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Pitcher NJ, Feder A, Bolden N, Zirbes CF, Pamatmat AJ, Boyken L, Hill JJ, Bartels AR, Thurman AL, Reeb VC, Porterfield HS, Moustafa AM, Planet PJ, Fischer AJ. Parallel evolution of linezolid-resistant Staphylococcus aureus in patients with cystic fibrosis. Microbiol Spectr 2023; 11:e0208423. [PMID: 37724867 PMCID: PMC10581212 DOI: 10.1128/spectrum.02084-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/10/2023] [Indexed: 09/21/2023] Open
Abstract
Linezolid is an antibiotic used to treat serious Staphylococcus aureus infections. Resistance to linezolid is considered rare but could emerge with repeated dosing. We recently reported widespread prescription of linezolid for a cohort of patients with cystic fibrosis (CF). The goals of this study were to determine the incidence of linezolid-resistant methicillin-resistant Staphylococcus aureus (MRSA) in CF and identify molecular mechanisms for linezolid resistance. We identified patients who cultured S. aureus resistant to linezolid with minimum inhibitory concentration (MIC) >4 at the University of Iowa CF Center between 2008 and 2018. We obtained isolates from these patients and retested susceptibility to linezolid using broth microdilution. We used whole genome sequencing to perform phylogenetic analysis of linezolid-resistant isolates and examine sequences for mutations or accessory genes that confer linezolid resistance. Between 2008 and 2018, 111 patients received linezolid, and 4 of these patients cultured linezolid-resistant S. aureus. We sequenced 11 resistant and 21 susceptible isolates from these 4 subjects. Phylogenetic analysis indicated that linezolid resistance developed in ST5 or ST105 backgrounds. Three individuals had linezolid-resistant S. aureus with a G2576T mutation in 23S rRNA. One of these subjects additionally had a mutS- mutL- hypermutating S. aureus that produced five resistant isolates with multiple ribosomal subunit mutations. In one subject, the genetic basis for linezolid resistance was unclear. We conclude that linezolid resistant S. aureus can occur through multiple genetic mechanisms in patients with repeated exposure to this antibiotic. IMPORTANCE Patients with cystic fibrosis have persistent lung infections with Staphylococcus aureus that require extensive antibiotic treatments. Linezolid, an antibiotic given by oral or intravenous route, is prescribed repeatedly for patients whose lung disease has progressed. After treatment with linezolid, S. aureus strains can evolve antibiotic resistance through multiple genetic mechanisms. In addition to a common mutation in the 23S ribosomal RNA known to confer linezolid resistance, S. aureus strains can evolve novel resistance based on a combination of mutations affecting the bacterial ribosome. This combination of mutations was observed in a strain that exhibited hypermutation owing to the loss of the DNA repair genes mutS and mutL. In this cohort of patients with cystic fibrosis, linezolid resistance was transient, possibly due to the growth disadvantage of resistant strains. However, ongoing chronic exposure to linezolid may create optimal conditions for the future emergence of resistance to this critical antibiotic.
