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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] [What about the content of this article? (0)] [Affiliation(s)] [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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zirbes CF, Pitcher NJ, Davis JC, Bartels AR, Krogh JD, Teresi M, Farber T, Milavetz F, Pamatmat AJ, Rozen AL, Reinhardt LD, Boyken L, Singh SB, Twait E, Reeb VC, Ford BA, Fischer AJ. Staphylococcus aureus detection from CF respiratory samples is improved using alternative media. J Cyst Fibros 2022; 21:888-889. [PMID: 35491319 PMCID: PMC10152491 DOI: 10.1016/j.jcf.2022.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
Affiliation(s)
- Christian F Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Nicholas J Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Joseph C Davis
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Alyssa R Bartels
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Justin D Krogh
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Mary Teresi
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Tyler Farber
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Francesca Milavetz
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Anthony J Pamatmat
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Alexis L Rozen
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Lindsey D Reinhardt
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Linda Boyken
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Sachinkumar B Singh
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Erik Twait
- State Hygienic Laboratory at the University of Iowa, Coralville, IA, United States
| | - Valérie C Reeb
- State Hygienic Laboratory at the University of Iowa, Coralville, IA, United States
| | - Bradley A Ford
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Anthony J Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States.
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Porterfield HS, Maakestad LJ, LaMarche MM, Thurman AL, Kienenberger ZE, Pitcher NJ, Hansen AR, Zirbes CF, Boyken L, Muyskens BL, Pezzulo AA, Singh SB, Twait E, Ford B, Diekema DJ, Reeb V, Fischer AJ. MRSA strains with distinct accessory genes predominate at different ages in cystic fibrosis. Pediatr Pulmonol 2021; 56:2868-2878. [PMID: 34219414 PMCID: PMC8395597 DOI: 10.1002/ppul.25559] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 01/30/2023]
Abstract
RATIONALE Methicillin resistant Staphylococcus aureus (MRSA) is prevalent and consequential in cystic fibrosis (CF). Whole genome sequencing (WGS) could reveal genomic differences in MRSA associated with poorer outcomes or detect MRSA transmission. OBJECTIVES To identify MRSA genes associated with low lung function and potential MRSA transmission in CF. METHODS We collected 97 MRSA isolates from 74 individuals with CF from 2017 and performed short-read WGS. We determined sequence type (ST) and the phylogenetic relationship between isolates. We aligned accessory genes from 25 reference genomes to genome assemblies, classified isolates by accessory gene content, and correlated the accessory genome to clinical outcomes. RESULTS The most prevalent ST were ST5 (N = 55), ST8 (N = 15), and ST105 (N = 14). Closely related MRSA strains were shared by family members with CF, but rarely between unrelated individuals. Three clusters of MRSA were identified by accessory genome content. Cluster A, including ST5 and ST105, was highly prevalent at all ages. Cluster B, including ST8, was more limited to younger patients. Cluster C included 6 distantly related strains. Patients 20 years old and younger infected with Cluster A had lower forced expiratory volume in the first second (FEV1 ) and higher sputum biomass compared to similar-aged patients with Cluster B. CONCLUSIONS In this CF cohort, we identified MRSA subtypes that predominate at different ages and differ by accessory gene content. The most prevalent cluster of MRSA, including ST5 and ST105, was associated with lower FEV1 . ST8 MRSA was more common in younger patients and thus has the potential to rise in prevalence as these patients age.
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Affiliation(s)
- Harry S Porterfield
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA.,Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Lucas J Maakestad
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Mason M LaMarche
- 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, Iowa, USA
| | - Zoe E Kienenberger
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Nicholas J Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Alexis R Hansen
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Christian F Zirbes
- 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, Iowa, USA
| | - Bethany L Muyskens
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Alejandro A Pezzulo
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Sachinkumar B Singh
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Erik Twait
- State Hygienic Laboratory at the University of Iowa, Iowa City, Iowa, USA
| | - Bradley Ford
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Daniel J Diekema
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Valérie Reeb
- State Hygienic Laboratory at the University of Iowa, Iowa City, Iowa, USA
| | - Anthony J Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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