1
|
Hira J, Singh B, Halder T, Mahmutovic A, Ajayi C, Sekh AA, Hegstad K, Johannessen M, Lentz CS. Single-cell phenotypic profiling and backtracing exposes and predicts clinically relevant subpopulations in isogenic Staphylococcus aureus communities. Commun Biol 2024; 7:1228. [PMID: 39354092 PMCID: PMC11445386 DOI: 10.1038/s42003-024-06894-z] [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: 12/04/2023] [Accepted: 09/13/2024] [Indexed: 10/03/2024] Open
Abstract
Isogenic bacterial cell populations are phenotypically heterogenous and may include subpopulations of antibiotic tolerant or heteroresistant cells. The reversibility of these phenotypes and lack of biomarkers to differentiate functionally different, but morphologically identical cells is a challenge for research and clinical detection. To overcome this, we present ´Cellular Phenotypic Profiling and backTracing (CPPT)´, a fluorescence-activated cell sorting platform that uses fluorescent probes to visualize and quantify cellular traits and connects this phenotypic profile with a cell´s experimentally determined fate in single cell-derived growth and antibiotic susceptibility analysis. By applying CPPT on Staphylococcus aureus we phenotypically characterized dormant cells, exposed bimodal growth patterns in colony-derived cells and revealed different culturability of single cells on solid compared to liquid media. We demonstrate that a fluorescent vancomycin conjugate marks cellular subpopulations of vancomycin-intermediate S. aureus with increased likelihood to survive antibiotic exposure, showcasing the value of CPPT for discovery of clinically relevant biomarkers.
Collapse
Affiliation(s)
- Jonathan Hira
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Bhupender Singh
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Tirthankar Halder
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Anel Mahmutovic
- Early Biometrics & Statistical Innovation Data Science & AI AstraZeneca, Biopharmaceuticals RD AstraZeneca, Mölndal, Sweden
| | - Clement Ajayi
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | | | - Kristin Hegstad
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, 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
| | - Mona Johannessen
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Christian S Lentz
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway.
| |
Collapse
|
2
|
Xue J, Li S, Wang L, Zhao Y, Zhang L, Zheng Y, Zhang W, Chen Z, Jiang T, Sun Y. Enhanced fatty acid biosynthesis by Sigma28 in stringent responses contributes to multidrug resistance and biofilm formation in Helicobacter pylori. Antimicrob Agents Chemother 2024; 68:e0085024. [PMID: 39046242 PMCID: PMC11373199 DOI: 10.1128/aac.00850-24] [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: 06/20/2024] [Accepted: 07/08/2024] [Indexed: 07/25/2024] Open
Abstract
The metabolic state of bacteria significantly contributes to their resistance to antibiotics; however, the specific metabolic mechanisms conferring antimicrobial resistance in Helicobacter pylori remain largely understudied. Employing transcriptomic and non-targeted metabolomics, we characterized the metabolic reprogramming of H. pylori when challenged with antibiotic agents. We observed a notable increase in both genetic and key proteomic components involved in fatty acid biosynthesis. Inhibition of this pathway significantly enhanced the antibiotic susceptibility of the sensitive and multidrug-resistant H. pylori strains while also disrupting their biofilm-forming capacities. Further analysis revealed that antibiotic treatment induced a stringent response, triggering the expression of the hp0560-hp0557 operon regulated by Sigma28 (σ28). This activation in turn stimulated the fatty acid biosynthetic pathway, thereby enhancing the antibiotic tolerance of H. pylori. Our findings reveal a novel adaptive strategy employed by H. pylori to withstand antibiotic stress.
Collapse
Affiliation(s)
- Junyuan Xue
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Microbiology, School of Basic Medical Science, Shandong University, Jinan, Shandong, China
| | - Shutong Li
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Liyuan Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Microbiology, School of Basic Medical Science, Shandong University, Jinan, Shandong, China
| | - Yican Zhao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Microbiology, School of Basic Medical Science, Shandong University, Jinan, Shandong, China
| | - Lu Zhang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Microbiology, School of Basic Medical Science, Shandong University, Jinan, Shandong, China
| | - Yantong Zheng
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Microbiology, School of Basic Medical Science, Shandong University, Jinan, Shandong, China
| | - Wenxin Zhang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Microbiology, School of Basic Medical Science, Shandong University, Jinan, Shandong, China
| | - Zhenghong Chen
- Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou, Guizhou Medical University, Guiyang, China
| | - Ting Jiang
- Jiangsu Luye Diagnostic Technology, Wuxi, China
| | - Yundong Sun
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Microbiology, School of Basic Medical Science, Shandong University, Jinan, Shandong, China
| |
Collapse
|
3
|
Laborda P, Gil‐Gil T, Martínez JL, Hernando‐Amado S. Preserving the efficacy of antibiotics to tackle antibiotic resistance. Microb Biotechnol 2024; 17:e14528. [PMID: 39016996 PMCID: PMC11253305 DOI: 10.1111/1751-7915.14528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
Different international agencies recognize that antibiotic resistance is one of the most severe human health problems that humankind is facing. Traditionally, the introduction of new antibiotics solved this problem but various scientific and economic reasons have led to a shortage of novel antibiotics at the pipeline. This situation makes mandatory the implementation of approaches to preserve the efficacy of current antibiotics. The concept is not novel, but the only action taken for such preservation had been the 'prudent' use of antibiotics, trying to reduce the selection pressure by reducing the amount of antibiotics. However, even if antibiotics are used only when needed, this will be insufficient because resistance is the inescapable outcome of antibiotics' use. A deeper understanding of the alterations in the bacterial physiology upon acquisition of resistance and during infection will help to design improved strategies to treat bacterial infections. In this article, we discuss the interconnection between antibiotic resistance (and antibiotic activity) and bacterial metabolism, particularly in vivo, when bacteria are causing infection. We discuss as well how understanding evolutionary trade-offs, as collateral sensitivity, associated with the acquisition of resistance may help to define evolution-based therapeutic strategies to fight antibiotic resistance and to preserve currently used antibiotics.
Collapse
Affiliation(s)
- Pablo Laborda
- Department of Clinical MicrobiologyRigshospitaletCopenhagenDenmark
| | | | | | | |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Sanz-García F, Gil-Gil T, Laborda P, Blanco P, Ochoa-Sánchez LE, Baquero F, Martínez JL, Hernando-Amado S. Translating eco-evolutionary biology into therapy to tackle antibiotic resistance. Nat Rev Microbiol 2023; 21:671-685. [PMID: 37208461 DOI: 10.1038/s41579-023-00902-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance is currently one of the most important public health problems. The golden age of antibiotic discovery ended decades ago, and new approaches are urgently needed. Therefore, preserving the efficacy of the antibiotics currently in use and developing compounds and strategies that specifically target antibiotic-resistant pathogens is critical. The identification of robust trends of antibiotic resistance evolution and of its associated trade-offs, such as collateral sensitivity or fitness costs, is invaluable for the design of rational evolution-based, ecology-based treatment approaches. In this Review, we discuss these evolutionary trade-offs and how such knowledge can aid in informing combination or alternating antibiotic therapies against bacterial infections. In addition, we discuss how targeting bacterial metabolism can enhance drug activity and impair antibiotic resistance evolution. Finally, we explore how an improved understanding of the original physiological function of antibiotic resistance determinants, which have evolved to reach clinical resistance after a process of historical contingency, may help to tackle antibiotic resistance.
