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Madden DE, Baird T, Bell SC, McCarthy KL, Price EP, Sarovich DS. Keeping up with the pathogens: improved antimicrobial resistance detection and prediction from Pseudomonas aeruginosa genomes. Genome Med 2024; 16:78. [PMID: 38849863 PMCID: PMC11157771 DOI: 10.1186/s13073-024-01346-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 05/20/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is an intensifying threat that requires urgent mitigation to avoid a post-antibiotic era. Pseudomonas aeruginosa represents one of the greatest AMR concerns due to increasing multi- and pan-drug resistance rates. Shotgun sequencing is gaining traction for in silico AMR profiling due to its unambiguity and transferability; however, accurate and comprehensive AMR prediction from P. aeruginosa genomes remains an unsolved problem. METHODS We first curated the most comprehensive database yet of known P. aeruginosa AMR variants. Next, we performed comparative genomics and microbial genome-wide association study analysis across a Global isolate Dataset (n = 1877) with paired antimicrobial phenotype and genomic data to identify novel AMR variants. Finally, the performance of our P. aeruginosa AMR database, implemented in our AMR detection and prediction tool, ARDaP, was compared with three previously published in silico AMR gene detection or phenotype prediction tools-abritAMR, AMRFinderPlus, ResFinder-across both the Global Dataset and an analysis-naïve Validation Dataset (n = 102). RESULTS Our AMR database comprises 3639 mobile AMR genes and 728 chromosomal variants, including 75 previously unreported chromosomal AMR variants, 10 variants associated with unusual antimicrobial susceptibility, and 281 chromosomal variants that we show are unlikely to confer AMR. Our pipeline achieved a genotype-phenotype balanced accuracy (bACC) of 85% and 81% across 10 clinically relevant antibiotics when tested against the Global and Validation Datasets, respectively, vs. just 56% and 54% with abritAMR, 58% and 54% with AMRFinderPlus, and 60% and 53% with ResFinder. ARDaP's superior performance was predominantly due to the inclusion of chromosomal AMR variants, which are generally not identified with most AMR identification tools. CONCLUSIONS Our ARDaP software and associated AMR variant database provides an accurate tool for predicting AMR phenotypes in P. aeruginosa, far surpassing the performance of current tools. Implementation of ARDaP for routine AMR prediction from P. aeruginosa genomes and metagenomes will improve AMR identification, addressing a critical facet in combatting this treatment-refractory pathogen. However, knowledge gaps remain in our understanding of the P. aeruginosa resistome, particularly the basis of colistin AMR.
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Affiliation(s)
- Danielle E Madden
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Timothy Baird
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Respiratory Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Scott C Bell
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia
- Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, Queensland, Australia
| | - Kate L McCarthy
- University of Queensland Medical School, Herston, QLD, Australia
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Erin P Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Derek S Sarovich
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia.
