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Best W, Ferrell M, Boris A, Heydarian N, Panlilio H, Rice CV. Acquisition of Resistance to PEGylated Branched Polyethylenimine Increases Pseudomonas Aeruginosa Susceptibility to Aminoglycosides. ChemMedChem 2024; 19:e202300689. [PMID: 38806411 PMCID: PMC11368615 DOI: 10.1002/cmdc.202300689] [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: 12/06/2023] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024]
Abstract
PEGylated branched polyethylenimine (PEG-BPEI) has antibacterial and antibiofilm properties. Exposure to PEG-BPEI through serial passage leads to resistant P. aeruginosa strains. The minimum inhibitory concentration (MIC) of 600 Da BPEI and PEGylated 600 Da BPEI (PEG-BPEI) in the wild-type PAO1 strain is 16 μg/ml while, after 15 serial passages, the MIC increased to 1024 μg/mL. An additional 15 rounds of serial passage in the absence of BPEI or PEG-BPEI did not change the 1024 μg/mL MIC. Gentamicin, Neomycin, and Tobramycin, cationic antibiotics that inhibit protein synthesis, have a 16-32 fold reduction of MIC values in PEG350-BPEI resistant strains, suggesting increased permeation. The influx of these antibiotics occurs using a self-mediated uptake mechanism, suggesting changes to the outer membrane Data show that resistance causes changes in genes related to outer membrane lipopolysaccharide (LPS) assembly. Mutations were noted in the gene coding for the polymerase Wzy that participates in the assembly of the O-antigen region. Other mutations were noted with wbpE and wbpI of the Wbp pathway responsible for the enzymatic synthesis of ManNAc(3NAc)A in the LPS of P. aeruginosa. These changes suggest that an altered gene product could lead to PEG-BPEI resistance. Nevertheless, the increased susceptibility to aminoglycosides could prevent the emergence of PEG-BPEI resistant bacterial populations.
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Affiliation(s)
- William Best
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
| | - Maya Ferrell
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
| | - Andrew Boris
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
| | - Neda Heydarian
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
| | - Hannah Panlilio
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
| | - Charles V. Rice
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
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2
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Najari E, Zamani S, Sheikh Arabi M, Ardebili A. Antimicrobial photodynamic effect of the photosensitizer riboflavin, alone and in combination with colistin, against pandrug-resistant Pseudomonas aeruginosa clinical isolates. J Infect Chemother 2024; 30:892-898. [PMID: 38432556 DOI: 10.1016/j.jiac.2024.03.001] [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: 07/07/2023] [Revised: 02/05/2024] [Accepted: 03/01/2024] [Indexed: 03/05/2024]
Abstract
INTRODUCTION Development of multi-, extensively-, and pandrug-resistant (MDR, XDR, and PDR) strains of Pseudomonas aeruginosa remains a major problem in medical care. The present study evaluated the effect of antimicrobial photodynamic therapy (aPDT) as a monotherapy and in combination with colistin against P. aeruginosa isolates. METHODS Two P. aeruginosa isolates recovered from patients with respiratory tract infections were examined in this study. Minimum inhibitory concentration (MIC) of colistin was determined by the colistin broth disk elution (CBDE) and the reference broth microdilution (rBMD) methods. aPDT was performed using the photosensitizer (Ps) riboflavin at several concentrations and a light-emitting diode (LED) emitting blue light for different irradiation times with or without colistin at 1/2 × MIC concentration. RESULTS Both PA1 and PA2 isolates were identified as colistin-resistant P. aeruginosa with a MIC ≥4 μg/mL by the CBDE and MICs of 512 μg/mL and 256 μg/mL, respectively, by the rBMD. In aPDT, neither riboflavin nor LED light alone had antibacterial effects. The values of colony forming units per milliliter (CFU/mL) in both isolates were significantly reduced by LED + Ps treatments in a time-dependent manner (LED irradiation time) and dose-dependent manner (Ps concentration). In comparison with control, treatment with Ps (50 μM) + LED (120 s) and Ps (100 μM) + LED (120 s) resulted in 0.27 log10 CFU/mL and 0.43 log10 CFU/mL reductions in PA1, and 0.28 log10 CFU/mL and 0.34 log10 CFU/mL reductions in PA2, respectively, (P < 0.01). The best results were obtained after the combination of aPDT followed by colistin, which increased bacterial reduction, resulting in a 0.41-0.7 log10 CFU/mL reduction for PA1 and 0.35-0.83 log10 CFU/mL reduction for PA2 (P = 0.001). CONCLUSIONS This study suggests the potential implications of aPDT in combination with antibiotics, such as colistin for treatment of difficult-to-treat P. aeruginosa infections.
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Affiliation(s)
- Ehsan Najari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran; Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Samin Zamani
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran; Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Mehdi Sheikh Arabi
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Abdollah Ardebili
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran; Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran.
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Diani E, Bianco G, Gatti M, Gibellini D, Gaibani P. Colistin: Lights and Shadows of an Older Antibiotic. Molecules 2024; 29:2969. [PMID: 38998921 PMCID: PMC11243602 DOI: 10.3390/molecules29132969] [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: 05/29/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
The emergence of antimicrobial resistance represents a serious threat to public health and for infections due to multidrug-resistant (MDR) microorganisms, representing one of the most important causes of death worldwide. The renewal of old antimicrobials, such as colistin, has been proposed as a valuable therapeutic alternative to the emergence of the MDR microorganisms. Although colistin is well known to present several adverse toxic effects, its usage in clinical practice has been reconsidered due to its broad spectrum of activity against Gram-negative (GN) bacteria and its important role of "last resort" agent against MDR-GN. Despite the revolutionary perspective of treatment with this old antimicrobial molecule, many questions remain open regarding the emergence of novel phenotypic traits of resistance and the optimal usage of the colistin in clinical practice. In last years, several forward steps have been made in the understanding of the resistance determinants, clinical usage, and pharmacological dosage of this molecule; however, different points regarding the role of colistin in clinical practice and the optimal pharmacokinetic/pharmacodynamic targets are not yet well defined. In this review, we summarize the mode of action, the emerging resistance determinants, and its optimal administration in the treatment of infections that are difficult to treat due to MDR Gram-negative bacteria.
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Affiliation(s)
- Erica Diani
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Gabriele Bianco
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
| | - Milo Gatti
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Davide Gibellini
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Paolo Gaibani
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
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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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Breen SKJ, Harper M, López-Causapé C, Rogers KE, Tait JR, Smallman TR, Lang Y, Lee WL, Zhou J, Zhang Y, Bulitta JB, Nation RL, Oliver A, Boyce JD, Landersdorfer CB. Synergistic effects of inhaled aztreonam plus tobramycin on hypermutable cystic fibrosis Pseudomonas aeruginosa isolates in a dynamic biofilm model evaluated by mechanism-based modelling and whole genome sequencing. Int J Antimicrob Agents 2024; 63:107161. [PMID: 38561094 DOI: 10.1016/j.ijantimicag.2024.107161] [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: 01/19/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVE Hypermutable Pseudomonas aeruginosa strains are highly prevalent in chronic lung infections of patients with cystic fibrosis (CF). Acute exacerbations of these infections have limited treatment options. This study aimed to investigate inhaled aztreonam and tobramycin against clinical hypermutable P. aeruginosa strains using the CDC dynamic in vitro biofilm reactor (CBR), mechanism-based mathematical modelling (MBM) and genomic studies. METHODS Two CF multidrug-resistant strains were investigated in a 168 h CBR (n = 2 biological replicates). Regimens were inhaled aztreonam (75 mg 8-hourly) and tobramycin (300 mg 12-hourly) in monotherapies and combination. The simulated pharmacokinetic profiles of aztreonam and tobramycin (t1/2 = 3 h) were based on published lung fluid concentrations in patients with CF. Total viable and resistant counts were determined for planktonic and biofilm bacteria. MBM of total and resistant bacterial counts and whole genome sequencing were completed. RESULTS Both isolates showed reproducible bacterial regrowth and resistance amplification for the monotherapies by 168 h. The combination performed synergistically, with minimal resistant subpopulations compared to the respective monotherapies at 168 h. Mechanistic synergy appropriately described the antibacterial effects of the combination regimen in the MBM. Genomic analysis of colonies recovered from monotherapy regimens indicated noncanonical resistance mechanisms were likely responsible for treatment failure. CONCLUSION The combination of aztreonam and tobramycin was required to suppress the regrowth and resistance of planktonic and biofilm bacteria in all biological replicates of both hypermutable multidrug-resistant P. aeruginosa CF isolates. The developed MBM could be utilised for future investigations of this promising inhaled combination.
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Affiliation(s)
- Siobhonne K J Breen
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Marina Harper
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitario Son Espases-IdISBa, Palma de Mallorca, Spain; CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Kate E Rogers
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Jessica R Tait
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Thomas R Smallman
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yinzhi Lang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Wee L Lee
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Jieqiang Zhou
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Yongzhen Zhang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Jurgen B Bulitta
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Roger L Nation
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases-IdISBa, Palma de Mallorca, Spain; CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - John D Boyce
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Cornelia B Landersdorfer
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
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Hsieh YYP, Sun W, Young JM, Cheung R, Hogan DA, Dandekar AA, Malik HS. Widespread fungal-bacterial competition for magnesium lowers bacterial susceptibility to polymyxin antibiotics. PLoS Biol 2024; 22:e3002694. [PMID: 38900845 PMCID: PMC11218974 DOI: 10.1371/journal.pbio.3002694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/02/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024] Open
Abstract
Fungi and bacteria coexist in many polymicrobial communities, yet the molecular basis of their interactions remains poorly understood. Here, we show that the fungus Candida albicans sequesters essential magnesium ions from the bacterium Pseudomonas aeruginosa. To counteract fungal Mg2+ sequestration, P. aeruginosa expresses the Mg2+ transporter MgtA when Mg2+ levels are low. Thus, loss of MgtA specifically impairs P. aeruginosa in co-culture with C. albicans, but fitness can be restored by supplementing Mg2+. Using a panel of fungi and bacteria, we show that Mg2+ sequestration is a general mechanism of fungal antagonism against gram-negative bacteria. Mg2+ limitation enhances bacterial resistance to polymyxin antibiotics like colistin, which target gram-negative bacterial membranes. Indeed, experimental evolution reveals that P. aeruginosa evolves C. albicans-dependent colistin resistance via non-canonical means; antifungal treatment renders resistant bacteria colistin-sensitive. Our work suggests that fungal-bacterial competition could profoundly impact polymicrobial infection treatment with antibiotics of last resort.
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Affiliation(s)
- Yu-Ying Phoebe Hsieh
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Wanting Sun
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Janet M. Young
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Robin Cheung
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Ajai A. Dandekar
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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7
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Padhy I, Dwibedy SK, Mohapatra SS. A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development. Microbiol Res 2024; 283:127679. [PMID: 38508087 DOI: 10.1016/j.micres.2024.127679] [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: 07/31/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
With the rising incidences of antimicrobial resistance (AMR) and the diminishing options of novel antimicrobial agents, it is paramount to decipher the molecular mechanisms of action and the emergence of resistance to the existing drugs. Polymyxin, a cationic antimicrobial lipopeptide, is used to treat infections by Gram-negative bacterial pathogens as a last option. Though polymyxins were identified almost seventy years back, their use has been restricted owing to toxicity issues in humans. However, their clinical use has been increasing in recent times resulting in the rise of polymyxin resistance. Moreover, the detection of "mobile colistin resistance (mcr)" genes in the environment and their spread across the globe have complicated the scenario. The mechanism of polymyxin action and the development of resistance is not thoroughly understood. Specifically, the polymyxin-bacterial lipopolysaccharide (LPS) interaction is a challenging area of investigation. The use of advanced biophysical techniques and improvement in molecular dynamics simulation approaches have furthered our understanding of this interaction, which will help develop polymyxin analogs with better bactericidal effects and lesser toxicity in the future. In this review, we have delved deeper into the mechanisms of polymyxin-LPS interactions, highlighting several models proposed, and the mechanisms of polymyxin resistance development in some of the most critical Gram-negative pathogens.
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Affiliation(s)
- Indira Padhy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India.
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Oliver A, Rojo-Molinero E, Arca-Suarez J, Beşli Y, Bogaerts P, Cantón R, Cimen C, Croughs PD, Denis O, Giske CG, Graells T, Daniel Huang TD, Iorga BI, Karatuna O, Kocsis B, Kronenberg A, López-Causapé C, Malhotra-Kumar S, Martínez LM, Mazzariol A, Meyer S, Naas T, Notermans DW, Oteo-Iglesias J, Pedersen T, Pirš M, Poeta P, Poirel L, Pournaras S, Sundsfjord A, Szabó D, Tambić-Andrašević A, Vatcheva-Dobrevska R, Vitkauskienė A, Jeannot K. Pseudomonasaeruginosa antimicrobial susceptibility profiles, resistance mechanisms and international clonal lineages: update from ESGARS-ESCMID/ISARPAE Group. Clin Microbiol Infect 2024; 30:469-480. [PMID: 38160753 DOI: 10.1016/j.cmi.2023.12.026] [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: 10/13/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
SCOPE Pseudomonas aeruginosa, a ubiquitous opportunistic pathogen considered one of the paradigms of antimicrobial resistance, is among the main causes of hospital-acquired and chronic infections associated with significant morbidity and mortality. This growing threat results from the extraordinary capacity of P. aeruginosa to develop antimicrobial resistance through chromosomal mutations, the increasing prevalence of transferable resistance determinants (such as the carbapenemases and the extended-spectrum β-lactamases), and the global expansion of epidemic lineages. The general objective of this initiative is to provide a comprehensive update of P. aeruginosa resistance mechanisms, especially for the extensively drug-resistant (XDR)/difficult-to-treat resistance (DTR) international high-risk epidemic lineages, and how the recently approved β-lactams and β-lactam/β-lactamase inhibitor combinations may affect resistance mechanisms and the definition of susceptibility profiles. METHODS To address this challenge, the European Study Group for Antimicrobial Resistance Surveillance (ESGARS) from the European Society of Clinical Microbiology and Infectious Diseases launched the 'Improving Surveillance of Antibiotic-Resistant Pseudomonas aeruginosa in Europe (ISARPAE)' initiative in 2022, supported by the Joint programming initiative on antimicrobial resistance network call and included a panel of over 40 researchers from 18 European Countries. Thus, a ESGARS-ISARPAE position paper was designed and the final version agreed after four rounds of revision and discussion by all panel members. QUESTIONS ADDRESSED IN THE POSITION PAPER To provide an update on (a) the emerging resistance mechanisms to classical and novel anti-pseudomonal agents, with a particular focus on β-lactams, (b) the susceptibility profiles associated with the most relevant β-lactam resistance mechanisms, (c) the impact of the novel agents and resistance mechanisms on the definitions of resistance profiles, and (d) the globally expanding XDR/DTR high-risk lineages and their association with transferable resistance mechanisms. IMPLICATION The evidence presented herein can be used for coordinated epidemiological surveillance and decision making at the European and global level.