Collapse
Affiliation(s)
- Fernando Sanz-García
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Universidad de Zaragoza, Zaragoza, Spain
| | - Teresa Gil-Gil
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
- Programa de Doctorado en Biociencias Moleculares, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Clinical Microbiology, 9301, Rigshospitalet, Copenhagen, Denmark
| | - Paula Blanco
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | | | | |
Collapse
|
6
|
Martínez JL, Baquero F. What are the missing pieces needed to stop antibiotic resistance? Microb Biotechnol 2023; 16:1900-1923. [PMID: 37417823 PMCID: PMC10527211 DOI: 10.1111/1751-7915.14310] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/21/2023] [Accepted: 06/25/2023] [Indexed: 07/08/2023] Open
Abstract
As recognized by several international agencies, antibiotic resistance is nowadays one of the most relevant problems for human health. While this problem was alleviated with the introduction of new antibiotics into the market in the golden age of antimicrobial discovery, nowadays few antibiotics are in the pipeline. Under these circumstances, a deep understanding on the mechanisms of emergence, evolution and transmission of antibiotic resistance, as well as on the consequences for the bacterial physiology of acquiring resistance is needed to implement novel strategies, beyond the development of new antibiotics or the restriction in the use of current ones, to more efficiently treat infections. There are still several aspects in the field of antibiotic resistance that are not fully understood. In the current article, we make a non-exhaustive critical review of some of them that we consider of special relevance, in the aim of presenting a snapshot of the studies that still need to be done to tackle antibiotic resistance.
Collapse
Affiliation(s)
| | - Fernando Baquero
- Ramón y Cajal Institute for Health Research (IRYCIS), Department of MicrobiologyRamón y Cajal University Hospital, CIBER en Epidemiología y Salud Pública (CIBERESP)MadridSpain
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Kim JW, Lee KJ. Development of a Single-nucleotide Polymorphism Genotyping Assay for the Rapid Detection of Vancomycin-intermediate Resistance in Staphylococcus aureus Epidemic Lineage ST5. Ann Lab Med 2023; 43:355-363. [PMID: 36843404 PMCID: PMC9989536 DOI: 10.3343/alm.2023.43.4.355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/25/2022] [Accepted: 01/04/2023] [Indexed: 02/28/2023] Open
Abstract
Background Vancomycin is a treatment option for patients with severe methicillin-resistant Staphylococcus aureus (MRSA) infection. Unfortunately, reduced susceptibility to vancomycin in S. aureus is becoming increasingly common. We developed a method for the rapid and accurate diagnosis of vancomycin-intermediate resistant S. aureus (VISA). Methods We performed a microbial genome-wide association study to discriminate between VISA and vancomycin-susceptible S. aureus (VSSA) using 42 whole-genome sequences. A TaqMan single-nucleotide polymorphism (SNP) genotyping assay was developed to detect target SNPs in VISA strains. Results Four SNPs in the VISA strains resulting in nonsynonymous amino-acid substitutions were associated with reduced susceptibility to vancomycin: SA_RS01235 (G203S), SA_RS09725 (V171A), SA_RS12250 (I48F), and SA_RS12550 (G478A). These four SNPs were mainly detected in the typical hospital-associated sequence type (ST)5 clonal lineage. The TaqMan assay successfully detected all four SNPs using as little as 0.2 ng DNA per reaction. Using 10 VSSA and VISA clinical strains each, we validated that the assay accurately discriminates between VISA and VSSA. Conclusions The TaqMan SNP genotyping assay targeting four SNPs may be an alternative to current standard methods for the rapid detection of vancomycin-intermediate resistance in S. aureus epidemic lineage ST5.
Collapse
Affiliation(s)
- Jung Wook Kim
- Division of Antimicrobial Resistance Research, Center for Infectious Diseases Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - Kwang Jun Lee
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Diseases Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Korea
| |
Collapse
|
9
|
Zeden MS, Gallagher LA, Bueno E, Nolan AC, Ahn J, Shinde D, Razvi F, Sladek M, Burke Ó, O’Neill E, Fey PD, Cava F, Thomas VC, O’Gara JP. Metabolic reprogramming and altered cell envelope characteristics in a pentose phosphate pathway mutant increases MRSA resistance to β-lactam antibiotics. PLoS Pathog 2023; 19:e1011536. [PMID: 37486930 PMCID: PMC10399904 DOI: 10.1371/journal.ppat.1011536] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 08/03/2023] [Accepted: 07/04/2023] [Indexed: 07/26/2023] Open
Abstract
Central metabolic pathways control virulence and antibiotic resistance, and constitute potential targets for antibacterial drugs. In Staphylococcus aureus the role of the pentose phosphate pathway (PPP) remains largely unexplored. Mutation of the 6-phosphogluconolactonase gene pgl, which encodes the only non-essential enzyme in the oxidative phase of the PPP, significantly increased MRSA resistance to β-lactam antibiotics, particularly in chemically defined media with physiologically-relevant concentrations of glucose, and reduced oxacillin (OX)-induced lysis. Expression of the methicillin-resistance penicillin binding protein 2a and peptidoglycan architecture were unaffected. Carbon tracing and metabolomics revealed extensive metabolic reprogramming in the pgl mutant including increased flux to glycolysis, the TCA cycle, and several cell envelope precursors, which was consistent with increased β-lactam resistance. Morphologically, pgl mutant cells were smaller than wild-type with a thicker cell wall and ruffled surface when grown in OX. The pgl mutation reduced resistance to Congo Red, sulfamethoxazole and oxidative stress, and increased resistance to targocil, fosfomycin and vancomycin. Levels of lipoteichoic acids (LTAs) were significantly reduced in pgl, which may limit cell lysis, while the surface charge of pgl cells was significantly more positive. A vraG mutation in pgl reversed the increased OX resistance phenotype, and partially restored wild-type surface charge, but not LTA levels. Mutations in vraF or graRS from the VraFG/GraRS complex that regulates DltABCD-mediated d-alanylation of teichoic acids (which in turn controls β-lactam resistance and surface charge), also restored wild-type OX susceptibility. Collectively these data show that reduced levels of LTAs and OX-induced lysis combined with a VraFG/GraRS-dependent increase in cell surface positive charge are accompanied by significantly increased OX resistance in an MRSA pgl mutant.