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Hujer AM, Marshall SH, Mack AR, Hujer KM, Bakthavatchalam YD, Umarkar K, Palwe SR, Takalkar S, Joshi PR, Shrivastava R, Periasamy H, Bhagwat SS, Patel MV, Veeraraghavan B, Bonomo RA. Transcending the challenge of evolving resistance mechanisms in Pseudomonas aeruginosa through β-lactam-enhancer-mechanism-based cefepime/zidebactam. mBio 2023; 14:e0111823. [PMID: 37889005 PMCID: PMC10746216 DOI: 10.1128/mbio.01118-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/14/2023] [Indexed: 10/28/2023] Open
Abstract
Multi-drug resistant (MDR) Pseudomonas aeruginosa harbor a complex array of β-lactamases and non-enzymatic resistance mechanisms. In this study, the activity of a β-lactam/β-lactam-enhancer, cefepime/zidebactam, and novel β-lactam/β-lactamase inhibitor combinations was determined against an MDR phenotype-enriched, challenge panel of P. aeruginosa (n = 108). Isolates were multi-clonal as they belonged to at least 29 distinct sequence types (STs) and harbored metallo-β-lactamases, serine β-lactamases, penicillin binding protein (PBP) mutations, and other non-enzymatic resistance mechanisms. Ceftazidime/avibactam, ceftolozane/tazobactam, imipenem/relebactam, and cefepime/taniborbactam demonstrated MIC90s of >128 mg/L, while cefepime/zidebactam MIC90 was 16 mg/L. In a neutropenic-murine lung infection model, a cefepime/zidebactam human epithelial-lining fluid-simulated regimen achieved or exceeded a translational end point of 1-log10 kill for the isolates with elevated cefepime/zidebactam MICs (16-32 mg/L), harboring VIM-2 or KPC-2 and alterations in PBP2 and PBP3. In the same model, to assess the impact of zidebactam on the pharmacodynamic (PD) requirement of cefepime, dose-fractionation studies were undertaken employing cefepime-susceptible P. aeruginosa isolates. Administered alone, cefepime required 47%-68% fT >MIC for stasis to ~1 log10 kill effect, while cefepime in the presence of zidebactam required just 8%-16% for >2 log10 kill effect, thus, providing the pharmacokinetic/PD basis for in vivo efficacy of cefepime/zidebactam against isolates with MICs up to 32 mg/L. Unlike β-lactam/β-lactamase inhibitors, β-lactam enhancer mechanism-based cefepime/zidebactam shows a potential to transcend the challenge of ever-evolving resistance mechanisms by targeting multiple PBPs and overcoming diverse β-lactamases including carbapenemases in P. aeruginosa.IMPORTANCECompared to other genera of Gram-negative pathogens, Pseudomonas is adept in acquiring complex non-enzymatic and enzymatic resistance mechanisms thus remaining a challenge to even novel antibiotics including recently developed β-lactam and β-lactamase inhibitor combinations. This study shows that the novel β-lactam enhancer approach enables cefepime/zidebactam to overcome both non-enzymatic and enzymatic resistance mechanisms associated with a challenging panel of P. aeruginosa. This study highlights that the β-lactam enhancer mechanism is a promising alternative to the conventional β-lactam/β-lactamase inhibitor approach in combating ever-evolving MDR P. aeruginosa.
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Affiliation(s)
- Andrea M. Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Steven H. Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
| | - Andrew R. Mack
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Kristine M. Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | | | - Kushal Umarkar
- Wockhardt Research Centre, Aurangabad, Maharashtra, India
| | | | | | | | | | | | | | | | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Departments of Pharmacology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
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Rodríguez A, Moreno G, Bodi M, Martín-Loeches I. Antibiotics in development for multiresistant gram-negative bacilli. Med Intensiva 2022; 46:630-640. [PMID: 36302707 DOI: 10.1016/j.medine.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/26/2022] [Indexed: 06/16/2023]
Abstract
The rapid increase in antibiotic(ATB) resistance among Gram-negative bacilli(BGN), especially in strains of Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii, with high resistance patterns (XDR), poses a huge threat to health systems worldwide. In the last decade, different ATBs have been developed against XDR, some of which combine a lactam β along with a β-lactamase inhibitor, while others use non-β-lactam inhibitors. Most of them have adequate "in vitro" activity on several β-lactamases of class A, C and D of Ambler. However, combinations such as Ceftazidime/avibactam, Ceftolozane/Tazobactam and Meropenem/vaborbactam have no activity against metallo-β-lactamases(MβL). New combinations such as Aztreonan/AVI, Cefepime/Zidebactam, or new cephalosporins such as Cefiderocol, have efficacy against MβL enzymes. Although some of these combinations are already approved and in the commercialization phase, many of them have yet to define their place within the treatment of microorganisms with high resistance through clinical studies.
