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Mishra NN, de Paula Baptista R, Tran TT, Lapitan CK, Garcia-de-la-Maria C, Miró JM, Proctor RA, Bayer AS. Membrane Phenotypic, Metabolic and Genotypic Adaptations of Streptococcus oralis Strains Destined to Rapidly Develop Stable, High-Level Daptomycin Resistance during Daptomycin Exposures. Antibiotics (Basel) 2023; 12:1083. [PMID: 37508179 PMCID: PMC10376253 DOI: 10.3390/antibiotics12071083] [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: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
The Streptococcus mitis-oralis subgroup of viridans group streptococci are important human pathogens. We previously showed that a substantial portion of S. mitis-oralis strains (>25%) are 'destined' to develop rapid, high-level, and stable daptomycin (DAP) resistance (DAP-R) during DAP exposures in vitro. Such DAP-R is often accompanied by perturbations in distinct membrane phenotypes and metabolic pathways. The current study evaluated two S. oralis bloodstream isolates, 73 and 205. Strain 73 developed stable, high-level DAP-R (minimum inhibitory concentration [MIC] > 256 µg/mL) within 2 days of in vitro DAP passage ("high level" DAP-R [HLDR]). In contrast, strain 205 evolved low-level and unstable DAP-R (MIC = 8 µg/mL) under the same exposure conditions in vitro ("non-HLDR"). Comparing the parental 73 vs. 73-D2 (HLDR) strain-pair, we observed the 73-D2 had the following major differences: (i) altered cell membrane (CM) phospholipid profiles, featuring the disappearance of phosphatidylglycerol (PG) and cardiolipin (CL), with accumulation of the PG-CL pathway precursor, phosphatidic acid (PA); (ii) enhanced CM fluidity; (iii) increased DAP surface binding; (iv) reduced growth rates; (v) decreased glucose utilization and lactate accumulation; and (vi) increased enzymatic activity within the glycolytic (i.e., lactate dehydrogenase [LDH]) and lipid biosynthetic (glycerol-3-phosphate dehydrogenase [GPDH]) pathways. In contrast, the 205 (non-HLDR) strain-pair did not show these same phenotypic or metabolic changes over the 2-day DAP exposure. WGS analyses confirmed the presence of mutations in genes involved in the above glycolytic and phospholipid biosynthetic pathways in the 73-D2 passage variant. These data suggest that S. oralis strains which are 'destined' to rapidly develop HLDR do so via a conserved cadre of genotypic, membrane phenotypic, and metabolic adaptations.
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Affiliation(s)
- Nagendra N Mishra
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, 1124 West Carson St. MRL Bldg. Room 224, Torrance, CA 90502, USA
- The David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Rodrigo de Paula Baptista
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX 77030, USA
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Medicine, Weill-Cornell Medical College, New York, NY 10065, USA
| | - Truc T Tran
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX 77030, USA
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Medicine, Weill-Cornell Medical College, New York, NY 10065, USA
| | - Christian K Lapitan
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, 1124 West Carson St. MRL Bldg. Room 224, Torrance, CA 90502, USA
| | - Cristina Garcia-de-la-Maria
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Jose M Miró
- CIBERINFEC, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Richard A Proctor
- The Department of Medicine, University of Wisconsin School of Medicine, Madison, WI 53705, USA
| | - Arnold S Bayer
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, 1124 West Carson St. MRL Bldg. Room 224, Torrance, CA 90502, USA
- The David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
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Yang B, Yao H, Li D, Liu Z. The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface. Curr Res Struct Biol 2021; 3:312-323. [PMID: 34901881 PMCID: PMC8640168 DOI: 10.1016/j.crstbi.2021.