Collapse
Affiliation(s)
- Merve S. Zeden
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Laura A. Gallagher
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Emilio Bueno
- Department of Molecular Biology, Umeå University, MIMS—Laboratory for Molecular Infection Medicine Sweden, Umeå, Sweden
| | - Aaron C. Nolan
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Jongsam Ahn
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Dhananjay Shinde
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Fareha Razvi
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Margaret Sladek
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Órla Burke
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Eoghan O’Neill
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, MIMS—Laboratory for Molecular Infection Medicine Sweden, Umeå, Sweden
| | - Vinai C. Thomas
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - James P. O’Gara
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| |
Collapse
|
10
|
Iu HTV, Fong PM, Yam HCB, Gao P, Yan B, Lai PM, Tang VYM, Li KH, Ma CW, Ng KHK, Sze KH, Yang D, Davies J, Kao RYT. Identification of a Small Molecule Compound Active against Antibiotic-Tolerant Staphylococcus aureus by Boosting ATP Synthesis. Int J Mol Sci 2023; 24:ijms24076242. [PMID: 37047217 PMCID: PMC10094146 DOI: 10.3390/ijms24076242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Antibiotic tolerance poses a threat to current antimicrobial armamentarium. Bacteria at a tolerant state survive in the presence of antibiotic treatment and account for persistence, relapse and recalcitrance of infections. Antibiotic treatment failure may occur due to antibiotic tolerance. Persistent infections are difficult to treat and are often associated with poor prognosis, imposing an enormous burden on the healthcare system. Effective strategies targeting antibiotic-tolerant bacteria are therefore highly warranted. In this study, small molecule compound SA-558 was identified to be effective against Staphylococcus aureus that are tolerant to being killed by conventional antibiotics. SA-558 mediated electroneutral transport across the membrane and led to increased ATP and ROS generation, resulting in a reduction of the population of antibiotic-tolerant bacteria. In a murine chronic infection model, of which vancomycin treatment failed, we demonstrated that SA-558 alone and in combination with vancomycin caused significant reduction of MRSA abundance. Our results indicate that SA-558 monotherapy or combinatorial therapy with vancomycin is an option for managing persistent S. aureus bacteremia infection and corroborate that bacterial metabolism is an important target for counteracting antibiotic tolerance.
Collapse
|
11
|
Zeden MS, Gallagher LA, Bueno E, Nolan AC, Ahn J, Shinde D, Razvi F, Sladek M, Burke Ó, O'Neill E, Fey PD, Cava F, Thomas VC, O'Gara JP. Metabolic reprogramming and flux to cell envelope precursors in a pentose phosphate pathway mutant increases MRSA resistance to β-lactam antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.03.530734. [PMID: 36945400 PMCID: PMC10028837 DOI: 10.1101/2023.03.03.530734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Central metabolic pathways controls virulence and antibiotic resistance, and constitute potential targets for antibacterial drugs. In Staphylococcus aureus the role of the pentose phosphate pathway (PPP) remains largely unexplored. Mutation of the 6-phosphogluconolactonase gene pgl, which encodes the only non-essential enzyme in the oxidative phase of the PPP, significantly increased MRSA resistance to β-lactam antibiotics, particularly in chemically defined media with glucose, and reduced oxacillin (OX)-induced lysis. Expression of the methicillin-resistance penicillin binding protein 2a and peptidoglycan architecture were unaffected. Carbon tracing and metabolomics revealed extensive metabolic reprogramming in the pgl mutant including increased flux to glycolysis, the TCA cycle, and several cell envelope precursors, which was consistent with increased β-lactam resistance. Morphologically, pgl mutant cells were smaller than wild-type with a thicker cell wall and ruffled surface when grown in OX. Further evidence of the pleiotropic effect of the pgl mutation was reduced resistance to Congo Red, sulfamethoxazole and oxidative stress, and increased resistance to targocil, fosfomycin and vancomycin. Reduced binding of wheat germ agglutinin (WGA) to pgl was indicative of lower wall teichoic acid/lipoteichoic acid levels or altered teichoic acid structures. Mutations in the vraFG or graRS loci reversed the increased OX resistance phenotype and restored WGA binding to wild-type levels. VraFG/GraRS was previously implicated in susceptibility to cationic antimicrobial peptides and vancomycin, and these data reveal a broader role for this multienzyme membrane complex in the export of cell envelope precursors or modifying subunits required for resistance to diverse antimicrobial agents. Altogether our study highlights important roles for the PPP and VraFG/GraRS in β-lactam resistance, which will support efforts to identify new drug targets and reintroduce β-lactams in combination with adjuvants or other antibiotics for infections caused by MRSA and other β-lactam resistant pathogens. Author summary High-level resistance to penicillin-type (β-lactam) antibiotics significantly limits the therapeutic options for patients with MRSA infections necessitating the use of newer agents, for which reduced susceptibility has already been described. Here we report for the first time that the central metabolism pentose phosphate pathway controls MRSA resistance to penicillin-type antibiotics. We comprehensively demonstrated that mutation of the PPP gene pgl perturbed metabolism in MRSA leading to increased flux to cell envelope precursors to drive increased antibiotic resistance. Moreover, increased resistance was dependent on the VraRG/GraRS multienzyme membrane complex previously implicated in resistance to antimicrobial peptides and vancomycin. Our data thus provide new insights on MRSA mechanisms of β-lactam resistance, which will support efforts to expand the treatment options for infections caused by this and other antimicrobial resistant pathogens.
Collapse
|
12
|
Fan L, Pan Z, Liao X, Zhong Y, Guo J, Pang R, Chen X, Ye G, Su Y. Uracil restores susceptibility of methicillin-resistant Staphylococcus aureus to aminoglycosides through metabolic reprogramming. Front Pharmacol 2023; 14:1133685. [PMID: 36762116 PMCID: PMC9902350 DOI: 10.3389/fphar.2023.1133685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Background: Methicillin-resistant Staphylococcus aureus (MRSA) has now become a major nosocomial pathogen bacteria and resistant to many antibiotics. Therefore, Development of novel approaches to combat the disease is especially important. The present study aimed to provide a novel approach involving the use of nucleotide-mediated metabolic reprogramming to tackle intractable methicillin-resistant S. aureus (MRSA) infections. Objective: This study aims to explore the bacterial effects and mechanism of uracil and gentamicin in S. aureus. Methods: Antibiotic bactericidal assays was used to determine the synergistic bactericidal effect of uracil and gentamicin. How did uracil regulate bacterial metabolism including the tricarboxylic acid (TCA) cycle by GC-MS-based metabolomics. Next, genes and activity of key enzymes in the TCA cycle, PMF, and intracellular aminoglycosides were measured. Finally, bacterial respiration, reactive oxygen species (ROS), and ATP levels were also assayed in this study. Results: In the present study, we found that uracil could synergize with aminoglycosides to kill MRSA (USA300) by 400-fold. Reprogramming metabolomics displayed uracil reprogrammed bacterial metabolism, especially enhanced the TCA cycle to elevate NADH production and proton motive force, thereby promoting the uptake of antibiotics. Furthermore, uracil increased cellular respiration and ATP production, resulting the generation of ROS. Thus, the combined activity of uracil and antibiotics induced bacterial death. Inhibition of the TCA cycle or ROS production could attenuate bactericidal efficiency. Moreover, uracil exhibited bactericidal activity in cooperation with aminoglycosides against other pathogenic bacteria. In a mouse mode of MRSA infection, the combination of gentamicin and uracil increased the survival rate of infected mice. Conclusion: Our results suggest that uracil enhances the activity of bactericidal antibiotics to kill Gram-positive bacteria by modulating bacterial metabolism.