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Affiliation(s)
- Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Estrella Rojo-Molinero
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Arca-Suarez
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Yeşim Beşli
- Department of Medical Microbiology, Amerikan Hastanesi, Istanbul, Turkey
| | - Pierre Bogaerts
- National Center for Antimicrobial Resistance in Gram, CHU UCL Namur, Yvoir, Belgium
| | - Rafael Cantón
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Cansu Cimen
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany; Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter D Croughs
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Olivier Denis
- Department of Microbiology, CHU Namur Site-Godinne, Université Catholique de Louvain, Yvoir, Belgium; Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Tíscar Graells
- Department of Neurobiology, Care Sciences and Society (NVS), Division of Family Medicine and Primary Care, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Te-Din Daniel Huang
- National Center for Antimicrobial Resistance in Gram, CHU UCL Namur, Yvoir, Belgium
| | - Bogdan I Iorga
- CNRS, Institut de Chimie des Substances Naturelles, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Onur Karatuna
- EUCAST Development Laboratory, Clinical Microbiology, Central Hospital, Växjö, Sweden
| | - Béla Kocsis
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Andreas Kronenberg
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Luis Martínez Martínez
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Unidad de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, e Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | - Annarita Mazzariol
- Microbiology and Virology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Sylvain Meyer
- INSERM UMR 1092 and Université of Limoges, Limoges, France
| | - Thierry Naas
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques: Entérobactéries Résistantes aux Carbapénèmes, Le Kremlin-Bicêtre, France; Équipe INSERM ReSIST, Faculté de Médecine, Université Paris-Saclay, Paris, France
| | - Daan W Notermans
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jesús Oteo-Iglesias
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Mateja Pirš
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Patricia Poeta
- MicroART-Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, Portugal; Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; University of Trás-os-Montes and Alto Douro, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Vila Real, Portugal
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland; University of Fribourg, Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
| | - Spyros Pournaras
- Laboratory of Clinical Microbiology, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dora Szabó
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary; Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary
| | - Arjana Tambić-Andrašević
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Zagreb, Croatia; School of Dental Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Astra Vitkauskienė
- Department of Laboratory Medicine, Faculty of Medicine, Medical Academy, Lithuanian University of Health Science, Kaunas, Lithuania
| | - Katy Jeannot
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, Besançon, France; Laboratoire associé du Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France; Chrono-environnement UMR 6249, CNRS, Université Franche-Comté, Besançon, France
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9
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Janet-Maitre M, Job V, Bour M, Robert-Genthon M, Brugière S, Triponney P, Cobessi D, Couté Y, Jeannot K, Attrée I. Pseudomonas aeruginosa MipA-MipB envelope proteins act as new sensors of polymyxins. mBio 2024; 15:e0221123. [PMID: 38345374 PMCID: PMC10936184 DOI: 10.1128/mbio.02211-23] [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: 08/16/2023] [Accepted: 01/09/2024] [Indexed: 03/14/2024] Open
Abstract
Due to the rising incidence of antibiotic-resistant infections, the last-line antibiotics, polymyxins, have resurged in the clinics in parallel with new bacterial strategies of escape. The Gram-negative opportunistic pathogen Pseudomonas aeruginosa develops resistance to colistin/polymyxin B by distinct molecular mechanisms, mostly through modification of the lipid A component of the LPS by proteins encoded within the arnBCDATEF-ugd (arn) operon. In this work, we characterized a polymyxin-induced operon named mipBA, present in P. aeruginosa strains devoid of the arn operon. We showed that mipBA is activated by the ParR/ParS two-component regulatory system in response to polymyxins. Structural modeling revealed that MipA folds as an outer-membrane β-barrel, harboring an internal negatively charged channel, able to host a polymyxin molecule, while the lipoprotein MipB adopts a β-lactamase fold with two additional C-terminal domains. Experimental work confirmed that MipA and MipB localize to the bacterial envelope, and they co-purify in vitro. Nano differential scanning fluorimetry showed that polymyxins stabilized MipA in a specific and dose-dependent manner. Mass spectrometry-based quantitative proteomics on P. aeruginosa membranes demonstrated that ∆mipBA synthesized fourfold less MexXY-OprA proteins in response to polymyxin B compared to the wild-type strain. The decrease was a direct consequence of impaired transcriptional activation of the mex operon operated by ParR/ParS. We propose MipA/MipB to act as membrane (co)sensors working in concert to activate ParS histidine kinase and help the bacterium to cope with polymyxin-mediated envelope stress through synthesis of the efflux pump, MexXY-OprA.IMPORTANCEDue to the emergence of multidrug-resistant isolates, antibiotic options may be limited to polymyxins to eradicate Gram-negative infections. Pseudomonas aeruginosa, a leading opportunistic pathogen, has the ability to develop resistance to these cationic lipopeptides by modifying its lipopolysaccharide through proteins encoded within the arn operon. Herein, we describe a sub-group of P. aeruginosa strains lacking the arn operon yet exhibiting adaptability to polymyxins. Exposition to sub-lethal polymyxin concentrations induced the expression and production of two envelope-associated proteins. Among those, MipA, an outer-membrane barrel, is able to specifically bind polymyxins with an affinity in the 10-µM range. Using membrane proteomics and phenotypic assays, we showed that MipA and MipB participate in the adaptive response to polymyxins via ParR/ParS regulatory signaling. We propose a new model wherein the MipA-MipB module functions as a novel polymyxin sensing mechanism.
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Affiliation(s)
- Manon Janet-Maitre
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Viviana Job
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Maxime Bour
- UMR6249 Chrono-Environnement, UFR Santé, University of Franche-Comté, Besançon, France
- French National Reference Center for Antibiotic Resistance, Besançon, France
| | - Mylène Robert-Genthon
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
| | - Sabine Brugière
- University Grenoble Alpes, CEA, INSERM, UA13 BGE, CNRS, CEA, FranceGrenoble
| | - Pauline Triponney
- French National Reference Center for Antibiotic Resistance, Besançon, France
| | - David Cobessi
- University Grenoble Alpes, IBS, UMR5075, Team Synchrotron, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, CEA, INSERM, UA13 BGE, CNRS, CEA, FranceGrenoble
| | - Katy Jeannot
- UMR6249 Chrono-Environnement, UFR Santé, University of Franche-Comté, Besançon, France
- French National Reference Center for Antibiotic Resistance, Besançon, France
- Department of Bacteriology, Teaching Hospital of Besançon, Besançon, France
| | - Ina Attrée
- Team Bacterial Pathogenesis and Cellular Responses, University Grenoble Alpes, IBS, UMR5075, Grenoble, France
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10
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Graham CI, MacMartin TL, de Kievit TR, Brassinga AKC. Molecular regulation of virulence in Legionella pneumophila. Mol Microbiol 2024; 121:167-195. [PMID: 37908155 DOI: 10.1111/mmi.15172] [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: 05/31/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 11/02/2023]
Abstract
Legionella pneumophila is a gram-negative bacteria found in natural and anthropogenic aquatic environments such as evaporative cooling towers, where it reproduces as an intracellular parasite of cohabiting protozoa. If L. pneumophila is aerosolized and inhaled by a susceptible person, bacteria may colonize their alveolar macrophages causing the opportunistic pneumonia Legionnaires' disease. L. pneumophila utilizes an elaborate regulatory network to control virulence processes such as the Dot/Icm Type IV secretion system and effector repertoire, responding to changing nutritional cues as their host becomes depleted. The bacteria subsequently differentiate to a transmissive state that can survive in the environment until a replacement host is encountered and colonized. In this review, we discuss the lifecycle of L. pneumophila and the molecular regulatory network that senses nutritional depletion via the stringent response, a link to stationary phase-like metabolic changes via alternative sigma factors, and two-component systems that are homologous to stress sensors in other pathogens, to regulate differentiation between the intracellular replicative phase and more transmissible states. Together, we highlight how this prototypic intracellular pathogen offers enormous potential in understanding how molecular mechanisms enable intracellular parasitism and pathogenicity.
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Affiliation(s)
- Christopher I Graham
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Teassa L MacMartin
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Teresa R de Kievit
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ann Karen C Brassinga
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, Manitoba, Canada
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11
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Ghassani A, Triponney P, Bour M, Plésiat P, Jeannot K. Mutations in genes lpxL1, bamA, and pmrB impair the susceptibility of cystic fibrosis strains of Pseudomonas aeruginosa to murepavadin. Antimicrob Agents Chemother 2024; 68:e0129823. [PMID: 38092672 PMCID: PMC10790571 DOI: 10.1128/aac.01298-23] [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: 10/06/2023] [Accepted: 11/06/2023] [Indexed: 01/11/2024] Open
Abstract
Murepavadin is a peptidomimetic exhibiting specific inhibitory activity against Pseudomonas species. In the present study, its in vitro activity was assessed on 230 cystic fibrosis (CF) strains of Pseudomonas aeruginosa isolated from 12 French hospitals, in comparison with 12 other antipseudomonal antibiotics. Although murepavadin is still in preclinical stage of development, 9.1% (n = 21) of strains had a minimum inhibitory concentration (MIC) >4 mg/L, a level at least 128-fold higher than the modal MIC value of the whole collection (≤0.06 mg/L). Whole-genome sequencing of these 21 strains along with more susceptible isogenic counterparts coexisting in the same patients revealed diverse mutations in genes involved in the synthesis (lpxL1 and lpxL2) or transport of lipopolysaccharides (bamA, lptD, and msbA), or encoding histidine kinases of two-component systems (pmrB and cbrA). Allelic replacement experiments with wild-type reference strain PAO1 confirmed that alteration of genes lpxL1, bamA, and/or pmrB can decrease the murepavadin susceptibility from 8- to 32-fold. Furthermore, we found that specific amino acid substitutions in histidine kinase PmrB (G188D, Q105P, and D45E) reduce the susceptibility of P. aeruginosa to murepavadin, colistin, and tobramycin, three antibiotics used or intended to be used (murepavadin) in aerosols to treat colonized CF patients. Whether colistin or tobramycin may select mutants resistant to murepavadin or the opposite needs to be addressed by clinical studies.
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Affiliation(s)
- Aya Ghassani
- UMR6249 CNRS Chrono-environnement, Université de Franche-Comté, Besançon, France
| | - Pauline Triponney
- Laboratoire associé au Centre National de Référence de la résistance aux antibiotiques, Besançon, France
| | - Maxime Bour
- Laboratoire associé au Centre National de Référence de la résistance aux antibiotiques, Besançon, France
| | - Patrick Plésiat
- UMR6249 CNRS Chrono-environnement, Université de Franche-Comté, Besançon, France
| | - Katy Jeannot
- UMR6249 CNRS Chrono-environnement, Université de Franche-Comté, Besançon, France
- Laboratoire associé au Centre National de Référence de la résistance aux antibiotiques, Besançon, France
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire Jean Minjoz, Besançon, France
| | - MucoMicrobes study GroupCardot-MartinEmilie1CattoirVincent2CrémetLise3Doléan-JordheimAnne4FerroniAgnès5GarnierFabien6Guet-RevilletHélène7GuillardThomas8Hery-ArnaudGeneviève9ImbertGuenièvre10MarianiPatricia11Centre Hospitalier Universitaire Foch, Paris, FranceCentre Hospitalier Universitaire de Rennes, Rennes, FranceCentre Hospitalier Universitaire de Nantes, Nantes, FranceHospices civils de Lyon, Lyon, FranceCentre Hospitalier Universitaire de Necker, Paris, FranceCentre Hospitalier Universitaire de Limoges, Limoges, FranceCentre Hospitalier Universitaire de Toulouse, Toulouse, FranceCentre Hospitalier Universitaire de Reims, Reims, FranceCentre Hospitalier Universitaire de Brest, Brest, FranceCentre Hospitalier de Toulon, Toulon, FranceCentre Hospitalier Universitaire Robert Debré, Paris, France
- UMR6249 CNRS Chrono-environnement, Université de Franche-Comté, Besançon, France
- Laboratoire associé au Centre National de Référence de la résistance aux antibiotiques, Besançon, France
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire Jean Minjoz, Besançon, France
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12
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Disney-McKeethen S, Seo S, Mehta H, Ghosh K, Shamoo Y. Experimental evolution of Pseudomonas aeruginosa to colistin in spatially confined microdroplets identifies evolutionary trajectories consistent with adaptation in microaerobic lung environments. mBio 2023; 14:e0150623. [PMID: 37847036 PMCID: PMC10746239 DOI: 10.1128/mbio.01506-23] [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: 06/16/2023] [Accepted: 09/08/2023] [Indexed: 10/18/2023] Open
Abstract
IMPORTANCE Antibiotic resistance remains one of the great challenges confronting public health in the world today. Individuals with compromised immune systems or underlying health conditions are often at an increased for bacterial infections. Patients with cystic fibrosis (CF) produce thick mucus that clogs airways and provides a very favorable environment for infection by bacteria that further decrease lung function and, ultimately, mortality. CF patients are often infected by bacteria such as Pseudomonas aeruginosa early in life and experience a series of chronic infections that, over time, become increasingly difficult to treat due to increased antibiotic resistance. Colistin is a major antibiotic used to treat CF patients. Clinical and laboratory studies have identified PmrA/PmrB and PhoP/PhoQ as responsible for increased resistance to colistin. Both have been identified in CF patient lungs, but why, in some cases, is it one and not the other? In this study, we show that distinct evolutionary trajectories to colistin resistance may be favored by the microaerobic partitioning found within the damaged CF lung.
