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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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Kienenberger ZE, Farber TO, Teresi ME, Milavetz F, Singh SB, Larson Ode K, Thoma T, Weiner RL, Burlage KR, Fischer AJ. Patient and Caregiver Perceptions of Airway Clearance Methods Used for Cystic Fibrosis. Can Respir J 2023; 2023:1422319. [PMID: 37547298 PMCID: PMC10403321 DOI: 10.1155/2023/1422319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/06/2023] [Accepted: 06/24/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction Cystic Fibrosis Foundation guidelines recommend people with CF perform daily airway clearance. This can be difficult for patients, as some find it time consuming or uncomfortable. Data comparing airway clearance methods are limited. We surveyed patients and their families to understand which methods are preferred and identify obstacles to performing airway clearance. Methods We designed a REDCap survey and enrolled participants in 2021. Respondents reported information on airway clearance usage, time commitment, and medication use. They rated airway clearance methods for effectiveness, comfort, time commitment, importance, and compatibility with other treatments. The analysis included descriptive statistics and clustering. Results 60 respondents started and 52 completed the survey. The median patient age was 20 years. Respondents experienced a median of four airway clearance methods in their lifetime, including chest wall oscillation (vest, 92%), manual chest physical therapy (CPT, 88%), forced expiration technique (huff or cough, 77%), and exercise (75%). Past 30-day use was highest for exercise (62%) and vest (57%). The time commitment was generally less than 2 hours daily. Of those eligible for CFTR modulators, 53% reported decreased time commitment to airway clearance after starting treatment. On a scale of 0-100, respondents rated CFTR modulators as their most important treatment (median 99.5), followed by exercise (88). Discussion. Patients and caregivers are familiar with several methods of airway clearance for CF. They report distinct strengths and limitations of each method. Exercise and vest are the most common methods of airway clearance. The use of CFTR modulators may reduce patient-reported time commitment to airway clearance.
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Affiliation(s)
- Zoe E. Kienenberger
- Pediatrics, University of Iowa, Iowa City, IA, USA
- Department of Physical Therapy and Rehabilitation Science, University of Iowa, Iowa City, IA, USA
| | | | | | | | | | | | | | | | - Kathryn R. Burlage
- Department of Physical Therapy and Rehabilitation Science, University of Iowa, Iowa City, IA, 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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Bonn CM, Rafiqullah IM, Crawford JA, Qian YM, Guthrie JL, Matuszewska M, Robinson DA, McGavin MJ. Repeated Emergence of Variant TetR Family Regulator, FarR, and Increased Resistance to Antimicrobial Unsaturated Fatty Acid among Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0074922. [PMID: 36744906 PMCID: PMC10019231 DOI: 10.1128/aac.00749-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Resistance-nodulation-division (RND) superfamily efflux pumps promote antibiotic resistance in Gram-negative pathogens, but their role in Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) is undocumented. However, recent in vitro selections for resistance of S. aureus to an antimicrobial fatty acid, linoleic acid, and an antibiotic, rhodomyrtone, identified H121Y and C116R substitution variants, respectively, in a TetR family regulator, FarR, promoting increased expression of the RND pump FarE. Hypothesizing that in vivo selection pressures have also promoted the emergence of FarR variants, we searched available genome data and found that strains with FarRH121Y from human and bovine hosts have emerged sporadically in clonal complexes (CCs) CC1, CC30, CC8, CC22, and CC97, whereas multiple FarR variants have occurred within CC5 hospital-associated (HA)-MRSA. Of these, FarRE160G and FarRE93EE were exclusive to CC5, while FarRC116Y, FarRP165L, and FarRG166D also occurred in nonrelated CCs, primarily from bovine hosts. Within CC5, FarRC116Y and FarRG166D strains were polyphyletic, each exhibiting two emergence events. FarRC116Y and FarRE160G were individually sufficient to confer increased expression of FarE and enhanced resistance to linoleic acid (LA). Isolates with FarRE93EE were most closely related to S. aureus N315 MRSA and exhibited increased resistance independently of FarRE93EE. Accumulation of pseudogenes and additional polymorphisms in FarRE93EE strains contributed to a multiresistance phenotype which included fosfomycin and fusidic acid resistance in addition to increased linoleic acid resistance. These findings underscore the remarkable adaptive capacity of CC5 MRSA, which includes the polyphyletic USA100 lineage of HA-MRSA that is endemic in the Western hemisphere and known for the acquisition of multiple resistance phenotypes.
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Affiliation(s)
- Camryn M. Bonn
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
| | - Iftekhar M. Rafiqullah
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - John A. Crawford
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Yi Meng Qian
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
| | - Jennifer L. Guthrie
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Marta Matuszewska
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Martin J. McGavin
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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Small Colonies, Bigger Problems? New Evidence That Staphylococcus aureus Small Colony Variants Can Worsen Lung Inflammation in Cystic Fibrosis Rats. Infect Immun 2022; 90:e0041322. [PMID: 36286497 PMCID: PMC9670989 DOI: 10.1128/iai.00413-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus
is the most prevalent cystic fibrosis (CF) pathogen. During chronic airway infections,
S. aureus
adaptation to antibiotics includes evolving small colony variants (SCVs).
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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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