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Anna E Sheppard
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,NIHR Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom
| | - Sanuki Perera
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Jane Charlesworth
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom
| | - Tanya Golubchik
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - John Paul
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Timothy E Peto
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Martin J Llewelyn
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, United Kingdom.,Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - David H Wyllie
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,Centre for Molecular and Cellular Physiology, Jenner Institute, Oxford, United Kingdom
| | - Daniel J Wilson
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.,Institute for Emerging Infections, Oxford Martin School, University of Oxford, Oxford, United Kingdom
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VraR Binding to the Promoter Region of agr Inhibits Its Function in Vancomycin-Intermediate Staphylococcus aureus (VISA) and Heterogeneous VISA. Antimicrob Agents Chemother 2017; 61:AAC.02740-16. [PMID: 28289032 DOI: 10.1128/aac.02740-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/04/2017] [Indexed: 11/20/2022] Open
Abstract
Acquisition of vancomycin resistance in Staphylococcus aureus is often accompanied by a reduction in virulence, but the mechanisms underlying this change remain unclear. The present study was undertaken to investigate this process in a clinical heterogeneous vancomycin-intermediate S. aureus (hVISA) strain, 10827; an hVISA reference strain, Mu3; and a VISA reference strain, Mu50, along with their respective series of vancomycin-induced resistant strains. In these strains, increasing MICs of vancomycin were associated with increased expression of the vancomycin resistance-associated regulator gene (vraR) and decreased expression of virulence genes (hla, hlb, and coa) and virulence-regulated genes (RNAIII, agrA, and saeR). These results suggested that VraR might have a direct or indirect effect on virulence in S. aureus In electrophoretic mobility shift assays, VraR did not bind to promoter sequences of hla, hlb, and coa genes, but it did bind to the agr promoter region. In DNase I footprinting assays, VraR protected a 15-nucleotide (nt) sequence in the intergenic region between the agr P2 and P3 promoters. These results indicated that when S. aureus is subject to induction by vancomycin, expression of vraR is upregulated, and VraR binding inhibits the function of the Agr quorum-sensing system, causing reductions in the virulence of VISA/hVISA strains. Our results suggested that VraR in S. aureus is involved not only in the regulation of vancomycin resistance but also in the regulation of virulence.
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Characterization of a vraG Mutant in a Genetically Stable Staphylococcus aureus Small-Colony Variant and Preliminary Assessment for Use as a Live-Attenuated Vaccine against Intrammamary Infections. PLoS One 2016; 11:e0166621. [PMID: 27855187 PMCID: PMC5113970 DOI: 10.1371/journal.pone.0166621] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 11/01/2016] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus is a leading cause of bovine intramammary infections (IMIs) that can evolve into difficult-to-treat chronic mastitis. To date, no vaccine formulation has shown high protective efficacy against S. aureus IMI, partly because this bacterium can efficiently evade the immune system. For instance, S. aureus small colony variants (SCVs) have intracellular abilities and can persist without producing invasive infections. As a first step towards the development of a live vaccine, this study describes the elaboration of a novel attenuated mutant of S. aureus taking advantage of the SCV phenotype. A genetically stable SCV was created through the deletion of the hemB gene, impairing its ability to adapt and revert to the invasive phenotype. Further attenuation was obtained through inactivation of gene vraG (SACOL0720) which we previously showed to be important for full virulence during bovine IMIs. After infection of bovine mammary epithelial cells (MAC-T), the double mutant (ΔvraGΔhemB) was less internalized and caused less cell destruction than that seen with ΔhemB and ΔvraG, respectively. In a murine IMI model, the ΔvraGΔhemB mutant was strongly attenuated, with a reduction of viable counts of up to 5-log10 CFU/g of mammary gland when compared to the parental strain. A complete clearance of ΔvraGΔhemB from glands was observed whereas mortality rapidly (48h) occurred with the wild-type strain. Immunization of mice using subcutaneous injections of live ΔvraGΔhemB raised a strong immune response as judged by the high total IgG titers measured against bacterial cell extracts and by the high IgG2a/IgG1 ratio observed against the IsdH protein. Also, ΔvraGΔhemB had sufficient common features with bovine mastitis strains so that the antibody response also strongly recognized strains from a variety of mastitis associated spa types. This double mutant could serve as a live-attenuated component in vaccines to improve cell-mediated immune responses against S. aureus IMIs.
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Tan XE, Neoh HM, Looi ML, Chin SF, Cui L, Hiramatsu K, Hussin S, Jamal R. Activated ADI pathway: the initiator of intermediate vancomycin resistance in Staphylococcus aureus. Can J Microbiol 2016; 63:260-264. [PMID: 28059579 DOI: 10.1139/cjm-2016-0439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Comparative proteomic profiling between 2 vancomycin-intermediate Staphylococcus aureus (VISA) strains, Mu50Ω-vraSm and Mu50Ω-vraSm-graRm, and vancomycin-susceptible S. aureus (VSSA) strain Mu50Ω revealed upregulated levels of catabolic ornithine carbamoyltransferase (ArcB) of the arginine catabolism pathway in VISA strains. Subsequent analyses showed that the VISA strains have higher levels of cellular ATP and ammonia, which are by-products of arginine catabolism, and displayed thicker cell walls. We postulate that elevated cytoplasmic ammonia and ATP molecules, resulting from activated arginine catabolism upon acquisition of vraS and graR mutations, are important requirements facilitating cell wall biosynthesis, thereby contributing to thickened cell wall and consequently reduced vancomycin susceptibility in VISA strains.