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Affiliation(s)
| | - Seokju Seo
- Department of Biosciences, Rice University, Houston , Texas , USA
| | - Heer Mehta
- Department of Biosciences, Rice University, Houston , Texas , USA
| | - Karukriti Ghosh
- Department of Biosciences, Rice University, Houston , Texas , USA
| | - Yousif Shamoo
- Department of Biosciences, Rice University, Houston , Texas , USA
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13
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Erdmann MB, Gardner PP, Lamont IL. The PitA protein contributes to colistin susceptibility in Pseudomonas aeruginosa. PLoS One 2023; 18:e0292818. [PMID: 37824582 PMCID: PMC10569645 DOI: 10.1371/journal.pone.0292818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes a wide range of problematic infections in individuals with predisposing conditions. Infections can be treated with colistin but some isolates are resistant to this antibiotic. To better understand the genetic basis of resistance, we experimentally evolved 19 independent resistant mutants from the susceptible laboratory strain PAO1. Whole genome sequencing identified mutations in multiple genes including phoQ and pmrB that have previously been associated with resistance, pitA that encodes a phosphate transporter, and carB and eno that encode enzymes of metabolism. Individual mutations were engineered into the genome of strain PAO1. Mutations in pitA, pmrB and phoQ increased the minimum inhibitory concentration (MIC) for colistin 8-fold, making the bacteria resistant. Engineered pitA/phoQ and pitA/pmrB double mutants had higher MICs than single mutants, demonstrating additive effects on colistin susceptibility. Single carB and eno mutations did not increase the MIC suggesting that their effect is dependent on the presence of other mutations. Many of the resistant mutants had increased susceptibility to β-lactams and lower growth rates than the parental strain demonstrating that colistin resistance can impose a fitness cost. Two hundred and fourteen P. aeruginosa isolates from a range of sources were tested and 18 (7.8%) were colistin resistant. Sequence variants in genes identified by experimental evolution were present in the 18 resistant isolates and may contribute to resistance. Overall our results identify pitA mutations as novel contributors to colistin resistance and demonstrate that resistance can reduce fitness of the bacteria.
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Affiliation(s)
| | - Paul P. Gardner
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Iain L. Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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14
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Awori RM, Hendre P, Amugune NO. The genome of a steinernematid-associated Pseudomonas piscis bacterium encodes the biosynthesis of insect toxins. Access Microbiol 2023; 5:000659.v3. [PMID: 37970093 PMCID: PMC10634486 DOI: 10.1099/acmi.0.000659.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/15/2023] [Indexed: 11/17/2023] Open
Abstract
Several species of soil-dwelling Steinernema nematodes are used in the biocontrol of crop pests, due to their natural capacity to kill diverse lepidopteran species. Although this insect-killing trait is known to be augmented by the nematodes' Xenorhabdus endosymbionts, the role of other steinernematid-associated bacterial genera in the nematode lifecycle remains unclear. This genomic study aimed to determine the potential of Pseudomonas piscis to contribute to the entomopathogenicity of its Steinernema host. Insect larvae were infected with three separate Steinernema cultures. From each of the three treatments, the prevalent bacteria in the haemocoel of cadavers, four days post-infection, were isolated. These three bacterial isolates were morphologically characterised. DNA was extracted from each of the three bacterial isolates and used for long-read genome sequencing and assembly. Assemblies were used to delineate species and identify genes that encode insect toxins, antimicrobials, and confer antibiotic resistance. We assembled three complete genomes. Through digital DNA-DNA hybridisation analyses, we ascertained that the haemocoels of insect cadavers previously infected with Steinernema sp. Kalro, Steinernema sp. 75, and Steinernema sp. 97 were dominated by Xenorhabdus griffiniae Kalro, Pseudomonas piscis 75, and X. griffiniae 97, respectively. X. griffiniae Kalro and X. griffiniae 97 formed a subspecies with other X. griffiniae symbionts of steinernematids from Kenya. P. piscis 75 phylogenetically clustered with pseudomonads that are characterised by high insecticidal activity. The P. piscis 75 genome encoded the production pathway of insect toxins such as orfamides and rhizoxins, antifungals such as pyrrolnitrin and pyoluteorin, and the broad-spectrum antimicrobial 2,4-diacetylphloroglucinol. The P. piscis 75 genome encoded resistance to over ten classes of antibiotics, including cationic lipopeptides. Steinernematid-associated P. piscis bacteria hence have the biosynthetic potential to contribute to nematode entomopathogenicity.
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Affiliation(s)
- Ryan Musumba Awori
- Elakistos Biosciences, P. O. Box 19301-00100, Nairobi, Kenya
- International Centre for Research on Agroforestry, P. O. Box 30677-00100, Nairobi, Kenya
| | - Prasad Hendre
- International Centre for Research on Agroforestry, P. O. Box 30677-00100, Nairobi, Kenya
| | - Nelson O. Amugune
- Department of Biology, University of Nairobi, P. O. Box 30197-00100, Nairobi, Kenya
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15
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Wei X, Gao J, Xu C, Pan X, Jin Y, Bai F, Cheng Z, Lamont IL, Pletzer D, Wu W. Murepavadin induces envelope stress response and enhances the killing efficacies of β-lactam antibiotics by impairing the outer membrane integrity of Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0125723. [PMID: 37668398 PMCID: PMC10581190 DOI: 10.1128/spectrum.01257-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/08/2023] [Indexed: 09/06/2023] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen that can cause a variety of acute and chronic infections. The bacterium is highly resistant to numerous antibiotics. Murepavadin is a peptidomimetic antibiotic that blocks the function of P. aeruginosa lipopolysaccharide (LPS) transport protein D (LptD), thus inhibiting the insertion of LPS into the outer membrane. In this study, we demonstrated that sublethal concentrations of murepavadin enhance the bacterial outer membrane permeability. Proteomic analyses revealed the alteration of protein composition in bacterial inner and outer membranes following murepavadin treatment. The antisigma factor MucA was upregulated by murepavadin. In addition, the expression of the sigma E factor gene algU and the alginate synthesis gene algD was induced by murepavadin. Deletion of the algU gene reduces bacterial survival following murepavadin treatment, indicating a role of the envelope stress response in bacterial tolerance. We further demonstrated that murepavadin enhances the bactericidal activities of β-lactam antibiotics by promoting drug influx across the outer membrane. In a mouse model of acute pneumonia, the murepavadin-ceftazidime/avibactam combination showed synergistic therapeutic effect against P. aeruginosa infection. In addition, the combination of murepavadin with ceftazidime/avibactam slowed down the resistance development. In conclusion, our results reveal the response mechanism of P. aeruginosa to murepavadin and provide a promising antibiotic combination for the treatment of P. aeruginosa infections.IMPORTANCEThe ever increasing resistance of bacteria to antibiotics poses a serious threat to global public health. Novel antibiotics and treatment strategies are urgently needed. Murepavadin is a novel antibiotic that blocks the assembly of lipopolysaccharide (LPS) into the Pseudomonas aeruginosa outer membrane by inhibiting LPS transport protein D (LptD). Here, we demonstrated that murepavadin impairs bacterial outer membrane integrity, which induces the envelope stress response. We further found that the impaired outer membrane integrity increases the influx of β-lactam antibiotics, resulting in enhanced bactericidal effects. In addition, the combination of murepavadin and a β-lactam/β-lactamase inhibitor mixture (ceftazidime/avibactam) slowed down the resistance development of P. aeruginosa. Overall, this study demonstrates the bacterial response to murepavadin and provides a new combination strategy for effective treatment.
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Affiliation(s)
- Xiaoya Wei
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jiacong Gao
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Congjuan Xu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Iain L. Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Daniel Pletzer
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
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16
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Huang YT, Mao YC, Tseng CH, Liu CW, Liu PY. Identification of combinatorial mutations associated with colistin resistance in Shewanella algae. Microbes Infect 2023; 25:105143. [PMID: 37085044 DOI: 10.1016/j.micinf.2023.105143] [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: 01/13/2023] [Revised: 04/11/2023] [Accepted: 04/16/2023] [Indexed: 04/23/2023]
Abstract
Colistin is a last-resort antibiotic used to treat infections caused by drug-resistant gram-negative bacteria. However, the genetic mechanisms underlying colistin resistance in Shewanella algae are not well understood. In this study, we sequenced and compared the genomes of 23 mcr-negative colistin-resistant and sensitive S. algae samples from various sources. We applied a computational approach to identify combinatorial mutations associated with colistin resistance. Our analysis revealed a combination of three mutations (PmrB 451, PmrE168, PmrH292) that were strongly associated with colistin resistance in S. algae. This study provides insights into the genetic mechanisms of colistin resistance in S. algae and demonstrates the utility of a computational approach for identifying epistatic interactions among mutations. Identifying the genetic mutations responsible for colistin resistance in S. algae can inform the development of new treatments or strategies to combat infections caused by this emerging pathogen.
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Affiliation(s)
- Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Daxue Road Section 1, Minxiong Township, Chiayi County 62102, Taiwan
| | - Yan-Chiao Mao
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, 1650 Taiwan Boulevard Section 4, Xitun District, Taichung 40705, Taiwan
| | - Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, 1650 Taiwan Boulevard Section 4, Xitun District, Taichung 40705, Taiwan
| | - Chia-Wei Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, 1650 Taiwan Boulevard Section 4, Xitun District, Taichung 40705, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, 1650 Taiwan Boulevard Section 4, Xitun District, Taichung 40705, Taiwan; Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, 145 Xingda Rd, South District, Taichung 40227, Taiwan; Ph.D. Program in Translational Medicine, National Chung Hsing University, 145 Xingda Rd, South District, Taichung 40227, Taiwan; Department of Post-Baccalaureate Medicine, National Chung Hsing University, 145 Xingda Rd, South District, Taichung 40227, Taiwan; Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, 1650 Taiwan Boulevard Section 4. Xitun District, Taichung 40705, Taiwan.
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17
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Mozaheb N, Rasouli P, Kaur M, Van Der Smissen P, Larrouy-Maumus G, Mingeot-Leclercq MP. A Mildly Acidic Environment Alters Pseudomonas aeruginosa Virulence and Causes Remodeling of the Bacterial Surface. Microbiol Spectr 2023; 11:e0483222. [PMID: 37278652 PMCID: PMC10433952 DOI: 10.1128/spectrum.04832-22] [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] [Received: 11/23/2022] [Accepted: 05/14/2023] [Indexed: 06/07/2023] Open
Abstract
Pseudomonas aeruginosa is a versatile pathogen that resists environmental stress, such as suboptimal pH. As a result of exposure to environmental stress, P. aeruginosa shows an altered virulence-related phenotype. This study investigated the modifications that P. aeruginosa undertakes at a mildly low pH (pH 5.0) compared with the bacteria grown in a neutral medium (pH 7.2). Results indicated that in a mildly acidic environment, expression of two-component system genes (phoP/phoQ and pmrA/pmrB), lipid A remodeling genes such as arnT and pagP and virulence genes, i.e., pqsE and rhlA, were induced. Moreover, lipid A of the bacteria grown at a mildly low pH is modified by adding 4-amino-arabinose (l-Ara4N). Additionally, the production of virulence factors such as rhamnolipid, alginate, and membrane vesicles is significantly higher in a mildly low-pH environment than in a neutral medium. Interestingly, at a mildly low pH, P. aeruginosa produces a thicker biofilm with higher biofilm biomass. Furthermore, studies on inner membrane viscosity and permeability showed that a mildly low pH causes a decrease in the inner membrane permeability and increases its viscosity. Besides, despite the importance of PhoP, PhoQ, PmrA, and PmrB in Gram-negative bacteria for responding to low pH stress, we observed that the absence of each of these two-component systems does not meaningfully impact the remodeling of the P. aeruginosa envelope. Given that P. aeruginosa is likely to encounter mildly acidic environments during infection in its host, the alterations that the bacterium undertakes under such conditions must be considered in designing antibacterial strategies against P. aeruginosa. IMPORTANCE P. aeruginosa encounters environments with acidic pH when establishing infections in hosts. The bacterium develops an altered phenotype to tolerate a moderate decrease in the environmental pH. At the level of the bacterial envelope, modified lipid A composition and a reduction of the bacterial inner membrane permeability and fluidity are among the changes P. aeruginosa undergoes at a mildly low pH. Also, the bacterium is more likely to form biofilm in a mildly acidic environment. Overall, these alterations in the P. aeruginosa phenotype put obstacles in the way of antibacterial activities. Thus, considering physiological changes in the bacterium at low pH helps design and implement antimicrobial approaches against this hostile microorganism.
