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Cheng MJ, Wu YY, Zeng H, Zhang TH, Hu YX, Liu SY, Cui RQ, Hu CX, Zou QM, Li CC, Ye WC, Huang W, Wang L. Asymmetric total synthesis of polycyclic xanthenes and discovery of a WalK activator active against MRSA. Nat Commun 2024; 15:5879. [PMID: 38997253 PMCID: PMC11245619 DOI: 10.1038/s41467-024-49629-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 06/13/2024] [Indexed: 07/14/2024] Open
Abstract
The development of new antibiotics continues to pose challenges, particularly considering the growing threat of multidrug-resistant Staphylococcus aureus. Structurally diverse natural products provide a promising source of antibiotics. Herein, we outline a concise approach for the collective asymmetric total synthesis of polycyclic xanthene myrtucommulone D and five related congeners. The strategy involves rapid assembly of the challenging benzopyrano[2,3-a]xanthene core, highly diastereoselective establishment of three contiguous stereocenters through a retro-hemiketalization/double Michael cascade reaction, and a Mitsunobu-mediated chiral resolution approach with high optical purity and broad substrate scope. Quantum mechanical calculations provide insight into stereoselective construction mechanism of the three contiguous stereocenters. Additionally, this work leads to the discovery of an antibacterial agent against both drug-sensitive and drug-resistant S. aureus. This compound operates through a unique mechanism that promotes bacterial autolysis by activating the two-component sensory histidine kinase WalK. Our research holds potential for future antibacterial drug development.
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Affiliation(s)
- Min-Jing Cheng
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P. R. China
- Center for Bioactive Natural Molecules and Innovative Drugs, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China
| | - Yan-Yi Wu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P. R. China
- Center for Bioactive Natural Molecules and Innovative Drugs, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China
| | - Hao Zeng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, P. R. China
| | - Tian-Hong Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P. R. China
- Center for Bioactive Natural Molecules and Innovative Drugs, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China
| | - Yan-Xia Hu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P. R. China
- Center for Bioactive Natural Molecules and Innovative Drugs, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China
| | - Shi-Yi Liu
- Department of Medical Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, P. R. China
| | - Rui-Qin Cui
- Department of Medical Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, P. R. China
| | - Chun-Xia Hu
- Department of Medical Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, P. R. China
| | - Quan-Ming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, Chongqing, 400038, P. R. China.
| | - Chuang-Chuang Li
- Department of Chemistry, Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen, 518055, P. R. China.
| | - Wen-Cai Ye
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P. R. China.
- Center for Bioactive Natural Molecules and Innovative Drugs, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China.
| | - Wei Huang
- Department of Medical Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, P. R. China.
| | - Lei Wang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P. R. China.
- Center for Bioactive Natural Molecules and Innovative Drugs, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China.
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Freeman CD, Hansen T, Urbauer R, Wilkinson BJ, Singh VK, Hines KM. Defective pgsA contributes to increased membrane fluidity and cell wall thickening in Staphylococcus aureus with high-level daptomycin resistance. mSphere 2024; 9:e0011524. [PMID: 38752757 DOI: 10.1128/msphere.00115-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/17/2024] [Indexed: 05/28/2024] Open
Abstract
Daptomycin is a membrane-targeting last-resort antimicrobial therapeutic for the treatment of infections caused by methicillin- and/or vancomycin-resistant Staphylococcus aureus. In the rare event of failed daptomycin therapy, the source of resistance is often attributable to mutations directly within the membrane phospholipid biosynthetic pathway of S. aureus or in the regulatory systems that control cell envelope response and membrane homeostasis. Here we describe the structural changes to the cell envelope in a daptomycin-resistant isolate of S. aureus strain N315 that has acquired mutations in the genes most commonly reported associated with daptomycin resistance: mprF, yycG, and pgsA. In addition to the decreased phosphatidylglycerol (PG) levels that are the hallmark of daptomycin resistance, the mutant with high-level daptomycin resistance had increased branched-chain fatty acids (BCFAs) in its membrane lipids, increased membrane fluidity, and increased cell wall thickness. However, the successful utilization of isotope-labeled straight-chain fatty acids (SCFAs) in lipid synthesis suggested that the aberrant BCFA:SCFA ratio arose from upstream alteration in fatty acid synthesis rather than a structural preference in PgsA. Transcriptomics studies revealed that expression of pyruvate dehydrogenase (pdhB) was suppressed in the daptomycin-resistant isolate, which is known to increase BCFA levels. While complementation with an additional copy of pdhB had no effect, complementation of the pgsA mutation resulted in increased PG formation, reduction in cell wall thickness, restoration of normal BCFA levels, and increased daptomycin susceptibility. Collectively, these results demonstrate that pgsA contributes to daptomycin resistance through its influence on membrane fluidity and cell wall thickness, in addition to phosphatidylglycerol levels. IMPORTANCE The cationic lipopeptide antimicrobial daptomycin has become an essential tool for combating infections with Staphylococcus aureus that display reduced susceptibility to β-lactams or vancomycin. Since daptomycin's activity is based on interaction with the negatively charged membrane of S. aureus, routes to daptomycin-resistance occur through mutations in the lipid biosynthetic pathway surrounding phosphatidylglycerols and the regulatory systems that control cell envelope homeostasis. Therefore, there are many avenues to achieve daptomycin resistance and several different, and sometimes contradictory, phenotypes of daptomycin-resistant S. aureus, including both increased and decreased cell wall thickness and membrane fluidity. This study is significant because it demonstrates the unexpected influence of a lipid biosynthesis gene, pgsA, on membrane fluidity and cell wall thickness in S. aureus with high-level daptomycin resistance.
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Affiliation(s)
| | - Tayte Hansen
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, Missouri, USA
| | - Ramona Urbauer
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Brian J Wilkinson
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Vineet K Singh
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, Missouri, USA
| | - Kelly M Hines
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
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Fait A, Silva SF, Abrahamsson JÅH, Ingmer H. Staphylococcus aureus response and adaptation to vancomycin. Adv Microb Physiol 2024; 85:201-258. [PMID: 39059821 DOI: 10.1016/bs.ampbs.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Antibiotic resistance is an increasing challenge for the human pathogen Staphylococcus aureus. Methicillin-resistant S. aureus (MRSA) clones have spread globally, and a growing number display decreased susceptibility to vancomycin, the favoured antibiotic for treatment of MRSA infections. These vancomycin-intermediate S. aureus (VISA) or heterogeneous vancomycin-intermediate S. aureus (hVISA) strains arise from accumulation of a variety of point mutations, leading to cell wall thickening and reduced vancomycin binding to the cell wall building block, Lipid II, at the septum. They display only minor changes in vancomycin susceptibility, with varying tolerance between cells in a population, and therefore, they can be difficult to detect. In this review, we summarize current knowledge of VISA and hVISA. We discuss the role of genetic strain background or epistasis for VISA development and the possibility of strains being 'transient' VISA with gene expression changes mediated by, for example, VraTSR, GraXSR, or WalRK signal transduction systems, leading to temporary vancomycin tolerance. Additionally, we address collateral susceptibility to other antibiotics than vancomycin. Specifically, we estimate how mutations in rpoB, encoding the β-subunit of the RNA polymerase, affect overall protein structure and compare changes with rifampicin resistance. Ultimately, such in-depth analysis of VISA and hVISA strains in terms of genetic and transcriptional changes, as well as changes in protein structures, may pave the way for improved detection and guide antibiotic therapy by revealing strains at risk of VISA development. Such tools will be valuable for keeping vancomycin an asset also in the future.
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Affiliation(s)
- Anaëlle Fait
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark; Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Stephanie Fulaz Silva
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
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Hoffmann A, Steffens U, Maček B, Franz-Wachtel M, Nieselt K, Harbig TA, Scherlach K, Hertweck C, Sahl HG, Bierbaum G. The unusual mode of action of the polyketide glycoside antibiotic cervimycin C. mSphere 2024; 9:e0076423. [PMID: 38722162 PMCID: PMC11237698 DOI: 10.1128/msphere.00764-23] [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: 01/02/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
Cervimycins A-D are bis-glycosylated polyketide antibiotics produced by Streptomyces tendae HKI 0179 with bactericidal activity against Gram-positive bacteria. In this study, cervimycin C (CmC) treatment caused a spaghetti-like phenotype in Bacillus subtilis 168, with elongated curved cells, which stayed joined after cell division, and exhibited a chromosome segregation defect, resulting in ghost cells without DNA. Electron microscopy of CmC-treated Staphylococcus aureus (3 × MIC) revealed swollen cells, misshapen septa, cell wall thickening, and a rough cell wall surface. Incorporation tests in B. subtilis indicated an effect on DNA biosynthesis at high cervimycin concentrations. Indeed, artificial downregulation of the DNA gyrase subunit B gene (gyrB) increased the activity of cervimycin in agar diffusion tests, and, in high concentrations (starting at 62.5 × MIC), the antibiotic inhibited S. aureus DNA gyrase supercoiling activity in vitro. To obtain a more global view on the mode of action of CmC, transcriptomics and proteomics of cervimycin treated versus untreated S. aureus cells were performed. Interestingly, 3 × MIC of cervimycin did not induce characteristic responses, which would indicate disturbance of the DNA gyrase activity in vivo. Instead, cervimycin induced the expression of the CtsR/HrcA heat shock operon and the expression of autolysins, exhibiting similarity to the ribosome-targeting antibiotic gentamicin. In summary, we identified the DNA gyrase as a target, but at low concentrations, electron microscopy and omics data revealed a more complex mode of action of cervimycin, which comprised induction of the heat shock response, indicating protein stress in the cell.IMPORTANCEAntibiotic resistance of Gram-positive bacteria is an emerging problem in modern medicine, and new antibiotics with novel modes of action are urgently needed. Secondary metabolites from Streptomyces species are an important source of antibiotics, like the cervimycin complex produced by Streptomyces tendae HKI 0179. The phenotypic response of Bacillus subtilis and Staphylococcus aureus toward cervimycin C indicated a chromosome segregation and septum formation defect. This effect was at first attributed to an interaction between cervimycin C and the DNA gyrase. However, omics data of cervimycin treated versus untreated S. aureus cells indicated a different mode of action, because the stress response did not include the SOS response but resembled the response toward antibiotics that induce mistranslation or premature chain termination and cause protein stress. In summary, these results point toward a possibly novel mechanism that generates protein stress in the cells and subsequently leads to defects in cell and chromosome segregation.
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Affiliation(s)
- Alina Hoffmann
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| | - Ursula Steffens
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| | - Boris Maček
- University of Tübingen, Proteome Center Tübingen, Tübingen, Germany
| | | | - Kay Nieselt
- University of Tübingen, Interfaculty Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
| | - Theresa Anisja Harbig
- University of Tübingen, Interfaculty Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
- Friedrich Schiller University Jena, Institute of Microbiology, Faculty of Biological Sciences, Jena, Germany
| | - Hans-Georg Sahl
- University of Bonn, Institute for Pharmaceutical Microbiology, Bonn, Germany
| | - Gabriele Bierbaum
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
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Ahator SD, Hegstad K, Lentz CS, Johannessen M. Deciphering Staphylococcus aureus-host dynamics using dual activity-based protein profiling of ATP-interacting proteins. mSystems 2024; 9:e0017924. [PMID: 38656122 PMCID: PMC11097646 DOI: 10.1128/msystems.00179-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
The utilization of ATP within cells plays a fundamental role in cellular processes that are essential for the regulation of host-pathogen dynamics and the subsequent immune response. This study focuses on ATP-binding proteins to dissect the complex interplay between Staphylococcus aureus and human cells, particularly macrophages (THP-1) and keratinocytes (HaCaT), during an intracellular infection. A snapshot of the various protein activity and function is provided using a desthiobiotin-ATP probe, which targets ATP-interacting proteins. In S. aureus, we observe enrichment in pathways required for nutrient acquisition, biosynthesis and metabolism of amino acids, and energy metabolism when located inside human cells. Additionally, the direct profiling of the protein activity revealed specific adaptations of S. aureus to the keratinocytes and macrophages. Mapping the differentially activated proteins to biochemical pathways in the human cells with intracellular bacteria revealed cell-type-specific adaptations to bacterial challenges where THP-1 cells prioritized immune defenses, autophagic cell death, and inflammation. In contrast, HaCaT cells emphasized barrier integrity and immune activation. We also observe bacterial modulation of host processes and metabolic shifts. These findings offer valuable insights into the dynamics of S. aureus-host cell interactions, shedding light on modulating host immune responses to S. aureus, which could involve developing immunomodulatory therapies. IMPORTANCE This study uses a chemoproteomic approach to target active ATP-interacting proteins and examines the dynamic proteomic interactions between Staphylococcus aureus and human cell lines THP-1 and HaCaT. It uncovers the distinct responses of macrophages and keratinocytes during bacterial infection. S. aureus demonstrated a tailored response to the intracellular environment of each cell type and adaptation during exposure to professional and non-professional phagocytes. It also highlights strategies employed by S. aureus to persist within host cells. This study offers significant insights into the human cell response to S. aureus infection, illuminating the complex proteomic shifts that underlie the defense mechanisms of macrophages and keratinocytes. Notably, the study underscores the nuanced interplay between the host's metabolic reprogramming and immune strategy, suggesting potential therapeutic targets for enhancing host defense and inhibiting bacterial survival. The findings enhance our understanding of host-pathogen interactions and can inform the development of targeted therapies against S. aureus infections.