Collapse
Affiliation(s)
- Lvyuan Fan
- MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zhiyu Pan
- MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xu Liao
- Center for Excellence in Regional Atmospheric Environment, and Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yilin Zhong
- MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Juan Guo
- MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinhai Chen
- Institute of Infectious Diseases Shenzhen Bay Laboratory, Shenzhen, China
| | - Guozhu Ye
- Center for Excellence in Regional Atmospheric Environment, and Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China,*Correspondence: Yubin Su, ; Guozhu Ye,
| | - Yubin Su
- MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China,*Correspondence: Yubin Su, ; Guozhu Ye,
| |
Collapse
|
13
|
Liu J, Qi M, Yuan Z, Wong TY, Song X, Lam H. Nontargeted metabolomics reveals differences in the metabolite profiling among methicillin-resistant and methicillin-susceptible Staphylococcus aureus in response to antibiotics. Mol Omics 2022; 18:948-956. [PMID: 36218091 DOI: 10.1039/d2mo00229a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Staphylococcus aureus (S. aureus) causes infections and can be fatal. In the long-term struggle against antibiotics, S. aureus has acquired resistance toward antibiotics and become more difficult to kill. Metabolomics could directly reflect the responses of S. aureus toward antibiotics, which is effective for studying the resistance mechanism of S. aureus. In this study, based on a nontargeted metabolic figure printing technique, the metabolome of a pair of isogenic methicillin-susceptible and resistant S. aureus strains ATCC25923 (MSSA) and ATCC43300 (MRSA) treated with or without oxacillin was characterized. 7 and 29 significantly changed metabolites in MRSA and MSSA were identified by combined accurate mass and mass fragmentation analysis. Pathway enrichment analysis suggested that DNA repair and flavin biosynthesis are the universal pathways of both MSSA and MRSA under antibiotic stress. MRSA systematically and effectively fights against oxacillin through precise control of energy production, PBP2a substrate biosynthesis and antioxidant function. In contrast, MSSA lacks effective defense pathways against oxacillin. The different metabolome responses of MSSA and MRSA toward antibiotics provide us with new insights into how S. aureus develops antibiotic resistance.
Collapse
Affiliation(s)
- Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China. .,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Mingyang Qi
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
| | - Zichen Yuan
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Tin Yan Wong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| |
Collapse
|
14
|
Fait A, Seif Y, Mikkelsen K, Poudel S, Wells JM, Palsson BO, Ingmer H. Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories. Proc Natl Acad Sci U S A 2022; 119:e2118262119. [PMID: 35858453 PMCID: PMC9335240 DOI: 10.1073/pnas.2118262119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 05/11/2022] [Indexed: 11/27/2022] Open
Abstract
Human infections with methicillin-resistant Staphylococcus aureus (MRSA) are commonly treated with vancomycin, and strains with decreased susceptibility, designated as vancomycin-intermediate S. aureus (VISA), are associated with treatment failure. Here, we profiled the phenotypic, mutational, and transcriptional landscape of 10 VISA strains adapted by laboratory evolution from one common MRSA ancestor, the USA300 strain JE2. Using functional and independent component analysis, we found that: 1) despite the common genetic background and environmental conditions, the mutational landscape diverged between evolved strains and included mutations previously associated with vancomycin resistance (in vraT, graS, vraFG, walKR, and rpoBCD) as well as novel adaptive mutations (SAUSA300_RS04225, ssaA, pitAR, and sagB); 2) the first wave of mutations affected transcriptional regulators and the second affected genes involved in membrane biosynthesis; 3) expression profiles were predominantly strain-specific except for sceD and lukG, which were the only two genes significantly differentially expressed in all clones; 4) three independent virulence systems (φSa3, SaeR, and T7SS) featured as the most transcriptionally perturbed gene sets across clones; 5) there was a striking variation in oxacillin susceptibility across the evolved lineages (from a 10-fold increase to a 63-fold decrease) that also arose in clinical MRSA isolates exposed to vancomycin and correlated with susceptibility to teichoic acid inhibitors; and 6) constitutive expression of the VraR regulon explained cross-susceptibility, while mutations in walK were associated with cross-resistance. Our results show that adaptation to vancomycin involves a surprising breadth of mutational and transcriptional pathways that affect antibiotic susceptibility and possibly the clinical outcome of infections.
Collapse
Affiliation(s)
- Anaëlle Fait
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, 1870 Denmark
| | - Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
- Merck & Co., Inc., South San Francisco, CA 94080
| | - Kasper Mikkelsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, 1870 Denmark
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Jerry M. Wells
- Host-Microbe Interactomics, Animal Sciences Group, Wageningen University, Wageningen, The Netherlands
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, 1870 Denmark
| |
Collapse
|
15
|
Li Y, Lu W, Zheng X, Zhang L, Dong W, Zhao X, Zhao Z, Zhang Z. Norvancomycin for the Treatment of Central Nervous System MRSA Infections: a Randomized Controlled Trial: Norvancomycin for the Treatment of Central nervous system MRSA infections. Eur J Pharm Sci 2022; 177:106266. [PMID: 35868433 DOI: 10.1016/j.ejps.2022.106266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022]
Abstract
Combined intravenous and intrathecal administration of norvancomycin (NVCM) is routinely employed in treating methicillin-resistant Staphylococcus aureus (MRSA) ventriculitis in patients following craniotomy. However, the optimal dosing regimen, the pharmacokinetics (PK) of NVCM in cerebrospinal fluid (CSF), and the clinical outcome are yet to be elucidated. Herein, a single-center randomized controlled trial was conducted in the Neurosurgery Department of the Second Hospital of Hebei Medical University (Shijiazhuang, China). Patients with MRSA ventriculitis after craniotomy were randomly assigned to two groups. The control group received 800 mg NVCM intravenously every 12 h, and the experimental group received 800 mg NVCM intravenously every 12 h and 16 mg NVCM intrathecal administration every 24 h. The primary outcome was the length of therapy, while the secondary outcomes included the area under the concentration-time curve in 0-24 h/minimum inhibitory concentration ratio (AUC0-24h/MIC) of NVCM in CSF. A total of 29 patients (14 in the experimental group and 15 in the control group) were included in this study. Of these, 24 constituted the final analysis population, with 12 in each group. The average length of therapy in the experimental group was markedly shorter than that of the control group (11.2 ± 2.6 days vs. 16.6 ± 5.2 days, P = 0.005), while the AUC0-24h/MIC in the experimental group was significantly higher than that in the control group (2306.57 ± 928.58 vs. 46.83 ± 27.48, P <0.001) with no increase in adverse reactions. Combined intravenous and intrathecal administration can shorten the treatment time of intracranial infection without higher adverse reaction risks in our research. Further studies with larger sample size are warranted to verify its safety and efficacy.