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Affiliation(s)
- Negar Mozaheb
- Université catholique de Louvain, Louvain Drug Research Institute, Cellular & Molecular Pharmacology Unit (FACM), Brussels, Belgium
| | - Paria Rasouli
- Université catholique de Louvain, Louvain Drug Research Institute, Cellular & Molecular Pharmacology Unit (FACM), Brussels, Belgium
| | - Mandeep Kaur
- Université catholique de Louvain, Louvain Drug Research Institute, Cellular & Molecular Pharmacology Unit (FACM), Brussels, Belgium
| | - Patrick Van Der Smissen
- Université catholique de Louvain, de Duve Institute, CELL Unit and PICT Platform, Brussels, Belgium
| | - Gerald Larrouy-Maumus
- Imperial College London, Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Faculty of Natural Science, London, United Kingdom
| | - Marie-Paule Mingeot-Leclercq
- Université catholique de Louvain, Louvain Drug Research Institute, Cellular & Molecular Pharmacology Unit (FACM), Brussels, Belgium
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Shepherd MJ, Reynolds M, Pierce AP, Rice AM, Taylor TB. Transcription factor expression levels and environmental signals constrain transcription factor innovation. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001378. [PMID: 37584667 PMCID: PMC10482368 DOI: 10.1099/mic.0.001378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
Evolutionary innovation of transcription factors frequently drives phenotypic diversification and adaptation to environmental change. Transcription factors can gain or lose connections to target genes, resulting in novel regulatory responses and phenotypes. However the frequency of functional adaptation varies between different regulators, even when they are closely related. To identify factors influencing propensity for innovation, we utilise a Pseudomonas fluorescens SBW25 strain rendered incapable of flagellar mediated motility in soft-agar plates via deletion of the flagellar master regulator (fleQ ). This bacterium can evolve to rescue flagellar motility via gene regulatory network rewiring of an alternative transcription factor to rescue activity of FleQ. Previously, we have identified two members (out of 22) of the RpoN-dependent enhancer binding protein (RpoN-EBP) family of transcription factors (NtrC and PFLU1132) that are capable of innovating in this way. These two transcription factors rescue motility repeatably and reliably in a strict hierarchy – with NtrC the only route in a ∆fleQ background, and PFLU1132 the only route in a ∆fleQ ∆ntrC background. However, why other members in the same transcription factor family have not been observed to rescue flagellar activity is unclear. Previous work shows that protein homology cannot explain this pattern within the protein family (RpoN-EBPs), and mutations in strains that rescued motility suggested high levels of transcription factor expression and activation drive innovation. We predict that mutations that increase expression of the transcription factor are vital to unlock evolutionary potential for innovation. Here, we construct titratable expression mutant lines for 11 of the RpoN-EBPs in P. fluorescens . We show that in five additional RpoN-EBPs (FleR, HbcR, GcsR, DctD, AauR and PFLU2209), high expression levels result in different mutations conferring motility rescue, suggesting alternative rewiring pathways. Our results indicate that expression levels (and not protein homology) of RpoN-EBPs are a key constraining factor in determining evolutionary potential for innovation. This suggests that transcription factors that can achieve high expression through few mutational changes, or transcription factors that are active in the selective environment, are more likely to innovate and contribute to adaptive gene regulatory network evolution.
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Affiliation(s)
- Matthew J. Shepherd
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Mitchell Reynolds
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Aidan P. Pierce
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Alan M. Rice
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tiffany B. Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
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19
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Schumann A, Cohn AR, Gaballa A, Wiedmann M. Escherichia coli B-Strains Are Intrinsically Resistant to Colistin and Not Suitable for Characterization and Identification of mcr Genes. Microbiol Spectr 2023; 11:e0089423. [PMID: 37199645 PMCID: PMC10269513 DOI: 10.1128/spectrum.00894-23] [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: 03/02/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Antimicrobial resistance is an increasing threat to human and animal health. Due to the rise of multi-, extensive, and pandrug resistance, last resort antibiotics, such as colistin, are extremely important in human medicine. While the distribution of colistin resistance genes can be tracked through sequencing methods, phenotypic characterization of putative antimicrobial resistance (AMR) genes is still important to confirm the phenotype conferred by different genes. While heterologous expression of AMR genes (e.g., in Escherichia coli) is a common approach, so far, no standard methods for heterologous expression and characterization of mcr genes exist. E. coli B-strains, designed for optimum protein expression, are frequently utilized. Here, we report that four E. coli B-strains are intrinsically resistant to colistin (MIC 8-16 μg/mL). The three tested B-strains that encode T7 RNA polymerase show growth defects when transformed with empty or mcr-expressing pET17b plasmids and grown in the presence of IPTG; K-12 or B-strains without T7 RNA polymerase do not show these growth defects. E. coli SHuffle T7 express carrying empty pET17b also skips wells in colistin MIC assays in the presence of IPTG. These phenotypes could explain why B-strains were erroneously reported as colistin susceptible. Analysis of existing genome data identified one nonsynonymous change in each pmrA and pmrB in all four E. coli B-strains; the E121K change in PmrB has previously been linked to intrinsic colistin resistance. We conclude that E. coli B-strains are not appropriate heterologous expression hosts for identification and characterization of mcr genes. IMPORTANCE Given the rise in multidrug, extensive drug, and pandrug resistance in bacteria and the increasing use of colistin to treat human infections, occurrence of mcr genes threatens human health, and characterization of these resistance genes becomes more important. We show that three commonly used heterologous expression strains are intrinsically resistant to colistin. This is important because these strains have previously been used to characterize and identify new mobile colistin resistance (mcr) genes. We also show that expression plasmids (i.e., pET17b) without inserts cause cell viability defects when carried by B-strains with T7 RNA polymerase and grown in the presence of IPTG. Our findings are important as they will facilitate improved selection of heterologous strains and plasmid combinations for characterizing AMR genes, which will be particularly important with a shift to Culture-independent diagnostic tests where bacterial isolates become increasingly less available for characterization.
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Affiliation(s)
- Anna Schumann
- Department of Food Science, Cornell University, Ithaca, New York, USA
- Graduate Field of Biomedical and Biological Sciences, Cornell University, Ithaca, New York, USA
| | - Alexa R. Cohn
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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20
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Yang F, Zhou Y, Bai Y, Pan X, Ha UH, Cheng Z, Wu W, Jin Y, Bai F. MvfR Controls Tolerance to Polymyxin B by Regulating rfaD in Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0042623. [PMID: 37039709 PMCID: PMC10269820 DOI: 10.1128/spectrum.00426-23] [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: 01/31/2023] [Accepted: 02/18/2023] [Indexed: 04/12/2023] Open
Abstract
Polymyxins are currently the last-resort antibiotics for the treatment of multidrug-resistant Gram-negative bacterial infections. To expand the understanding of the intrinsic resistance mechanism against polymyxins, a laboratory strain of Pseudomonas aeruginosa PAO1 was subjected to serial passage in the presence of sublethal doses of polymyxin B over a period of 30 days. By whole-genome sequencing of successively isolated polymyxin B-resistant isolates, we identified a frameshift mutation (L183fs) in the mvfR gene that further increased polymyxin resistance in the pmrB mutant background. A ΔmvfR mutation alone showed higher tolerance to polymyxin B due to altered lipopolysaccharide (LPS) on the surface of bacterial cells, which decreases its outer membrane permeability. In the ΔmvfR mutant, polymyxin B treatment caused the upregulation of rfaD, the gene involved in LPS core oligosaccharide synthesis, which is responsible for polymyxin tolerance. To the best of our knowledge, this is the first report of mvfR mutation conferring polymyxin resistance in P. aeruginosa via increased integrity of bacterial outer membrane. IMPORTANCE Antibiotic resistance imposes a considerable challenge for the treatment of P. aeruginosa infections. Polymyxins are the last-resort antibiotics for the treatment of multidrug-resistant P. aeruginosa infections. Understanding the development and mechanisms of bacterial resistance to polymyxins may provide clues for the development of new or improved therapeutic strategies effective against P. aeruginosa. In this study, using an in vitro evolution assay in combination with whole-genome sequencing, we demonstrated that MvfR controls tolerance to polymyxin B by regulating the rfaD gene in P. aeruginosa. Our results reveal a novel mechanism employed by P. aeruginosa in the defense against polymyxin antibiotics.
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Affiliation(s)
- Fan Yang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuchen Zhou
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuxi Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Un-Hwan Ha
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
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21
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Ling KM, Stick SM, Kicic A. Pulmonary bacteriophage and cystic fibrosis airway mucus: friends or foes? Front Med (Lausanne) 2023; 10:1088494. [PMID: 37265479 PMCID: PMC10230084 DOI: 10.3389/fmed.2023.1088494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/11/2023] [Indexed: 06/03/2023] Open
Abstract
For those born with cystic fibrosis (CF), hyper-concentrated mucus with a dysfunctional structure significantly impacts CF airways, providing a perfect environment for bacterial colonization and subsequent chronic infection. Early treatment with antibiotics limits the prevalence of bacterial pathogens but permanently alters the CF airway microenvironment, resulting in antibiotic resistance and other long-term consequences. With little investment into new traditional antibiotics, safe and effective alternative therapeutic options are urgently needed. One gathering significant traction is bacteriophage (phage) therapy. However, little is known about which phages are effective for respiratory infections, the dynamics involved between phage(s) and the host airway, and associated by-products, including mucus. Work utilizing gut cell models suggest that phages adhere to mucus components, reducing microbial colonization and providing non-host-derived immune protection. Thus, phages retained in the CF mucus layer result from the positive selection that enables them to remain in the mucus layer. Phages bind weakly to mucus components, slowing down the diffusion motion and increasing their chance of encountering bacterial species for subsequent infection. Adherence of phage to mucus could also facilitate phage enrichment and persistence within the microenvironment, resulting in a potent phage phenotype or vice versa. However, how the CF microenvironment responds to phage and impacts phage functionality remains unknown. This review discusses CF associated lung diseases, the impact of CF mucus, and chronic bacterial infection. It then discusses the therapeutic potential of phages, their dynamic relationship with mucus and whether this may enhance or hinder airway bacterial infections in CF.
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Affiliation(s)
- Kak-Ming Ling
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
- Occupation, Environment and Safety, School of Population Health, Curtin University, Perth, WA, Australia
| | - Stephen Michael Stick
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
- Division of Paediatrics, Medical School, The University of Western Australia, Perth, WA, Australia
- Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Nedlands, WA, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
- Occupation, Environment and Safety, School of Population Health, Curtin University, Perth, WA, Australia
- Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Nedlands, WA, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Perth, WA, Australia
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22
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Armengol E, Kragh KN, Tolker-Nielsen T, Sierra JM, Higazy D, Ciofu O, Viñas M, Høiby N. Colistin Enhances Rifampicin's Antimicrobial Action in Colistin-Resistant Pseudomonas aeruginosa Biofilms. Antimicrob Agents Chemother 2023; 67:e0164122. [PMID: 36856424 PMCID: PMC10112245 DOI: 10.1128/aac.01641-22] [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] [Received: 12/07/2022] [Accepted: 01/30/2023] [Indexed: 03/02/2023] Open
Abstract
The emergence of multidrug-resistant Pseudomonas aeruginosa infections has urged the need to find new strategies, such as the use of combinations of antibiotics. Among these, the combination of colistin with other antibiotics has been studied. Here, the action of combinations of colistin and rifampicin on both planktonic and sessile cells of colistin-resistant P. aeruginosa was studied. Dynamic biofilms were formed and treated with such a combination, resulting in an active killing effect of both colistin-resistant and colistin-susceptible P. aeruginosa in biofilms. The results suggest that the action of colistin on the outer membrane facilitates rifampicin penetration, regardless of the colistin-resistant phenotype. Based on these in vitro data, we propose a colistin-rifampicin combination as a promising treatment for infections caused by colistin-resistant P. aeruginosa.
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Affiliation(s)
- Eva Armengol
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School and IDIBELL, University of Barcelona, Hospitalet de Llobregat, Spain
| | - Kasper Nørskov Kragh
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Josep M. Sierra
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School and IDIBELL, University of Barcelona, Hospitalet de Llobregat, Spain
| | - Doaa Higazy
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Oana Ciofu
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Miguel Viñas
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School and IDIBELL, University of Barcelona, Hospitalet de Llobregat, Spain
| | - Niels Høiby
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
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23
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Romano K, Hung D. Targeting LPS biosynthesis and transport in gram-negative bacteria in the era of multi-drug resistance. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119407. [PMID: 36543281 PMCID: PMC9922520 DOI: 10.1016/j.bbamcr.2022.119407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Gram-negative bacteria pose a major threat to human health in an era fraught with multi-drug resistant bacterial infections. Despite extensive drug discovery campaigns over the past decades, no new antibiotic target class effective against gram-negative bacteria has become available to patients since the advent of the carbapenems in 1985. Antibiotic discovery efforts against gram-negative bacteria have been hampered by limited intracellular accumulation of xenobiotics, in large part due to the impermeable cell envelope comprising lipopolysaccharide (LPS) in the outer leaflet of the outer membrane, as well as a panoply of efflux pumps. The biosynthesis and transport of LPS are essential to the viability and virulence of most gram-negative bacteria. Thus, both LPS biosynthesis and transport are attractive pathways to target therapeutically. In this review, we summarize the LPS biosynthesis and transport pathways and discuss efforts to find small molecule inhibitors against targets within these pathways.
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Affiliation(s)
- K.P. Romano
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA,The Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - D.T. Hung
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA,Corresponding author at: The Broad Institute of MIT and Harvard, Cambridge, MA, USA. (D.T. Hung)
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24
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Regulatory Landscape of the Pseudomonas aeruginosa Phosphoethanolamine Transferase Gene eptA in the Context of Colistin Resistance. Antibiotics (Basel) 2023; 12:antibiotics12020200. [PMID: 36830112 PMCID: PMC9952513 DOI: 10.3390/antibiotics12020200] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa has the genetic potential to acquire colistin resistance through the modification of lipopolysaccharide by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) or phosphoethanolamine (PEtN), mediated by the arn operon or the eptA gene, respectively. However, in vitro evolution experiments and genetic analysis of clinical isolates indicate that lipopolysaccharide modification with L-Ara4N is invariably preferred over PEtN addition as the colistin resistance mechanism in this bacterium. Since little is known about eptA regulation in P. aeruginosa, we generated luminescent derivatives of the reference strain P. aeruginosa PAO1 to monitor arn and eptA promoter activity. We performed transposon mutagenesis assays to compare the likelihood of acquiring mutations leading to arn or eptA induction and to identify eptA regulators. The analysis revealed that eptA was slightly induced under certain stress conditions, such as arginine or biotin depletion and accumulation of the signal molecule diadenosine tetraphosphate, but the induction did not confer colistin resistance. Moreover, we demonstrated that spontaneous mutations leading to colistin resistance invariably triggered arn rather than eptA expression, and that eptA was not induced in resistant mutants upon colistin exposure. Overall, these results suggest that the contribution of eptA to colistin resistance in P. aeruginosa may be limited by regulatory restraints.