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Affiliation(s)
- Xin-Ee Tan
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| | - Hui-Min Neoh
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia.,b Department of Bacteriology, School of Medicine, Juntendo University, Japan
| | - Mee-Lee Looi
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia.,c Taylor's University Lakeside Campus, School of Biosciences, Malaysia
| | - Siok Fong Chin
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| | - Longzhu Cui
- d Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Japan
| | - Keiichi Hiramatsu
- b Department of Bacteriology, School of Medicine, Juntendo University, Japan
| | - Salasawati Hussin
- e Department of Medical Microbiology and Immunology, Universiti Kebangsaan Malaysia, Malaysia
| | - Rahman Jamal
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
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Hu Q, Peng H, Rao X. Molecular Events for Promotion of Vancomycin Resistance in Vancomycin Intermediate Staphylococcus aureus. Front Microbiol 2016; 7:1601. [PMID: 27790199 PMCID: PMC5062060 DOI: 10.3389/fmicb.2016.01601] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/26/2016] [Indexed: 12/14/2022] Open
Abstract
Vancomycin has been used as the last resort in the clinical treatment of serious Staphylococcus aureus infections. Vancomycin-intermediate S. aureus (VISA) was discovered almost two decades ago. Aside from the vancomycin-intermediate phenotype, VISA strains from the clinic or laboratory exhibited common characteristics, such as thickened cell walls, reduced autolysis, and attenuated virulence. However, the genetic mechanisms responsible for the reduced vancomycin susceptibility in VISA are varied. The comparative genomics of vancomycin-susceptible S. aureus (VSSA)/VISA pairs showed diverse genetic mutations in VISA; only a small number of these mutations have been experimentally verified. To connect the diversified genotypes and common phenotypes in VISA, we reviewed the genetic alterations in the relative determinants, including mutations in the vraTSR, graSR, walKR, stk1/stp1, rpoB, clpP, and cmk genes. Especially, we analyzed the mechanism through which diverse mutations mediate vancomycin resistance. We propose a unified model that integrates diverse gene functions and complex biochemical processes in VISA upon the action of vancomycin.
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Affiliation(s)
- Qiwen Hu
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University Chongqing, China
| | - Huagang Peng
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University Chongqing, China
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University Chongqing, China
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Kim JW, Kim HK, Kang GS, Kim IH, Kim HS, Lee YS, Yoo JI. The SAV1322 gene from Staphylococcus aureus: genomic and proteomic approaches to identification and characterization of gene function. BMC Microbiol 2016; 16:206. [PMID: 27599615 PMCID: PMC5013637 DOI: 10.1186/s12866-016-0824-2] [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: 08/12/2015] [Accepted: 08/29/2016] [Indexed: 11/18/2022] Open
Abstract
Background Bacterial two-component regulatory systems (TCRS) are associated with the expression of virulence factors and antibiotic susceptibility. In Staphylococcus aureus, 16 TCRS types have been identified. The histidine kinase/response regulator SAV1321/SAV1322 in the S. aureus shares considerable homology with the TCRS DesKR in Bacillus subtilis. However, a function for the SAV1322 locus has not yet been assigned. Results Deletion of the SAV1322 locus in S. aureus results in reduced growth when cultured under low (25 °C) and high (46 °C) temperature conditions. The sav1322 deletion mutant is more tolerant to oxidative stress in vitro and is less pathogenic in a murine infection model when compared with wild-type parent strain Mu50. Furthermore, the sav1322 mutant exhibits lower MICs for gentimicin, tetracyclines and glycopeptides, increased autolysis, and a thinner cell wall when compared with the wild-type strain. Microarray and proteomic analyses show that the expression of cell-wall-associated genes glmS and murZ are lower, and the expression of heat shock and stress-related genes (hrcA, ctsR, dnaK, dnaJ, grpE, clpB, and clpC) are higher in the sav1322 mutant when compared with the wild-type strain. In addition, the sav1322 mutant displays altered expression of proteins involved in carbohydrate/energy metabolism, cell wall metabolism, and stress or heat shock response, as well as other metabolic processes including lipid metabolism, amino acid biosynthesis, purine or pyrimidine metabolism, transcription, and protein biosynthesis. Conclusions The S. aureus SAV1322 locus plays a pronounced role in temperature adaptation, antibiotic resistance, and virulence by regulating a wide range of genes and proteins involved in metabolism and stress tolerance. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0824-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jung Wook Kim
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Centers for Disease Control and Prevention, Cheongju, South Korea
| | - Hyun-Kyung Kim
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Centers for Disease Control and Prevention, Cheongju, South Korea
| | - Gi Su Kang
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Centers for Disease Control and Prevention, Cheongju, South Korea
| | - Il-Hwan Kim
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Centers for Disease Control and Prevention, Cheongju, South Korea
| | - Hwa Su Kim
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Centers for Disease Control and Prevention, Cheongju, South Korea
| | - Yeong Seon Lee
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Centers for Disease Control and Prevention, Cheongju, South Korea
| | - Jae Il Yoo
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Centers for Disease Control and Prevention, Cheongju, South Korea. .,Korea National Research Institute of Health, Osong Health Technology Administration Complex, 187, Osongsaengmyeong2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 363-700, South Korea.