Collapse
Affiliation(s)
- Yaqian Li
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wenpeng Lu
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xuecheng Zheng
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Linhui Zhang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Weichong Dong
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiaoxiao Zhao
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zongmao Zhao
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
| | - Zhiqing Zhang
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
| |
Collapse
|
16
|
Chen YT, Yang KX, Dai ZY, Yi H, Peng XX, Li H, Chen ZG. Repressed Central Carbon Metabolism and Its Effect on Related Metabolic Pathways in Cefoperazone/Sulbactam-Resistant Pseudomonas aeruginosa. Front Microbiol 2022; 13:847634. [PMID: 35308347 PMCID: PMC8927769 DOI: 10.3389/fmicb.2022.847634] [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: 01/03/2022] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
Metabolic shift and antibiotic resistance have been reported in Pseudomonas aeruginosa. However, the global metabolic characteristics remain largely unknown. The present study characterizes the central carbon metabolism and its effect on other metabolic pathways in cefoperazone-sulbactam (SCF)-resistant P. aeruginosa (PA-RSCF). GC-MS-based metabolomics shows a repressed central carbon metabolism in PA-RSCF, which is confirmed by measuring expression of genes and activity of enzymes in the metabolism. Furthermore, expression of the genes that encode the enzymes for the first step of fatty acid biosynthesis, glutamate metabolism, and electron transport chain is reduced, confirmed by their enzymatic activity assay, and the key enzyme for riboflavin metabolism is also reduced, indicating the decreased metabolic flux to the four related metabolic pathways. Moreover, the role of the reduced riboflavin metabolism, being related to ROS generation, in SCF resistance is explored. Exogenous H2O2 potentiates SCF-mediated killing in a dose-dependent manner, suggesting that the decreased ROS resulted from the reduced riboflavin metabolism that contributed to the resistance. These results indicate that the repressed central carbon metabolism and related riboflavin metabolism contribute to SCF resistance, but increasing ROS can restore SCF sensitivity. These findings characterize the repressed central carbon metabolism and its effect on other metabolic pathways as the global metabolic features in PA-RSCF.
Collapse
Affiliation(s)
- Yue-tao Chen
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou, China
| | - Ke-xin Yang
- Department of Pediatrics, Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhen-yuan Dai
- Department of Pediatrics, Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huan Yi
- Department of Pediatrics, Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuan-xian Peng
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hui Li
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Hui Li,
| | - Zhuang-gui Chen
- Department of Pediatrics, Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Zhuang-gui Chen,
| |
Collapse
|
17
|
Gil-Gil T, Ochoa-Sánchez LE, Baquero F, Martínez JL. Antibiotic resistance: Time of synthesis in a post-genomic age. Comput Struct Biotechnol J 2021; 19:3110-3124. [PMID: 34141134 PMCID: PMC8181582 DOI: 10.1016/j.csbj.2021.05.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance has been highlighted by international organizations, including World Health Organization, World Bank and United Nations, as one of the most relevant global health problems. Classical approaches to study this problem have focused in infected humans, mainly at hospitals. Nevertheless, antibiotic resistance can expand through different ecosystems and geographical allocations, hence constituting a One-Health, Global-Health problem, requiring specific integrative analytic tools. Antibiotic resistance evolution and transmission are multilayer, hierarchically organized processes with several elements (from genes to the whole microbiome) involved. However, their study has been traditionally gene-centric, each element independently studied. The development of robust-economically affordable whole genome sequencing approaches, as well as other -omic techniques as transcriptomics and proteomics, is changing this panorama. These technologies allow the description of a system, either a cell or a microbiome as a whole, overcoming the problems associated with gene-centric approaches. We are currently at the time of combining the information derived from -omic studies to have a more holistic view of the evolution and spread of antibiotic resistance. This synthesis process requires the accurate integration of -omic information into computational models that serve to analyse the causes and the consequences of acquiring AR, fed by curated databases capable of identifying the elements involved in the acquisition of resistance. In this review, we analyse the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.
Collapse
Affiliation(s)
- Teresa Gil-Gil
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
| | | |
Collapse
|
18
|
Bellaviti G, Balsamo F, Iosa M, Vella D, Pistarini C. Influence of systemic infection and comorbidities on rehabilitation outcomes in severe acquired brain injury. Eur J Phys Rehabil Med 2020; 57:69-77. [PMID: 33165309 DOI: 10.23736/s1973-9087.20.05939-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Severe infectious complications are a frequent problem in patients with disability due to a severe acquired brain injury. Previous studies reported that the rehabilitation outcome is significantly lower in patients colonized or infected. However, these results could be influenced by comorbidities of those patients admitted in rehabilitation hospital with a lower functional status. AIM To explore the influence of systemic infection, in particular concerning multidrug resistant bacteria and analyze the role of comorbidities, as a risk factor for the development of systemic infection, on rehabilitation outcomes in patients with severe brain injury. DESIGN This research is a cohort, prospective-observational study, comparing patients with and without systemic infections, in terms of rehabilitation outcomes. SETTING An Italian Intensive Care Rehabilitation Department. POPULATION A group of 221 patients (mean age: 59 years, range: 16-93 years, 127 males, 94 females) with severe acquired brain injury admitted to rehabilitation hospital. METHODS We compared the rehabilitation outcomes between patients with and without a systemic infection (at least a positive blood culture) during the rehabilitation period. A secondary analysis was performed on 70 patients with infection versus 70 patients without infection, matched for functional status at admission. The used clinical scores were: Cumulative Illness Rating Scale for Geriatrics (CIRS-G), Coma Recovery Scale Revised (CRS-R), Glasgow Coma Scale (GCS), Functional Independence Measure (FIM), Glasgow Outcome Scale (GOS), Disability Rating Scale (DRS), Levels of Cognitive Functioning (LCF) administered at admission and discharge. Length of hospitalization and the role of comorbidities were also considered. RESULTS The group of patients with systemic infection (in particular due to Gram-negative bacteria) had a significantly lower outcome for 5 out 6 clinical scales and with a more than doubled length of hospitalization (P<0.001). However, these patients with, at least, a positive blood culture resulted having lower functional status at admission. In the secondary analysis, worst outcome was found in patients with positive blood culture in terms of FIM (P=0.033), GOS (P=0.048), and CRS-R (P=0.001). CONCLUSIONS Systemic infections during rehabilitation increased the length of hospitalization and reduce the rehabilitative outcomes, even when the analysis was performed on groups matched for the functional status at admission. Moreover, the cardiological and endocrine metabolic comorbidities seem to influence the outcome, without representing a further risk factor for systemic infection. CLINICAL REHABILITATION IMPACT The impact of infections during rehabilitation inpatient should be more taken into account, with specific procedures and suitable environments to avoid the diffusions of infections.
