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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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Jafari-Ramedani S, Nazari M, Arzanlou M, Peeri-Dogaheh H, Sahebkar A, Khademi F. Prevalence and molecular characterization of colistin resistance in Pseudomonas aeruginosa isolates: insights from a study in Ardabil hospitals. BMC Microbiol 2024; 24:152. [PMID: 38702660 PMCID: PMC11067120 DOI: 10.1186/s12866-024-03309-1] [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: 12/20/2023] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is a common cause of nosocomial infections. However, the emergence of multidrug-resistant strains has complicated the treatment of P. aeruginosa infections. While polymyxins have been the mainstay for treatment, there is a global increase in resistance to these antibiotics. Therefore, our study aimed to determine the prevalence and molecular details of colistin resistance in P. aeruginosa clinical isolates collected between June 2019 and May 2023, as well as the genetic linkage of colistin-resistant P. aeruginosa isolates. RESULTS The resistance rate to colistin was 9% (n = 18) among P. aeruginosa isolates. All 18 colistin-resistant isolates were biofilm producers and carried genes associated with biofilm formation. Furthermore, the presence of genes encoding efflux pumps, TCSs, and outer membrane porin was observed in all colistin-resistant P. aeruginosa strains, while the mcr-1 gene was not detected. Amino acid substitutions were identified only in the PmrB protein of multidrug- and colistin-resistant strains. The expression levels of mexA, mexC, mexE, mexY, phoP, and pmrA genes in the 18 colistin-resistant P. aeruginosa strains were as follows: 88.8%, 94.4%, 11.1%, 83.3%, 83.3%, and 38.8%, respectively. Additionally, down-regulation of the oprD gene was observed in 44.4% of colistin-resistant P. aeruginosa strains. CONCLUSION This study reports the emergence of colistin resistance with various mechanisms among P. aeruginosa strains in Ardabil hospitals. We recommend avoiding unnecessary use of colistin to prevent potential future increases in colistin resistance.
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Affiliation(s)
- Saghar Jafari-Ramedani
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Maryam Nazari
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mohsen Arzanlou
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hadi Peeri-Dogaheh
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzad Khademi
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran.
- Arthropod-Borne Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
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3
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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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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: 17] [Impact Index Per Article: 8.5] [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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Wan F, Xu L, Ruan Z, Luo Q. Genomic and Transcriptomic Analysis of Colistin-Susceptible and Colistin-Resistant Isolates Identify Two-Component System EvgS/EvgA Associated with Colistin Resistance in Escherichia coli. Infect Drug Resist 2021; 14:2437-2447. [PMID: 34234474 PMCID: PMC8254184 DOI: 10.2147/idr.s316963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/15/2021] [Indexed: 12/02/2022] Open
Abstract
Purpose Colistin is one of the last-resort antimicrobial agents that combat the increasing threat of multi-drug resistant (MDR) gram-negative bacteria. Based on the known mechanism of colistin resistance which contributes to chromosomal mutations involved in the synthesis and modification of lipopolysaccharide (LPS), we explored the regulatory genes mediate colistin resistance, by whole genome sequencing and transcriptome analysis. Materials and Methods In this study, a colistin-resistant (Colr) strain Escherichia coli ATCC 25922-R was generated from colistin-sensible (Cols) strain E. coli ATCC 25922 by colistin induction. We compared the genome and transcriptome sequencing result from Cols and Colr strain. MALDI-TOF mass spectrometry was used to detect LPS. Results Genomic analysis and complementation experiment demonstrated the PmrB amino acid substitution in ATCC 25922-R (L14R) conferred the colistin resistance phenotype. Results of RNA sequencing (RNA-Seq) and comparative transcriptome analysis indicated that the two-component system EvgS/EvgA is highly involved in the global regulation of colistin resistance. Conclusion This study demonstrated that PmrB L14R amino acid substitution resulted in colistin resistance, and two-component system EvgS/EvgA might participate in colistin resistance in E. coli.
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Affiliation(s)
- Fen Wan
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, People's Republic of China
| | - Linna Xu
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, People's Republic of China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, People's Republic of China
| | - Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, 310003, People's Republic of China
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6
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Various Novel Colistin Resistance Mechanisms Interact To Facilitate Adaptation of Aeromonas hydrophila to Complex Colistin Environments. Antimicrob Agents Chemother 2021; 65:e0007121. [PMID: 33903105 PMCID: PMC8373241 DOI: 10.1128/aac.00071-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aeromonas hydrophila, a heterotrophic and Gram-negative bacterium, has attracted considerable attention owing to the increasing prevalence of reported infections. Colistin is a last-resort antibiotic that can treat life-threatening infections caused by multidrug-resistant Gram-negative bacteria. However, the mechanisms underlying colistin resistance in A. hydrophila remain unclear. The present study reveals four novel colistin resistance mechanisms in A. hydrophila: (i) EnvZ/OmpR upregulates the expression of the arnBCADTEF operon to mediate lipopolysaccharide (LPS) modification by 4-amino-4-deoxy-l-arabinose, (ii) EnvZ/OmpR regulates the expression of the autotransporter gene3832 to decrease outer membrane permeability in response to colistin, (iii) deletion of envZ/ompR activates PhoP/PhoQ, which functions as a substitute two-component system to mediate the addition of phosphoethanolamine to lipid A via pmrC, and (iv) the mlaFD173A mutant confers high-level colistin resistance via upregulation of the Mla pathway. The EnvZ/OmpR two-component system-mediated resistance mechanism is the leading form of colistin resistance in A. hydrophila, which enables it to rapidly generate low- to medium-level colistin resistance. As colistin concentrations in the environment continue to rise, antibiotic resistance mediated by EnvZ/OmpR becomes insufficient to ensure bacterial survival. Consequently, A. hydrophila has developed an mlaF mutation that results in high-level colistin resistance. Our findings indicate that A. hydrophila can thrive in a complex environment through various colistin resistance mechanisms.