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25
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Determination of Mutational Timing of Colistin-Resistance Genes through Klebsiella pneumoniae Evolution. Pharmaceutics 2023; 15:pharmaceutics15010270. [PMID: 36678901 PMCID: PMC9862994 DOI: 10.3390/pharmaceutics15010270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/16/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
The emergence and dissemination of carbapenem-resistant Klebsiella pneumoniae (KP), one of the carbapenem-resistant Enterobacteriaceae (CRE), is now an emerging cause of antibiotic-resistant nosocomial infections associated with high rates of morbidity and mortality. Colistin, or polymyxin E, is a last-resort peptide antibiotic used to treat multidrug-resistant (MDR) Gram-negative bacterial infections including KP. Unfortunately, resistance to colistin is rising with increasing use in the clinical setting. Although clinical evidence links certain mutations to colistin resistance (COL-R) in KP, the origination and association of the mutations remain unclear. We hypothesize that the timing of COL-R mutations influences the development and progression of KP resistance to colistin. We performed planktonic and biofilm in vitro experimental evolutions of KP strain ATCC 43816 under increasing colistin concentrations to characterize the temporal regulation of critical COL-R mutations throughout COL-R progression. The resistance generation and mutation profiles of independently evolved bacterial populations with different lifestyles were compared. Genes with various functions theorize the timeline in which key mutations are generated and their roles in the progression of COL-R. Our results aim to advance the research and development of effective therapeutics to treat MDR bacterial infection as the dissemination of CRE continues to be a severe public health threat.
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26
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Cameron DR, Pitton M, Oberhaensli S, Schlegel K, Prod’hom G, Blanc DS, Jakob SM, Que YA. Parallel Evolution of Pseudomonas aeruginosa during a Prolonged ICU-Infection Outbreak. Microbiol Spectr 2022; 10:e0274322. [PMID: 36342287 PMCID: PMC9769503 DOI: 10.1128/spectrum.02743-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Most knowledge about Pseudomonas aeruginosa pathoadaptation is derived from studies on airway colonization in cystic fibrosis; little is known about adaptation in acute settings. P. aeruginosa frequently affects burned patients and the burn wound niche has distinct properties that likely influence pathoadaptation. This study aimed to genetically and phenotypically characterize P. aeruginosa isolates collected during an outbreak of infection in a burn intensive care unit (ICU). Sequencing reads from 58 isolates of ST1076 P. aeruginosa taken from 23 patients were independently mapped to a complete reference genome for the lineage (H25338); genetic differences were identified and were used to define the population structure. Comparative genomic analysis at single-nucleotide resolution identified pathoadaptive genes that evolved multiple, independent mutations. Three key phenotypic assays (growth performance, motility, carbapenem resistance) were performed to complement the genetic analysis for 47 unique isolates. Population structure for the ST1076 lineage revealed 11 evolutionary sublineages. Fifteen pathoadaptive genes evolved mutations in at least two sublineages. The most prominent functional classes affected were transcription/two-component regulatory systems, and chemotaxis/motility and attachment. The most frequently mutated gene was oprD, which codes for outer membrane porin involved in uptake of carbapenems. Reduced growth performance and motility were found to be adaptive phenotypic traits, as was high level of carbapenem resistance, which correlated with higher carbapenem consumption during the outbreak. Multiple prominent linages evolved each of the three traits in parallel providing evidence that they afford a fitness advantage for P. aeruginosa in the context of human burn infection. IMPORTANCE Pseudomonas aeruginosa is a Gram-negative pathogen causing infections in acutely burned patients. The precise mechanisms required for the establishment of infection in the burn setting, and adaptive traits underpinning prolonged outbreaks are not known. We have assessed genotypic data from 58 independent P. aeruginosa isolates taken from a single lineage that was responsible for an outbreak of infection in a burn ICU that lasted for almost 2.5 years and affected 23 patients. We identified a core set of 15 genes that we predict to control pathoadaptive traits in the burn infection based on the frequency with which independent mutations evolved. We combined the genotypic data with phenotypic data (growth performance, motility, antibiotic resistance) and clinical data (antibiotic consumption) to identify adaptive phenotypes that emerged in parallel. High-level carbapenem resistance evolved rapidly, and frequently, in response to high clinical demand for this antibiotic class during the outbreak.
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Affiliation(s)
- David R. Cameron
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Melissa Pitton
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Bern, Switzerland
| | - Simone Oberhaensli
- Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Katja Schlegel
- Institute of Psychology, University of Bern, Bern, Switzerland
| | - Guy Prod’hom
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dominique S. Blanc
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stephan M. Jakob
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yok-Ai Que
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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27
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Liu Q, Yin L, Zhang X, Zhu G, Liu H, Bai F, Cheng Z, Wu W, Jin Y. Reversion of Ceftazidime Resistance in Pseudomonas aeruginosa under Clinical Setting. Microorganisms 2022; 10:microorganisms10122395. [PMID: 36557649 PMCID: PMC9782964 DOI: 10.3390/microorganisms10122395] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is an important nosocomial pathogen which frequently becomes resistant to most antibiotics used in chemotherapy, resulting in treatment failure among infected individuals. Although the evolutionary trajectory and molecular mechanisms for becoming β-lactam resistant have been well established for P. aeruginosa, the molecular basis of reversion from β-lactam resistant to susceptible is largely unexplored. In this study, we investigated the molecular mechanisms by which a ceftazidime-resistant clinical strain is converted to a ceftazidime-susceptible isolate under the clinical setting. RNA sequencing and genomic DNA reference mapping were conducted to compare the transcriptional profiles and chromosomal mutations between these two isolates. Our results demonstrate that a gain-of-function mutation in ampD, via deletion of a 53 bp duplicated nucleotide sequence, is the contributory factor for the conversion. Furthermore, we show for the first time that AmpD is involved in intraspecies competitiveness in P. aeruginosa. We also found that AmpD is not responsible for phenotypic changes between R1 and S2, including growth rate, motilities, pyocyanin, rhamnolipid, and biofilm production. This finding provides novel insights into the alteration of β-lactam sensitivity in P. aeruginosa under the clinical setting.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Liwen Yin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xinxin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guangbo Zhu
- Tianjin Union Medical Center, Nankai University Affiliated Hospital, Tianjin 300100, China
| | - Huimin Liu
- Tianjin Union Medical Center, Nankai University Affiliated Hospital, Tianjin 300100, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
- Correspondence:
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Hasan CM, Pottenger S, Green AE, Cox AA, White JS, Jones T, Winstanley C, Kadioglu A, Wright MH, Neill DR, Fothergill JL. Pseudomonas aeruginosa utilizes the host-derived polyamine spermidine to facilitate antimicrobial tolerance. JCI Insight 2022; 7:158879. [PMID: 36194492 PMCID: PMC9746822 DOI: 10.1172/jci.insight.158879] [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: 01/27/2022] [Accepted: 09/27/2022] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa undergoes diversification during infection of the cystic fibrosis (CF) lung. Understanding these changes requires model systems that capture the complexity of the CF lung environment. We previously identified loss-of-function mutations in the 2-component regulatory system sensor kinase gene pmrB in P. aeruginosa from CF lung infections and from experimental infection of mice. Here, we demonstrate that, while such mutations lowered in vitro minimum inhibitory concentrations for multiple antimicrobial classes, this was not reflected in increased antibiotic susceptibility in vivo. Loss of PmrB impaired aminoarabinose modification of LPS, increasing the negative charge of the outer membrane and promoting uptake of cationic antimicrobials. However, in vivo, this could be offset by increased membrane binding of other positively charged molecules present in lungs. The polyamine spermidine readily coated the surface of PmrB-deficient P. aeruginosa, reducing susceptibility to antibiotics that rely on charge differences to bind the outer membrane and increasing biofilm formation. Spermidine was elevated in lungs during P. aeruginosa infection in mice and during episodes of antimicrobial treatment in people with CF. These findings highlight the need to study antimicrobial resistance under clinically relevant environmental conditions. Microbial mutations carrying fitness costs in vitro may be advantageous during infection, where host resources can be utilized.
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Affiliation(s)
- Chowdhury M. Hasan
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Sian Pottenger
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Angharad E. Green
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Adrienne A. Cox
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Jack S. White
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Trevor Jones
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Craig Winstanley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Megan H. Wright
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Daniel R. Neill
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Joanne L. Fothergill
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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Colistin Resistance Mechanisms in Human and Veterinary Klebsiella pneumoniae Isolates. Antibiotics (Basel) 2022; 11:antibiotics11111672. [DOI: 10.3390/antibiotics11111672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Colistin (polymyxin E) is increasingly used as a last-resort antibiotic for the treatment of severe infections with multidrug-resistant Gram-negative bacteria. In contrast to human medicine, colistin is also used in veterinary medicine for metaphylaxis. Our objective was to decipher common colistin resistance mechanisms in Klebsiella pneumoniae isolates from animals. In total, 276 veterinary K. pneumoniae isolates, derived from companion animals or livestock, and 12 isolates from human patients were included for comparison. Six out of 276 veterinary isolates were colistin resistant (2.2%). Human isolates belonging to high-risk clonal lineages (e.g., ST15, ST101, ST258), displayed multidrug-resistant phenotypes and harboured many resistance genes compared to the veterinary isolates. However, the common colistin resistance mechanism in both human and animal K. pneumoniae isolates were diverse alterations of MgrB, a critical regulator of lipid A modification. Additionally, deleterious variations of lipopolysaccharide (LPS)-associated proteins (e.g., PmrB P95L, PmrE P89L, LpxB A152T) were identified. Phylogenetic analysis and mutation patterns in genes encoding LPS-associated proteins indicated that colistin resistance mechanisms developed independently in human and animal isolates. Since only very few antibiotics remain to treat infections with MDR bacteria, it is important to further analyse resistance mechanisms and the dissemination within different isolates and sources.
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Genomic Characterization of Colistin-Resistant Isolates from the King Fahad Medical City, Kingdom of Saudi Arabia. Antibiotics (Basel) 2022; 11:antibiotics11111597. [DOI: 10.3390/antibiotics11111597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Whole-genome sequencing is one of the best ways to investigate resistance mechanisms of clinical isolates as well as to detect and identify circulating multi-drug-resistant (MDR) clones or sub-clones in a given hospital setting. Methods: Here, we sequenced 37 isolates of Acinetobacter baumannii, 10 Klebsiella pneumoniae, and 5 Pseudomonas aeruginosa collected from the biobank of the hospital setting of the King Fahad Medical City. Complete phenotypic analyses were performed, including MALDI-TOF identification and antibiotic susceptibility testing. After the genome assembly of raw data, exhaustive genomic analysis was conducted including full resistome determination, genomic SNP (gSNP) analysis, and comparative genomics. Results: Almost all isolates were highly resistant to all tested antibiotics, including carbapenems and colistin. Resistome analysis revealed many antibiotic resistance genes, including those with resistance to β-lactams, aminoglycosides, macrolides, tetracyclines, sulfamids, quinolones, and phenicols. In A. baumannii isolates, the endemic carbapenemase blaOXA-23 gene was detected in 36 of the 37 isolates. Non-synonymous mutations in pmrB were detected in almost all of the isolates and likely mediated colistin resistance. Interestingly, while classical analyses, such as MLST, revealed the predominance of an ST2 clone in A. baumannii isolates, the genomic analysis revealed the presence of five circulating sub-clones and identified several isolate transmissions between patients. In the 10 K. pneumoniae isolates, several resistance genes were identified, and the observed carbapenem resistance was likely mediated by overexpression of the detected extended-spectrum-β-lactamase (ESBL) genes associated with low membrane permeability as few carbapenemase genes were detected with just blaOXA-48 in three isolates. Colistin resistance was mediated either by non-synonymous mutations in the MgrB regulator, PmrA, PmrB, and PhoQ proteins or the presence of the MCR-1 protein. Here, gSNP analysis also revealed the existence of bacterial clones and cases of isolate transmissions between patients. The five analyzed P. aeruginosa isolates were highly resistant to all tested antibiotics, including carbapenems mediated by loss or truncated OprD porin, and colistin resistance was associated with mutations in the genes encoding the PmrA, PmrB, or PhoQ proteins. Conclusion: We demonstrate here the usefulness of whole-genome sequencing to exhaustively investigate the dissemination of MDR isolates at the sub-clone level. Thus, we suggest implementing such an approach to monitor the emergence and spread of new clones or sub-clones, which classical molecular analyses cannot detect. Moreover, we recommend increasing the surveillance of the endemic and problematic colistin resistance mcr-1 gene to avoid extensive dissemination.
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Schneider-Futschik EK, Spriet I, Zhou H. Editorial: Women in pharmacology of infectious diseases: 2021. Front Pharmacol 2022; 13:1038369. [PMID: 36278180 PMCID: PMC9583128 DOI: 10.3389/fphar.2022.1038369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/20/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Elena K. Schneider-Futschik
- Cystic Fibrosis Pharmacology Laboratory, Department of Biochemistry and Pharmacology, Melbourne University, Melbourne, VIC, Australia
- *Correspondence: Elena K. Schneider-Futschik,
| | - Isabel Spriet
- Pharmacy Department, University Hospitals Leuven, Leuven and Department of Pharmaceutical and Pharmacological Sciences, KU Leuven – University of Leuven, Leuven, Belgium
| | - Hong Zhou
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
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32
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Wang D, Ning Q, Deng Z, Zhang M, You J. Role of environmental stresses in elevating resistance mutations in bacteria: Phenomena and mechanisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119603. [PMID: 35691443 DOI: 10.1016/j.envpol.2022.119603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/28/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Mutations are an important origin of antibiotic resistance in bacteria. While there is increasing evidence showing promoted resistance mutations by environmental stresses, no retrospective research has yet been conducted on this phenomenon and its mechanisms. Herein, we summarized the phenomena of stress-elevated resistance mutations in bacteria, generalized the regulatory mechanisms and discussed the environmental and human health implications. It is shown that both chemical pollutants, such as antibiotics and other pharmaceuticals, biocides, metals, nanoparticles and disinfection byproducts, and non-chemical stressors, such as ultraviolet radiation, electrical stimulation and starvation, are capable of elevating resistance mutations in bacteria. Notably, resistance mutations are more likely to occur under sublethal or subinhibitory levels of these stresses, suggesting a considerable environmental concern. Further, mechanisms for stress-induced mutations are summarized in several points, namely oxidative stress, SOS response, DNA replication and repair systems, RpoS regulon and biofilm formation, all of which are readily provoked by common environmental stresses. Given bacteria in the environment are confronted with a variety of unfavorable conditions, we propose that the stress-elevated resistance mutations are a universal phenomenon in the environment and represent a nonnegligible risk factor for ecosystems and human health. The present review identifies a need for taking into account the pollutants' ability to elevate resistance mutations when assessing their environmental and human health risks and highlights the necessity of including resistance mutations as a target to prevent antibiotic resistance evolution.
