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Rojas LJ, Yasmin M, Benjamino J, Marshall SM, DeRonde KJ, Krishnan NP, Perez F, Colin AA, Cardenas M, Martinez O, Pérez-Cardona A, Rhoads DD, Jacobs MR, LiPuma JJ, Konstan MW, Vila AJ, Smania A, Mack AR, Scott JG, Adams MD, Abbo LM, Bonomo RA. Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing. PLoS One 2022; 17:e0265129. [PMID: 35358221 PMCID: PMC8970513 DOI: 10.1371/journal.pone.0265129] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is a persistent and difficult-to-treat pathogen in many patients, especially those with Cystic Fibrosis (CF). Herein, we describe a longitudinal analysis of a series of multidrug resistant (MDR) P. aeruginosa isolates recovered in a 17-month period, from a young female CF patient who underwent double lung transplantation. Our goal was to understand the genetic basis of the observed resistance phenotypes, establish the genomic population diversity, and define the nature of sequence evolution over time. METHODS Twenty-two sequential P. aeruginosa isolates were obtained within a 17-month period, before and after a double-lung transplant. At the end of the study period, antimicrobial susceptibility testing, whole genome sequencing (WGS), phylogenetic analyses and RNAseq were performed in order to understand the genetic basis of the observed resistance phenotypes, establish the genomic population diversity, and define the nature of sequence changes over time. RESULTS The majority of isolates were resistant to almost all tested antibiotics. A phylogenetic reconstruction revealed 3 major clades representing a genotypically and phenotypically heterogeneous population. The pattern of mutation accumulation and variation of gene expression suggested that a group of closely related strains was present in the patient prior to transplantation and continued to change throughout the course of treatment. A trend toward accumulation of mutations over time was observed. Different mutations in the DNA mismatch repair gene mutL consistent with a hypermutator phenotype were observed in two clades. RNAseq performed on 12 representative isolates revealed substantial differences in the expression of genes associated with antibiotic resistance and virulence traits. CONCLUSIONS The overwhelming current practice in the clinical laboratories setting relies on obtaining a pure culture and reporting the antibiogram from a few isolated colonies to inform therapy decisions. Our analyses revealed significant underlying genomic heterogeneity and unpredictable evolutionary patterns that were independent of prior antibiotic treatment, highlighting the need for comprehensive sampling and population-level analysis when gathering microbiological data in the context of CF P. aeruginosa chronic infection. Our findings challenge the applicability of antimicrobial stewardship programs based on single-isolate resistance profiles for the selection of antibiotic regimens in chronic infections such as CF.
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Affiliation(s)
- Laura J. Rojas
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, United States of America
| | - Mohamad Yasmin
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | - Jacquelynn Benjamino
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - Steven M. Marshall
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | - Kailynn J. DeRonde
- Jackson Memorial Hospital, Jackson Health System, Miami, Florida, United States of America
| | - Nikhil P. Krishnan
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Departments of Translational Hematology and Oncology Research and Radiation Oncology, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Federico Perez
- Medical Service, Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, United States of America
- CONICET, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Division of Infectious Diseases and HIV Medicine, Cleveland, Ohio, United States of America
- GRECC Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | - Andrew A. Colin
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Monica Cardenas
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Octavio Martinez
- Jackson Memorial Hospital, Jackson Health System, Miami, Florida, United States of America
- Division of Pulmonology, Department of Pathology University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Armando Pérez-Cardona
- Jackson Memorial Hospital, Jackson Health System, Miami, Florida, United States of America
| | - Daniel D. Rhoads
- Department of Laboratory Medicine and Infection Biology Program, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Pathology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University Cleveland, Ohio, United States of America
| | - Michael R. Jacobs
- Department of Pathology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University Cleveland, Ohio, United States of America
| | - John J. LiPuma
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Michael W. Konstan
- Department of Pediatrics, Case Western Reserve University School of Medicine and Rainbow Babies and Children’s Hospital, Cleveland, Ohio, United States of America
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
| | - Andrea Smania
- CONICET, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica, Córdoba, Argentina
| | - Andrew R. Mack
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | - Jacob G. Scott
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Departments of Translational Hematology and Oncology Research and Radiation Oncology, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Mark D. Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - Lilian M. Abbo
- Jackson Memorial Hospital, Jackson Health System, Miami, Florida, United States of America
- Division of Infectious Diseases Department of Medicine University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Robert A. Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, United States of America
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Medical Service, Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, United States of America
- Division of Infectious Diseases and HIV Medicine, Cleveland, Ohio, United States of America
- GRECC Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
- Department of Pharmacology, Cleveland, Ohio, United States of America
- Department of Biochemistry Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
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