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Nair ZJ, Gao IH, Firras A, Chong KKL, Hill ED, Choo PY, Colomer-Winter C, Chen Q, Manzano C, Pethe K, Kline KA. An essential protease, FtsH, influences daptomycin resistance acquisition in Enterococcus faecalis. Mol Microbiol 2024. [PMID: 38527904 DOI: 10.1111/mmi.15253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024]
Abstract
Daptomycin is a last-line antibiotic commonly used to treat vancomycin-resistant Enterococci, but resistance evolves rapidly and further restricts already limited treatment options. While genetic determinants associated with clinical daptomycin resistance (DAPR) have been described, information on factors affecting the speed of DAPR acquisition is limited. The multiple peptide resistance factor (MprF), a phosphatidylglycerol-modifying enzyme involved in cationic antimicrobial resistance, is linked to DAPR in pathogens such as methicillin-resistant Staphylococcus aureus. Since Enterococcus faecalis encodes two paralogs of mprF and clinical DAPR mutations do not map to mprF, we hypothesized that functional redundancy between the paralogs prevents mprF-mediated resistance and masks other evolutionary pathways to DAPR. Here, we performed in vitro evolution to DAPR in mprF mutant background. We discovered that the absence of mprF results in slowed DAPR evolution and is associated with inactivating mutations in ftsH, resulting in the depletion of the chaperone repressor HrcA. We also report that ftsH is essential in the parental, but not in the ΔmprF, strain where FtsH depletion results in growth impairment in the parental strain, a phenotype associated with reduced extracellular acidification and reduced ability for metabolic reduction. This presents FtsH and HrcA as enticing targets for developing anti-resistance strategies.
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Affiliation(s)
- Zeus Jaren Nair
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Iris Hanxing Gao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Aslam Firras
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kelvin Kian Long Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, Singapore, Singapore
| | - Eric D Hill
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Pei Yi Choo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Cristina Colomer-Winter
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Qingyan Chen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Caroline Manzano
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kevin Pethe
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
| | - Kimberly A Kline
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gotoh K, Mayura IPB, Enomoto Y, Iio K, Matsushita O, Otsuka F, Hagiya H. Detection of in-frame mutation by IS30-family insertion sequence in the phospholipid phosphatidylglycerol synthase gene (pgsA2) of high-level daptomycin-resistant Corynebacterium striatum. Eur J Clin Microbiol Infect Dis 2021; 41:331-333. [PMID: 34671843 DOI: 10.1007/s10096-021-04369-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/15/2021] [Indexed: 10/20/2022]
Abstract
The emergence of high-level daptomycin (DAP)-resistant (HLDR) Corynebacterium striatum has been reported as a result of loss-of-function point mutations or premature stop codon mutations in a responsible gene, pgsA2. We herein describe the novel detection of an HLDR C. striatum clinical isolate, in which IS30-insertion was corroborated to cause destruction of pgsA2 gene. We isolated an HLDR C. striatum from a critically ill patient with underlying mycosis fungoides who had been treated with DAP for 10 days. With a sequence investigation, IS30-insertion was discovered to split pgsA2 in the HLDR C. striatum strain, which may cause disrupted phospholipid phosphatidylglycerol (PG) production. Future studies should survey the prevalence of IS-mediated gene inactivation among HLDR C. striatum clinical isolates.
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Affiliation(s)
- Kazuyoshi Gotoh
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - I Putu Bayu Mayura
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Yusaku Enomoto
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Koji Iio
- Microbiology Division, Clinical Laboratory, Okayama University Hospital, Okayama, 700-8558, Japan
| | - Osamu Matsushita
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Fumio Otsuka
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Hideharu Hagiya
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan.