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Affiliation(s)
- A Rodríguez
- Servicio de Medicina Intensiva, Hospital Universitario Joan XXIII, Tarragona, Spain; IISPV/CIBERES, Tarragona, Spain.
| | - G Moreno
- Servicio de Medicina Intensiva, Hospital Universitario Joan XXIII, Tarragona, Spain
| | - M Bodi
- Servicio de Medicina Intensiva, Hospital Universitario Joan XXIII, Tarragona, Spain; IISPV/CIBERES, Tarragona, Spain
| | - I Martín-Loeches
- Trinity College Dublin, School of Medicine, Intensive Care Medicine St James's Hospital, Dublín, Ireland
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Díaz Santos E, Mora Jiménez C, Del Río-Carbajo L, Vidal-Cortés P. Treatment of severe multi-drug resistant Pseudomonas aeruginosa infections. Med Intensiva 2022; 46:508-520. [PMID: 35840495 DOI: 10.1016/j.medine.2022.06.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 06/15/2023]
Abstract
Pseudomonas aeruginosa is the microorganism most frequently involved in the main ICU-acquired infections, with special importance in ventilator associated pneumonia. Its importance lies, in addition to its high incidence in critically ill patients, in the severity of the infections it causes and in the difficulty of its antimicrobial treatment, directly related to the high percentage of resistance to antibiotics classically considered first-line. New active antibiotics have recently been developed against Pseudomonas aeruginosa, even against multi-drug resistant strains. This review analyzes both the differential characteristics of Pseudomonas aeruginosa infections and the new therapeutic options, focusing on multi-drug resistant Pseudomonas aeruginosa.
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Affiliation(s)
- E Díaz Santos
- Medicina Intensiva, Consorci Corporació Sanitaria Parc Taulí, Sabadell, Barcelona, Spain; Departamento de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - C Mora Jiménez
- Medicina Intensiva, Consorci Corporació Sanitaria Parc Taulí, Sabadell, Barcelona, Spain
| | - L Del Río-Carbajo
- Medicina Intensiva, Complexo Hospitalario Universitario de Ourense, Ourense, Spain
| | - P Vidal-Cortés
- Medicina Intensiva, Complexo Hospitalario Universitario de Ourense, Ourense, Spain.
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Comparative In Vitro Activity of Ceftolozane/Tazobactam against Clinical Isolates of Pseudomonas aeruginosa and Enterobacterales from Five Latin American Countries. Antibiotics (Basel) 2022; 11:antibiotics11081101. [PMID: 36009970 PMCID: PMC9405202 DOI: 10.3390/antibiotics11081101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Ceftolozane/tazobactam (C/T) is a combination of an antipseudomonal oxyiminoaminothiazolyl cephalosporin with potent in vitro activity against Pseudomonas aeruginosa and tazobactam, a known β-lactamase inhibitor. The aim of this study was to evaluate the activity of C/T against clinical isolates of P. aeruginosa and Enterobacterales collected from five Latin American countries between 2016 and 2017, before its clinical use in Latin America, and to compare it with the activity of other available broad-spectrum antimicrobial agents. Methods: a total of 2760 clinical isolates (508 P. aeruginosa and 2252 Enterobacterales) were consecutively collected from 20 hospitals and susceptibility to C/T and comparator agents was tested and interpreted following the current guidelines. Results: according to the CLSI breakpoints, 68.1% (346/508) of P. aeruginosa and 83.9% (1889/2252) of Enterobacterales isolates were susceptible to C/T. Overall, C/T demonstrated higher in vitro activity than currently available cephalosporins, piperacillin/tazobactam and carbapenems when tested against P. aeruginosa, and its performance in vitro was comparable to fosfomycin. When tested against Enterobacterales, it showed higher activity than cephalosporins and piperacillin/tazobactam, and similar activity to ertapenem. Conclusions: these results show that C/T is an active β-lactam agent against clinical isolates of P. aeruginosa and Enterobacterales.