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Complete Reconstitution of the Vancomycin-Intermediate Staphylococcus aureus Phenotype of Strain Mu50 in Vancomycin-Susceptible S. aureus. Antimicrob Agents Chemother 2016; 60:3730-42. [PMID: 27067329 PMCID: PMC4879404 DOI: 10.1128/aac.00420-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/01/2016] [Indexed: 12/23/2022] Open
Abstract
Complete reconstitution of the vancomycin-intermediate Staphylococcus aureus (VISA) phenotype of strain Mu50 was achieved by sequentially introducing mutations into six genes of vancomycin-susceptible S. aureus (VSSA) strain N315ΔIP. The six mutated genes were detected in VISA strain Mu50 but not in N315ΔIP. Introduction of the mutation Ser329Leu into vraS, encoding the sensor histidine kinase of the vraSR two-component regulatory (TCR) system, and another mutation, Glu146Lys, into msrR, belonging to the LytR-CpsA-Psr (LCP) family, increased the level of vancomycin resistance to that detected in heterogeneous vancomycin-intermediate S. aureus (hVISA) strain Mu3. Introduction of two more mutations, Asn197Ser into graR of the graSR TCR system and His481Tyr into rpoB, encoding the β subunit of RNA polymerase, converted the hVISA strain into a VISA strain with the same level of vancomycin resistance as Mu50. Surprisingly, however, the constructed quadruple mutant strain ΔIP4 did not have a thickened cell wall, a cardinal feature of the VISA phenotype. Subsequent study showed that cell wall thickening was an inducible phenotype in the mutant strain, whereas it was a constitutive one in Mu50. Finally, introduction of the Ala297Val mutation into fdh2, which encodes a putative formate dehydrogenase, or a 67-amino-acid sequence deletion into sle1 [sle1(Δ67aa)], encoding the hydrolase of N-acetylmuramyl-l-alanine amidase in the peptidoglycan, converted inducible cell wall thickening into constitutive cell wall thickening. sle1(Δ67aa) was found to cause a drastic decrease in autolysis activity. Thus, all six mutated genes required for acquisition of the VISA phenotype were directly or indirectly involved in the regulation of cell physiology. The VISA phenotype seemed to be achieved through multiple genetic events accompanying drastic changes in cell physiology.
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Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates. Proteomes 2016; 4:proteomes4010011. [PMID: 28248221 PMCID: PMC5217363 DOI: 10.3390/proteomes4010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/05/2016] [Accepted: 03/01/2016] [Indexed: 01/20/2023] Open
Abstract
Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control.
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Rapid Detection of Vancomycin-Intermediate Staphylococcus aureus by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2016; 54:883-90. [PMID: 26763961 DOI: 10.1128/jcm.02428-15] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/04/2016] [Indexed: 12/16/2022] Open
Abstract
Vancomycin is the standard of care for the treatment of invasive methicillin-resistantStaphylococcus aureus(MRSA) infections. Infections with vancomycin-nonsusceptible MRSA, including vancomycin-intermediateS. aureus(VISA) and heterogeneous VISA (hVISA), are clinically challenging and are associated with poor patient outcomes. The identification of VISA in the clinical laboratory depends on standard susceptibility testing, which takes at least 24 h to complete after isolate subculture, whereas hVISA is not routinely detected in clinical labs. We therefore sought to determine whether VISA and hVISA can be differentiated from vancomycin-susceptibleS. aureus(VSSA) using the spectra produced by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Strains of MRSA were characterized for vancomycin susceptibility phenotype by broth microdilution and modified population analysis. We tested 21 VISA, 21 hVISA, and 38 VSSA isolates by MALDI-TOF MS. Susceptibility phenotypes were separated by using a support vector machine (SVM) machine learning algorithm. The resulting model was validated by leave-one-out cross validation. Models were developed and validated by using spectral profiles generated under various subculture conditions, as well as with and without hVISA strains. Using SVM, we correctly identified 100% of the VISA and 97% of the VSSA isolates with an overall classification accuracy of 98%. Addition of hVISA to the model resulted in 76% hVISA identification, 100% VISA identification, and 89% VSSA identification, for an overall classification accuracy of 89%. We conclude that VISA/hVISA and VSSA isolates are separable by MALDI-TOF MS with SVM analysis.