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Affiliation(s)
- Stephen Dela Ahator
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Christian S. Lentz
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Mona Johannessen
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
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Zhou C, Pawline MB, Pironti A, Morales SM, Perault AI, Ulrich RJ, Podkowik M, Lejeune A, DuMont A, Stubbe FX, Korman A, Jones DR, Schluter J, Richardson AR, Fey PD, Drlica K, Cadwell K, Torres VJ, Shopsin B. Microbiota and metabolic adaptation shape Staphylococcus aureus virulence and antimicrobial resistance during intestinal colonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.593044. [PMID: 38766195 PMCID: PMC11100824 DOI: 10.1101/2024.05.11.593044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Depletion of microbiota increases susceptibility to gastrointestinal colonization and subsequent infection by opportunistic pathogens such as methicillin-resistant Staphylococcus aureus (MRSA). How the absence of gut microbiota impacts the evolution of MRSA is unknown. The present report used germ-free mice to investigate the evolutionary dynamics of MRSA in the absence of gut microbiota. Through genomic analyses and competition assays, we found that MRSA adapts to the microbiota-free gut through sequential genetic mutations and structural changes that enhance fitness. Initially, these adaptations increase carbohydrate transport; subsequently, evolutionary pathways largely diverge to enhance either arginine metabolism or cell wall biosynthesis. Increased fitness in arginine pathway mutants depended on arginine catabolic genes, especially nos and arcC, which promote microaerobic respiration and ATP generation, respectively. Thus, arginine adaptation likely improves redox balance and energy production in the oxygen-limited gut environment. Findings were supported by human gut metagenomic analyses, which suggest the influence of arginine metabolism on colonization. Surprisingly, these adaptive genetic changes often reduced MRSA's antimicrobial resistance and virulence. Furthermore, resistance mutation, typically associated with decreased virulence, also reduced colonization fitness, indicating evolutionary trade-offs among these traits. The presence of normal microbiota inhibited these adaptations, preserving MRSA's wild-type characteristics that effectively balance virulence, resistance, and colonization fitness. The results highlight the protective role of gut microbiota in preserving a balance of key MRSA traits for long-term ecological success in commensal populations, underscoring the potential consequences on MRSA's survival and fitness during and after host hospitalization and antimicrobial treatment.
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Affiliation(s)
- Chunyi Zhou
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Miranda B. Pawline
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alejandro Pironti
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
- Microbial Computational Genomic Core Lab, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sabrina M. Morales
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Andrew I. Perault
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Robert J. Ulrich
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Magdalena Podkowik
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alannah Lejeune
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ashley DuMont
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | | | - Aryeh Korman
- Metabolomics Core Resource Laboratory, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Drew R. Jones
- Metabolomics Core Resource Laboratory, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jonas Schluter
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Anthony R. Richardson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Karl Drlica
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07102, USA
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07102, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine, New York, NY 10016, USA
| | - Victor J. Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Bo Shopsin
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
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Ali L, Abdel Aziz MH. Crosstalk involving two-component systems in Staphylococcus aureus signaling networks. J Bacteriol 2024; 206:e0041823. [PMID: 38456702 PMCID: PMC11025333 DOI: 10.1128/jb.00418-23] [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] [Indexed: 03/09/2024] Open
Abstract
Staphylococcus aureus poses a serious global threat to human health due to its pathogenic nature, adaptation to environmental stress, high virulence, and the prevalence of antimicrobial resistance. The signaling network in S. aureus coordinates and integrates various internal and external inputs and stimuli to adapt and formulate a response to the environment. Two-component systems (TCSs) of S. aureus play a central role in this network where surface-expressed histidine kinases (HKs) receive and relay external signals to their cognate response regulators (RRs). Despite the purported high fidelity of signaling, crosstalk within TCSs, between HK and non-cognate RR, and between TCSs and other systems has been detected widely in bacteria. The examples of crosstalk in S. aureus are very limited, and there needs to be more understanding of its molecular recognition mechanisms, although some crosstalk can be inferred from similar bacterial systems that share structural similarities. Understanding the cellular processes mediated by this crosstalk and how it alters signaling, especially under stress conditions, may help decipher the emergence of antibiotic resistance. This review highlights examples of signaling crosstalk in bacteria in general and S. aureus in particular, as well as the effect of TCS mutations on signaling and crosstalk.
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Affiliation(s)
- Liaqat Ali
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - May H. Abdel Aziz
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
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Freeman CD, Hansen T, Urbauer R, Wilkinson BJ, Singh VK, Hines KM. Defective pgsA contributes to increased membrane fluidity and cell wall thickening in S. aureus with high-level daptomycin resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.11.536441. [PMID: 37090586 PMCID: PMC10120677 DOI: 10.1101/2023.04.11.536441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Daptomycin is a membrane-targeting last-resort antimicrobial therapeutic for the treatment of infections caused by methicillin- and/or vancomycin-resistant Staphylococcus aureus. In the rare event of failed daptomycin therapy, the source of resistance is often attributable to mutations directly within the membrane phospholipid biosynthetic pathway of S. aureus or in the regulatory systems that control cell envelope response and membrane homeostasis. Here we describe the structural changes to the cell envelope in a daptomycin-resistant isolate of S. aureus strain N315 that has acquired mutations in the genes most commonly reported associated with daptomycin-resistance: mprF, yycG, and pgsA. In addition to the decreased phosphatidylglycerol (PG) levels that are the hallmark of daptomycin-resistance, the mutant with high-level daptomycin resistance had increased branched-chain fatty acids (BCFAs) in its membrane lipids, increased membrane fluidity, and increased cell wall thickness. However, the successful utilization of isotope-labeled straight-chain fatty acids (SCFAs) in lipid synthesis suggested that the aberrant BCFA:SCFA ratio arose from upstream alteration in fatty acid synthesis rather than a structural preference in PgsA. RT-qPCR studies revealed that expression of pyruvate dehydrogenase (pdhB) was suppressed in the daptomycin-resistant isolate, which is known to increase BCFA levels. While complementation with an additional copy of pdhB had no effect, complementation of the pgsA mutation resulted in increased PG formation, reduction in cell wall thickness, restoration of normal BCFA levels, and increased daptomycin susceptibility. Collectively, these results demonstrate that pgsA contributes to daptomycin resistance through its influence on membrane fluidity and cell wall thickness, in addition to phosphatidylglycerol levels.
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Affiliation(s)
| | - Tayte Hansen
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, MO, USA
| | - Ramona Urbauer
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Brian J. Wilkinson
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Vineet K. Singh
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, MO, USA
| | - Kelly M. Hines
- Department of Chemistry, University of Georgia, Athens, GA, USA
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9
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Wu W, Pang CNI, Mediati DG, Tree JJ. The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin-tolerant Staphylococcus aureus. mSystems 2024; 9:e0097123. [PMID: 38534138 PMCID: PMC11019875 DOI: 10.1128/msystems.00971-23] [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: 09/11/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Small RNAs have been found to control a broad range of bacterial phenotypes including tolerance to antibiotics. Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance is poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. At steady-state, protein and mRNA abundances are often highly correlated and lower than expected protein abundance may indicate translational repression of an mRNA. To identify sRNA-mRNA interactions that regulate mRNA translation, we examined the correlation between gene transcript abundance, ribosome occupancy, and protein levels. We used the machine learning technique self-organizing maps (SOMs) to cluster genes with similar transcription and translation patterns and identified a cluster of mRNAs that appeared to be post-transcriptionally repressed. By integrating our clustering with sRNA-mRNA interactome data generated in vancomycin-tolerant S. aureus by RNase III-CLASH, we identified sRNAs that may be mediating translational repression. We have confirmed sRNA-dependant post-transcriptional repression of several mRNAs in this cluster. Two of these interactions are mediated by RsaOI, a sRNA that is highly upregulated by vancomycin. We demonstrate the regulation of HPr and the cell-wall autolysin Atl. These findings suggest that RsaOI coordinates carbon metabolism and cell wall turnover during vancomycin treatment. IMPORTANCE The emergence of multidrug-resistant Staphylococcus aureus (MRSA) is a major public health concern. Current treatment is dependent on the efficacy of last-line antibiotics like vancomycin. The most common cause of vancomycin treatment failure is strains with intermediate resistance or tolerance that arise through the acqusition of a diverse repertoire of point mutations. These strains have been shown to altered small RNA (sRNA) expression in response to antibiotic treatment. Here, we have used a technique termed RNase III-CLASH to capture sRNA interactions with their target mRNAs. To understand the function of these interactions, we have looked at RNA and protein abundance for mRNAs targeted by sRNAs. Messenger RNA and protein levels are generally well correlated and we use deviations from this correlation to infer post-transcriptional regulation and the function of individual sRNA-mRNA interactions. Using this approach we identify mRNA targets of the vancomycin-induced sRNA, RsaOI, that are repressed at the translational level. We find that RsaOI represses the cell wall autolysis Atl and carbon transporter HPr suggestion a link between vancomycin treatment and suppression of cell wall turnover and carbon metabolism.
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Affiliation(s)
- Winton Wu
- School of Biotechnology and Biomolecular Sciences, Sydney, New South Wales, Australia
| | | | - Daniel G. Mediati
- School of Biotechnology and Biomolecular Sciences, Sydney, New South Wales, Australia
| | - Jai Justin Tree
- School of Biotechnology and Biomolecular Sciences, Sydney, New South Wales, Australia
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10
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Moreira L, Guimarães NM, Santos RS, Loureiro JA, Pereira MC, Azevedo NF. Promising strategies employing nucleic acids as antimicrobial drugs. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102122. [PMID: 38333674 PMCID: PMC10850860 DOI: 10.1016/j.omtn.2024.102122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Antimicrobial resistance (AMR) is a growing concern because it causes microorganisms to develop resistance to drugs commonly used to treat infections. This results in increased difficulty in treating infections, leading to higher mortality rates and significant economic effects. Investing in new antimicrobial agents is, therefore, necessary to prevent and control AMR. Antimicrobial nucleic acids have arisen as potential key players in novel therapies for AMR infections. They have been designed to serve as antimicrobials and to act as adjuvants to conventional antibiotics or to inhibit virulent mechanisms. This new category of antimicrobial drugs consists of antisense oligonucleotides and oligomers, DNAzymes, and transcription factor decoys, differing in terms of structure, target molecules, and mechanisms of action. They are synthesized using nucleic acid analogs to enhance their resistance to nucleases. Because bacterial envelopes are generally impermeable to oligonucleotides, delivery into the cytoplasm typically requires the assistance of nanocarriers, which can affect their therapeutic potency. Given that numerous factors contribute to the success of these antimicrobial drugs, this review aims to provide a summary of the key advancements in the use of oligonucleotides for treating bacterial infections. Their mechanisms of action and the impact of factors such as nucleic acid design, target sequence, and nanocarriers on the antimicrobial potency are discussed.
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Affiliation(s)
- Luís Moreira
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nuno M. Guimarães
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Rita S. Santos
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Joana A. Loureiro
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Maria C. Pereira
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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11
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Mattos-Graner RO, Klein MI, Alves LA. The complement system as a key modulator of the oral microbiome in health and disease. Crit Rev Microbiol 2024; 50:138-167. [PMID: 36622855 DOI: 10.1080/1040841x.2022.2163614] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/10/2023]
Abstract
In this review, we address the interplay between the complement system and host microbiomes in health and disease, focussing on oral bacteria known to contribute to homeostasis or to promote dysbiosis associated with dental caries and periodontal diseases. Host proteins modulating complement activities in the oral environment and expression profiles of complement proteins in oral tissues were described. In addition, we highlight a sub-set of bacterial proteins involved in complement evasion and/or dysregulation previously characterized in pathogenic species (or strains), but further conserved among prototypical commensal species of the oral microbiome. Potential roles of these proteins in host-microbiome homeostasis and in the emergence of commensal strain lineages with increased virulence were also addressed. Finally, we provide examples of how commensal bacteria might exploit the complement system in competitive or cooperative interactions within the complex microbial communities of oral biofilms. These issues highlight the need for studies investigating the effects of the complement system on bacterial behaviour and competitiveness during their complex interactions within oral and extra-oral host sites.