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/24/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Phosphatidylglycerol is a crucial phospholipid found ubiquitously in biological membranes of prokaryotic and eukaryotic cells. The phosphatidylglycerol phosphate (PGP) synthase (PgsA), a membrane-embedded enzyme, catalyzes the primary reaction of phosphatidylglycerol biosynthesis. Mutations in pgsA frequently correlate with daptomycin resistance in Staphylococcus aureus and other prevalent infectious pathogens. Here we report the crystal structures of S. aureus PgsA (SaPgsA) captured at two distinct states of the catalytic process, with lipid substrate (cytidine diphosphate-diacylglycerol, CDP-DAG) or product (PGP) bound to the active site within a trifurcated amphipathic cavity. The hydrophilic head groups of CDP-DAG and PGP occupy two different pockets in the cavity, inducing local conformational changes. An elongated membrane-exposed surface groove accommodates the fatty acyl chains of CDP-DAG/PGP and opens a lateral portal for lipid entry/release. Remarkably, the daptomycin resistance-related mutations mostly cluster around the active site, causing reduction of enzymatic activity. Our results provide detailed mechanistic insights into the dynamic catalytic process of PgsA and structural frameworks beneficial for development of antimicrobial agents targeting PgsA from pathogenic bacteria. PgsA uses a trifurcated amphipathic cavity for binding of substrates or products. Conversion of CDP-DAG to PGP induces local conformational changes in PgsA. Daptomycin-resistant mutations of PgsA mostly lead to reduced catalytic activity. A structure-based five-state model is proposed for the synthesis of PGP by PgsA.
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Affiliation(s)
- Bowei Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hebang Yao
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 201210, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 201210, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenfeng Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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Brazeau NF, Levinson KJ, Schranz A, Moser KA, Hollis I, Iyer P, Chien C, Bowen A, van Duin D, Lachiewicz A, Andermann T, Jones M, Miller M, Juliano JJ, Bartelt LA. Loss of daptomycin susceptibility in clinical Staphylococcus epidermidis infection coincided with variants in WalK. EVOLUTION MEDICINE AND PUBLIC HEALTH 2020; 2020:219-224. [PMID: 33214904 PMCID: PMC7658547 DOI: 10.1093/emph/eoaa031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/07/2020] [Indexed: 01/25/2023]
Abstract
Daptomycin (DAP) is key in treating multidrug-resistant Staphylococcus infections. Diminished susceptibility to DAP is emerging among Staphylococcus epidermidis strains although mechanisms for non-susceptibility (NS) remain poorly understood. We report a case of persistent S. epidermidis bacteremia in which loss of DAP susceptibility arose during prolonged treatment. Whole genome sequencing identified two mutations, Q371del and P415L, in a single-affected gene, WalK, that coincided with the emergence of DAP-NS. Protein modeling of the mutations predicted a disruption of WalK protein configuration. The emergence of mutations in a single-gene during DAP exposure raises concerns in an era of increasingly treatment-resistant infections. Lay summary: Daptomycin is an important antibiotic for fighting Staphylococcus infections. We identified variants in the WalK gene that were coincident with resistance in a clinical Staphylococcus epidermidis infection. Clinicians, hospital epidemiologists, and microbiology laboratories need to be aware of the potential for the evolution of drug resistance during prolonged daptomycin therapy.
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Affiliation(s)
- Nicholas F Brazeau
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kara J Levinson
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Asher Schranz
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kara A Moser
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ian Hollis
- University of North Carolina Health, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Prashanth Iyer
- University of North Carolina Health, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Christopher Chien
- Division of Cardiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Amanda Bowen
- Division of Cardiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David van Duin
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anne Lachiewicz
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tessa Andermann
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Melissa Jones
- Clinical Microbiology Laboratory, University of North Carolina Health Care, Chapel Hill, NC 27599, USA
| | - Melissa Miller
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Luther A Bartelt
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Gostev VV, Sopova YV, Kalinogorskaya OS, Tsvetkova IA, Sidorenko SV. Selection of Resistance to Daptomycin in Methicillin-Resistant Staphylococcus aureus: Role of Homo- and Hetero-Mutations. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420030060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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