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RNAIII of the Staphylococcus aureus agr system activates global regulator MgrA by stabilizing mRNA. Proc Natl Acad Sci U S A 2015; 112:14036-41. [PMID: 26504242 DOI: 10.1073/pnas.1509251112] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNAIII, the effector of the agr quorum-sensing system, plays a key role in virulence gene regulation in Staphylococcus aureus, but how RNAIII transcriptionally regulates its downstream genes is not completely understood. Here, we show that RNAIII stabilizes mgrA mRNA, thereby increasing the production of MgrA, a global transcriptional regulator that affects the expression of many genes. The mgrA gene is transcribed from two promoters, P1 and P2, to produce two mRNA transcripts with long 5' UTR. Two adjacent regions of the mgrA mRNA UTR transcribed from the upstream P2 promoter, but not the P1 promoter, form a stable complex with two regions of RNAIII near the 5' and 3' ends. We further demonstrate that the interaction has several biological effects. We propose that MgrA can serve as an intermediary regulator through which agr exerts its regulatory function.
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Manuse S, Fleurie A, Zucchini L, Lesterlin C, Grangeasse C. Role of eukaryotic-like serine/threonine kinases in bacterial cell division and morphogenesis. FEMS Microbiol Rev 2015; 40:41-56. [DOI: 10.1093/femsre/fuv041] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2015] [Indexed: 11/14/2022] Open
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35
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Gene network analysis reveals the association of important functional partners involved in antibiotic resistance: A report on an important pathogenic bacterium Staphylococcus aureus. Gene 2015; 575:253-63. [PMID: 26342962 DOI: 10.1016/j.gene.2015.08.068] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/30/2015] [Accepted: 08/31/2015] [Indexed: 12/27/2022]
Abstract
Staphylococcus aureus (S. aureus) is an emerging concern in hospital settings as it causes serious human infections. The multidrug resistance (MDR) in S. aureus is a complicated problem that is difficult to overcome due to the presence of numerous antibiotic resistance genes and it exhibit resistance to most of the currently available antibiotics. Presently, the resistance mechanisms of these genes/proteins are not completely understood. Therefore, identifying and understanding the functional relationship between the antibiotic resistant genes and their associated proteins might provide necessary information on resistance mechanisms and thereby help in designing successful drugs to combat the antibiotic resistance. In this study, we propose a model based on protein/gene network to identify genes/proteins associated with drug resistance in S. aureus. We filtered 50 functional partners in NorA, aacA-aphD (aac6ie), aad9ib (ant), aadd (knt), baca (uppP), bl2a_pc (blaZ), ble, ermA, SAV0052 (ermb), ermc, fosB, mecA (mecI), mecR (mecr1), mepA, msrA1, qacA, vraR (str), tet38 and tetM while 40 functional partners are identified in tet and aphA-3 (aph3iiia). The average shortest path length and betweenness centrality of functional partners in the clusters are calculated and they are functionally enriched with the Gene Ontology (GO) terms with a p-value cut-off ≤0.05. Interestingly, the constructed network reveals many associated antibiotic resistant genes and proteins and their role in resistance mechanisms. Thus, our results might provide a better understanding of the molecular mechanisms of action and their mode of drug resistance that will be useful for researchers exploring in the field of antibiotic resistance mechanisms.
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Lee CR, Lee JH, Park KS, Jeong BC, Lee SH. Quantitative proteomic view associated with resistance to clinically important antibiotics in Gram-positive bacteria: a systematic review. Front Microbiol 2015; 6:828. [PMID: 26322035 PMCID: PMC4531251 DOI: 10.3389/fmicb.2015.00828] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/27/2015] [Indexed: 11/13/2022] Open
Abstract
The increase of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) poses a worldwide and serious health threat. Although new antibiotics, such as daptomycin and linezolid, have been developed for the treatment of infections of Gram-positive pathogens, the emergence of daptomycin-resistant and linezolid-resistant strains during therapy has now increased clinical treatment failures. In the past few years, studies using quantitative proteomic methods have provided a considerable progress in understanding antibiotic resistance mechanisms. In this review, to understand the resistance mechanisms to four clinically important antibiotics (methicillin, vancomycin, linezolid, and daptomycin) used in the treatment of Gram-positive pathogens, we summarize recent advances in studies on resistance mechanisms using quantitative proteomic methods, and also examine proteins playing an important role in the bacterial mechanisms of resistance to the four antibiotics. Proteomic researches can identify proteins whose expression levels are changed in the resistance mechanism to only one antibiotic, such as LiaH in daptomycin resistance and PrsA in vancomycin resistance, and many proteins simultaneously involved in resistance mechanisms to various antibiotics. Most of resistance-related proteins, which are simultaneously associated with resistance mechanisms to several antibiotics, play important roles in regulating bacterial envelope biogenesis, or compensating for the fitness cost of antibiotic resistance. Therefore, proteomic data confirm that antibiotic resistance requires the fitness cost and the bacterial envelope is an important factor in antibiotic resistance.