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Affiliation(s)
- Nicholas J. Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Andries Feder
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nicholas Bolden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christian F. Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Anthony J. Pamatmat
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Linda Boyken
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, lowa, USA
| | - Jared J. Hill
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Alyssa R. Bartels
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Andrew L. Thurman
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, lowa, USA
| | - Valerie C. Reeb
- State Hygienic Laboratory at the University of Iowa, Coralville, lowa, USA
| | | | - Ahmed M. Moustafa
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paul J. Planet
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Anthony J. Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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Pitcher NJ, Feder A, Bolden N, Zirbes CF, Pamatmat AJ, Boyken L, Hill JJ, Thurman AL, Reeb VC, Porterfield HS, Moustafa AM, Planet PJ, Fischer AJ. Parallel Evolution of Linezolid Resistant Staphylococcus aureus in Patients with Cystic Fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539145. [PMID: 37205485 PMCID: PMC10187253 DOI: 10.1101/2023.05.02.539145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Background Linezolid is an antibiotic used to treat serious Staphylococcus aureus infections. Resistance to linezolid is considered rare but could emerge with repeated dosing. We recently reported widespread prescription of linezolid for a cohort of patients with cystic fibrosis (CF). Objectives The goals of this study were to determine the incidence of linezolid resistance in CF and identify molecular mechanisms for linezolid resistance. Methods We identified patients with S. aureus resistant to linezolid (MIC > 4) at the University of Iowa CF Center between 2008 and 2018. We obtained isolates from these patients and retested susceptibility to linezolid using broth microdilution. We used whole genome sequencing to perform phylogenetic analysis of linezolid resistant isolates and examine sequences for mutations or accessory genes that confer linezolid resistance. Main Results Between 2008 and 2018, 111 patients received linezolid and 4 of these patients cultured linezolid resistant S. aureus . We sequenced 11 resistant and 21 susceptible isolates from these 4 subjects. Phylogenetic analysis indicated that linezolid resistance developed in ST5 or ST105 backgrounds. Three individuals had linezolid resistant S. aureus with a G2576T mutation in 23S rRNA. One of these subjects additionally had a mutS - mutL - hypermutating S. aureus that produced 5 resistant isolates with multiple ribosomal subunit mutations. In one subject, the genetic basis for linezolid resistance was unclear. Conclusions Linezolid resistance evolved in 4 of 111 patients in this study. Linezolid resistance occurred by multiple genetic mechanisms. All resistant strains developed in ST5 or ST105 MRSA backgrounds. Key Point Linezolid resistance arises through multiple genetic mechanisms and could be facilitated by mutator phenotypes. Linezolid resistance was transient, possibly due to growth disadvantage.
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Affiliation(s)
- Nicholas J. Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Andries Feder
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Nicholas Bolden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Christian F. Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Anthony J. Pamatmat
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Linda Boyken
- Pathology. University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Jared J. Hill
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Andrew L. Thurman
- Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Valérie C. Reeb
- State Hygienic Laboratory at the University of Iowa, Coralville, IA 52241
| | - Harry S. Porterfield
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Ahmed M. Moustafa
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul J. Planet
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Anthony J. Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
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Zhang L, Yang W, Chu Y, Wen B, Cheng Y, Mahmood T, Bao M, Ge F, Li L, Yi J, Du C, Lu C, Tan Y. The Inhibition Effect of Linezolid With Reyanning Mixture on MRSA and its Biofilm is More Significant than That of Linezolid Alone. Front Pharmacol 2022; 12:766309. [PMID: 35046807 PMCID: PMC8762264 DOI: 10.3389/fphar.2021.766309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 12/01/2021] [Indexed: 12/02/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a superbacterium, and when it forms biofilms, it is difficult to treat even with the first-line of antibiotic linezolid (LNZ). Reyanning mixture (RYN), a compound-based Chinese medicine formula, has been found to have inhibitory effects on biofilms. This study aims to explore the synergistic inhibitory effect and corresponding mechanisms of their (LNZ&RYN) combination on the planktonic as well as biofilm cells of MRSA. Broth microdilution and chessboard methods were employed for the determination of minimum inhibitory concentrations (MICs) and synergistic concentration of LNZ&RYN, respectively. The effect of the combined medication on biofilm and mature biofilm of MRSA were observed by biofilm morphology and permeability experiments, respectively. To unveil the molecular mechanism of action of the synergistic combination of LNZ and RYN, RT-PCR based biofilm-related gene expression analysis and ultra-high pressure liquid chromatography-time-of-flight mass spectrometry based endogenous metabonomic analysis were deployed. The results indicated that 1/16RYN as the best combined dose reduced LNZ (4 μg/ml) to 2 μg/ml. The combined treatment inhibited living MRSA before and after biofilm formation, removed the residual structure of dead bacteria in MRSA biofilms and affected the shape and size of bacteria, resulting in the improvement of biofilm permeability. The mechanism was that biofilm-related genes such as agrC, atlA, and sarA, as well as amino acid uptake associated with the metabolism of 3-dehydrocarnitine, kynurenine, L-leucine, L-lysine and sebacic acid were inhibited. This study provides evidence for the treatment of MRSA and its biofilms with LNZ combined with RYN.