Collapse
Affiliation(s)
- Gianluca Bellaviti
- Neurorehabilitation Division, ICS Maugeri SPA SB, Institute of Pavia, IRCCS, Pavia, Italy -
| | - Francesca Balsamo
- Neurorehabilitation Division, ICS Maugeri SPA SB, Institute of Veruno, IRCCS, Novara, Italy.,Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Marco Iosa
- Clinical Laboratory of Experimental Neurorehabilitation, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Danila Vella
- Laboratory of Informatics and Systems Engineering for Clinical Research, ICS Maugeri SPA SB, Institute of Pavia, IRCCS, Pavia, Italy
| | - Caterina Pistarini
- Head of Severe Brain Injury Rehabilitation Unit, ICS Maugeri SPA SB, Institute of Nervi, IRCCS, Genoa, Italy
| |
Collapse
|
19
|
Reed JM, Gardner SG, Mishra NN, Bayer AS, Somerville GA. Metabolic interventions for the prevention and treatment of daptomycin non-susceptibility in Staphylococcus aureus. J Antimicrob Chemother 2020; 74:2274-2283. [PMID: 31074482 DOI: 10.1093/jac/dkz194] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/03/2019] [Accepted: 04/07/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND A major developing problem in the treatment of Staphylococcus aureus infections is the emergence of resistance during treatment with daptomycin. Previous metabolomic analyses of isogenic S. aureus strains prior to and after evolution into a daptomycin non-susceptible (DapNS) state provided important metabolic information about this transition (e.g. perturbations of the tricarboxylic acid cycle). OBJECTIVES To assess the significance of these metabolic changes, in vitro susceptibility to daptomycin was determined in daptomycin-susceptible (DapS) and DapNSS. aureus strains cultivated with metabolic inhibitors targeting these changes. METHODS Only inhibitors that are approved for use in humans were chosen (i.e. fosfomycin, valproate, trimetazidine and 6-mercaptopurine) to assess the importance of metabolic pathways for daptomycin non-susceptibility. The ability of these inhibitors to forestall the emergence of DapNS strains was also assessed. RESULTS The combination of daptomycin and fosfomycin synergistically killed both DapS and DapNS strains in vitro and enhanced the in vivo outcome against a DapNS strain in experimental endocarditis. Interestingly, fosfomycin acts on the peptidoglycan biosynthetic enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA); however, it also had a significant effect on the enzymatic activity of enolase, an essential enzyme in S. aureus. While fosfomycin acted synergistically with daptomycin, it failed to prevent the in vitro evolution of daptomycin non-susceptibility. In contrast, trimetazidine, an anti-angina drug that stimulates glucose oxidation, abolished the ability of DapSS. aureus strains to transition to a DapNS state. CONCLUSIONS These data reveal that metabolic adaptations associated with DapNS strains can be targeted to prevent the emergence of and/or reverse pre-existing resistance to daptomycin.
Collapse
Affiliation(s)
- Joseph M Reed
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0905, USA
| | - Stewart G Gardner
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0905, USA
| | - Nagendra N Mishra
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA.,Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Arnold S Bayer
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA.,Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Greg A Somerville
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0905, USA
| |
Collapse
|
20
|
Parrett A, Reed JM, Gardner SG, Mishra NN, Bayer AS, Powers R, Somerville GA. Metabolic changes associated with adaptive resistance to daptomycin in Streptococcus mitis-oralis. BMC Microbiol 2020; 20:162. [PMID: 32539684 PMCID: PMC7296729 DOI: 10.1186/s12866-020-01849-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/09/2020] [Indexed: 12/26/2022] Open
Abstract
Background Viridans group streptococci of the Streptococcus mitis-oralis subgroup are important endovascular pathogens. They can rapidly develop high-level and durable non-susceptibility to daptomycin both in vitro and in vivo upon exposure to daptomycin. Two consistent genetic adaptations associated with this phenotype (i.e., mutations in cdsA and pgsA) lead to the depletion of the phospholipids, phosphatidylglycerol and cardiolipin, from the bacterial membrane. Such alterations in phospholipid biosynthesis will modify carbon flow and change the bacterial metabolic status. To determine the metabolic differences between daptomycin-susceptible and non-susceptible bacteria, the physiology and metabolomes of S. mitis-oralis strains 351 (daptomycin-susceptible) and 351-D10 (daptomycin non-susceptible) were analyzed. S. mitis-oralis strain 351-D10 was made daptomycin non-susceptible through serial passage in the presence of daptomycin. Results Daptomycin non-susceptible S. mitis-oralis had significant alterations in glucose catabolism and a re-balancing of the redox status through amino acid biosynthesis relative to daptomycin susceptible S. mitis-oralis. These changes were accompanied by a reduced capacity to generate biomass, creating a fitness cost in exchange for daptomycin non-susceptibility. Conclusions S. mitis-oralis metabolism is altered in daptomycin non-susceptible bacteria relative to the daptomycin susceptible parent strain. As demonstrated in Staphylococcus aureus, inhibiting the metabolic changes that facilitate the transition from a daptomycin susceptible state to a non-susceptible one, inhibits daptomycin non-susceptibility. By preventing these metabolic adaptations in S. mitis-oralis, it should be possible to deter the formation of daptomycin non-susceptibility.
Collapse
Affiliation(s)
- Allison Parrett
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA
| | - Joseph M Reed
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0905, USA.,Present address: Chemical Testing Program, Wyoming Department of Health, Cheyenne, Wyoming, 82002, USA
| | - Stewart G Gardner
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0905, USA.,Present address: Department of Biological Sciences, Emporia State University, Emporia, Kansas, 66801, USA
| | - Nagendra N Mishra
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, 90502, USA.,David Geffen School of Medicine University of California Los Angeles, Los Angeles, California, 90095, USA
| | - Arnold S Bayer
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, 90502, USA.,David Geffen School of Medicine University of California Los Angeles, Los Angeles, California, 90095, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA. .,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA.
| | - Greg A Somerville
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0905, USA.
| |
Collapse
|
21
|
Zhang S, Yang MJ, Peng B, Peng XX, Li H. Reduced ROS-mediated antibiotic resistance and its reverting by glucose in Vibrio alginolyticus. Environ Microbiol 2020; 22:4367-4380. [PMID: 32441046 DOI: 10.1111/1462-2920.15085] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/13/2020] [Indexed: 01/16/2023]
Abstract
Antibiotic-resistant Vibrio alginolyticus poses a big challenge to human health and food safety. It is urgently needed to understand the mechanisms underlying antibiotic resistance to develop effective approaches for the control. Here we explored the metabolic difference between gentamicin-resistant V. alginolyticus (VA-RGEN ) and gentamicin-sensitive V. alginolyticus (VA-S), and found that the reactive oxygen species (ROS) generation was altered. Compared with VA-S, the ROS content in VA-RGEN was reduced due to the decreased generation and increased breakdown of ROS. The decreased production of ROS was attributed to the decreased central carbon metabolism, which is associated with the resistance to gentamicin. As such a mechanism, we exogenously administrated VA-RGEN with the glucose that activated the central carbon metabolism and promoted the generation of ROS, but decreased the breakdown of ROS in VA-RGEN . The gentamicin-mediated killing was increased with the elevation of the ROS level by a synergistic effect between gentamicin and exogenous glucose. The synergistic effect was inhibited by thiourea, a scavenger of ROS. These results reveal a reduced ROS-mediated antibiotic resistance mechanism and its reversal by exogenous glucose.