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Affiliation(s)
- Chang-Ro Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
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Abstract
The dramatic rise in the incidence of antibiotic resistance demands that new therapeutic options will have to be developed. One potentially interesting class of antimicrobials are the modified bacteriocins termed lantibiotics, which are bacterially produced, posttranslationally modified, lanthionine/methyllanthionine-containing peptides. It is interesting that low levels of resistance have been reported for lantibiotics compared with commercial antibiotics. Given that there are very few examples of naturally occurring lantibiotic resistance, attempts have been made to deliberately induce resistance phenotypes in order to investigate this phenomenon. Mechanisms that hinder the action of lantibiotics are often innate systems that react to the presence of any cationic peptides/proteins or ones which result from cell well damage, rather than being lantibiotic specific. Such resistance mechanisms often arise due to altered gene regulation following detection of antimicrobials/cell wall damage by sensory proteins at the membrane. This facilitates alterations to the cell wall or changes in the composition of the membrane. Other general forms of resistance include the formation of spores or biofilms, which are a common mechanistic response to many classes of antimicrobials. In rare cases, bacteria have been shown to possess specific antilantibiotic mechanisms. These are often species specific and include the nisin lytic protein nisinase and the phenomenon of immune mimicry.
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Affiliation(s)
- Lorraine A Draper
- School of Microbiology, University College Cork, Cork, Ireland Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Paul D Cotter
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - R Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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38
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A mutation of RNA polymerase β' subunit (RpoC) converts heterogeneously vancomycin-intermediate Staphylococcus aureus (hVISA) into "slow VISA". Antimicrob Agents Chemother 2015; 59:4215-25. [PMID: 25941225 DOI: 10.1128/aac.00135-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/28/2015] [Indexed: 12/13/2022] Open
Abstract
Various mutations in the rpoB gene, which encodes the RNA polymerase β subunit, are associated with increased vancomycin (VAN) resistance in vancomycin-intermediate Staphylococcus aureus (VISA) and heterogeneously VISA (hVISA) strains. We reported that rpoB mutations are also linked to the expression of the recently found "slow VISA" (sVISA) phenotype (M. Saito, Y. Katayama, T. Hishinuma, A. Iwamoto, Y. Aiba, K Kuwahara-Arai, L. Cui, M. Matsuo, N. Aritaka, and K. Hiramatsu, Antimicrob Agents Chemother 58:5024-5035, 2014, http://dx.doi.org/10.1128/AAC.02470-13). Because RpoC and RpoB are components of RNA polymerase, we examined the effect of the rpoC(P440L) mutation on the expression of the sVISA phenotype in the Mu3fdh2*V6-5 strain (V6-5), which was derived from a previously reported hVISA strain with the VISA phenotype. V6-5 had an extremely prolonged doubling time (DT) (72 min) and high vancomycin MIC (16 mg/liter). However, the phenotype of V6-5 was unstable, and the strain frequently reverted to hVISA with concomitant loss of low growth rate, cell wall thickness, and reduced autolysis. Whole-genome sequencing of phenotypic revertant strain V6-5-L1 and comparison with V6-5 revealed a second mutation, F562L, in rpoC. Introduction of the wild-type (WT) rpoC gene using a multicopy plasmid resolved the sVISA phenotype of V6-5, indicating that the rpoC(P440L) mutant expressed the sVISA phenotype in hVISA. To investigate the mechanisms of resistance in the sVISA strain, we independently isolated an additional 10 revertants to hVISA and VISA. In subsequent whole-genome analysis, we identified compensatory mutations in the genes of three distinct functional categories: the rpoC gene itself as regulatory mutations, peptidoglycan biosynthesis genes, and relQ, which is involved in the stringent response. It appears that the rpoC(P440L) mutation causes the sVISA phenotype by augmenting cell wall peptidoglycan synthesis and through the control of the stringent response.
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Santiago-Rodriguez TM, Naidu M, Jones MB, Ly M, Pride DT. Identification of staphylococcal phage with reduced transcription in human blood through transcriptome sequencing. Front Microbiol 2015; 6:216. [PMID: 26074882 PMCID: PMC4447126 DOI: 10.3389/fmicb.2015.00216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/03/2015] [Indexed: 12/29/2022] Open
Abstract
Many pathogenic bacteria have bacteriophage and other mobile genetic elements whose activity during human infections has not been evaluated. We investigated the gene expression patterns in human subjects with invasive Methicillin Resistant Staphylococcus aureus (MRSA) infections to determine the gene expression of bacteriophage and other mobile genetic elements. We developed an ex vivo technique that involved direct inoculation of blood from subjects with invasive bloodstream infections into culture media to reduce any potential laboratory adaptation. We compared ex vivo to in vitro profiles from 10 human subjects to determine MRSA gene expression in blood. Using RNA sequencing, we found that there were distinct and significant differences between ex vivo and in vitro MRSA gene expression profiles. Among the major differences between ex vivo and in vitro gene expression were virulence/disease/defense and mobile elements. While transposons were expressed at higher levels ex vivo, lysogenic bacteriophage had significantly higher in vitro expression. Five subjects had MRSA with bacteriophage that were inhibited by the presence of blood in the media, supporting that the lysogeny state was preferred in human blood. Some of the phage produced also had reduced infectivity, further supporting that phage were inhibited by blood. By comparing the gene expression cultured in media with and without the blood of patients, we gain insights into the specific adaptations made by MRSA and its bacteriophage to life in the human bloodstream.