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Affiliation(s)
- Dali Wang
- Guangdong Provincial Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | - Qing Ning
- Guangdong Provincial Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | | | - Meng Zhang
- Shenzhen Dapeng New District Center for Disease Control and Prevention, Shenzhen, 518000, China
| | - Jing You
- Guangdong Provincial Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China.
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Santos-Lopez A, Fritz MJ, Lombardo JB, Burr AHP, Heinrich VA, Marshall CW, Cooper VS. Evolved resistance to a novel cationic peptide antibiotic requires high mutation supply. Evol Med Public Health 2022; 10:266-276. [PMID: 35712084 PMCID: PMC9198447 DOI: 10.1093/emph/eoac022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/21/2022] [Indexed: 01/30/2023] Open
Abstract
Background and Objectives A key strategy for resolving the antibiotic resistance crisis is the development of new drugs with antimicrobial properties. The engineered cationic antimicrobial peptide WLBU2 (also known as PLG0206) is a promising broad-spectrum antimicrobial compound that has completed Phase I clinical studies. It has activity against Gram-negative and Gram-positive bacteria including infections associated with biofilm. No definitive mechanisms of resistance to WLBU2 have been identified. Methodology Here, we used experimental evolution under different levels of mutation supply and whole genome sequencing (WGS) to detect the genetic pathways and probable mechanisms of resistance to this peptide. We propagated populations of wild-type and hypermutator Pseudomonas aeruginosa in the presence of WLBU2 and performed WGS of evolved populations and clones. Results Populations that survived WLBU2 treatment acquired a minimum of two mutations, making the acquisition of resistance more difficult than for most antibiotics, which can be tolerated by mutation of a single target. Major targets of resistance to WLBU2 included the orfN and pmrB genes, previously described to confer resistance to other cationic peptides. More surprisingly, mutations that increase aggregation such as the wsp pathway were also selected despite the ability of WLBU2 to kill cells growing in a biofilm. Conclusions and implications The results show how experimental evolution and WGS can identify genetic targets and actions of new antimicrobial compounds and predict pathways to resistance of new antibiotics in clinical practice.
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Affiliation(s)
- Alfonso Santos-Lopez
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Present address: Department of Microbiology, Hospital Universitario Ramon y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Present address: Department of Microbial Biology, National Center of Biotechnology (CNB), Madrid, Spain
| | - Melissa J Fritz
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
| | - Jeffrey B Lombardo
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
| | - Ansen H P Burr
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
| | - Victoria A Heinrich
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
| | - Christopher W Marshall
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Present address: Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Investigations into the membrane activity of arenicin antimicrobial peptide AA139. Biochim Biophys Acta Gen Subj 2022; 1866:130156. [PMID: 35523364 DOI: 10.1016/j.bbagen.2022.130156] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/21/2022]
Abstract
Arenicin-3 is an amphipathic β-hairpin antimicrobial peptide that is produced by the lugworm Arenicola marina. In this study, we have investigated the mechanism of action of arenicin-3 and an optimized synthetic analogue, AA139, by studying their effects on lipid bilayer model membranes and Escherichia coli bacterial cells. The results show that simple amino acid changes can lead to subtle variations in their interaction with membranes and therefore alter their pre-clinical potency, selectivity and toxicity. While the mechanism of action of arenicin-3 is primarily dependent on universal membrane permeabilization, our data suggest that the analogue AA139 relies on more specific binding and insertion properties to elicit its improved antibacterial activity and lower toxicity, as exemplified by greater selectivity between lipid composition when inserting into model membranes i.e. the N-terminus of AA139 seems to insert deeper into lipid bilayers than arenicin-3 does, with a clear distinction between zwitterionic and negatively charged lipid bilayer vesicles, and AA139 demonstrates a cytoplasmic permeabilization dose response profile that is consistent with its greater antibacterial potency against E. coli cells compared to arenicin-3.
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Detection of Antimicrobial Resistance, Pathogenicity, and Virulence Potentials of Non-Typhoidal Salmonella Isolates at the Yaounde Abattoir Using Whole-Genome Sequencing Technique. Pathogens 2022; 11:pathogens11050502. [PMID: 35631023 PMCID: PMC9148033 DOI: 10.3390/pathogens11050502] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
One of the crucial public health problems today is the emerging and re-emerging of multidrug-resistant (MDR) bacteria coupled with a decline in the development of new antimicrobials. Non-typhoidal Salmonella (NTS) is classified among the MDR pathogens of international concern. To predict their MDR potentials, 23 assembled genomes of NTS from live cattle (n = 1), beef carcass (n = 19), butchers’ hands (n = 1) and beef processing environments (n = 2) isolated from 830 wet swabs at the Yaounde abattoir between December 2014 and November 2015 were explored using whole-genome sequencing. Phenotypically, while 22% (n = 5) of Salmonella isolates were streptomycin-resistant, 13% (n = 3) were MDR. Genotypically, all the Salmonella isolates possessed high MDR potentials against several classes of antibiotics including critically important drugs (carbapenems, third-generation cephalosporin and fluoroquinolone). Moreover, >31% of NTS exhibited resistance potentials to polymyxin, considered as the last resort drug. Additionally, ≤80% of isolates harbored “silent resistant genes” as a potential reservoir of drug resistance. Our isolates showed a high degree of pathogenicity and possessed key virulence factors to establish infection even in humans. Whole-genome sequencing unveiled both broader antimicrobial resistance (AMR) profiles and inference of pathogen characteristics. This study calls for the prudent use of antibiotics and constant monitoring of AMR of NTS.
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Lu T, Zheng X, Mao F, Cao Q, Cao Q, Zhu J, Li X, Lan L, Li B, Li J. Novel niclosamide-derived adjuvants elevating the efficacy of polymyxin B against MDR Pseudomonas aeruginosa DK2. Eur J Med Chem 2022; 236:114318. [DOI: 10.1016/j.ejmech.2022.114318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/04/2022]
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The Role of Colistin in the Era of New β-Lactam/β-Lactamase Inhibitor Combinations. Antibiotics (Basel) 2022; 11:antibiotics11020277. [PMID: 35203879 PMCID: PMC8868358 DOI: 10.3390/antibiotics11020277] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 02/06/2023] Open
Abstract
With the current crisis related to the emergence of carbapenem-resistant Gram-negative bacteria (CR-GNB), classical treatment approaches with so-called “old-fashion antibiotics” are generally unsatisfactory. Newly approved β-lactam/β-lactamase inhibitors (BLBLIs) should be considered as the first-line treatment options for carbapenem-resistant Enterobacterales (CRE) and carbapenem-resistant Pseudomonas aeruginosa (CRPA) infections. However, colistin can be prescribed for uncomplicated lower urinary tract infections caused by CR-GNB by relying on its pharmacokinetic and pharmacodynamic properties. Similarly, colistin can still be regarded as an alternative therapy for infections caused by carbapenem-resistant Acinetobacter baumannii (CRAB) until new and effective agents are approved. Using colistin in combination regimens (i.e., including at least two in vitro active agents) can be considered in CRAB infections, and CRE infections with high risk of mortality. In conclusion, new BLBLIs have largely replaced colistin for the treatment of CR-GNB infections. Nevertheless, colistin may be needed for the treatment of CRAB infections and in the setting where the new BLBLIs are currently unavailable. In addition, with the advent of rapid diagnostic methods and novel antimicrobials, the application of personalized medicine has gained significant importance in the treatment of CRE infections.
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O'Leary MK, Sundaram V, LiPuma JJ, Dörr T, Westblade LF, Alabi CA. Mechanism of Action and Resistance Evasion of an Antimicrobial Oligomer against Multidrug-Resistant Gram-Negative Bacteria. ACS APPLIED BIO MATERIALS 2022; 5:1159-1168. [PMID: 35167257 DOI: 10.1021/acsabm.1c01217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The last resort for treating multidrug-resistant (MDR) Pseudomonas aeruginosa and other MDR Gram-negative bacteria is a class of antibiotics called the polymyxins; however, polymyxin-resistant isolates have emerged. In response, antimicrobial peptides (AMPs) and their synthetic mimetics have been investigated as alternative therapeutic options. Oligothioetheramides (oligoTEAs) are a class of synthetic, sequence-defined oligomers composed of N-allylacrylamide monomers and an abiotic dithiol backbone that is resistant to serum degradation. Characteristic of other AMP mimetics, the precise balance between charge and hydrophobicity has afforded cationic oligoTEAs potent antimicrobial activity, particularly for the compound BDT-4G, which consists of a 1,4-butanedithiol backbone and guanidine pendant groups, the latter of which provides a cationic charge at physiological pH. However, the activity and mechanism of cationic oligoTEAs against MDR Gram-negative isolates have yet to be fully investigated. Herein, we demonstrated the potent antimicrobial activity of BDT-4G against clinical isolates of P. aeruginosa with a range of susceptibility profiles, assessed the kinetics of bactericidal activity, and further elucidated its mechanism of action. Activity was also evaluated against a panel of polymyxin-resistant isolates, including intrinsically-resistant species. We demonstrate that BDT-4G can evade some of the mechanisms conferring resistance to polymyxin B and thus may have therapeutic potential.
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Affiliation(s)
- Meghan K O'Leary
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Vishal Sundaram
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, New York 14853, United States.,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States.,Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York 14853, United States
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10065, United States.,Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Christopher A Alabi
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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Savin M, Bierbaum G, Schmithausen RM, Heinemann C, Kreyenschmidt J, Schmoger S, Akbaba I, Käsbohrer A, Hammerl JA. Slaughterhouse wastewater as a reservoir for extended-spectrum β-lactamase (ESBL)-producing, and colistin-resistant Klebsiella spp. and their impact in a "One Health" perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150000. [PMID: 34517324 DOI: 10.1016/j.scitotenv.2021.150000] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 05/28/2023]
Abstract
Klebsiella spp. are ubiquitous bacteria capable of colonizing humans and animals, and sometimes leading to severe infections in both. Due to their high adaptability against environmental/synthetic conditions as well as their potential in aquiring antimicrobial/metal/biocide resistance determinants, Klebsiella spp. are recognized as an emerging threat to public health, worldwide. Currently, scarce information on the impact of livestock for the spread of pathogenic Klebsiella spp. is available. Thus, the phenotypic and genotypic properties of extended-spectrum β-lactamase-producing, and colistin-resistant Klebsiella strains (n = 185) from process- and wastewater of two poultry and pig slaughterhouses as well as their receiving municipal wastewater treatment plants (mWWTPs) were studied to determine the diversity of isolates that might be introduced into the food-production chain or that are released into the environment by surviving the wastewater treatment. Selectively-isolated Klebsiella spp. from slaughterhouses including effluents and receiving waterbodies of mWWTPs were assigned to various lineages, including high-risk clones involved in human outbreaks, and exhibited highly heterogeneous antibiotic-resistance patterns. While isolates originating from poultry slaughterhouses showed the highest rate of colistin resistance (32.4%, 23/71), carbapenem-resistant Klebsiella spp. were only detected in mWWTP samples (n = 76). The highest diversity of resistance genes (n = 77) was detected in Klebsiella spp. from mWWTPs, followed by isolates from pig (n = 56) and poultry slaughterhouses (n = 52). Interestingly, no carbapenemase-encoding genes were detected and mobile colistin resistance genes were only obeserved in isolates from poultry and pig slaughterhouses. Our study provides in-depth information into the clonality of livestock-associated Klebsiella spp. and their determinants involved in antimicrobial resistance and virulence development. On the basis of their pathogenic potential and clinical importance there is a potential risk of colonization and/or infection of wildlife, livestock and humans exposed to contaminated food and/or surface waters.
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Affiliation(s)
- Mykhailo Savin
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, Germany; Institute of Animal Sciences, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | | | | | - Judith Kreyenschmidt
- Institute of Animal Sciences, University of Bonn, Bonn, Germany; Hochschule Geisenheim University, Department of Fresh Produce Logistics, Geisenheim, Germany
| | - Silvia Schmoger
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Inna Akbaba
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annemarie Käsbohrer
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany; Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, AT-1210 Vienna, Austria
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.