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Affiliation(s)
- Renata O Mattos-Graner
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Sao Paulo, Brazil
| | - Marlise I Klein
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Sao Paulo, Brazil
| | - Lívia Araújo Alves
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Sao Paulo, Brazil
- School of Dentistry, Cruzeiro do Sul University (UNICSUL), Sao Paulo, Brazil
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12
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Crozier D, Gray JM, Maltas JA, Bonomo RA, Burke ZDC, Card KJ, Scott JG. The evolution of diverse antimicrobial responses in vancomycin-intermediate Staphylococcus aureus and its therapeutic implications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.30.569373. [PMID: 38077036 PMCID: PMC10705500 DOI: 10.1101/2023.11.30.569373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Staphylococcus aureus causes endocarditis, osteomyelitis, and bacteremia. Clinicians often prescribe vancomycin as an empiric therapy to account for methicillin-resistant S. aureus (MRSA) and narrow treatment based on culture susceptibility results. However, these results reflect a single time point before empiric treatment and represent a limited subset of the total bacterial population within the patient. Thus, while they may indicate that the infection is susceptible to a particular drug, this recommendation may no longer be accurate during therapy. Here, we addressed how antibiotic susceptibility changes over time by accounting for evolution. We evolved 18 methicillin-susceptible S. aureus (MSSA) populations under increasing vancomycin concentrations until they reached intermediate resistance levels. Sequencing revealed parallel mutations that affect cell membrane stress response and cell-wall biosynthesis. The populations exhibited repeated cross-resistance to daptomycin and varied responses to meropenem, gentamicin, and nafcillin. We accounted for this variability by deriving likelihood estimates that express a population's probability of exhibiting a drug response following vancomycin treatment. Our results suggest antistaphylococcal penicillins are preferable first-line treatments for MSSA infections but also highlight the inherent uncertainty that evolution poses to effective therapies. Infections may take varied evolutionary paths; therefore, considering evolution as a probabilistic process should inform our therapeutic choices.
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13
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Jiang JH, Cameron DR, Nethercott C, Aires-de-Sousa M, Peleg AY. Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages. Clin Microbiol Rev 2023; 36:e0014822. [PMID: 37982596 PMCID: PMC10732075 DOI: 10.1128/cmr.00148-22] [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] [Indexed: 11/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of severe and often fatal infections. MRSA epidemics have occurred in waves, whereby a previously successful lineage has been replaced by a more fit and better adapted lineage. Selection pressures in both hospital and community settings are not uniform across the globe, which has resulted in geographically distinct epidemiology. This review focuses on the mechanisms that trigger the establishment and maintenance of current, dominant MRSA lineages across the globe. While the important role of antibiotic resistance will be mentioned throughout, factors which influence the capacity of S. aureus to colonize and cause disease within a host will be the primary focus of this review. We show that while MRSA possesses a diverse arsenal of toxins including alpha-toxin, the success of a lineage involves more than just producing toxins that damage the host. Success is often attributed to the acquisition or loss of genetic elements involved in colonization and niche adaptation such as the arginine catabolic mobile element, as well as the activity of regulatory systems, and shift metabolism accordingly (e.g., the accessory genome regulator, agr). Understanding exactly how specific MRSA clones cause prolonged epidemics may reveal targets for therapies, whereby both core (e.g., the alpha toxin) and acquired virulence factors (e.g., the Panton-Valentine leukocidin) may be nullified using anti-virulence strategies.
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Affiliation(s)
- Jhih-Hang Jiang
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - David R. Cameron
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Cara Nethercott
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Marta Aires-de-Sousa
- Laboratory of Molecular Genetics, Institutode Tecnologia Químicae Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
- Escola Superior de Saúde da Cruz Vermelha Portuguesa-Lisboa (ESSCVP-Lisboa), Lisbon, Portugal
| | - Anton Y. Peleg
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton, Melbourne, Victoria, Australia
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14
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Kang YR, Chung DR, Ko JH, Huh K, Cho SY, Kang CI, Peck KR. Genetic alterations in methicillin-susceptible Staphylococcus aureus associated with high vancomycin minimum inhibitory concentration. Int J Antimicrob Agents 2023; 62:106971. [PMID: 37716577 DOI: 10.1016/j.ijantimicag.2023.106971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/21/2023] [Accepted: 09/09/2023] [Indexed: 09/18/2023]
Abstract
BACKGROUND There are many reports on gene mutations observed in methicillin-resistant Staphylococcus aureus (MRSA) showing reduced susceptibility to vancomycin. However, there are limited studies on the genetic alterations that contribute to high vancomycin minimum inhibitory concentrations (MICs) in methicillin-susceptible S. aureus (MSSA). This study aimed to compare MSSA strains with high vancomycin MICs with those with low MICs, and to identify specific genetic alterations associated with increased vancomycin MICs. METHODS In total, 124 MSSA strains were analysed, with 62 having vancomycin MICs of 1-2 mg/L (MS-HV) and the remaining 62 having MICs <1 mg/L (MS-LV) as control. Polymerase chain reaction amplification and sequencing were conducted to identify point mutations and amino acid changes in the vraSR, graRS and walRK operons and rpoB gene. The number of single nucleotide polymorphisms (SNPs) and specific mutations in the indicated gene were compared between the two groups. RESULTS The MS-HV strains had a significantly higher median number of SNPs in studied genes than the MS-LV strains (5 vs 3; P < 0.0001), with higher frequency of SNPs in the graR and walK genes. The MS-HV strains also displayed a significantly higher prevalence of specific mutations in the graR gene (V135I, I136V and V136I) compared with the MS-LV strains. The odds of having a high vancomycin MIC was 5.54 times higher in strains with a mutation in the graR gene, and 5.32 times higher in strains with a mutation in the walK gene, compared with those without these mutations. CONCLUSIONS Mutations in the graR and walK genes may contribute to reduced vancomycin susceptibility in MSSA. This study gives key insights into the mechanisms underlying this phenomenon.
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Affiliation(s)
- Yu Ri Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Asia Pacific Foundation for Infectious Diseases, Seoul, Republic of Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Asia Pacific Foundation for Infectious Diseases, Seoul, Republic of Korea; Centre for Infection Prevention and Control, Samsung Medical Centre, Seoul, Republic of Korea.
| | - Jae-Hoon Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Asia Pacific Foundation for Infectious Diseases, Seoul, Republic of Korea
| | - Sun Young Cho
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Centre for Infection Prevention and Control, Samsung Medical Centre, Seoul, Republic of Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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15
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Zhang R, Ashford NK, Li A, Ross DH, Werth BJ, Xu L. High-throughput analysis of lipidomic phenotypes of methicillin-resistant Staphylococcus aureus by coupling in situ 96-well cultivation and HILIC-ion mobility-mass spectrometry. Anal Bioanal Chem 2023; 415:6191-6199. [PMID: 37535099 PMCID: PMC11059195 DOI: 10.1007/s00216-023-04890-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
Antimicrobial resistance is a major threat to human health as resistant pathogens spread globally, and the development of new antimicrobials is slow. Since many antimicrobials function by targeting cell wall and membrane components, high-throughput lipidomics for bacterial phenotyping is of high interest for researchers to unveil lipid-mediated pathways when dealing with a large number of lab-selected or clinical strains. However, current practice for lipidomic analysis requires the cultivation of bacteria on a large scale, which does not replicate the growth conditions for high-throughput bioassays that are normally carried out in 96-well plates, such as susceptibility tests, growth curve measurements, and biofilm quantitation. Analysis of bacteria grown under the same condition as other bioassays would better inform the differences in susceptibility and other biological metrics. In this work, a high-throughput method for cultivation and lipidomic analysis of antimicrobial-resistant bacteria was developed for standard 96-well plates exemplified by methicillin-resistant Staphylococcus aureus (MRSA). By combining a 30-mm liquid chromatography (LC) column with ion mobility (IM) separation, elution time could be dramatically shortened to 3.6 min for a single LC run without losing major lipid features. Peak capacity was largely rescued by the addition of the IM dimension. Through multi-linear calibration, the deviation of retention time can be limited to within 5%, making database-based automatic lipid identification feasible. This high-throughput method was further validated by characterizing the lipidomic phenotypes of antimicrobial-resistant mutants derived from the MRSA strain, W308, grown in a 96-well plate.
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Affiliation(s)
- Rutan Zhang
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Nate K Ashford
- Department of Pharmacy, University of Washington, Seattle, WA, 98195, USA
| | - Amy Li
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Dylan H Ross
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, WA, 99352, Richland, USA
| | - Brian J Werth
- Department of Pharmacy, University of Washington, Seattle, WA, 98195, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA.
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16
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Giulieri SG, Guérillot R, Holmes NE, Baines SL, Hachani A, Hayes AS, Daniel DS, Seemann T, Davis JS, Van Hal S, Tong SYC, Stinear TP, Howden BP. A statistical genomics framework to trace bacterial genomic predictors of clinical outcomes in Staphylococcus aureus bacteremia. Cell Rep 2023; 42:113069. [PMID: 37703880 DOI: 10.1016/j.celrep.2023.113069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 06/29/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023] Open
Abstract
Outcomes of severe bacterial infections are determined by the interplay between host, pathogen, and treatments. While human genomics has provided insights into host factors impacting Staphylococcus aureus infections, comparatively little is known about S. aureus genotypes and disease severity. Building on the hypothesis that bacterial pathoadaptation is a key outcome driver, we developed a genome-wide association study (GWAS) framework to identify adaptive mutations associated with treatment failure and mortality in S. aureus bacteremia (1,358 episodes). Our research highlights the potential of vancomycin-selected mutations and vancomycin minimum inhibitory concentration (MIC) as key explanatory variables to predict infection severity. The contribution of bacterial variation was much lower for clinical outcomes (heritability <5%); however, GWASs allowed us to identify additional, MIC-independent candidate pathogenesis loci. Using supervised machine learning, we were able to quantify the predictive potential of these adaptive signatures. Our statistical genomics framework provides a powerful means to capture adaptive mutations impacting severe bacterial infections.
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Affiliation(s)
- Stefano G Giulieri
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia.
| | - Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Natasha E Holmes
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Ashleigh S Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Diane S Daniel
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Joshua S Davis
- Department of Infectious Diseases, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia; Menzies School of Health Research, Charles Darwin University, Casuarina, NT 0810, Australia
| | - Sebastiaan Van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia
| | - Steven Y C Tong
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
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17
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Gómez-Arrebola C, Hernandez SB, Culp EJ, Wright GD, Solano C, Cava F, Lasa I. Staphylococcus aureus susceptibility to complestatin and corbomycin depends on the VraSR two-component system. Microbiol Spectr 2023; 11:e0037023. [PMID: 37646518 PMCID: PMC10581084 DOI: 10.1128/spectrum.00370-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/30/2023] [Indexed: 09/01/2023] Open
Abstract
The overuse of antibiotics in humans and livestock has driven the emergence and spread of antimicrobial resistance and has therefore prompted research on the discovery of novel antibiotics. Complestatin (Cm) and corbomycin (Cb) are glycopeptide antibiotics with an unprecedented mechanism of action that is active even against methicillin-resistant and daptomycin-resistant Staphylococcus aureus. They bind to peptidoglycan and block the activity of peptidoglycan hydrolases required for remodeling the cell wall during growth. Bacterial signaling through two-component transduction systems (TCSs) has been associated with the development of S. aureus antimicrobial resistance. However, the role of TCSs in S. aureus susceptibility to Cm and Cb has not been previously addressed. In this study, we determined that, among all 16 S. aureus TCSs, VraSR is the only one controlling the susceptibility to Cm and Cb. Deletion of vraSR increased bacterial susceptibility to both antibiotics. Epistasis analysis with members of the vraSR regulon revealed that deletion of spdC, which encodes a membrane protein that scaffolds SagB for cleavage of peptidoglycan strands to achieve physiological length, in the vraSR mutant restored Cm and Cb susceptibility to wild-type levels. Moreover, deletion of either spdC or sagB in the wild-type strain increased resistance to both antibiotics. Further analyses revealed a significant rise in the relative amount of peptidoglycan and its total degree of cross-linkage in ΔspdC and ΔsagB mutants compared to the wild-type strain, suggesting that these changes in the cell wall provide resistance to the damaging effect of Cm and Cb. IMPORTANCE Although Staphylococcus aureus is a common colonizer of the skin and digestive tract of humans and many animals, it is also a versatile pathogen responsible for causing a wide variety and number of infections. Treatment of these infections requires the bacteria to be constantly exposed to antibiotic treatment, which facilitates the selection of antibiotic-resistant strains. The development of new antibiotics is, therefore, urgently needed. In this paper, we investigated the role of the sensory system of S. aureus in susceptibility to two new antibiotics: corbomycin and complestatin. The results shed light on the cell-wall synthesis processes that are affected by the presence of the antibiotic and the sensory system responsible for coordinating their activity.
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Affiliation(s)
- Carmen Gómez-Arrebola
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Sara B. Hernandez
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Elizabeth J. Culp
- Department of Biochemistry and Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Gerard D. Wright
- Department of Biochemistry and Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Cristina Solano
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Felipe Cava
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
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18
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Fait A, Andersson DI, Ingmer H. Evolutionary history of Staphylococcus aureus influences antibiotic resistance evolution. Curr Biol 2023; 33:3389-3397.e5. [PMID: 37494936 DOI: 10.1016/j.cub.2023.06.082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/05/2023] [Accepted: 06/29/2023] [Indexed: 07/28/2023]
Abstract
Antibiotic resistance often confers a fitness cost to the resistant cell and thus raises key questions of how resistance is maintained in the absence of antibiotics and, if lost, whether cells are genetically primed for re-evolving resistance. To address these questions, we have examined vancomycin-intermediate Staphylococcus aureus (VISA) strains that arise during vancomycin therapy. VISA strains harbor a broad spectrum of mutations, and they are known to be unstable both in patients and in the laboratory. Here, we show that loss of resistance in VISA strains is correlated with a fitness increase and is attributed to adaptive mutations, leaving the initial VISA-adaptive mutations intact. Importantly, upon a second exposure to vancomycin, such revertants evolve significantly faster to become VISA, and they reach higher resistance levels than vancomycin-naive cells. Further, we find that sub-lethal concentrations of vancomycin stabilize the VISA phenotype, as do the human β-defensin 3 (hBD-3) and the bacteriocin nisin that both, like vancomycin, bind to the peptidoglycan building block, lipid II. Thus, factors binding lipid II may stabilize VISA both in vivo and in vitro, and in case resistance is lost, mutations remain that predispose to resistance development. These findings may explain why VISA infections often are re-occurring and suggest that previous vancomycin adaptation should be considered a risk factor when deciding on antimicrobial chemotherapy.