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Affiliation(s)
| | - Mayuri Naidu
- Department of Pathology, University of California San Diego, CA, USA
| | | | - Melissa Ly
- Department of Pathology, University of California San Diego, CA, USA
| | - David T Pride
- Department of Pathology, University of California San Diego, CA, USA ; Department of Medicine, University of California San Diego, CA, USA
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Kononova LI, Korobov VP. Physiological properties of the vancomycin-resistant strain Staphylococcus epidermidis 33 GISK VANR. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715010063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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41
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Hattangady DS, Singh AK, Muthaiyan A, Jayaswal RK, Gustafson JE, Ulanov AV, Li Z, Wilkinson BJ, Pfeltz RF. Genomic, Transcriptomic and Metabolomic Studies of Two Well-Characterized, Laboratory-Derived Vancomycin-Intermediate Staphylococcus aureus Strains Derived from the Same Parent Strain. Antibiotics (Basel) 2015; 4:76-112. [PMID: 27025616 PMCID: PMC4790321 DOI: 10.3390/antibiotics4010076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 11/20/2014] [Accepted: 12/10/2014] [Indexed: 11/16/2022] Open
Abstract
Complete genome comparisons, transcriptomic and metabolomic studies were performed on two laboratory-selected, well-characterized vancomycin-intermediate Staphylococcus aureus (VISA) derived from the same parent MRSA that have changes in cell wall composition and decreased autolysis. A variety of mutations were found in the VISA, with more in strain 13136p(-)m⁺V20 (vancomycin MIC = 16 µg/mL) than strain 13136p(-)m⁺V5 (MIC = 8 µg/mL). Most of the mutations have not previously been associated with the VISA phenotype; some were associated with cell wall metabolism and many with stress responses, notably relating to DNA damage. The genomes and transcriptomes of the two VISA support the importance of gene expression regulation to the VISA phenotype. Similarities in overall transcriptomic and metabolomic data indicated that the VISA physiologic state includes elements of the stringent response, such as downregulation of protein and nucleotide synthesis, the pentose phosphate pathway and nutrient transport systems. Gene expression for secreted virulence determinants was generally downregulated, but was more variable for surface-associated virulence determinants, although capsule formation was clearly inhibited. The importance of activated stress response elements could be seen across all three analyses, as in the accumulation of osmoprotectant metabolites such as proline and glutamate. Concentrations of potential cell wall precursor amino acids and glucosamine were increased in the VISA strains. Polyamines were decreased in the VISA, which may facilitate the accrual of mutations. Overall, the studies confirm the wide variability in mutations and gene expression patterns that can lead to the VISA phenotype.
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Affiliation(s)
- Dipti S Hattangady
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | - Atul K Singh
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | - Arun Muthaiyan
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | | | - John E Gustafson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Alexander V Ulanov
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61807, USA.
| | - Zhong Li
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61807, USA.
| | - Brian J Wilkinson
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | - Richard F Pfeltz
- BD Diagnostic Systems, Microbiology Research and Development, Sparks, MD 21152, USA.
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42
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The Role of Two-Component Signal Transduction Systems in Staphylococcus aureus Virulence Regulation. Curr Top Microbiol Immunol 2015; 409:145-198. [PMID: 26728068 DOI: 10.1007/82_2015_5019] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Staphylococcus aureus is a versatile, opportunistic human pathogen that can asymptomatically colonize a human host but can also cause a variety of cutaneous and systemic infections. The ability of S. aureus to adapt to such diverse environments is reflected in the presence of complex regulatory networks fine-tuning metabolic and virulence gene expression. One of the most widely distributed mechanisms is the two-component signal transduction system (TCS) which allows a pathogen to alter its gene expression profile in response to environmental stimuli. The simpler TCSs consist of only a transmembrane histidine kinase (HK) and a cytosolic response regulator. S. aureus encodes a total of 16 conserved pairs of TCSs that are involved in diverse signalling cascades ranging from global virulence gene regulation (e.g. quorum sensing by the Agr system), the bacterial response to antimicrobial agents, cell wall metabolism, respiration and nutrient sensing. These regulatory circuits are often interconnected and affect each other's expression, thus fine-tuning staphylococcal gene regulation. This manuscript gives an overview of the current knowledge of staphylococcal environmental sensing by TCS and its influence on virulence gene expression and virulence itself. Understanding bacterial gene regulation by TCS can give major insights into staphylococcal pathogenicity and has important implications for knowledge-based drug design and vaccine formulation.
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43
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Hosseinkhan N, Zarrineh P, Masoudi-Nejad A. Analysis of Genome-scale Expression Network in Four Major Bacterial Residents of Cystic Fibrosis Lung. Curr Genomics 2014; 15:408-18. [PMID: 25435803 PMCID: PMC4245700 DOI: 10.2174/1389202915666140818205444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/06/2014] [Accepted: 08/15/2014] [Indexed: 11/22/2022] Open
Abstract
In polymicrobial communities where several species co-exist in a certain niche and consequently the possibility of interactions among species is very high, gene expression data sources can give better insights in to underlying adaptation mechanisms assumed by bacteria. Furthermore, several possible synergistic or antagonistic interactions among species can be investigated through gene expression comparisons. Lung is one of the habitats harboring several distinct pathogens during severe pulmonary disorders such as chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF). Expression data analysis of these lung residents can help to gain a better understanding on how these species interact with each other within the host cells. The first part of this paper deals with introducing available data sources for the major bacteria responsible for causing lung diseases and their genomic relations. In the second part, the main focus is on the studies concerning gene expression analyses of these species.