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Huang W, Zhang J, Liu S, Hu C, Zhang M, Cheng S, Yu H, Zheng M, Wu J, Lu Y, Zou Q, Cui R. Disulfiram Enhances the Activity of Polymyxin B Against Klebsiella pneumoniae by Inhibiting Lipid A Modification. Infect Drug Resist 2022; 15:295-306. [PMID: 35115797 PMCID: PMC8802902 DOI: 10.2147/idr.s342641] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background The use of antibiotic adjuvants is a complementary strategy to the development of new antibiotics. The essential role of the ArnA dehydrogenase domain (ArnA_DH) in the addition of 4-amino-L-arabinose (L-Ara4N) to lipid A makes it a potential target in polymyxin adjuvant design. Purpose This study aimed to identify a dehydrogenase inhibitor that enhances the antibacterial effect of polymyxin B (PB) and to further understand the mechanism of this drug combination. Methods A susceptible K. pneumoniae strain, ATCC13883, was used to screen a dehydrogenase inhibitor library based on 3-(4,5)-dimethylthiazol(-z-y1)-2,5-diphenyltetrazolium bromide (MTT) and chequerboard assays. The protein- and cell-based effects of disulfiram (DSF) on ArnA activity were assessed, and the transcription levels of genes in the arn operon were evaluated by quantitative real-time polymerase chain reaction (qRT–PCR). Lipid A was isolated, and a structural analysis was performed. The cell wall function was evaluated through membrane integrity and bacterial viability assays. The in vivo antibacterial activity was evaluated using a mouse pulmonary infection model. Results We screened a dehydrogenase inhibitor library and found that the anti-alcoholism drug DSF significantly enhanced the antibacterial activity of PB in vitro and in vivo. The protein-based enzyme activity assay showed that DSF exerted no direct effect on the dehydrogenase activity of ArnA. Treatment with the combination of DSF and PB but not with PB alone decreased both the transcription level of genes in the arn operon and the modification level of lipid A. DSF also strengthened the disruption of the cell membrane integrity of PB. Moreover, the enhanced PB antibacterial activity was effective against clinical PB-resistant strains. Conclusion We identified a new drug combination that can be used to reduce the necessary dosage of PB and overcome PB resistance, and this drug combination has good prospects for clinical application.
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Affiliation(s)
- Wei Huang
- Bacteriology & Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Diseases, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
- Department of Clinical Microbiology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
| | - Jinyong Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, People’s Republic of China
| | - Shiyi Liu
- Bacteriology & Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Diseases, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
| | - Chunxia Hu
- Bacteriology & Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Diseases, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
| | - Min Zhang
- Bacteriology & Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Diseases, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
| | - Shumin Cheng
- Bacteriology & Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Diseases, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
| | - Huijuan Yu
- Bacteriology & Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Diseases, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
- Department of Clinical Microbiology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
| | - Manling Zheng
- Bacteriology & Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Diseases, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
| | - Jinsong Wu
- Department of Clinical Microbiology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
| | - Yuemei Lu
- Department of Clinical Microbiology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, People’s Republic of China
- Correspondence: Quanming Zou; Ruiqin Cui, Email ;
| | - Ruiqin Cui
- Bacteriology & Antibacterial Resistance Surveillance Laboratory, Shenzhen Institute of Respiratory Diseases, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
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Cervoni M, Lo Sciuto A, Bianchini C, Mancone C, Imperi F. Exogenous and Endogenous Phosphoethanolamine Transferases Differently Affect Colistin Resistance and Fitness in Pseudomonas aeruginosa. Front Microbiol 2021; 12:778968. [PMID: 34777328 PMCID: PMC8578941 DOI: 10.3389/fmicb.2021.778968] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/07/2021] [Indexed: 12/15/2022] Open
Abstract
Colistin represents a last-line treatment option for infections caused by multidrug resistant Gram-negative pathogens, including Pseudomonas aeruginosa. Colistin resistance generally involves the modification of the lipid A moiety of lipopolysaccharide (LPS) with positively charged molecules, namely phosphoethanolamine (PEtN) or 4-amino-4-deoxy-L-arabinose (Ara4N), that reduce colistin affinity for its target. Several lines of evidence highlighted lipid A aminoarabinosylation as the primary colistin resistance mechanism in P. aeruginosa, while the contribution of phosphoethanolamination remains elusive. PEtN modification can be due to either endogenous (chromosomally encoded) PEtN transferase(s) (e.g., EptA in P. aeruginosa) or plasmid borne MCR enzymes, commonly found in enterobacteria. By individually cloning eptA and mcr-1 into a plasmid for inducible gene expression, we demonstrated that MCR-1 and EptA have comparable PEtN transferase activity in P. aeruginosa and confer colistin resistance levels similar to those provided by lipid A aminoarabinosylation. Notably, EptA, but not MCR-1, negatively affects P. aeruginosa growth and, to a lesser extent, cell envelope integrity when expressed at high levels. Mutagenesis experiments revealed that PEtN transferase activity does not account for the noxious effects of EptA overexpression, that instead requires a C-terminal tail unique to P. aeruginosa EptA, whose function remains unknown. Overall, this study shows that both endogenous and exogenous PEtN transferases can promote colistin resistance in P. aeruginosa, and that PEtN and MCR-1 mediated resistance has no impact on growth and cell envelope homeostasis, suggesting that there may be no fitness barriers to the spread of mcr-1 in P. aeruginosa.
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Affiliation(s)
| | | | | | - Carmine Mancone
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, Rome, Italy.,IRCCS Fondazione Santa Lucia, Rome, Italy
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Shprung T, Wani NA, Wilmes M, Mangoni ML, Bitler A, Shimoni E, Sahl HG, Shai Y. Opposing Effects of PhoPQ and PmrAB on the Properties of Salmonella enterica serovar Typhimurium: Implications on Resistance to Antimicrobial Peptides. Biochemistry 2021; 60:2943-2955. [PMID: 34547893 PMCID: PMC8638962 DOI: 10.1021/acs.biochem.1c00287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The increasing number of resistant
bacteria is a major threat worldwide,
leading to the search for new antibiotic agents. One of the leading
strategies is the use of antimicrobial peptides (AMPs), cationic and
hydrophobic innate immune defense peptides. A major target of AMPs
is the bacterial membrane. Notably, accumulating data suggest that
AMPs can activate the two-component systems (TCSs) of Gram-negative
bacteria. These include PhoP-PhoQ (PhoPQ) and PmrA-PmrB (PmrAB), responsible
for remodeling of the bacterial cell surface. To better understand
this mechanism, we utilized bacteria deficient either in one system
alone or in both and biophysical tools including fluorescence spectroscopy,
single-cell atomic force microscopy, electron microscopy, and mass
spectrometry (MoskowitzS. M.;Antimicrob. Agents Chemother.2012, 56, 1019−103022106224; ChengH. Y.;J. Biomed. Sci.2010, 17, 6020653976). Our data suggested that the two systems have opposing
effects on the properties of Salmonella enterica. The knockout of PhoPQ made the bacteria more susceptible to AMPs
by making the surface less rigid, more polarized, and permeable with
a slightly more negatively charged cell wall. In addition, the periplasmic
space is thinner. In contrast, the knockout of PmrAB did not affect
its susceptibility, while it made the bacterial outer layer very rigid,
less polarized, and less permeable than the other two mutants, with
a negatively charged cell wall similar to the WT. Overall, the data
suggest that the coexistence of systems with opposing effects on the
biophysical properties of the bacteria contribute to their membrane
flexibility, which, on the one hand, is important to accommodate changing
environments and, on the other hand, may inhibit the development of
meaningful resistance to AMPs.
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Affiliation(s)
- Tal Shprung
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naiem Ahmad Wani
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miriam Wilmes
- Pharmaceutical Microbiology Section, Institute for Medical Microbiology, Immunology and Parasitology, University of Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
| | - Maria Luisa Mangoni
- Department of Biochemical Sciences A. Rossi Fanelli, Faculty of Pharmacy and Medicine, Sapienza University of Rome, CU27, 00185 Roma, Italy
| | - Arkadi Bitler
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hans-Georg Sahl
- Pharmaceutical Microbiology Section, Institute for Medical Microbiology, Immunology and Parasitology, University of Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
| | - Yechiel Shai
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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43
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Zhang W, Yuan Y, Li S, Deng B, Zhang J, Li Z. Comparative transcription analysis of resistant mutants against four different antibiotics in Pseudomonas aeruginosa. Microb Pathog 2021; 160:105166. [PMID: 34480983 DOI: 10.1016/j.micpath.2021.105166] [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: 06/10/2021] [Revised: 08/26/2021] [Accepted: 08/29/2021] [Indexed: 11/28/2022]
Abstract
The emergence of antibiotic resistance has severely impaired the treatment of infections caused by Pseudomonas aeruginosa. There are few studies related to comparing the antibiotics resistance mechanisms of P. aeruginosa against different antibiotics. In this study, RNA sequencing was used to investigate the differences of transcriptome between wild strain and four antibiotics resistant strains of P. aeruginosa PAO1 (polymyxin B, ciprofloxacin, doxycycline, and ceftriaxone). Compared to the wild strain, 1907, 495, 2402, and 116 differentially expressed genes (DEGs) were identified in polymyxin B, ciprofloxacin, doxycycline, and ceftriaxone resistant PAO1, respectively. After analysis of genes related to antimicrobial resistance, we found genes implicated in biofilm formation (pelB, pelC, pelD, pelE, pelF, pelG, algA, algF, and alg44) were significantly upregulated in polymyxin B-resistant PAO1, efflux pump genes (mexA, mexB, oprM) and biofilm formation genes (pslJ, pslK and pslN) were upregulated in ciprofloxacin-resistant PAO1; other efflux pump genes (mexC, mexD, oprJ) were upregulated in doxycycline-resistant PAO1; ampC were upregulated in ceftriaxone-resistant PAO1. As a consequence of antibiotic resistance, genes related to virulence factors such as type Ⅱ secretion system (lasA, lasB and piv) were significantly upregulated in polymyxin B-resistant PAO1, and type Ⅲ secretion system (exoS, exoT, exoY, exsA, exsB, exsC, exsD, pcrV, popB, popD, pscC, pscE, pscG, and pscJ) were upregulated in doxycycline-resistant PAO1. While, ampC were upregulated in ceftriaxone-resistant PAO1. In addition, variants were obtained in wild type and four antibiotics resistant PAO1. Our findings provide a comparative transcriptome analysis of antibiotic resistant mutants selected by different antibiotics, and might assist in identifying potential therapeutic strategies for P. aeruginosa infection.
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Affiliation(s)
- Wenlu Zhang
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China
| | - Yaping Yuan
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China
| | - Shasha Li
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China
| | - Bo Deng
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China
| | - Jiaming Zhang
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China
| | - Zhongjie Li
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China.
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Genotyping of paired KPC-producing Klebsiella pneumoniae isolates with and without divergent polymyxin B susceptibility profiles. Braz J Microbiol 2021; 52:1981-1989. [PMID: 34460074 DOI: 10.1007/s42770-021-00600-5] [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: 04/26/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022] Open
Abstract
Polymyxins are still used mainly in treating infections caused by carbapenem-resistant Klebsiella pneumoniae worldwide. The most frequent mechanism of acquired resistance to polymyxins in Gram-negative bacilli is the occurrence of mutations in chromosomal genes regulating operons responsible for lipopolysaccharide modification. As we observed at Santa Casa de São Paulo hospital the occurrence of infections caused by isolates resistant to polymyxins in patients previously treated with this antimicrobial, and new infections caused by the same polymyxin-susceptible species, in this study, we aimed to determine the clonality of consecutive K. pneumoniae isolates from the same patients and characterize the molecular determinants of polymyxin resistance in paired or clonal isolates. A total of 24 pairs and one trio of K. pneumoniae isolates were included in this study. Species identification was achieved by mass spectrometry and multiplex PCR. Polymyxin B minimal inhibitory concentrations were determined by broth microdilution. Clonality was evaluated using pulsed-field gel electrophoresis. The presence of insertions in mgrB gene was tested by PCR, and mutations on pmrA, pmrB, phoP, and phoQ were evaluated by PCR and complete nucleotide sequencing. A fraction of 23.8% of strains resistant to polymyxin B had an insertion in mgrB. Amino acid substitution F204L in PmrB may be implicated in polymyxin resistance. Substitutions T246A and R256G in PmrB were not implicated in polymyxin resistance. In this study, polymyxin resistance after a first susceptible isolate was detected was most frequently due to an infection caused by a distinct clone.
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45
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Jeannot K, Hagart K, Dortet L, Kostrzewa M, Filloux A, Plesiat P, Larrouy-Maumus G. Detection of Colistin Resistance in Pseudomonas aeruginosa Using the MALDIxin Test on the Routine MALDI Biotyper Sirius Mass Spectrometer. Front Microbiol 2021; 12:725383. [PMID: 34531843 PMCID: PMC8438524 DOI: 10.3389/fmicb.2021.725383] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022] Open
Abstract
Colistin is frequently a last resort treatment for Pseudomonas aeruginosa infections caused by multidrug-resistant (MDR) and extensively drug resistant (XDR) strains, and detection of colistin resistance is essential for the management of infected patients. Therefore, we evaluated the recently developed MALDIxin test for the detection of colistin resistance in P. aeruginosa clinical strains using the routine matrix-assisted laser desorption ionization (MALDI) Biotyper Sirius system. The test is based on the detection by mass spectrometry of modified lipid A by the addition of 4-amino-l-arabinose (l-ara4N) molecules on one or two phosphate groups, in strains resistant to colistin. Overproduction of l-Ara4N molecules is mainly due to the constitutive activation of the histidine kinase (PmrB) or the response regulator (PmrA) following an amino-acid substitution in clinical strains. The performance of the test was determined on a panel of 14 colistin-susceptible and 14 colistin-resistant P. aeruginosa clinical strains, the reference strain PAO1 and positive control mutants PmrB (V28G), PmrB (D172), PhoQ (D240-247), and ParR (M59I). In comparison with the broth microdilution (BMD) method, all the susceptible strains (n=14) and 8/14 colistin-resistant strains were detected in less than 1h, directly on whole bacteria. The remaining resistant strains (n=6) were all detected after a short pre-exposure (4h) to colistin before sample preparation. Validation of the method on a larger panel of strains will be the next step before its use in diagnostics laboratories. Our data showed that the MALDIxin test offers rapid and efficient detection of colistin resistant P. aeruginosa and is thus a valuable diagnostics tool to control the spread of these emerging resistant strains.