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Affiliation(s)
- Anaëlle Fait
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark.
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19
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Ganesan N, Mishra B, Felix L, Mylonakis E. Antimicrobial Peptides and Small Molecules Targeting the Cell Membrane of Staphylococcus aureus. Microbiol Mol Biol Rev 2023; 87:e0003722. [PMID: 37129495 PMCID: PMC10304793 DOI: 10.1128/mmbr.00037-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Clinical management of Staphylococcus aureus infections presents a challenge due to the high incidence, considerable virulence, and emergence of drug resistance mechanisms. The treatment of drug-resistant strains, such as methicillin-resistant S. aureus (MRSA), is further complicated by the development of tolerance and persistence to antimicrobial agents in clinical use. To address these challenges, membrane disruptors, that are not generally considered during drug discovery for agents against S. aureus, should be explored. The cell membrane protects S. aureus from external stresses and antimicrobial agents, but membrane-targeting antimicrobial agents are probably less likely to promote bacterial resistance. Nontypical linear cationic antimicrobial peptides (AMPs), highly modified AMPs such as daptomycin (lipopeptide), bacitracin (cyclic peptide), and gramicidin S (cyclic peptide), are currently in clinical use. Recent studies have demonstrated that AMPs and small molecules can penetrate the cell membrane of S. aureus, inhibit phospholipid biosynthesis, or block the passage of solutes between the periplasm and the exterior of the cell. In addition to their primary mechanism of action (MOA) that targets the bacterial membrane, AMPs and small molecules may also impact bacteria through secondary mechanisms such as targeting the biofilm, and downregulating virulence genes of S. aureus. In this review, we discuss the current state of research into cell membrane-targeting AMPs and small molecules and their potential mechanisms of action against drug-resistant physiological forms of S. aureus, including persister cells and biofilms.
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Affiliation(s)
- Narchonai Ganesan
- Infectious Diseases Division, Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Biswajit Mishra
- Infectious Diseases Division, Alpert Medical School, Brown University, Providence, Rhode Island, USA
- Department of Medicine, The Miriam Hospital, Providence, Rhode Island, USA
| | - LewisOscar Felix
- Infectious Diseases Division, Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Eleftherios Mylonakis
- Infectious Diseases Division, Alpert Medical School, Brown University, Providence, Rhode Island, USA
- Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
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20
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Liu C, Zhang H, Peng X, Blackledge MS, Furlani RE, Li H, Su Z, Melander RJ, Melander C, Michalek S, Wu H. Small Molecule Attenuates Bacterial Virulence by Targeting Conserved Response Regulator. mBio 2023; 14:e0013723. [PMID: 37074183 PMCID: PMC10294662 DOI: 10.1128/mbio.00137-23] [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: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 04/20/2023] Open
Abstract
Antibiotic tolerance within a biofilm community presents a serious public health challenge. Here, we report the identification of a 2-aminoimidazole derivative that inhibits biofilm formation by two pathogenic Gram-positive bacteria, Streptococcus mutans and Staphylococcus aureus. In S. mutans, the compound binds to VicR, a key response regulator, at the N-terminal receiver domain, and concurrently inhibits expression of vicR and VicR-regulated genes, including the genes that encode the key biofilm matrix producing enzymes, Gtfs. The compound inhibits S. aureus biofilm formation via binding to a Staphylococcal VicR homolog. In addition, the inhibitor effectively attenuates S. mutans virulence in a rat model of dental caries. As the compound targets bacterial biofilms and virulence through a conserved transcriptional factor, it represents a promising new class of anti-infective agents that can be explored to prevent or treat a host of bacterial infections. IMPORTANCE Antibiotic resistance is a major public health issue due to the growing lack of effective anti-infective therapeutics. New alternatives to treat and prevent biofilm-driven microbial infections, which exhibit high tolerance to clinically available antibiotics, are urgently needed. We report the identification of a small molecule that inhibits biofilm formation by two important pathogenic Gram-positive bacteria, Streptococcus mutans and Staphylococcus aureus. The small molecule selectively targets a transcriptional regulator leading to attenuation of a biofilm regulatory cascade and concurrent reduction of bacterial virulence in vivo. As the regulator is highly conserved, the finding has broad implication for the development of antivirulence therapeutics that selectively target biofilms.
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Affiliation(s)
- Chang Liu
- Department of Pediatric Dentistry, University of Alabama at Birmingham Schools of Dentistry and Medicine, Birmingham, Alabama, USA
- Department of Microbiology, University of Alabama at Birmingham Schools of Dentistry and Medicine, Birmingham, Alabama, USA
| | - Hua Zhang
- Department of Pediatric Dentistry, University of Alabama at Birmingham Schools of Dentistry and Medicine, Birmingham, Alabama, USA
- Department of Integrative Biomedical & Diagnostic Sciences, Oregon Health & Science University School of Dentistry, Portland, Oregon, USA
- Department of Microbiology, University of Alabama at Birmingham Schools of Dentistry and Medicine, Birmingham, Alabama, USA
| | - Xian Peng
- Department of Pediatric Dentistry, University of Alabama at Birmingham Schools of Dentistry and Medicine, Birmingham, Alabama, USA
- Department of Microbiology, University of Alabama at Birmingham Schools of Dentistry and Medicine, Birmingham, Alabama, USA
| | - Meghan S. Blackledge
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Robert E. Furlani
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Haoting Li
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Zhaoming Su
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Roberta J. Melander
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Christian Melander
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Suzanne Michalek
- Department of Integrative Biomedical & Diagnostic Sciences, Oregon Health & Science University School of Dentistry, Portland, Oregon, USA
| | - Hui Wu
- Department of Pediatric Dentistry, University of Alabama at Birmingham Schools of Dentistry and Medicine, Birmingham, Alabama, USA
- Department of Integrative Biomedical & Diagnostic Sciences, Oregon Health & Science University School of Dentistry, Portland, Oregon, USA
- Department of Microbiology, University of Alabama at Birmingham Schools of Dentistry and Medicine, Birmingham, Alabama, USA
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21
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Xu L, Henriksen C, Mebus V, Guérillot R, Petersen A, Jacques N, Jiang JH, Derks RJE, Sánchez-López E, Giera M, Leeten K, Stinear TP, Oury C, Howden BP, Peleg AY, Frees D. A Clinically Selected Staphylococcus aureus clpP Mutant Survives Daptomycin Treatment by Reducing Binding of the Antibiotic and Adapting a Rod-Shaped Morphology. Antimicrob Agents Chemother 2023; 67:e0032823. [PMID: 37184389 PMCID: PMC10269151 DOI: 10.1128/aac.00328-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Daptomycin is a last-resort antibiotic used for the treatment of infections caused by Gram-positive antibiotic-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA). Treatment failure is commonly linked to accumulation of point mutations; however, the contribution of single mutations to resistance and the mechanisms underlying resistance remain incompletely understood. Here, we show that a single nucleotide polymorphism (SNP) selected during daptomycin therapy inactivates the highly conserved ClpP protease and is causing reduced susceptibility of MRSA to daptomycin, vancomycin, and β-lactam antibiotics as well as decreased expression of virulence factors. Super-resolution microscopy demonstrated that inactivation of ClpP reduced binding of daptomycin to the septal site and diminished membrane damage. In both the parental strain and the clpP strain, daptomycin inhibited the inward progression of septum synthesis, eventually leading to lysis and death of the parental strain while surviving clpP cells were able to continue synthesis of the peripheral cell wall in the presence of 10× MIC daptomycin, resulting in a rod-shaped morphology. To our knowledge, this is the first demonstration that synthesis of the outer cell wall continues in the presence of daptomycin. Collectively, our data provide novel insight into the mechanisms behind bacterial killing and resistance to this important antibiotic. Also, the study emphasizes that treatment with last-line antibiotics is selective for mutations that, like the SNP in clpP, favor antibiotic resistance over virulence gene expression.
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Affiliation(s)
- Lijuan Xu
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Henriksen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Viktor Mebus
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Romain Guérillot
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Nicolas Jacques
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Jhih-Hang Jiang
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Rico J. E. Derks
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| | - Elena Sánchez-López
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| | - Kirsten Leeten
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Cécile Oury
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Anton Y. Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Dorte Frees
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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22
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Dong W, Peng Q, Tang X, Zhong T, Lin S, Zhi Z, Ye J, Yang B, Sun N, Yuan W. Identification and Characterization of a Vancomycin Intermediate-Resistant Staphylococcus haemolyticus Isolated from Guangzhou, China. Infect Drug Resist 2023; 16:3639-3647. [PMID: 37313263 PMCID: PMC10259589 DOI: 10.2147/idr.s411860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023] Open
Abstract
Background Staphylococcus haemolyticus is an opportunistic pathogen that belongs to coagulase-negative Staphylococci (CoNS). Increasing infection and multi-drug resistance cases caused by this strain have been reported and thus it poses a great health threat. Methods The third-generation sequencing technology was performed on a S. haemolyticus SH-1 isolated from a clinical sample to analyze the drug resistance genes, which included vancomycin resistance related genes. In addition, antimicrobial susceptibility tests, transmission electron microscopy and Triton X-100 stimulated autolysis were conducted to understand its biological characteristics. Results The study shows that this clinical isolate is a vancomycin intermediate-resistant strain. Genome comparison also revealed that WalK(N70K) and WalK(R280Q) mutations may contribute to the vancomycin resistant phenotype. Besides, S. haemolyticus SH-1 exhibit common features of thicker cell wall and decreased autolytic activity. Conclusion S. haemolyticus SH-1 with WalKR mutations shows typical characteristics of vancomycin resistant strains. Combining the genome features and biological properties, our findings may provide important information for the understanding of the molecular mechanism of S. haemolyticus to vancomycin intermediate-resistance.
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Affiliation(s)
- Wanyang Dong
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China
| | - Qi Peng
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China
| | - Xiaohua Tang
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China
- Third Affiliated Hospital of Guangzhou Medical University, Department of Clinical Laboratory, Guangzhou, 510150, People’s Republic of China
| | - Tian Zhong
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China
| | - Shunan Lin
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China
| | - Ziling Zhi
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China
| | - Jingyi Ye
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China
| | - Bixia Yang
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China
| | - Ning Sun
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China
- Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, People’s Republic of China
| | - Wenchang Yuan
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China
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23
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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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24
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Gostev V, Kalinogorskaya O, Sopova J, Sulian O, Chulkova P, Velizhanina M, Tsvetkova I, Ageevets I, Ageevets V, Sidorenko S. Adaptive Laboratory Evolution of Staphylococcus aureus Resistance to Vancomycin and Daptomycin: Mutation Patterns and Cross-Resistance. Antibiotics (Basel) 2023; 12:antibiotics12050928. [PMID: 37237831 DOI: 10.3390/antibiotics12050928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Vancomycin and daptomycin are first-line drugs for the treatment of complicated methicillin-resistant Staphylococcus aureus (MRSA) infections, including bacteremia. However, their effectiveness is limited not only by their resistance to each antibiotic but also by their associated resistance to both drugs. It is unknown whether novel lipoglycopeptides can overcome this associated resistance. Resistant derivatives from five S. aureus strains were obtained during adaptive laboratory evolution with vancomycin and daptomycin. Both parental and derivative strains were subjected to susceptibility testing, population analysis profiles, measurements of growth rate and autolytic activity, and whole-genome sequencing. Regardless of whether vancomycin or daptomycin was selected, most of the derivatives were characterized by a reduced susceptibility to daptomycin, vancomycin, telavancin, dalbavancin, and oritavancin. Resistance to induced autolysis was observed in all derivatives. Daptomycin resistance was associated with a significant reduction in growth rate. Resistance to vancomycin was mainly associated with mutations in the genes responsible for cell wall biosynthesis, and resistance to daptomycin was associated with mutations in the genes responsible for phospholipid biosynthesis and glycerol metabolism. However, mutations in walK and mprF were detected in derivatives selected for both antibiotics.