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Affiliation(s)
- Nazanin Hosseinkhan
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Peyman Zarrineh
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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44
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Hiramatsu K, Kayayama Y, Matsuo M, Aiba Y, Saito M, Hishinuma T, Iwamoto A. Vancomycin-intermediate resistance in Staphylococcus aureus. J Glob Antimicrob Resist 2014; 2:213-224. [DOI: 10.1016/j.jgar.2014.04.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/11/2014] [Accepted: 04/22/2014] [Indexed: 10/25/2022] Open
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45
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Muzamal U, Gomez D, Kapadia F, Golemi-Kotra D. Diversity of two-component systems: insights into the signal transduction mechanism by the Staphylococcus aureus two-component system GraSR. F1000Res 2014; 3:252. [PMID: 25685323 PMCID: PMC4314665 DOI: 10.12688/f1000research.5512.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/17/2014] [Indexed: 12/13/2022] Open
Abstract
The response to cationic antimicrobial peptides (CAMPs) in Staphylococcus aureus relies on a two-component system (TCS), GraSR, an auxiliary protein GraX and an ATP-binding cassette (ABC) transporter, VraF/G. To understand the signal transduction mechanism by GraSR, we investigated the kinase activity of the cytoplasmic domain of histidine kinase GraS and the interaction with its cognate response regulator GraR. We also investigated interactions among the auxiliary protein GraX, GraS/R and the ATPase protein of the ABC transporter, VraF. We found that GraS lacks autophosphorylation activity, unlike a similar histidine kinase, BceS, of Bacillus subtilis. In addition, the interaction between GraS and GraR is very weak in comparison to the stronger interaction observed between BceS and its conjugated response regulator, BceR, suggesting that CAMP signaling may not flow directly from GraS to GraR. We found that the auxiliary protein GraX interacts with VraF and GraR, and requires the histidine phosphotransfer and dimerization domain of GraS to interact with this protein. Further, VraF requires the GraS region that connects the membrane-bound domain with the cytoplasmic domain of this protein for interaction with GraS. The interactions of GraX with GraS/R and VraF indicate that GraX may serve as a scaffold to bring these proteins in close proximity to GraS, plausibly to facilitate activation of GraS to ultimately transduce the signal to GraR.
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Affiliation(s)
- Uzma Muzamal
- Departments of Biology, York University, Toronto, Toronto, ON, M3J 1P3, Canada
| | - Daniel Gomez
- Department of Chemistry, York University, Toronto, Toronto, ON, M3J 1P3, Canada
| | - Fenika Kapadia
- Departments of Biology, York University, Toronto, Toronto, ON, M3J 1P3, Canada
| | - Dasantila Golemi-Kotra
- Departments of Biology, York University, Toronto, Toronto, ON, M3J 1P3, Canada ; Department of Chemistry, York University, Toronto, Toronto, ON, M3J 1P3, Canada
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46
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Muzamal U, Gomez D, Kapadia F, Golemi-Kotra D. Diversity of two-component systems: insights into the signal transduction mechanism by the Staphylococcus aureus two-component system GraSR. F1000Res 2014; 3:252. [PMID: 25685323 DOI: 10.12688/f1000research.5512.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/21/2014] [Indexed: 11/20/2022] Open
Abstract
The response to cationic antimicrobial peptides (CAMPs) in Staphylococcus aureus relies on a two-component system (TCS), GraSR, an auxiliary protein GraX and an ATP-binding cassette (ABC) transporter, VraF/G. To understand the signal transduction mechanism by GraSR, we investigated the kinase activity of the cytoplasmic domain of histidine kinase GraS and the interaction with its cognate response regulator GraR. We also investigated interactions among the auxiliary protein GraX, GraS/R and the ATPase protein of the ABC transporter, VraF. We found that GraS lacks autophosphorylation activity, unlike a similar histidine kinase, BceS, of Bacillus subtilis. In addition, the interaction between GraS and GraR is very weak in comparison to the stronger interaction observed between BceS and its conjugated response regulator, BceR, suggesting that CAMP signaling may not flow directly from GraS to GraR. We found that the auxiliary protein GraX interacts with VraF and GraR, and requires the histidine phosphotransfer and dimerization domain of GraS to interact with this protein. Further, VraF requires the GraS region that connects the membrane-bound domain with the cytoplasmic domain of this protein for interaction with GraS. The interactions of GraX with GraS/R and VraF indicate that GraX may serve as a scaffold to bring these proteins in close proximity to GraS, plausibly to facilitate activation of GraS to ultimately transduce the signal to GraR.