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Affiliation(s)
- Lulu Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.,Key Laboratory for Research on Active Ingredients in Natural Medicine of Jiangxi Province, Yichun University, Yichun, China
| | - Weifeng Yang
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yajun Chu
- Tsing Hua De Ren Xi an Happiness Pharmaceutical Co., Ltd., Xi'an, China
| | - Bo Wen
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yungchi Cheng
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | - Tariq Mahmood
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Mei Bao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.,Key Laboratory for Research on Active Ingredients in Natural Medicine of Jiangxi Province, Yichun University, Yichun, China
| | - Feng Ge
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jianfeng Yi
- Key Laboratory for Research on Active Ingredients in Natural Medicine of Jiangxi Province, Yichun University, Yichun, China
| | - Chengqiang Du
- Tsing Hua De Ren Xi an Happiness Pharmaceutical Co., Ltd., Xi'an, China
| | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yong Tan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
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Boudet A, Sorlin P, Pouget C, Chiron R, Lavigne JP, Dunyach-Remy C, Marchandin H. Biofilm Formation in Methicillin-Resistant Staphylococcus aureus Isolated in Cystic Fibrosis Patients Is Strain-Dependent and Differentially Influenced by Antibiotics. Front Microbiol 2021; 12:750489. [PMID: 34721354 PMCID: PMC8554194 DOI: 10.3389/fmicb.2021.750489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease with lung abnormalities making patients particularly predisposed to pulmonary infections. Staphylococcus aureus is the most frequently identified pathogen, and multidrug-resistant strains (MRSA, methicillin-resistant S. aureus) have been associated with more severe lung dysfunction leading to eradication recommendations. Diverse bacterial traits and adaptive skills, including biofilm formation, may, however, make antimicrobial therapy challenging. In this context, we compared the ability of a collection of genotyped MRSA isolates from CF patients to form biofilm with and without antibiotics (ceftaroline, ceftobiprole, linezolid, trimethoprim, and rifampicin). Our study used standardized approaches not previously applied to CF MRSA, the BioFilm Ring test® (BRT®), the Antibiofilmogram®, and the BioFlux™ 200 system which were adapted for use with the artificial sputum medium (ASM) mimicking conditions more relevant to the CF lung. We included 63 strains of 10 multilocus sequence types (STs) isolated from 35 CF patients, 16 of whom had chronic colonization. The BRT® showed that 27% of the strains isolated in 37% of the patients were strong biofilm producers. The Antibiofilmogram® performed on these strains showed that broad-spectrum cephalosporins had the lowest minimum biofilm inhibitory concentrations (bMIC) on a majority of strains. A focus on four chronically colonized patients with inclusion of successively isolated strains showed that ceftaroline, ceftobiprole, and/or linezolid bMICs may remain below the resistance thresholds over time. Studying the dynamics of biofilm formation by strains isolated 3years apart in one of these patients using BioFlux™ 200 showed that inhibition of biofilm formation was observed for up to 36h of exposure to bMIC and ceftaroline and ceftobiprole had a significantly greater effect than linezolid. This study has brought new insights into the behavior of CF MRSA which has been little studied for its ability to form biofilm. Biofilm formation is a common characteristic of prevalent MRSA clones in CF. Early biofilm formation was strain-dependent, even within a sample, and not only observed during chronic colonization. Ceftaroline and ceftobiprole showed a remarkable activity with a long-lasting inhibitory effect on biofilm formation and a conserved activity on certain strains adapted to the CF lung environment after years of colonization.
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Affiliation(s)
- Agathe Boudet
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Pauline Sorlin
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Département de Microbiologie, CHU de Nîmes, Montpellier, France
| | | | - Raphaël Chiron
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, Montpellier, France
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Catherine Dunyach-Remy
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Hélène Marchandin
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Département de Microbiologie, CHU de Nîmes, Montpellier, France
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Rumpf C, Lange J, Schwartbeck B, Kahl BC. Staphylococcus aureus and Cystic Fibrosis-A Close Relationship. What Can We Learn from Sequencing Studies? Pathogens 2021; 10:pathogens10091177. [PMID: 34578208 PMCID: PMC8466686 DOI: 10.3390/pathogens10091177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023] Open
Abstract
Staphylococcus aureus is next to Pseudomonas aeruginosa the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant S. aureus clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. S. aureus is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. S. aureus is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant S. aureus are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using S. aureus isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or spa-sequence typing (spa-typing) to follow the population dynamics of S. aureus, elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of S. aureus with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of S. aureus and its evolution in the airways of individuals with CF.
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