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Affiliation(s)
- Vladimir Gostev
- Pediatric Research and Clinical Center for Infectious Diseases, Department of Medical Microbiology and Molecular Epidemiology, 197022 Saint Petersburg, Russia
- Department of Medical Microbiology, North-Western State Medical University named after I.I. Mechnikov, 195067 Saint Petersburg, Russia
| | - Olga Kalinogorskaya
- Pediatric Research and Clinical Center for Infectious Diseases, Department of Medical Microbiology and Molecular Epidemiology, 197022 Saint Petersburg, Russia
| | - Julia Sopova
- Center of Transgenesis and Genome Editing, Saint Petersburg State University, 199034 Saint Petersburg, Russia
- Saint Petersburg Branch of Vavilov Institute of General Genetics, Russian Academy of Sciences, 198504 Saint Petersburg, Russia
| | - Ofelia Sulian
- Pediatric Research and Clinical Center for Infectious Diseases, Department of Medical Microbiology and Molecular Epidemiology, 197022 Saint Petersburg, Russia
| | - Polina Chulkova
- Pediatric Research and Clinical Center for Infectious Diseases, Department of Medical Microbiology and Molecular Epidemiology, 197022 Saint Petersburg, Russia
| | - Maria Velizhanina
- Center of Transgenesis and Genome Editing, Saint Petersburg State University, 199034 Saint Petersburg, Russia
- Laboratory of Signal Regulation, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 Saint Petersburg, Russia
| | - Irina Tsvetkova
- Pediatric Research and Clinical Center for Infectious Diseases, Department of Medical Microbiology and Molecular Epidemiology, 197022 Saint Petersburg, Russia
| | - Irina Ageevets
- Pediatric Research and Clinical Center for Infectious Diseases, Department of Medical Microbiology and Molecular Epidemiology, 197022 Saint Petersburg, Russia
| | - Vladimir Ageevets
- Pediatric Research and Clinical Center for Infectious Diseases, Department of Medical Microbiology and Molecular Epidemiology, 197022 Saint Petersburg, Russia
| | - Sergey Sidorenko
- Pediatric Research and Clinical Center for Infectious Diseases, Department of Medical Microbiology and Molecular Epidemiology, 197022 Saint Petersburg, Russia
- Department of Medical Microbiology, North-Western State Medical University named after I.I. Mechnikov, 195067 Saint Petersburg, Russia
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25
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Poshvina DV, Dilbaryan DS, Vasilchenko AS. Gausemycin A-Resistant Staphylococcus aureus Demonstrates Affected Cell Membrane and Cell Wall Homeostasis. Microorganisms 2023; 11:1330. [PMID: 37317304 DOI: 10.3390/microorganisms11051330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023] Open
Abstract
Antibiotic resistance is a significant and pressing issue in the medical field, as numerous strains of infectious bacteria have become resistant to commonly prescribed antibiotics. Staphylococcus aureus is a bacterium that poses a grave threat, as it is responsible for a large number of nosocomial infections and has high mortality rates worldwide. Gausemycin A is a new lipoglycopeptide antibiotic that has considerable efficacy against multidrug-resistant S. aureus strains. Although the cellular targets of gausemycin A have been previously identified, detailing the molecular processes of action is still needed. We performed gene expression analysis to identify molecular mechanisms that may be involved in bacterial resistance to gausemycin A. In the present study, we observed that gausemycin A-resistant S. aureus in the late-exponential phase showed an increased expression of genes involved in cell wall turnover (sceD), membrane charge (dltA), phospholipid metabolism (pgsA), the two-component stress-response system (vraS), and the Clp proteolytic system (clpX). The increased expression of these genes implies that changes in the cell wall and cell membrane are essential for the bacterial resistance to gausemycin A. In the stationary phase, we observed a decrease in the expression of genes involved in the phospholipid metabolism (mprF) and Clp proteolytic system (clpX).
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Affiliation(s)
- Darya V Poshvina
- Laboratory of Antimicrobial Resistance, Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Diana S Dilbaryan
- Laboratory of Antimicrobial Resistance, Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Alexey S Vasilchenko
- Laboratory of Antimicrobial Resistance, Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
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26
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Calov S, Munzel F, Roehr AC, Frey O, Higuita LMS, Wied P, Rosenberger P, Haeberle HA, Ngamsri KC. Daptomycin Pharmacokinetics in Blood and Wound Fluid in Critical Ill Patients with Left Ventricle Assist Devices. Antibiotics (Basel) 2023; 12:antibiotics12050904. [PMID: 37237807 DOI: 10.3390/antibiotics12050904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/03/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Daptomycin is a cyclic lipopeptide antibiotic with bactericidal effects against multidrug-resistant Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE). For critically ill patients, especially in the presence of implants, daptomycin is an important therapeutic option. Left ventricle assist devices (LVADs) can be utilized for intensive care patients with end-stage heart failure as a bridge to transplant. We conducted a single-center prospective trial with critically ill adults with LVAD who received prophylactic anti-infective therapy with daptomycin. Our study aimed to evaluate the pharmacokinetics of daptomycin in the blood serum and wound fluids after LVAD implantation. Daptomycin concentration were assessed over three days using high-performance liquid chromatography (HPLC). We detected a high correlation between blood serum and wound fluid daptomycin concentration at 12 h (IC95%: 0.64 to 0.95; r = 0.86; p < 0.001) and 24 h (IC95%: -0.38 to 0.92; r = 0.76; p < 0.001) after antibiotic administration. Our pilot clinical study provides new insights into the pharmacokinetics of daptomycin from the blood into wound fluids of critically ill patients with LVADs.
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Affiliation(s)
- Stefanie Calov
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Tübingen, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Frederik Munzel
- Department of Anesthesiology and Intensive Care Medicine, BG Trauma Center, 72076 Tübingen, Germany
| | - Anka C Roehr
- Department of Pharmacy, General Hospital of Heidenheim, 89522 Heidenheim, Germany
| | - Otto Frey
- Department of Pharmacy, General Hospital of Heidenheim, 89522 Heidenheim, Germany
| | - Lina Maria Serna Higuita
- Department for Translational Bioinformatics and Medical Data Integration Center, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Petra Wied
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Tübingen, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Peter Rosenberger
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Tübingen, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Helene A Haeberle
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Tübingen, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Kristian-Christos Ngamsri
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Tübingen, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
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27
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Shu X, Shi Y, Huang Y, Yu D, Sun B. Transcription tuned by S-nitrosylation underlies a mechanism for Staphylococcus aureus to circumvent vancomycin killing. Nat Commun 2023; 14:2318. [PMID: 37085493 PMCID: PMC10120478 DOI: 10.1038/s41467-023-37949-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/06/2023] [Indexed: 04/23/2023] Open
Abstract
Treatment of Staphylococcus aureus infections is a constant challenge due to emerging resistance to vancomycin, a last-resort drug. S-nitrosylation, the covalent attachment of a nitric oxide (NO) group to a cysteine thiol, mediates redox-based signaling for eukaryotic cellular functions. However, its role in bacteria is largely unknown. Here, proteomic analysis revealed that S-nitrosylation is a prominent growth feature of vancomycin-intermediate S. aureus. Deletion of NO synthase (NOS) or removal of S-nitrosylation from the redox-sensitive regulator MgrA or WalR resulted in thinner cell walls and increased vancomycin susceptibility, which was due to attenuated promoter binding and released repression of genes involved in cell wall metabolism. These genes failed to respond to H2O2-induced oxidation, suggesting distinct transcriptional responses to alternative modifications of the cysteine residue. Furthermore, treatment with a NOS inhibitor significantly decreased vancomycin resistance in S. aureus. This study reveals that transcriptional regulation via S-nitrosylation underlies a mechanism for NO-mediated bacterial antibiotic resistance.
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Affiliation(s)
- Xueqin Shu
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China
- Department of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Yingying Shi
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China
- Department of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Yi Huang
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China
- Department of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Dan Yu
- Laboratory of Dermatology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's Health, Beijing, China.
| | - Baolin Sun
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China.
- Department of Life Science and Medicine, University of Science and Technology of China, Hefei, China.
- CAS Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, China.
- Hefei National Laboratory for Physical Sciences at Microscale, Hefei, China.
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Baran A, Kwiatkowska A, Potocki L. Antibiotics and Bacterial Resistance-A Short Story of an Endless Arms Race. Int J Mol Sci 2023; 24:ijms24065777. [PMID: 36982857 PMCID: PMC10056106 DOI: 10.3390/ijms24065777] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Despite the undisputed development of medicine, antibiotics still serve as first-choice drugs for patients with infectious disorders. The widespread use of antibiotics results from a wide spectrum of their actions encompassing mechanisms responsible for: the inhibition of bacterial cell wall biosynthesis, the disruption of cell membrane integrity, the suppression of nucleic acids and/or proteins synthesis, as well as disturbances of metabolic processes. However, the widespread availability of antibiotics, accompanied by their overprescription, acts as a double-edged sword, since the overuse and/or misuse of antibiotics leads to a growing number of multidrug-resistant microbes. This, in turn, has recently emerged as a global public health challenge facing both clinicians and their patients. In addition to intrinsic resistance, bacteria can acquire resistance to particular antimicrobial agents through the transfer of genetic material conferring resistance. Amongst the most common bacterial resistance strategies are: drug target site changes, increased cell wall permeability to antibiotics, antibiotic inactivation, and efflux pumps. A better understanding of the interplay between the mechanisms of antibiotic actions and bacterial defense strategies against particular antimicrobial agents is crucial for developing new drugs or drug combinations. Herein, we provide a brief overview of the current nanomedicine-based strategies that aim to improve the efficacy of antibiotics.
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Affiliation(s)
- Aleksandra Baran
- Department of Biotechnology, College of Natural Sciences, University of Rzeszów, Pigonia 1, 35-310 Rzeszow, Poland
| | - Aleksandra Kwiatkowska
- Institute of Physical Culture Studies, College of Medical Sciences, University of Rzeszów, ul. Towarnickiego 3, 35-959 Rzeszów, Poland
| | - Leszek Potocki
- Department of Biotechnology, College of Natural Sciences, University of Rzeszów, Pigonia 1, 35-310 Rzeszow, Poland
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29
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Howden BP, Giulieri SG, Wong Fok Lung T, Baines SL, Sharkey LK, Lee JYH, Hachani A, Monk IR, Stinear TP. Staphylococcus aureus host interactions and adaptation. Nat Rev Microbiol 2023; 21:380-395. [PMID: 36707725 PMCID: PMC9882747 DOI: 10.1038/s41579-023-00852-y] [Citation(s) in RCA: 114] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 01/28/2023]
Abstract
Invasive Staphylococcus aureus infections are common, causing high mortality, compounded by the propensity of the bacterium to develop drug resistance. S. aureus is an excellent case study of the potential for a bacterium to be commensal, colonizing, latent or disease-causing; these states defined by the interplay between S. aureus and host. This interplay is multidimensional and evolving, exemplified by the spread of S. aureus between humans and other animal reservoirs and the lack of success in vaccine development. In this Review, we examine recent advances in understanding the S. aureus-host interactions that lead to infections. We revisit the primary role of neutrophils in controlling infection, summarizing the discovery of new immune evasion molecules and the discovery of new functions ascribed to well-known virulence factors. We explore the intriguing intersection of bacterial and host metabolism, where crosstalk in both directions can influence immune responses and infection outcomes. This Review also assesses the surprising genomic plasticity of S. aureus, its dualism as a multi-mammalian species commensal and opportunistic pathogen and our developing understanding of the roles of other bacteria in shaping S. aureus colonization.
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Affiliation(s)
- Benjamin P. Howden
- grid.1008.90000 0001 2179 088XCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.410678.c0000 0000 9374 3516Department of Infectious Diseases, Austin Health, Heidelberg, Victoria Australia ,grid.416153.40000 0004 0624 1200Microbiology Department, Royal Melbourne Hospital, Melbourne, Victoria Australia
| | - Stefano G. Giulieri
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.416153.40000 0004 0624 1200Victorian Infectious Diseases Service, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Tania Wong Fok Lung
- grid.21729.3f0000000419368729Department of Paediatrics, Columbia University, New York, NY USA
| | - Sarah L. Baines
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Liam K. Sharkey
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Jean Y. H. Lee
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.419789.a0000 0000 9295 3933Department of Infectious Diseases, Monash Health, Clayton, Victoria Australia
| | - Abderrahman Hachani
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Ian R. Monk
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Timothy P. Stinear
- grid.1008.90000 0001 2179 088XCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
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Al Janabi J, Tevell S, Sieber RN, Stegger M, Söderquist B. Emerging resistance in Staphylococcus epidermidis during dalbavancin exposure: a case report and in vitro analysis of isolates from prosthetic joint infections. J Antimicrob Chemother 2023; 78:669-677. [PMID: 36611258 PMCID: PMC9978592 DOI: 10.1093/jac/dkac434] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/07/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Dalbavancin, a semisynthetic lipoglycopeptide with exceptionally long half-life and Gram-positive spectrum, is an attractive option for infections requiring prolonged therapy, including prosthetic joint infections (PJIs). OBJECTIVES To investigate the prevalence of reduced susceptibility to dalbavancin in a strain collection of Staphylococcus epidermidis from PJIs, and to investigate genomic variation in isolates with reduced susceptibility selected during growth under dalbavancin exposure. METHODS MIC determination was performed on S. epidermidis isolates from a strain collection (n = 64) and from one patient with emerging resistance during treatment (n = 4). These isolates were subsequently cultured on dalbavancin-containing agar and evaluated at 48 h; MIC determination was repeated if phenotypical heterogeneity was detected during growth. Population analysis profile (PAP-AUC) was performed in isolates where a ≥ 2-fold increase in MIC was detected, together with corresponding parental isolates (n = 21). Finally, WGS was performed. RESULTS All strains grew at 48 h on agar containing 0.125 mg/L dalbavancin. PAP-AUC demonstrated significant differences between parental and derived strains in four of the eight analysed groups. An amino acid change in the walK gene coinciding with emergence of phenotypic resistance was detected in the patient isolates, whereas no alterations were found in this region in the in vitro derived strains. CONCLUSIONS Exposure to dalbavancin may lead to reduced susceptibility to dalbavancin through either selection of pre-existing subpopulations, epigenetic changes or spontaneous mutations during antibiotic exposure. Source control combined with adequate antibiotic concentrations may be important to prevent emerging reduced susceptibility during dalbavancin treatment.