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Affiliation(s)
- Uzma Muzamal
- Departments of Biology, York University, Toronto, Toronto, ON, M3J 1P3, Canada
| | - Daniel Gomez
- Department of Chemistry, York University, Toronto, Toronto, ON, M3J 1P3, Canada
| | - Fenika Kapadia
- Departments of Biology, York University, Toronto, Toronto, ON, M3J 1P3, Canada
| | - Dasantila Golemi-Kotra
- Departments of Biology, York University, Toronto, Toronto, ON, M3J 1P3, Canada ; Department of Chemistry, York University, Toronto, Toronto, ON, M3J 1P3, Canada
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47
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Applications of flow cytometry to characterize bacterial physiological responses. BIOMED RESEARCH INTERNATIONAL 2014; 2014:461941. [PMID: 25276788 PMCID: PMC4174974 DOI: 10.1155/2014/461941] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/13/2014] [Accepted: 08/13/2014] [Indexed: 12/30/2022]
Abstract
Although reports of flow cytometry (FCM) applied to bacterial analysis are increasing, studies of FCM related to human cells still vastly outnumber other reports. However, current advances in FCM combined with a new generation of cellular reporter probes have made this technique suitable for analyzing physiological responses in bacteria. We review how FCM has been applied to characterize distinct physiological conditions in bacteria including responses to antibiotics and other cytotoxic chemicals and physical factors, pathogen-host interactions, cell differentiation during biofilm formation, and the mechanisms governing development pathways such as sporulation. Since FCM is suitable for performing studies at the single-cell level, we describe how this powerful technique has yielded invaluable information about the heterogeneous distribution of differently and even specialized responding cells and how it may help to provide insights about how cell interaction takes place in complex structures, such as those that prevail in bacterial biofilms.
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48
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The msaABCR operon regulates resistance in vancomycin-intermediate Staphylococcus aureus strains. Antimicrob Agents Chemother 2014; 58:6685-95. [PMID: 25155591 DOI: 10.1128/aac.03280-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vancomycin-intermediate Staphylococcus aureus (VISA) strains present an increasingly difficult problem in terms of public health. However, the molecular mechanism for this resistance is not yet understood. In this study, we define the role of the msaABCR operon in vancomycin resistance in three clinical VISA strains, i.e., Mu50, HIP6297, and LIM2. Deletion of the msaABCR operon resulted in significant decreases in the vancomycin MIC (from 6.25 to 1.56 μg/ml) and significant reductions of cell wall thickness in strains Mu50 and HIP6297. Growth of the mutants in medium containing vancomycin at concentrations greater than 2 μg/ml resulted in decreases in the growth rate, compared with the wild-type strains. Mutation of the msaABCR operon also reduced the binding capacity for vancomycin. We conclude that the msaABCR operon contributes to resistance to vancomycin and cell wall synthesis in S. aureus.
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49
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Glycopeptide antibiotics: Back to the future. J Antibiot (Tokyo) 2014; 67:631-44. [DOI: 10.1038/ja.2014.111] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 12/22/2022]
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50
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Huang Q, Fei J, Yu HJ, Gou YB, Huang XK. Effects of human β-defensin-3 on biofilm formation‑regulating genes dltB and icaA in Staphylococcus aureus. Mol Med Rep 2014; 10:825-31. [PMID: 24913184 DOI: 10.3892/mmr.2014.2309] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 04/08/2014] [Indexed: 11/06/2022] Open
Abstract
An understanding of the regulatory mechanisms that drive Staphylococcus aureus biofilm formation may lead to the development of an effective strategy to control the increasing number of refractory clinical infections it causes. The present study examined the effects of the antimicrobial agent human β‑defensin 3 (hBD‑3) and the antibiotics vancomycin and clindamycin on the expression of the S. aureus biofilm formation‑regulating genes, icaA and dltB, during bacterial adhesion and biofilm formation. Transcription (mRNA) levels of dlt and ica genes were measured using quantitative polymerase chain reaction, and slimes of S. aureus biofilm were examined with confocal scanning laser microscopy during S. aureus adhesion and biofilm formation. Although hBD‑3, vancomycin and clindamycin led to significantly attenuated biofilm formation, their treatment‑associated effects on the mRNA expression of dlt and ica were not identical. Vancomycin and clindamycin induced sustained expression of the dlt and ica genes, which may be harnessed to induce biofilm formation. However, hBD‑3 did not have a significant affect on the transcription level of dltB during either bacterial adhesion or biofilm formation. Therefore, the mechanism of hBD‑3 that regulated the suppression of biofilm formation appears to differ from the mechanisms of vancomycin and clindamycin.
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Affiliation(s)
- Qiang Huang
- Trauma Center of Daping Hospital, Third Military Medical University, Chongqing 404100, P.R. China
| | - Jun Fei
- Trauma Center of Daping Hospital, Third Military Medical University, Chongqing 404100, P.R. China
| | - Hong-Jun Yu
- Rehabilitation Department, Southwest Hospital, Third Military Medical University, Chongqing 404100, P.R. China
| | - Yuan-Bin Gou
- Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 404100, P.R. China
| | - Xian-Kai Huang
- Trauma Center of Daping Hospital, Third Military Medical University, Chongqing 404100, P.R. China
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