Collapse
Affiliation(s)
- Song Zhang
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, 510006, China
| | - Man-Jun Yang
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, 510006, China
| | - Bo Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, 510006, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Xuan-Xian Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, 510006, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Hui Li
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, 510006, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| |
Collapse
|
22
|
Tan X, Ramond E, Jamet A, Barnier JP, Decaux-Tramoni B, Dupuis M, Euphrasie D, Tros F, Nemazanyy I, Ziveri J, Nassif X, Charbit A, Coureuil M. Transketolase of Staphylococcus aureus in the Control of Master Regulators of Stress Response During Infection. J Infect Dis 2020; 220:1967-1976. [PMID: 31420648 DOI: 10.1093/infdis/jiz404] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/07/2019] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus aureus is a leading cause of both acute and chronic infections in humans. The importance of the pentose phosphate pathway (PPP) during S. aureus infection is currently largely unexplored. In the current study, we focused on one key PPP enzyme, transketolase (TKT). We showed that inactivation of the unique gene encoding TKT activity in S. aureus USA300 (∆tkt) led to drastic metabolomic changes. Using time-lapse video imaging and mice infection, we observed a major defect of the ∆tkt strain compared with wild-type strain in early intracellular proliferation and in the ability to colonize kidneys. Transcriptional activity of the 2 master regulators sigma B and RpiRc was drastically reduced in the ∆tkt mutant during host cells invasion. The concomitant increased RNAIII transcription suggests that TKT-or a functional PPP-strongly influences the ability of S. aureus to proliferate within host cells by modulating key transcriptional regulators.
Collapse
Affiliation(s)
- Xin Tan
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| | - Elodie Ramond
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| | - Anne Jamet
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| | - Jean-Philippe Barnier
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| | | | - Marion Dupuis
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| | - Daniel Euphrasie
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| | - Fabiola Tros
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| | - Ivan Nemazanyy
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris.,Plateforme Métabolomique Institut Necker, Structure Fédérative de Recherche Necker, Université Paris Descartes, France
| | - Jason Ziveri
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| | - Xavier Nassif
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| | - Alain Charbit
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| | - Mathieu Coureuil
- Université de Paris.,INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris
| |
Collapse
|
23
|
Valentin E, Bottomley AL, Chilambi GS, Harry EJ, Amal R, Sotiriou GA, Rice SA, Gunawan C. Heritable nanosilver resistance in priority pathogen: a unique genetic adaptation and comparison with ionic silver and antibiotics. NANOSCALE 2020; 12:2384-2392. [PMID: 31930233 DOI: 10.1039/c9nr08424j] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The past decade has seen the incorporation of antimicrobial nanosilver (NAg) into medical devices, and, increasingly, in everyday 'antibacterial' products. With the continued rise of antibiotic resistant bacteria, there are concerns that these priority pathogens will also develop resistance to the extensively commercialized nanoparticle antimicrobials. Herein, this work reports the emergence of stable resistance traits to NAg in the WHO-listed priority pathogen Staphylococcus aureus, which has previously been suggested to have no, or very low, capacity for silver resistance. With no native presence of genetically encoded silver defence mechanisms, the work showed that the bacterium is dependent on mutation of physiologically essential genes, including those involved in nucleotide synthesis and oxidative stress defence. While some mutations were uniquely associated with resistance to NAg, the study also found common mutations that could be protective against both NAg and ionic silver. This is consistent with the observation of NAg/ionic silver cross-resistance. These mutations were detected following withdrawal of the silver exposure, denoting heritable characteristics that allow for spread of the resistance traits even with discontinued silver use. Heritable silver resistance in priority pathogen cautions that these nanoparticle antimicrobials should only be used as needed, to preserve their efficacy for treating infections.
Collapse
Affiliation(s)
| | - Amy L Bottomley
- Ithree institute, University of Technology Sydney, NSW 2007, Australia.
| | | | - Elizabeth J Harry
- Ithree institute, University of Technology Sydney, NSW 2007, Australia.
| | - Rose Amal
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Georgios A Sotiriou
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Scott A Rice
- Ithree institute, University of Technology Sydney, NSW 2007, Australia. and Singapore Centre for Environmental Life Sciences Engineering, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore
| | - Cindy Gunawan
- Ithree institute, University of Technology Sydney, NSW 2007, Australia. and School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| |
Collapse
|
24
|
Qu Q, Wang J, Cui W, Zhou Y, Xing X, Che R, Liu X, Chen X, Bello-Onaghise G, Dong C, Li Z, Li X, Li Y. In vitro activity and In vivo efficacy of Isoliquiritigenin against Staphylococcus xylosus ATCC 700404 by IGPD target. PLoS One 2019; 14:e0226260. [PMID: 31860659 PMCID: PMC6924684 DOI: 10.1371/journal.pone.0226260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/23/2019] [Indexed: 12/16/2022] Open
Abstract
Staphylococcus xylosus (S. xylosus) is a type of coagulase-negative Staphylococcus, which was previously considered as non-pathogenic. However, recent studies have linked it with cases of mastitis in cows. Isoliquiritigenin (ISL) is a bioactive compound with pharmacological functions including antibacterial activity. In this study, we evaluated the effect of ISL on S. xylosus in vitro and in vivo. The MIC of ISL against S. xylosus was 80 μg/mL. It was observed that sub-MICs of ISL (1/2MIC, 1/4MIC, 1/8MIC) significantly inhibited the formation of S. xylosus biofilm in vitro. Previous studies have observed that inhibiting imidazole glycerol phosphate dehydratase (IGPD) concomitantly inhibited biofilm formation in S. xylosus. So, we designed experiments to target the formation of IGPD or inhibits its activities in S. xylosus ATCC 700404. The results indicated that the activity of IGPD and its histidine content decreased significantly under 1/2 MIC (40 μg/mL) ISL, and the expression of IGPD gene (hisB) and IGPD protein was significantly down-regulated. Furthermore, Bio-layer interferometry experiments showed that ISL directly interacted with IGPD protein (with strong affinity; KD = 234 μM). In addition, molecular docking was used to predict the binding mode of ISL and IGPD. In vivo tests revealed that, ISL significantly reduced TNF-α and IL-6 levels, mitigated the destruction of the mammary glands and reversed the production of inflammatory cells in mice. The results of the study suggest that, ISL may inhibit S. xylosus growth by acting on IGPD, which can be used as a target protein to treat infections caused by S. xylosus.