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Affiliation(s)
| | | | - Raphael Niklaus Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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Li G, Walker MJ, De Oliveira DMP. Vancomycin Resistance in Enterococcus and Staphylococcus aureus. Microorganisms 2022; 11:microorganisms11010024. [PMID: 36677316 PMCID: PMC9866002 DOI: 10.3390/microorganisms11010024] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.
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Cheng S, Fleres G, Chen L, Liu G, Hao B, Newbrough A, Driscoll E, Shields RK, Squires KM, Chu TY, Kreiswirth BN, Nguyen MH, Clancy CJ. Within-Host Genotypic and Phenotypic Diversity of Contemporaneous Carbapenem-Resistant Klebsiella pneumoniae from Blood Cultures of Patients with Bacteremia. mBio 2022; 13:e0290622. [PMID: 36445082 PMCID: PMC9765435 DOI: 10.1128/mbio.02906-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 12/02/2022] Open
Abstract
It is unknown whether bacterial bloodstream infections (BSIs) are commonly caused by single organisms or mixed microbial populations. We hypothesized that contemporaneous carbapenem-resistant Klebsiella pneumoniae (CRKP) strains from blood cultures of individual patients are genetically and phenotypically distinct. We determined short-read whole-genome sequences of 10 sequence type 258 (ST258) CRKP strains from blood cultures in each of 6 patients (Illumina HiSeq). Strains clustered by patient by core genome and pan-genome phylogeny. In 5 patients, there was within-host strain diversity by gene mutations, presence/absence of antibiotic resistance or virulence genes, and/or plasmid content. Accessory gene phylogeny revealed strain diversity in all 6 patients. Strains from 3 patients underwent long-read sequencing for genome completion (Oxford Nanopore) and phenotypic testing. Genetically distinct strains within individuals exhibited significant differences in carbapenem and other antibiotic responses, capsular polysaccharide (CPS) production, mucoviscosity, and/or serum killing. In 2 patients, strains differed significantly in virulence during mouse BSIs. Genetic or phenotypic diversity was not observed among strains recovered from blood culture bottles seeded with index strains from the 3 patients and incubated in vitro at 37°C. In conclusion, we identified genotypic and phenotypic variant ST258 CRKP strains from blood cultures of individual patients with BSIs, which were not detected by the clinical laboratory or in seeded blood cultures. The data suggest a new paradigm of CRKP population diversity during BSIs, at least in some patients. If validated for BSIs caused by other bacteria, within-host microbial diversity may have implications for medical, microbiology, and infection prevention practices and for understanding antibiotic resistance and pathogenesis. IMPORTANCE The long-standing paradigm for pathogenesis of bacteremia is that, in most cases, a single organism passes through a bottleneck and establishes itself in the bloodstream (single-organism hypothesis). In keeping with this paradigm, standard practice in processing positive microbiologic cultures is to test single bacterial strains from morphologically distinct colonies. This study is the first genome-wide analysis of within-host diversity of Klebsiella pneumoniae strains recovered from individual patients with bloodstream infections (BSIs). Our finding that positive blood cultures comprised genetically and phenotypically heterogeneous carbapenem-resistant K. pneumoniae strains challenges the single-organism hypothesis and suggests that at least some BSIs are caused by mixed bacterial populations that are unrecognized by the clinical laboratory. The data support a model of pathogenesis in which pressures in vivo select for strain variants with particular antibiotic resistance or virulence attributes and raise questions about laboratory protocols and treatment decisions directed against single strains.
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Affiliation(s)
- Shaoji Cheng
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Guojun Liu
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Binghua Hao
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | | | - Ryan K. Shields
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | - Ting-yu Chu
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Barry N. Kreiswirth
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - M. Hong Nguyen
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Cornelius J. Clancy
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
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Knockout of ykcB, a Putative Glycosyltransferase, Leads to Reduced Susceptibility to Vancomycin in Bacillus subtilis. J Bacteriol 2022; 204:e0038722. [PMID: 36409129 PMCID: PMC9765085 DOI: 10.1128/jb.00387-22] [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: 11/23/2022] Open
Abstract
Vancomycin resistance of Gram-positive bacteria poses a serious health concern around the world. In this study, we searched for vancomycin-tolerant mutants from a gene deletion library of a model Gram-positive bacterium, Bacillus subtilis, to elucidate the mechanism of vancomycin resistance. We found that knockout of ykcB, a glycosyltransferase that is expected to utilize C55-P-glucose to glycosylate cell surface components, caused reduced susceptibility to vancomycin in B. subtilis. Knockout of ykcB altered the susceptibility to multiple antibiotics, including sensitization to β-lactams and increased the pathogenicity to silkworms. Furthermore, the ykcB-knockout mutant had (i) a decreased amount of lipoteichoic acid, (ii) decreased biofilm formation, and (iii) an increased content of diglucosyl diacylglycerol, a glycolipid that shares a precursor with C55-P-glucose. These phenotypes and vancomycin tolerance were abolished by knockout of ykcC, a gene in the same operon with ykcB probably involved in C55-P-glucose synthesis. Overexpression of ykcC enhanced vancomycin tolerance in both the parent strain and the ykcB-knockout mutant. These findings suggest that ykcB deficiency induces structural changes of cell surface molecules depending on the ykcC function, leading to reduced susceptibility to vancomycin, decreased biofilm formation, and increased pathogenicity to silkworms. IMPORTANCE Although vancomycin is effective against Gram-positive bacteria, vancomycin-resistant bacteria are a major public health concern. While the vancomycin-resistance mechanisms of clinically important bacteria such as Staphylococcus aureus, Enterococcus faecium, and Streptococcus pneumoniae are well studied, they remain unclear in other Gram-positive bacteria. In the present study, we searched for vancomycin-tolerant mutants from a gene deletion library of a model Gram-positive bacterium, Bacillus subtilis, and found that knockout of a putative glycosyltransferase, ykcB, caused vancomycin tolerance in B. subtilis. Notably, unlike the previously reported vancomycin-resistant bacterial strains, ykcB-deficient B. subtilis exhibited increased virulence while maintaining its growth rate. Our results broaden the fundamental understanding of vancomycin-resistance mechanisms in Gram-positive bacteria.
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Mahjabeen F, Saha U, Mostafa MN, Siddique F, Ahsan E, Fathma S, Tasnim A, Rahman T, Faruq R, Sakibuzzaman M, Dilnaz F, Ashraf A. An Update on Treatment Options for Methicillin-Resistant Staphylococcus aureus (MRSA) Bacteremia: A Systematic Review. Cureus 2022; 14:e31486. [DOI: 10.7759/cureus.31486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2022] [Indexed: 11/16/2022] Open
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Zhang R, Polenakovik H, Barreras Beltran IA, Waalkes A, Salipante SJ, Xu L, Werth BJ. Emergence of Dalbavancin, Vancomycin, and Daptomycin Nonsusceptible Staphylococcus aureus in a Patient Treated With Dalbavancin: Case Report and Isolate Characterization. Clin Infect Dis 2022; 75:1641-1644. [PMID: 35510938 PMCID: PMC10200325 DOI: 10.1093/cid/ciac341] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Indexed: 12/29/2022] Open
Abstract
A patient with end-stage renal disease received 2 doses of dalbavancin for methicillin-resistant Staphylococcus aureus (MRSA) arteriovenous fistula infection and presented 5 weeks later with infective endocarditis secondary to vancomycin, daptomycin, and dalbavancin nonsusceptible MRSA. Resistance was associated with walK and scrA mutations, reduced long-chain lipid content, and reduced membrane fluidity.
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Affiliation(s)
- Rutan Zhang
- Department of Medicinal Chemistry, University of Washington School of Pharmacy, Seattle, Washington, USA
| | - Hari Polenakovik
- Veterans Affairs Medical Center, Dayton, Ohio, USA
- Department of Medicine, Wright State University Boonshoft School of Medicine, Dayton, Ohio, USA
| | | | - Adam Waalkes
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington School of Pharmacy, Seattle, Washington, USA
| | - Brian J Werth
- Department of Pharmacy, University of Washington School of Pharmacy, Seattle, Washington, USA
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Cervimycin-Resistant Staphylococcus aureus Strains Display Vancomycin-Intermediate Resistant Phenotypes. Microbiol Spectr 2022; 10:e0256722. [PMID: 36173303 PMCID: PMC9603734 DOI: 10.1128/spectrum.02567-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Resistance to antibiotics is an increasing problem and necessitates novel antibacterial therapies. The polyketide antibiotics cervimycin A to D are natural products of Streptomyces tendae HKI 0179 with promising activity against multidrug-resistant staphylococci and vancomycin-resistant enterococci. To initiate mode of action studies, we selected cervimycin C- and D-resistant (CmR) Staphylococcus aureus strains. Genome sequencing of CmR mutants revealed amino acid exchanges in the essential histidine kinase WalK, the Clp protease proteolytic subunit ClpP or the Clp ATPase ClpC, and the heat shock protein DnaK. Interestingly, all characterized CmR mutants harbored a combination of mutations in walK and clpP or clpC. In vitro and in vivo analyses showed that the mutations in the Clp proteins abolished ClpP or ClpC activity, and the deletion of clpP rendered S. aureus but not all Bacillus subtilis strains cervimycin-resistant. The essential gene walK was the second mutational hotspot in the CmR S. aureus strains, which decreased WalK activity in vitro and generated a vancomycin-intermediate resistant phenotype, with a thickened cell wall, a lower growth rate, and reduced cell lysis. Transcriptomic and proteomic analyses revealed massive alterations in the CmR strains compared to the parent strain S. aureus SG511, with major shifts in the heat shock regulon, the metal ion homeostasis, and the carbohydrate metabolism. Taken together, mutations in the heat shock genes clpP, clpC, and dnaK, and the walK kinase gene in CmR mutants induced a vancomycin-intermediate resistant phenotype in S. aureus, suggesting cell wall metabolism or the Clp protease system as primary target of cervimycin. IMPORTANCE Staphylococcus aureus is a frequent cause of infections in both the community and hospital setting. Resistance development of S. aureus to various antibiotics is a severe problem for the treatment of this pathogen worldwide. New powerful antimicrobial agents against Gram-positives are needed, since antibiotics like vancomycin fail to cure vancomycin-intermediate resistant S. aureus (VISA) and vancomycin-resistant enterococci (VRE) infections. One candidate substance with promising activity against these organisms is cervimycin, which is an antibiotic complex with a yet unknown mode of action. In our study, we provide first insights into the mode of action of cervimycins. By characterizing cervimycin-resistant S. aureus strains, we revealed the Clp system and the essential kinase WalK as mutational hotspots for cervimycin resistance in S. aureus. It further emerged that cervimycin-resistant S. aureus strains show a VISA phenotype, indicating a role of cervimycin in perturbing the bacterial cell envelope.
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Wu S, Qin B, Deng S, Liu Y, Zhang H, Lei L, Feng G. CodY is modulated by YycF and affects biofilm formation in Staphylococcus aureus. Front Microbiol 2022; 13:967567. [PMID: 36304951 PMCID: PMC9593060 DOI: 10.3389/fmicb.2022.967567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Background Staphylococcus aureus (S. aureus) is the leading cause of various infective diseases, including topical soft tissue infections. The goals of this study were to investigate the roles of YycF and CodY in the regulation of biofilm formation and pathogenicity. Methods Electrophoretic mobility shift assay (EMSA) was conducted to validate the bound promoter regions of YycF protein. We constructed the codY up-regulated or down-regulated S. aureus mutants. The biofilm biomass was determined by crystal violet microtiter assay and scanning electron microscopy (SEM). Quantitative RT-PCR analysis was used to detect the transcripts of biofilm-related genes. The live and dead cells of S. aureus biofilm were also investigated by confocal laser scanning microscopy (CLSM). We constructed an abscess infection in Sprague Dawley (SD) rat models to determine the effect of CodY on bacterial pathogenicity. We further used the RAW264.7, which were cocultured with S. aureus, to evaluate the effect of CodY on macrophages apoptosis. Result Quantitative RT-PCR analyses reveled that YycF negatively regulates codY expression. EMSA assays indicated that YycF protein directly binds to the promoter regions of codY gene. Quantitative RT-PCR confirmed the construction of dual- mutant stains codY + ASyycF and codY-ASyycF. The SEM results showed that the biofilm formation in the codY + ASyycF group was sparser than those in the other groups. The crystal violet assays indicated that the codY + ASyycF group formed less biofilms, which was consistent with the immunofluorescence results of the lowest live cell ration in the codY + ASyycF group. The expression levels of biofilm-associated icaA gene were significantly reduced in the codY + strain, indicating codY negatively regulates the biofilm formation. Furthermore, CodY impedes the pathogenicity in a rat-infection model. After cocultured with bacteria or 4-h in vitro, the apoptosis rates of macrophage cells were lowest in the codY + group. Conclusions YycF negatively regulate the expression of codY. By interaction with codY, YycF could modulate S. aureus biofilm formation via both eDNA- dependent and PIA- dependent pathways, which can be a significant target for antibiofilm. CodY not only impedes the pathogenicity but also has a role on immunoregulation. Thus, the current evidence may provide a supplementary strategy for managing biofilm infections.