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Rodríguez A, Moreno G, Bodi M, Martín-Loeches I. Antibióticos en desarrollo para bacilos gram negativos multirresistentes. Med Intensiva 2022. [DOI: 10.1016/j.medin.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bitar I, Salloum T, Merhi G, Hrabak J, Araj GF, Tokajian S. Genomic Characterization of Mutli-Drug Resistant Pseudomonas aeruginosa Clinical Isolates: Evaluation and Determination of Ceftolozane/Tazobactam Activity and Resistance Mechanisms. Front Cell Infect Microbiol 2022; 12:922976. [PMID: 35782142 PMCID: PMC9241553 DOI: 10.3389/fcimb.2022.922976] [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: 04/18/2022] [Accepted: 05/17/2022] [Indexed: 12/31/2022] Open
Abstract
Resistance to ceftolozane/tazobactam (C/T) in Pseudomonas aeruginosa is a health concern. In this study, we conducted a whole-genome-based molecular characterization to correlate resistance patterns and β-lactamases with C/T resistance among multi-drug resistant P. aeruginosa clinical isolates. Resistance profiles for 25 P. aeruginosa clinical isolates were examined using disk diffusion assay. Minimal inhibitory concentrations (MIC) for C/T were determined by broth microdilution. Whole-genome sequencing was used to check for antimicrobial resistance determinants and reveal their genetic context. The clonal relatedness was evaluated using MLST, PFGE, and serotyping. All the isolates were resistant to C/T. At least two β-lactamases were detected in each with the blaOXA-4, blaOXA-10, blaOXA-50, and blaOXA-395 being the most common. blaIMP-15, blaNDM-1, or blaVIM-2, metallo-β-lactamases, were associated with C/T MIC >256 μg/mL. Eight AmpC variants were identified, and PDC-3 was the most common. We also determined the clonal relatedness of the isolates and showed that they grouped into 11 sequence types (STs) some corresponding to widespread clonal complexes (ST111, ST233, and ST357). C/T resistance was likely driven by the acquired OXA β-lactamases such as OXA-10, and OXA-50, ESBLs GES-1, GES-15, and VEB-1, and metallo- β-lactamases IMP-15, NDM-1, and VIM-2. Collectively, our results revealed C/T resistance determinants and patterns in multi-drug resistant P. aeruginosa clinical isolates. Surveillance programs should be implemented and maintained to better track and define resistance mechanisms and how they accumulate and interact.
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Affiliation(s)
- Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, University Hospital Pilsen, Charles University, Pilsen, Czechia,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine, University Hospital Pilsen, Charles University, Pilsen, Czechia,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - George F. Araj
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon,*Correspondence: Sima Tokajian,
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Tratamiento de las infecciones graves por Pseudomonas aeruginosa multirresistente. Med Intensiva 2022. [DOI: 10.1016/j.medin.2022.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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β-lactam Resistance in Pseudomonas aeruginosa: Current Status, Future Prospects. Pathogens 2021; 10:pathogens10121638. [PMID: 34959593 PMCID: PMC8706265 DOI: 10.3390/pathogens10121638] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is a major opportunistic pathogen, causing a wide range of acute and chronic infections. β-lactam antibiotics including penicillins, carbapenems, monobactams, and cephalosporins play a key role in the treatment of P. aeruginosa infections. However, a significant number of isolates of these bacteria are resistant to β-lactams, complicating treatment of infections and leading to worse outcomes for patients. In this review, we summarize studies demonstrating the health and economic impacts associated with β-lactam-resistant P. aeruginosa. We then describe how β-lactams bind to and inhibit P. aeruginosa penicillin-binding proteins that are required for synthesis and remodelling of peptidoglycan. Resistance to β-lactams is multifactorial and can involve changes to a key target protein, penicillin-binding protein 3, that is essential for cell division; reduced uptake or increased efflux of β-lactams; degradation of β-lactam antibiotics by increased expression or altered substrate specificity of an AmpC β-lactamase, or by the acquisition of β-lactamases through horizontal gene transfer; and changes to biofilm formation and metabolism. The current understanding of these mechanisms is discussed. Lastly, important knowledge gaps are identified, and possible strategies for enhancing the effectiveness of β-lactam antibiotics in treating P. aeruginosa infections are considered.
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