Collapse
Affiliation(s)
- Qianwei Qu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Jinpeng Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Wenqiang Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Yonghui Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Xiaoxu Xing
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Ruixiang Che
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Xin Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Xueying Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - God’spower Bello-Onaghise
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Chunliu Dong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Zhengze Li
- Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, P. R. China
| | - Xiubo Li
- Feed Research Institute Chinese Academy of Agricultural Science, Harbin, Heilongjiang, P. R. China
| | - Yanhua Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
- * E-mail:
| |
Collapse
|
25
|
Abstract
Drug discovery is an extremely difficult and challenging endeavor with a very high failure rate. The task of identifying a drug that is safe, selective, and effective is a daunting proposition because disease biology is complex and highly variable across patients. Metabolomics enables the discovery of disease biomarkers, which provides insights into the molecular and metabolic basis of disease and may be used to assess treatment prognosis and outcome. In this regard, metabolomics has evolved to become an important component of the drug discovery process to resolve efficacy and toxicity issues and as a tool for precision medicine. A detailed description of an experimental protocol is presented that outlines the application of NMR metabolomics to the drug discovery pipeline. This includes (1) target identification by understanding the metabolic dysregulation in diseases, (2) predicting the mechanism of action of newly discovered or existing drug therapies, (3) and using metabolomics to screen a chemical lead to assess biological activity. Unlike other OMICS approaches, the metabolome is "fragile" and may be negatively impacted by improper sample collection, storage, and extraction procedures. Similarly, biologically irrelevant conclusions may result from incorrect data collection, preprocessing or processing procedures, or the erroneous use of univariate and multivariate statistical methods. These critical concerns are also addressed in the protocol.
Collapse
|
26
|
Bhinderwala F, Lei S, Woods J, Rose J, Marshall DD, Riekeberg E, Leite ADL, Morton M, Dodds ED, Franco R, Powers R. Metabolomics Analyses from Tissues in Parkinson's Disease. Methods Mol Biol 2019; 1996:217-257. [PMID: 31127560 DOI: 10.1007/978-1-4939-9488-5_19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabolomics has been successfully applied to study neurological and neurodegenerative disorders including Parkinson's disease for (1) the identification of potential biomarkers of onset and disease progression; (2) the identification of novel mechanisms of disease progression; and (3) the assessment of treatment prognosis and outcome. Reproducible and efficient extraction of metabolites is imperative to the success of any metabolomics investigation. Unlike other omics techniques, the composition of the metabolome can be negatively impacted by the preparation, processing, and handling of these samples. The proper choice of data collection, preprocessing, and processing protocols is similarly important to the design of an effective metabolomics experiment. Likewise, the correct application of univariate and multivariate statistical methods is essential for providing biologically relevant insights. In this chapter, we have outlined a detailed metabolomics workflow that addresses all of these issues. A step-by-step protocol from the preparation of neuronal cells and metabolomic tissue samples to their metabolic analyses using nuclear magnetic resonance, mass spectrometry, and chemometrics is presented.
Collapse
Affiliation(s)
- Fatema Bhinderwala
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Shulei Lei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jade Woods
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jordan Rose
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.,Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Eli Riekeberg
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Aline De Lima Leite
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Martha Morton
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Eric D Dodds
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rodrigo Franco
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA. .,Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA. .,Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, USA. .,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, USA.
| |
Collapse
|
27
|
Goad B, Harris LK. Identification and prioritization of macrolideresistance genes with hypothetical annotation inStreptococcus pneumoniae. Bioinformation 2018; 14:488-498. [PMID: 31223208 PMCID: PMC6563660 DOI: 10.6026/97320630014488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 11/23/2022] Open
Abstract
Macrolide resistant Streptococcus pneumoniae infections have limited treatment options. While some resistance mechanisms are well
established, ample understanding is limited by incomplete genome annotation (hypothetical genes). Some hypothetical genes encode a
domain of unknown function (DUF), a conserved protein domain with uncharacterized function. Here, we identify and confirm macrolide
resistance genes. We further explore DUFs from macrolide resistance hypothetical genes to prioritize them for experimental
characterization. We found gene similarities between two macrolide resistance gene signatures from untreated and either erythromycin- or
spiramycin-treated resistant Streptococcus pneumoniae. We confirmed the association of these gene sets with macrolide resistance through
comparison to gene signatures from (i) second erythromycin resistant Streptococcus pneumoniae strain, and (ii) erythromycin-treated
sensitive Streptococcus pneumoniae strain, both from non-overlapping datasets. Examination into which cellular processes these macrolide
resistance genes belong found connections to known resistance mechanisms such as increased amino acid biosynthesis and efflux genes,
and decreased ribonucleotide biosynthesis genes, highlighting the predictive ability of the method used. 22 genes had hypothetical
annotation with 10 DUFs associated with macrolide resistance. DUF characterization could uncover novel co-therapies that restore
macrolide efficacy across multiple macrolide resistant species. Application of the methods to other antibiotic resistances could
revolutionize treatment of resistant infections
Collapse
Affiliation(s)
- Blue Goad
- Davenport University, 200 S. Grand Ave, Lansing, MI, 48933, USA
| | - Laura K Harris
- Davenport University, 200 S. Grand Ave, Lansing, MI, 48933, USA
| |
Collapse
|
28
|
Gebregiworgis T, Bhinderwala F, Purohit V, Chaika NV, Singh PK, Powers R. Insights into gemcitabine resistance and the potential for therapeutic monitoring. Metabolomics 2018; 14:156. [PMID: 30830412 PMCID: PMC6620022 DOI: 10.1007/s11306-018-1452-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/19/2018] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Gemcitabine is an important component of pancreatic cancer clinical management. Unfortunately, acquired gemcitabine resistance is widespread and there are limitations to predicting and monitoring therapeutic outcomes. OBJECTIVE To investigate the potential of metabolomics to differentiate pancreatic cancer cells that develops resistance or respond to gemcitabine treatment. RESULTS We applied 1D 1H and 2D 1H-13C HSQC NMR methods to profile the metabolic signature of pancreatic cancer cells. 13C6-glucose labeling identified 30 key metabolites uniquely altered between wild-type and gemcitabine-resistant cells upon gemcitabine treatment. Gemcitabine resistance was observed to reprogram glucose metabolism and to enhance the pyrimidine synthesis pathway. Myo-inositol, taurine, glycerophosphocholine and creatinine phosphate exhibited a "binary switch" in response to gemcitabine treatment and acquired resistance. CONCLUSION Metabolic differences between naïve and resistant pancreatic cancer cells and, accordingly, their unique responses to gemcitabine treatment were revealed, which may be useful in the clinical setting for monitoring a patient's therapeutic response.
Collapse
Affiliation(s)
- Teklab Gebregiworgis
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Fatema Bhinderwala
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Vinee Purohit
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nina V Chaika
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Pankaj K Singh
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
| |
Collapse
|
29
|
Novais Â, Freitas AR, Rodrigues C, Peixe L. Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing. Eur J Clin Microbiol Infect Dis 2018; 38:427-448. [DOI: 10.1007/s10096-018-3431-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/11/2018] [Indexed: 01/25/2023]
|
30
|
The depressed central carbon and energy metabolisms is associated to the acquisition of levofloxacin resistance in Vibrio alginolyticus. J Proteomics 2018; 181:83-91. [DOI: 10.1016/j.jprot.2018.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 02/28/2018] [Accepted: 04/02/2018] [Indexed: 01/22/2023]
|