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Affiliation(s)
- Shizhou Wu
- Department of Orthopedics, Orthopaedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Boquan Qin
- Department of Orthopedics, Orthopaedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Shu Deng
- Boston University Henry M. Goldman School of Dental Medicine, Boston, MA, United States
| | - Yunjie Liu
- West China School of Public Health, Sichuan University, Chengdu, China
| | - Hui Zhang
- Department of Orthopedics, Orthopaedic Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Lei
- Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Lei Lei,
| | - Guoying Feng
- College of Electronics and Information Engineering, Sichuan University, Chengdu, China
- Guoying Feng,
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Heo S, Kim T, Na HE, Lee G, Lee JH, Jeong DW. Transcriptomic analysis of Staphylococcus equorum KM1031 from the high-salt fermented seafood jeotgal under chloramphenicol, erythromycin and lincomycin stresses. Sci Rep 2022; 12:15541. [PMID: 36109627 PMCID: PMC9477809 DOI: 10.1038/s41598-022-19897-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus equorum strain KM1031 is resistant to chloramphenicol, erythromycin and lincomycin. To shed light on the genetic factors underlying these antibiotic resistances, we determined the global gene expression profile of S. equorum KM1031 using RNA sequencing. During chloramphenicol, erythromycin and lincomycin treatment, 8.3% (183/2,336), 16.0% (354/2,336), and 2.9% (63/2,336) of S. equorum KM1031 genes exhibited significant differences in expression, respectively. These three antibiotics upregulated genes related to efflux and downregulated genes related to transporters. Antibiotic treatment also upregulated osmoprotectant-related genes involved in salt tolerance. To identify specific genes functionally related to antibiotic resistance, we compared the genome of strain KM1031 with those of three S. equorum strains that are sensitive to these three antibiotics. We identified three genes of particular interest: an antibiotic biosynthesis monooxygenase gene (abm, AWC34_RS01805) related to chloramphenicol resistance, an antibiotic ABC transporter ATP-binding protein gene (msr, AWC34_RS11115) related to erythromycin resistance, and a lincosamide nucleotydyltransferase gene (lnuA, AWC34_RS13300) related to lincomycin resistance. These genes were upregulated in response to the corresponding antibiotic; in particular, msr was upregulated more than fourfold by erythromycin treatment. Finally, the results of RNA sequencing were validated by quantitative real-time PCR. This transcriptomic analysis provides genetic evidence regarding antibiotic stress responses of S. equorum strain KM1031.
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Tan S, Cho K, Nodwell JR. A defect in cell wall recycling confers antibiotic resistance and sensitivity in Staphylococcus aureus. J Biol Chem 2022; 298:102473. [PMID: 36089064 PMCID: PMC9547203 DOI: 10.1016/j.jbc.2022.102473] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/17/2022] Open
Abstract
WalKR is a two-component system that is essential for viability in Gram-positive bacteria that regulates the all-important autolysins in cell wall homeostasis. Further investigation of this essential system is important for identifying ways to address antibiotic resistance. Here, we show that a T101M mutation in walR confers a defect in autolysis, a thickened cell wall, and decreased susceptibility to antibiotics that target lipid II cycle, a phenotype that is reminiscent of the clinical resistance form known as vancomycin intermediate-resistant Staphylococcus aureus. Importantly, this is accompanied by dramatic sensitization to tunicamycin. We demonstrate that this phenotype is due to partial collapse of a pathway consisting of autolysins, AtlA and Sle1, a transmembrane sugar permease, MurP, and GlcNAc recycling enzymes, MupG and MurQ. We suggest that this causes a shortage of substrate for the peptidoglycan biosynthesis enzyme MraY, causing it to be hypersensitive to competitive inhibition by tunicamycin. In conclusion, our results constitute a new molecular model for antibiotic sensitivity in S. aureus and a promising new route for antibiotic discovery.
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Affiliation(s)
- Stephanie Tan
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada, M5G 1M1
| | - Kelvin Cho
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada, M5G 1M1
| | - Justin R Nodwell
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada, M5G 1M1.
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Rao Y, Peng H, Shang W, Hu Z, Yang Y, Tan L, Li M, Zhou R, Rao X. A vancomycin resistance-associated WalK(S221P) mutation attenuates the virulence of vancomycin-intermediate Staphylococcus aureus. J Adv Res 2022; 40:167-178. [PMID: 36100324 PMCID: PMC9481939 DOI: 10.1016/j.jare.2021.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Vancomycin-intermediate Staphylococcus aureus (VISA) is typically associated with a decline in virulence. We previously reported a WalK(S221P) mutation that plays an important role in mediating vancomycin resistance in VISA XN108. Whether this mutation is implicated in bacterial virulence remains unknown. OBJECTIVES This study aimed to investigate the effect of WalK(S221P) mutation on the virulence of VISA and the underlying mechanism of this effect. METHODS The influence of WalK(S221P) mutation on VISA virulence and its underlying mechanism were explored using animal models, RNA-seq analysis, RT-qPCR, hemolytic assay, slide coagulase test, Western blot, β-galactosidase assay, and electrophoresis mobility shift assay (EMSA). RESULTS Compared with XN108, WalK(S221P)-reverted strain XN108-R exacerbated cutaneous infections with increased lesion size and extensive inflammatory infiltration in mouse models. The bacterial loads of S. aureus XN108-R in murine kidney increased compared with those of XN108. RNA-seq analysis showed upregulation of a set of virulence genes in XN108-R, which exhibited greater hemolytic and stronger coagulase activities compared with XN108. Introduction of WalK(S221P) to methicillin-resistant S. aureus USA300 and methicillin-susceptible strain Newman increased the vancomycin resistance of the mutants, which exhibited reduced hemolytic activities and decreased expression levels of many virulence factors compared with their progenitors. WalK(S221P) mutation weakened agr promoter-controlled β-galactosidase activity. EMSA results showed that WalK-phosphorylated WalR could directly bind to the agr promoter region, whereas WalK(S221P)-activated WalR reduced binding to the target promoter. Inactivation of agr in S. aureus did not affect their vancomycin susceptibility but mitigated the virulence alterations caused by WalK(S221P) mutation. CONCLUSION The results of our study indicate that WalK(S221P) mutation can enhance vancomycin resistance in S. aureus of diverse genetic backgrounds. WalK(S221P)- bearing S. aureus strains exhibit reduced virulence. WalK(S221P) mutation may directly impair the activation of the agr system by WalR, thereby decreasing the expression of virulence factors in VISA.
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Affiliation(s)
- Yifan Rao
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China; Department of Emergency Medicine, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Huagang Peng
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Weilong Shang
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Zhen Hu
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Yi Yang
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Li Tan
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Ming Li
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China.
| | - Renjie Zhou
- Department of Emergency Medicine, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China.
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China.
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Neto NAS, Oliveira JTA, Aguiar TKB, Bezerra LP, Branco LAC, Mesquita FP, Freitas CDT, Souza PFN. Synergistic Antibiofilm Activity between Synthetic Peptides and Ciprofloxacin against Staphylococcus aureus. Pathogens 2022; 11:pathogens11090995. [PMID: 36145427 PMCID: PMC9505254 DOI: 10.3390/pathogens11090995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus is a human pathogen known to be resistant to antibiotics since the mid-20th century and is constantly associated with hospital-acquired infections. S. aureus forms biofilms, which are complex surface-attached communities of bacteria held together by a self-produced polymer matrix consisting of proteins, extracellular DNA, and polysaccharides. Biofilms are resistance structures responsible for increasing bacterial resistance to drugs by 1000 times more than the planktonic lifestyle. Therefore, studies have been conducted to discover novel antibacterial molecules to prevent biofilm formation and/or degrade preformed biofilms. Synthetic antimicrobial peptides (SAMPs) have appeared as promising alternative agents to overcome increasing antibiotic resistance. Here, the antibiofilm activity of eight SAMPs, in combination with the antibiotic ciprofloxacin, was investigated in vitro. Biofilm formation by S. aureus was best inhibited (76%) by the combination of Mo-CBP3-PepIII (6.2 µg mL−1) and ciprofloxacin (0.39 µg mL−1). In contrast, the highest reduction (60%) of the preformed biofilm mass was achieved with RcAlb-PepII (1.56 µg mL−1) and ciprofloxacin (0.78 µg mL−1). Fluorescence microscopy analysis reinforced these results. These active peptides formed pores in the cellular membrane of S. aureus, which may be related to the enhanced ciprofloxacin’s antibacterial activity. Our findings indicated that these peptides may act with ciprofloxacin and are powerful co-adjuvant agents for the treatment of S. aureus infections.
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Affiliation(s)
- Nilton A. S. Neto
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451, CE, Brazil
| | - Jose T. A. Oliveira
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451, CE, Brazil
- Correspondence: (J.T.A.O.); (P.F.N.S.)
| | - Tawanny K. B. Aguiar
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451, CE, Brazil
| | - Leandro P. Bezerra
- Department of Fisheries Engineering, Federal University of Ceará, Fortaleza 60451, CE, Brazil
| | - Levi A. C. Branco
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451, CE, Brazil
| | - Felipe P. Mesquita
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Caixa, Fortaleza 60430, CE, Brazil
| | - Cleverson D. T. Freitas
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451, CE, Brazil
| | - Pedro F. N. Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451, CE, Brazil
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Caixa, Fortaleza 60430, CE, Brazil
- Correspondence: (J.T.A.O.); (P.F.N.S.)
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Mutation in the Two-Component System Regulator YycH Leads to Daptomycin Tolerance in Methicillin-Resistant Staphylococcus aureus upon Evolution with a Population Bottleneck. Microbiol Spectr 2022; 10:e0168722. [PMID: 35913149 PMCID: PMC9431245 DOI: 10.1128/spectrum.01687-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptive laboratory evolution (ALE) is a useful tool to study the evolution of antibiotic tolerance in bacterial populations under diverse environmental conditions. The role of population bottlenecks in the evolution of tolerance has been investigated in Escherichia coli, but not in a more clinically relevant pathogen, methicillin-resistant Staphylococcus aureus (MRSA). In this study, we used ALE to evolve MRSA under repetitive daptomycin treatment and incorporated population bottlenecks following antibiotic exposure. We observed that the populations finally attained a tolerance mutation in the yycH gene after 2 weeks of evolution with population bottlenecks, and additional mutations in yycI and several other genes further increased the tolerance level. The tolerant populations also became resistant to another glycopeptide antibiotic, vancomycin. Through proteomics, we showed that yycH and yycI mutations led to the loss of function of the proteins and downregulated the WalKR two-component system and the downstream players, including the autolysin Atl and amidase Sle1, which are important for cell wall metabolism. Overall, our study offers new insights into the evolution of daptomycin tolerance under population bottlenecking conditions, which are commonly faced by pathogens during infection; the study also identified new mutations conferring daptomycin tolerance and revealed the proteome alterations in the evolved tolerant populations. IMPORTANCE Although population bottlenecks are known to influence the evolutionary dynamics of microbial populations, how such bottlenecks affect the evolution of tolerance to antibiotics in a clinically relevant methicillin-resistant S. aureus (MRSA) pathogen are still unclear. Here, we performed in vitro evolution of MRSA under cyclic daptomycin treatment and applied population bottlenecks following the treatment. We showed that under these experimental conditions, MRSA populations finally attained mutations in yycH, yycI, and several other genes that led to daptomycin tolerance. The discovered yycH and yycI mutations caused early termination of the genes and loss of function of the proteins, and they subsequently downregulated the expression of proteins controlled by the WalKR two-component system, such as Atl and Sle1. In addition, we compared our proteomics data with multiple studies on distinct daptomycin-tolerant MRSA mutants to identify proteins with a consistent expression pattern that could serve as biological markers for daptomycin tolerance in MRSA.
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Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022; 10:microorganisms10061239. [PMID: 35744757 PMCID: PMC9228545 DOI: 10.3390/microorganisms10061239] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.