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Affiliation(s)
- Katy Jeannot
- UMR 6249 Chrono-Environnement, UFR Sciences Médicales et Pharmaceutiques, University of Bourgogne-Franche Comté, Besançon, France
- French National Reference Centre for Antibiotic Resistance, Besançon, France
- Department of Bacteriology, University Hospital of Besançon, Besançon, France
| | - Katheryn Hagart
- Department of Life Sciences, Faculty of Natural Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Laurent Dortet
- French National Reference Centre for Antibiotic Resistance, Besançon, France
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique – Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- EA7361 “Structure, Dynamic, Function and Expression of Broad Spectrum β-lactamases,” LabEx Lermit, Faculty of Medecine, Paris-Sud University, Le Kremlin-Bicêtre, France
| | | | - Alain Filloux
- Department of Life Sciences, Faculty of Natural Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Patrick Plesiat
- UMR 6249 Chrono-Environnement, UFR Sciences Médicales et Pharmaceutiques, University of Bourgogne-Franche Comté, Besançon, France
- French National Reference Centre for Antibiotic Resistance, Besançon, France
- Department of Bacteriology, University Hospital of Besançon, Besançon, France
| | - Gerald Larrouy-Maumus
- Department of Life Sciences, Faculty of Natural Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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Tabor LM, Grosser MR, Metruccio MMME, Kumar NG, Wu YT, Nieto V, Evans DJ, Fleiszig SMJ. Human tear fluid modulates the Pseudomonas aeruginosa transcriptome to alter antibiotic susceptibility. Ocul Surf 2021; 22:94-102. [PMID: 34332149 PMCID: PMC10139757 DOI: 10.1016/j.jtos.2021.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/08/2021] [Accepted: 07/26/2021] [Indexed: 11/24/2022]
Abstract
PURPOSE Previously, we showed that tear fluid protects corneal epithelial cells against Pseudomonas aeruginosa without suppressing bacterial viability. Here, we studied how tear fluid affects bacterial gene expression. METHODS RNA-sequencing was used to study the P. aeruginosa transcriptome after tear fluid exposure (5 h, 37 oC). Outcomes were further investigated by biochemical and physiological perturbations to tear fluid and tear-like fluid (TLF) and assessment of bacterial viability following tear/TLF pretreatment and antibiotic exposure. RESULTS Tear fluid deregulated ~180 P. aeruginosa genes ≥8 fold versus PBS including downregulating lasI, rhlI, qscR (quorum sensing/virulence), oprH, phoP, phoQ (antimicrobial resistance) and arnBCADTEF (polymyxin B resistance). Upregulated genes included algF (biofilm formation) and hemO (iron acquisition). qPCR confirmed tear down-regulation of oprH, phoP and phoQ. Tear fluid pre-treatment increased P. aeruginosa resistance to meropenem ~5-fold (4 μg/ml), but enhanced polymyxin B susceptibility ~180-fold (1 μg/ml), the latter activity reduced by dilution in PBS. Media containing a subset of tear components (TLF) also sensitized bacteria to polymyxin B, but only ~22.5-fold, correlating with TLF/tear fluid Ca2+ and Mg2+ concentrations. Accordingly, phoQ mutants were not sensitized by TLF or tear fluid. Superior activity of tear fluid versus TLF against wild-type P. aeruginosa was heat resistant but proteinase K sensitive. CONCLUSION P. aeruginosa responds to human tear fluid by upregulating genes associated with bacterial survival and adaptation. Meanwhile, tear fluid down-regulates multiple virulence-associated genes. Tears also utilize divalent cations and heat resistant/proteinase K sensitive component(s) to enhance P. aeruginosa sensitivity to polymyxin B.
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Affiliation(s)
- Lauren M Tabor
- School of Optometry, University of California, Berkeley, CA, USA
| | | | | | - Naren G Kumar
- School of Optometry, University of California, Berkeley, CA, USA
| | - Yvonne T Wu
- School of Optometry, University of California, Berkeley, CA, USA
| | - Vincent Nieto
- School of Optometry, University of California, Berkeley, CA, USA
| | - David J Evans
- School of Optometry, University of California, Berkeley, CA, USA; College of Pharmacy, Touro University California, Vallejo, CA, USA
| | - Suzanne M J Fleiszig
- School of Optometry, University of California, Berkeley, CA, USA; Graduate Groups in Vision Science, Microbiology, and Infectious Diseases & Immunity, University of California, Berkeley, CA, USA.
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Loss of RND-type multidrug efflux pumps triggers iron starvation and lipid A modifications in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2021; 65:e0059221. [PMID: 34252310 DOI: 10.1128/aac.00592-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Transporters belonging to the Resistance-Nodulation-Division (RND) superfamily of proteins are invariably present in the genomes of Gram-negative bacteria and are largely responsible for the intrinsic antibiotic resistance of these organisms. The number of genes encoding RND transporters per genome vary from one to sixteen and correlates with environmental versatilities of bacterial species. Pseudomonas aeruginosa PAO1 strain, a ubiquitous nosocomial pathogen, possesses twelve RND pumps, which are implicated in development of clinical multidrug resistance and known to contribute to virulence, quorum sensing and many other physiological functions. In this study, we analyzed how P. aeruginosa physiology adapts to the lack of RND-mediated efflux activities. A combination of transcriptomics, metabolomics, genetic and analytical approaches showed that the P. aeruginosa PΔ6 strain lacking six best characterized RND pumps activates a specific adaptation response that involves significant changes in abundance and activities of several transport systems, quorum sensing, iron acquisition and lipid A modifications. Our results demonstrate that these cells accumulate large quantities of pseudomonas quorum signal (PQS), which triggers iron starvation and activation of siderophore biosynthesis and acquisition pathways. The accumulation of iron in turn activates lipid A modification and membrane protection pathways. A transcriptionally regulated RND pump MuxABC-OpmB contributes to these transformations by controlling concentrations of coumarins. Our results suggest that these changes reduce the permeability barrier of the outer membrane and are needed to protect the cell envelope of efflux-deficient P. aeruginosa.
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Ghirga F, Stefanelli R, Cavinato L, Lo Sciuto A, Corradi S, Quaglio D, Calcaterra A, Casciaro B, Loffredo MR, Cappiello F, Morelli P, Antonelli A, Rossolini GM, Mangoni M, Mancone C, Botta B, Mori M, Ascenzioni F, Imperi F. A novel colistin adjuvant identified by virtual screening for ArnT inhibitors. J Antimicrob Chemother 2021; 75:2564-2572. [PMID: 32514531 PMCID: PMC7443731 DOI: 10.1093/jac/dkaa200] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/31/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
Background Colistin is a last-resort treatment option for many MDR Gram-negative bacteria. The covalent addition of l-aminoarabinose to the lipid A moiety of LPS is the main colistin resistance mechanism in the human pathogen Pseudomonas aeruginosa. Objectives Identification (by in silico screening of a chemical library) of potential inhibitors of ArnT, which catalyses the last committed step of lipid A aminoarabinosylation, and their validation in vitro as colistin adjuvants. Methods The available ArnT crystal structure was used for a docking-based virtual screening of an in-house library of natural products. The resulting putative ArnT inhibitors were tested in growth inhibition assays using a reference colistin-resistant P. aeruginosa strain. The most promising compound was further characterized for its range of activity, specificity and cytotoxicity. Additionally, the effect of the compound on lipid A aminoarabinosylation was verified by MS analyses of lipid A. Results A putative ArnT inhibitor (BBN149) was discovered by molecular docking and demonstrated to specifically potentiate colistin activity in colistin-resistant P. aeruginosa isolates, without relevant effect on colistin-susceptible strains. BBN149 also showed adjuvant activity against colistin-resistant Klebsiella pneumoniae and low toxicity to bronchial epithelial cells. Lipid A aminoarabinosylation was reduced in BBN149-treated cells, although only partially. Conclusions This study demonstrates that in silico screening targeting ArnT can successfully identify inhibitors of colistin resistance and provides a promising lead compound for the development of colistin adjuvants for the treatment of MDR bacterial infections.
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Affiliation(s)
- Francesca Ghirga
- Center for Life Nano Science@Sapienza, Italian Institute of Technology, Rome, Italy
| | - Roberta Stefanelli
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy.,Department of Sciences, 'Department of Excellence 2018 - 2022', Roma Tre University, Rome, Italy
| | - Luca Cavinato
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Alessandra Lo Sciuto
- Department of Sciences, 'Department of Excellence 2018 - 2022', Roma Tre University, Rome, Italy
| | - Silvia Corradi
- Center for Life Nano Science@Sapienza, Italian Institute of Technology, Rome, Italy.,Department of Chemistry and Technology of Drugs, 'Department of Excellence 2018 - 2022', Sapienza University of Rome, Rome, Italy
| | - Deborah Quaglio
- Department of Chemistry and Technology of Drugs, 'Department of Excellence 2018 - 2022', Sapienza University of Rome, Rome, Italy
| | - Andrea Calcaterra
- Department of Chemistry and Technology of Drugs, 'Department of Excellence 2018 - 2022', Sapienza University of Rome, Rome, Italy
| | - Bruno Casciaro
- Center for Life Nano Science@Sapienza, Italian Institute of Technology, Rome, Italy
| | - Maria Rosa Loffredo
- Department of Biochemical Sciences, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Floriana Cappiello
- Department of Biochemical Sciences, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Patrizia Morelli
- Microbiology Laboratory, Giannina Gaslini Institute, Genoa, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Marialuisa Mangoni
- Department of Biochemical Sciences, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Carmine Mancone
- Department of Molecular Medicine, 'Department of Excellence 2018 - 2022', Sapienza University of Rome, Rome, Italy
| | - Bruno Botta
- Department of Chemistry and Technology of Drugs, 'Department of Excellence 2018 - 2022', Sapienza University of Rome, Rome, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, 'Department of Excellence 2018 - 2022', University of Siena, Siena, Italy
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesco Imperi
- Department of Sciences, 'Department of Excellence 2018 - 2022', Roma Tre University, Rome, Italy
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Two-Component Signaling Systems Regulate Diverse Virulence-Associated Traits in Pseudomonas aeruginosa. Appl Environ Microbiol 2021; 87:AEM.03089-20. [PMID: 33771779 DOI: 10.1128/aem.03089-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/18/2021] [Indexed: 12/30/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can cause problematic infections at different sites throughout the human body. P. aeruginosa encodes a large suite of over 60 two-component signaling systems that enable cells to rapidly sense and respond to external signals. Previous work has shown that some of these sensory systems contribute to P. aeruginosa pathogenesis, but the virulence-associated processes and phenotypic traits that each of these systems controls are still largely unclear. To aid investigations of these sensory systems, we have generated deletion strains for each of 64 genes encoding histidine kinases and one histidine phosphotransferase in P. aeruginosa PA14. We carried out initial phenotypic characterizations of this collection by assaying these mutants for over a dozen virulence-associated traits, and we found that each of these phenotypes is regulated by multiple sensory systems. Our work highlights the usefulness of this collection for further studies of P. aeruginosa two-component signaling systems and provides insight into how these systems may contribute to P. aeruginosa infection.IMPORTANCE Pseudomonas aeruginosa can grow and survive under a wide range of conditions, including as a human pathogen. As such, P. aeruginosa must be able to sense and respond to diverse signals and cues in its environment. This sensory capability is endowed in part by the hundreds of two-component signaling proteins encoded in the P. aeruginosa genome, but the precise roles of each remain poorly defined. To facilitate systematic study of the signaling repertoire of P. aeruginosa PA14, we generated a library of deletion strains, each lacking one of the 64 histidine kinases. By subjecting these strains to a battery of phenotypic assays, we confirmed the functions of many and unveiled roles for dozens of previously uncharacterized histidine kinases in controlling various traits, many of which are associated with P. aeruginosa virulence. Thus, this work provides new insight into the functions of two-component signaling proteins and provides a resource for future investigations.
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Langendonk RF, Neill DR, Fothergill JL. The Building Blocks of Antimicrobial Resistance in Pseudomonas aeruginosa: Implications for Current Resistance-Breaking Therapies. Front Cell Infect Microbiol 2021; 11:665759. [PMID: 33937104 PMCID: PMC8085337 DOI: 10.3389/fcimb.2021.665759] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
P. aeruginosa is classified as a priority one pathogen by the World Health Organisation, and new drugs are urgently needed, due to the emergence of multidrug-resistant (MDR) strains. Antimicrobial-resistant nosocomial pathogens such as P. aeruginosa pose unwavering and increasing threats. Antimicrobial stewardship has been a challenge during the COVID-19 pandemic, with a majority of those hospitalized with SARS-CoV2 infection given antibiotics as a safeguard against secondary bacterial infection. This increased usage, along with increased handling of sanitizers and disinfectants globally, may further accelerate the development and spread of cross-resistance to antibiotics. In addition, P. aeruginosa is the primary causative agent of morbidity and mortality in people with the life-shortening genetic disease cystic fibrosis (CF). Prolonged periods of selective pressure, associated with extended antibiotic treatment and the actions of host immune effectors, results in widespread adaptive and acquired resistance in P. aeruginosa found colonizing the lungs of people with CF. This review discusses the arsenal of resistance mechanisms utilized by P. aeruginosa, how these operate under high-stress environments such as the CF lung and how their interconnectedness can result in resistance to multiple antibiotic classes. Intrinsic, adaptive and acquired resistance mechanisms will be described, with a focus on how each layer of resistance can serve as a building block, contributing to multi-tiered resistance to antimicrobial activity. Recent progress in the development of anti-resistance adjuvant therapies, targeting one or more of these building blocks, should lead to novel strategies for combatting multidrug resistant P. aeruginosa. Anti-resistance adjuvant therapy holds great promise, not least because resistance against such therapeutics is predicted to be rare. The non-bactericidal nature of anti-resistance adjuvants reduce the selective pressures that drive resistance. Anti-resistance adjuvant therapy may also be advantageous in facilitating efficacious use of traditional antimicrobials, through enhanced penetration of the antibiotic into the bacterial cell. Promising anti-resistance adjuvant therapeutics and targets will be described, and key remaining challenges highlighted. As antimicrobial stewardship becomes more challenging in an era of emerging and re-emerging infectious diseases and global conflict, innovation in antibiotic adjuvant therapy can play an important role in extending the shelf-life of our existing antimicrobial therapeutic agents.
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Affiliation(s)
- R. Frèdi Langendonk
- Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Liverpool, United Kingdom
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