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Egli A, Schmid H, Kuenzli E, Widmer AF, Battegay M, Plagge H, Frei R, Achermann R, Weisser M. Association of daptomycin use with resistance development in Enterococcus faecium bacteraemia-a 7-year individual and population-based analysis. Clin Microbiol Infect 2016; 23:118.e1-118.e7. [PMID: 27746397 DOI: 10.1016/j.cmi.2016.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 09/23/2016] [Accepted: 10/03/2016] [Indexed: 11/15/2022]
Abstract
OBJECTIVE In this study we aimed to analyse the association between use of daptomycin and MICs of daptomycin in Enterococcus faecium bacteraemia. METHODS We prospectively enrolled patients aged ≥18 years with E. faecium bacteraemia hospitalized at the University Hospital Basel from 2008 to 2014. We determined daptomycin MICs by Etests and used pulsed field gel electrophoresis to determine clonal relatedness. We recorded the defined daily dosages of daptomycin (DDDs) per 100 patient-days and clinical data from charts. We correlated daptomycin MIC with use of daptomycin in patients with recurrence/persistence. RESULTS In 195 E. faecium bacteraemias originating from 162 patients the median MIC for daptomycin was 2 mg/L (IQR 2-3); 30% (15.4%) isolates had a MIC ≥4 mg/L and 6 (3.1%) were resistant (MIC >4 mg/L) according to CLSI criteria. The usage of daptomycin increased more than four-fold from 0.36 DDDs/100 patient-days in 2008 to 1.6 in 2014. In 13 of 28 (42.9%) patients with a relapsing or persisting bacteraemia, the daptomycin MIC of the second isolate increased from a median of 2.0 to 2.5 mg/L (p 0.010); 3/13 (23.1%) developed resistance. All patients with the same clone in the first and second episode and an increase of daptomycin MIC had been treated with daptomycin (6/6 versus 1/7 p 0.005). CONCLUSIONS Daptomycin MICs and Daptomycin usage increased over time. On an individual patient level daptomycin exposure was associated with an increased MIC in subsequent bacteraemia episodes. Diversity did not indicate a clonal origin and argues for a de novo development of resistance.
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Affiliation(s)
- A Egli
- Clinical Microbiology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department Biomedicine, University of Basel, Switzerland
| | - H Schmid
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - E Kuenzli
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; Epidemiology, Biostatistics and Prevention Institute, University of Zürich, Zürich, Switzerland
| | - A F Widmer
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - M Battegay
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - H Plagge
- Hospital Pharmacy, University Hospital Basel, Basel, Switzerland
| | - R Frei
- Clinical Microbiology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - R Achermann
- Applied Microbiology Research, Department Biomedicine, University of Basel, Switzerland
| | - M Weisser
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; Department of Clinical Research, University Hospital Basel, Basel, Switzerland.
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Lellek H, Franke GC, Ruckert C, Wolters M, Wolschke C, Christner M, Büttner H, Alawi M, Kröger N, Rohde H. Emergence of daptomycin non-susceptibility in colonizing vancomycin-resistant Enterococcus faecium isolates during daptomycin therapy. Int J Med Microbiol 2015; 305:902-9. [PMID: 26454536 DOI: 10.1016/j.ijmm.2015.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/31/2015] [Accepted: 09/10/2015] [Indexed: 11/27/2022] Open
Abstract
Infections due to vancomycin-resistant enterococci (VRE) are of significant importance in high-risk populations, and daptomycin is a bactericidal antibiotic to treat multidrug-resistant VRE in these patients. The emergence of daptomycin non-susceptibility invasive VRE during daptomycin therapy is a major clinical issue. Here the hypothesis was tested that systemic daptomycin therapy also induces the emergence of daptomycin non-susceptible (DNS-) isolates in colonizing VRE populations. 11 vancomycin-resistant Enterococcus faecium strain pairs recovered from rectal swabs were available for analysis. All initial isolates exhibited daptomycin MICs within the wild type MIC distribution of E. faecium (MIC≤4 mg/L). In follow-up isolates from five patients a 4-16-fold daptomycin MIC increase was detected. All patients carrying DNS-VRE received daptomycin (14-28 days) at 4 mg/kg body weight, while two patients in whom no DNS-VRE emerged were only treated with daptomycin for 1 and 4 days, respectively. Comparative whole genome sequencing identified DNS-VRE-specific single nucleotide polymorphisms (SNP), including mutations in cardiolipin synthase (Cls), and additional SNPs in independent genes potentially relevant for the DNS phenotype. Mutations within cls were also identified in three additional, colonizing DNS-VRE. Of these, at least one strain was transmitted within the hospital. In none of the VRE isolates tested, pre-existing or de novo mutations in the liaFSR operon were detected. This is the first report documenting the emergence of DNS-VRE in colonizing strains during daptomycin treatment, putting the patient at risk for subsequent DNS-VRE infections and priming the spread of DNS-VRE within the hospital environment.
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Affiliation(s)
- Heinrich Lellek
- Klinik für Stammzelltransplantation, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Gefion C Franke
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Carolin Ruckert
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Manuel Wolters
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Christiane Wolschke
- Klinik für Stammzelltransplantation, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Martin Christner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Henning Büttner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Service Facility, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Nicolaus Kröger
- Klinik für Stammzelltransplantation, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.
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