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Giulieri SG, Guérillot R, Duchene S, Hachani A, Daniel D, Seemann T, Davis JS, Tong SYC, Young BC, Wilson DJ, Stinear TP, Howden BP. Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections. eLife 2022; 11:77195. [PMID: 35699423 PMCID: PMC9270034 DOI: 10.7554/elife.77195] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues and is exposed to new selective pressures, thus, potentially driving adaptive evolution. Previous studies have shown the key role of the agr locus in S. aureus pathoadaptation; however, a more comprehensive characterisation of genetic signatures of bacterial adaptation may enable prediction of clinical outcomes and reveal new targets for treatment and prevention of these infections. Here, we measured adaptation using within-host evolution analysis of 2590 S. aureus genomes from 396 independent episodes of infection. By capturing a comprehensive repertoire of single nucleotide and structural genome variations, we found evidence of a distinctive evolutionary pattern within the infecting populations compared to colonising bacteria. These invasive strains had up to 20-fold enrichments for genome degradation signatures and displayed significantly convergent mutations in a distinctive set of genes, linked to antibiotic response and pathogenesis. In addition to agr-mediated adaptation, we identified non-canonical, genome-wide significant loci including sucA-sucB and stp1. The prevalence of adaptive changes increased with infection extent, emphasising the clinical significance of these signatures. These findings provide a high-resolution picture of the molecular changes when S. aureus transitions from colonisation to severe infection and may inform correlation of infection outcomes with adaptation signatures. The bacterium Staphylococcus aureus lives harmlessly on our skin and noses. However, occasionally, it gets into our blood and internal organs, such as our bones and joints, where it causes severe, long-lasting infections that are difficult to treat. Over time, S. aureus acquire characteristics that help them to adapt to different locations, such as transitioning from the nose to the blood, and avoid being killed by antibiotics. Previous studies have identified changes, or ‘mutations’, in genes that are likely to play an important role in this evolutionary process. One of these genes, called accessory gene regulator (or agr for short), has been shown to control the mechanisms S. aureus use to infect cells and disseminate in the body. However, it is unclear if there are changes in other genes that also help S. aureus adapt to life inside the human body. To help resolve this mystery, Giulieri et al. collected 2,500 samples of S. aureus from almost 400 people. This included bacteria harmlessly living on the skin or in the nose, as well as strains that caused an infection. Gene sequencing revealed a small number of genes, referred to as ‘adaptive genes’, that often acquire mutations during infection. Of these, agr was the most commonly altered. However, mutations in less well-known genes were also identified: some of these genes are related to resistance to antibiotics, while others are involved in chemical processes that help the bacteria to process nutrients. Most mutations were caused by random errors being introduced in to the bacteria’s genetic code which stopped genes from working. However, in some cases, genes were turned off by small fragments of DNA moving around and inserting themselves into different parts of the genome. This study highlights a group of genes that help S. aureus to thrive inside the body and cause severe and prolonged infections. If these results can be confirmed, it may help to guide which antibiotics are used to treat different infections. Furthermore, understanding which genes are important for infection could lead to new strategies for eliminating this dangerous bacterium.
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Affiliation(s)
- Stefano G Giulieri
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Diane Daniel
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit, University of Melbourne, Melbourne, Australia
| | - Joshua S Davis
- Department of Infectious Diseases, John Hunter Hospital, Newcastle, Australia
| | - Steven Y C Tong
- Victorian Infectious Diseases Service, University of Melbourne, Melbourne, Australia
| | | | | | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
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Kong L, Su M, Sang J, Huang S, Wang M, Cai Y, Xie M, Wu J, Wang S, Foster SJ, Zhang J, Han A. The W-Acidic Motif of Histidine Kinase WalK Is Required for Signaling and Transcriptional Regulation in Streptococcus mutans. Front Microbiol 2022; 13:820089. [PMID: 35558126 PMCID: PMC9087282 DOI: 10.3389/fmicb.2022.820089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
In Streptococcus mutans, we find that the histidine kinase WalK possesses the longest C-terminal tail (CTT) among all 14 TCSs, and this tail plays a key role in the interaction of WalK with its response regulator WalR. We demonstrate that the intrinsically disordered CTT is characterized by a conserved tryptophan residue surrounded by acidic amino acids. Mutation in the tryptophan not only disrupts the stable interaction, but also impairs the efficient phosphotransferase and phosphatase activities of WalRK. In addition, the tryptophan is important for WalK to compete with DNA containing a WalR binding motif for the WalR interaction. We further show that the tryptophan is important for in vivo transcriptional regulation and bacterial biofilm formation by S. mutans. Moreover, Staphylococcus aureus WalK also has a characteristic CTT, albeit relatively shorter, with a conserved W-acidic motif, that is required for the WalRK interaction in vitro. Together, these data reveal that the W-acidic motif of WalK is indispensable for its interaction with WalR, thereby playing a key role in the WalRK-dependent signal transduction, transcriptional regulation and biofilm formation.
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Affiliation(s)
- Lingyuan Kong
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingyang Su
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiayan Sang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shanshan Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Min Wang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingquan Xie
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jun Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shida Wang
- State Key Laboratory for Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Simon J Foster
- Department of Molecular Biology and Biotechnology, The Florey Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Jiaqin Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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Elgrail MM, Chen E, Shaffer MG, Srinivasa V, Griffith MP, Mustapha MM, Shields RK, Van Tyne D, Culyba MJ. Convergent Evolution of Antibiotic Tolerance in Patients with Persistent Methicillin-Resistant Staphylococcus aureus Bacteremia. Infect Immun 2022; 90:e0000122. [PMID: 35285704 PMCID: PMC9022596 DOI: 10.1128/iai.00001-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/12/2022] [Indexed: 02/06/2023] Open
Abstract
Severe infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are often complicated by persistent bacteremia (PB) despite active antibiotic therapy. Antibiotic resistance rarely contributes to MRSA-PB, suggesting an important role for antibiotic tolerance pathways. To identify bacterial factors associated with PB, we sequenced the whole genomes of 206 MRSA isolates derived from 20 patients with PB and looked for genetic signatures of adaptive within-host evolution. We found that genes involved in the tricarboxylic acid cycle (citZ and odhA) and stringent response (rel) bore repeated, independent, protein-altering mutations across multiple infections, indicative of convergent evolution. Both pathways have been linked previously to antibiotic tolerance. Mutations in citZ were identified most frequently, and further study showed they caused antibiotic tolerance through the loss of citrate synthase activity. Isolates harboring mutant alleles (citZ, odhA, and rel) were sampled at a low frequency from each patient but were detected in 10 (50%) of the patients. These results suggest that subpopulations of antibiotic-tolerant mutants emerge commonly during MRSA-PB. Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of hospital-acquired infection. In severe cases, bacteria invade the bloodstream and cause bacteremia, a condition associated with high mortality. We analyzed the genomes of serial MRSA isolates derived from patients with bacteremia that persisted through active antibiotic therapy and found a frequent evolution of pathways leading to antibiotic tolerance. Antibiotic tolerance is distinct from antibiotic resistance, and the role of tolerance in clinical failure of antibiotic therapy is defined poorly. Our results show genetic evidence that perturbation of specific metabolic pathways plays an important role in the ability of MRSA to evade antibiotics during severe infection.
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Affiliation(s)
- Mitra M. Elgrail
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Edwin Chen
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marla G. Shaffer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vatsala Srinivasa
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marissa P. Griffith
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mustapha M. Mustapha
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ryan K. Shields
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daria Van Tyne
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Matthew J. Culyba
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Abstract
Urinary tract infection (UTI) is the most common type of urogenital disease. UTI affects the urethra, bladder, ureter, and kidney. A total of 13.3% of women, 2.3% of men, and 3.4% of children in the United States will require treatment for UTI. Traditionally, bladder (cystitis) and kidney (pyelonephritis) infections are considered independently. However, both infections induce host defenses that are either shared or coordinated across the urinary tract. Here, we review the chemical and biophysical mechanisms of bacteriostasis, which limit the duration and severity of the illness. Urinary bacteria attempt to overcome each of these defenses, complicating description of the natural history of UTI.
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Affiliation(s)
| | - Anne-Catrin Uhlemann
- Department of Medicine and Pathology and Urology, Columbia University, New York, NY, USA;
| | - Jonathan Barasch
- Department of Medicine and Pathology and Urology, Columbia University, New York, NY, USA;
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Wassmann CS, Rolsted AP, Lyngsie MC, Puig ST, Kronborg T, Vestergaard M, Ingmer H, Pontoppidan SP, Klitgaard JK. The menaquinone pathway is important for susceptibility of Staphylococcus aureus to the antibiotic adjuvant, cannabidiol. Microbiol Res 2022; 257:126974. [DOI: 10.1016/j.micres.2022.126974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 01/12/2023]
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Oliveira LT, Alves LA, Harth-Chu EN, Nomura R, Nakano K, Mattos-Graner RO. VicRK and CovR polymorphisms in Streptococcus mutans strains associated with cardiovascular infections. J Med Microbiol 2021; 70. [PMID: 34939562 DOI: 10.1099/jmm.0.001457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Introduction. Streptococcus mutans, a common species of the oral microbiome, expresses virulence genes promoting cariogenic dental biofilms, persistence in the bloodstream and cardiovascular infections.Gap statement. Virulence gene expression is variable among S. mutans strains and controlled by the transcription regulatory systems VicRK and CovR.Aim. This study investigates polymorphisms in the vicRK and covR loci in S. mutans strains isolated from the oral cavity or from the bloodstream, which were shown to differ in expression of covR, vicRK and downstream genes.Methodology. The transcriptional activities of covR, vicR and vicK were compared by RT-qPCR between blood and oral strains after exposure to human serum. PCR-amplified promoter and/or coding regions of covR and vicRK of 18 strains (11 oral and 7 blood) were sequenced and compared to the reference strain UA159.Results. Serum exposure significantly reduced covR and vicR/K transcript levels in most strains (P<0.05), but reductions were higher in oral than in blood strains. Single-nucleotide polymorphisms (SNPs) were detected in covR regulatory and coding regions, but SNPs affecting the CovR effector domain were only present in two blood strains. Although vicR was highly conserved, vicK showed several SNPs, and SNPs affecting VicK regions important for autokinase activity were found in three blood strains.Conclusions. This study reveals transcriptional and structural diversity in covR and vicR/K, and identifies polymorphisms of functional relevance in blood strains, indicating that covR and vicRK might be important loci for S. mutans adaptation to host selective pressures associated with virulence diversity.
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Affiliation(s)
- Letícia T Oliveira
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
| | - Lívia A Alves
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
| | - Erika N Harth-Chu
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
| | - Ryota Nomura
- Department of Pediatric Dentistry, Osaka University, Graduate School of Dentistry, Osaka, Japan
| | - Kazuhiko Nakano
- Department of Pediatric Dentistry, Osaka University, Graduate School of Dentistry, Osaka, Japan
| | - Renata O Mattos-Graner
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
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Wu S, Zhang J, Peng Q, Liu Y, Lei L, Zhang H. The Role of Staphylococcus aureus YycFG in Gene Regulation, Biofilm Organization and Drug Resistance. Antibiotics (Basel) 2021; 10:antibiotics10121555. [PMID: 34943766 PMCID: PMC8698359 DOI: 10.3390/antibiotics10121555] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/09/2021] [Accepted: 12/16/2021] [Indexed: 02/05/2023] Open
Abstract
Antibiotic resistance is a serious global health concern that may have significant social and financial consequences. Methicillin-resistant Staphylococcus aureus (MRSA) infection is responsible for substantial morbidity and leads to the death of 21.8% of infected patients annually. A lack of novel antibiotics has prompted the exploration of therapies targeting bacterial virulence mechanisms. The two-component signal transduction system (TCS) enables microbial cells to regulate gene expression and the subsequent metabolic processes that occur due to environmental changes. The YycFG TCS in S. aureus is essential for bacterial viability, the regulation of cell membrane metabolism, cell wall synthesis and biofilm formation. However, the role of YycFG-associated biofilm organization in S. aureus antimicrobial drug resistance and gene regulation has not been discussed in detail. We reviewed the main molecules involved in YycFG-associated cell wall biosynthesis, biofilm development and polysaccharide intercellular adhesin (PIA) accumulation. Two YycFG-associated regulatory mechanisms, accessory gene regulator (agr) and staphylococcal accessory regulator (SarA), were also discussed. We highlighted the importance of biofilm formation in the development of antimicrobial drug resistance in S. aureus infections. Data revealed that inhibition of the YycFG pathway reduced PIA production, biofilm formation and bacterial pathogenicity, which provides a potential target for the management of MRSA-induced infections.
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Affiliation(s)
- Shizhou Wu
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu 610041, China; (S.W.); (J.Z.); (Q.P.)
| | - Junqi Zhang
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu 610041, China; (S.W.); (J.Z.); (Q.P.)
| | - Qi Peng
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu 610041, China; (S.W.); (J.Z.); (Q.P.)
| | - Yunjie Liu
- West China School of Public Health, Sichuan University, Chengdu 610041, China;
| | - Lei Lei
- West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Correspondence: (L.L.); (H.Z.)
| | - Hui Zhang
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu 610041, China; (S.W.); (J.Z.); (Q.P.)
- Correspondence: (L.L.); (H.Z.)
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