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Ho J, Yeoh YK, Barua N, Chen Z, Lui G, Wong SH, Yang X, Chan MCW, Chan PKS, Hawkey PM, Ip M. Systematic review of human gut resistome studies revealed variable definitions and approaches. Gut Microbes 2020; 12:1700755. [PMID: 31942825 PMCID: PMC7524153 DOI: 10.1080/19490976.2019.1700755] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.
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Affiliation(s)
- Jeffery Ho
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yun Kit Yeoh
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nilakshi Barua
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Grace Lui
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,Department of Medicine & Therapeutics, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H Wong
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,Department of Medicine & Therapeutics, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Martin CW Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul KS Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peter M Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,CONTACT Margaret Ip Department of Microbiology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
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Ayoub Moubareck C. Polymyxins and Bacterial Membranes: A Review of Antibacterial Activity and Mechanisms of Resistance. MEMBRANES 2020; 10:membranes10080181. [PMID: 32784516 PMCID: PMC7463838 DOI: 10.3390/membranes10080181] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022]
Abstract
Following their initial discovery in the 1940s, polymyxin antibiotics fell into disfavor due to their potential clinical toxicity, especially nephrotoxicity. However, the dry antibiotic development pipeline, together with the rising global prevalence of infections caused by multidrug-resistant (MDR) Gram-negative bacteria have both rejuvenated clinical interest in these polypeptide antibiotics. Parallel to the revival of their use, investigations into the mechanisms of action and resistance to polymyxins have intensified. With an initial known effect on biological membranes, research has uncovered the detailed molecular and chemical interactions that polymyxins have with Gram-negative outer membranes and lipopolysaccharide structure. In addition, genetic and epidemiological studies have revealed the basis of resistance to these agents. Nowadays, resistance to polymyxins in MDR Gram-negative pathogens is well elucidated, with chromosomal as well as plasmid-encoded, transferrable pathways. The aims of the current review are to highlight the important chemical, microbiological, and pharmacological properties of polymyxins, to discuss their mechanistic effects on bacterial membranes, and to revise the current knowledge about Gram-negative acquired resistance to these agents. Finally, recent research, directed towards new perspectives for improving these old agents utilized in the 21st century, to combat drug-resistant pathogens, is summarized.
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Huang J, Li C, Song J, Velkov T, Wang L, Zhu Y, Li J. Regulating polymyxin resistance in Gram-negative bacteria: roles of two-component systems PhoPQ and PmrAB. Future Microbiol 2020; 15:445-459. [PMID: 32250173 DOI: 10.2217/fmb-2019-0322] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Polymyxins (polymyxin B and colistin) are last-line antibiotics against multidrug-resistant Gram-negative pathogens. Polymyxin resistance is increasing worldwide, with resistance most commonly regulated by two-component systems such as PmrAB and PhoPQ. This review discusses the regulatory mechanisms of PhoPQ and PmrAB in mediating polymyxin resistance, from receiving an external stimulus through to activation of genes responsible for lipid A modifications. By analyzing the reported nonsynonymous substitutions in each two-component system, we identified the domains that are critical for polymyxin resistance. Notably, for PmrB 71% of resistance-conferring nonsynonymous mutations occurred in the HAMP (present in histidine kinases, adenylate cyclases, methyl accepting proteins and phosphatase) linker and DHp (dimerization and histidine phosphotransfer) domains. These results enhance our understanding of the regulatory mechanisms underpinning polymyxin resistance and may assist with the development of new strategies to minimize resistance emergence.
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Affiliation(s)
- Jiayuan Huang
- Biomedicine Discovery Institute & Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Chen Li
- Biomedicine Discovery Institute & Department of Biochemistry & Molecular Biology, Monash University, Melbourne 3800, Australia.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Jiangning Song
- Biomedicine Discovery Institute & Department of Biochemistry & Molecular Biology, Monash University, Melbourne 3800, Australia
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry & Health Sciences, The University of Melbourne, Melbourne 3010, Australia
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yan Zhu
- Biomedicine Discovery Institute & Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Jian Li
- Biomedicine Discovery Institute & Department of Microbiology, Monash University, Melbourne 3800, Australia
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10
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The Efflux Pump MexXY/OprM Contributes to the Tolerance and Acquired Resistance of Pseudomonas aeruginosa to Colistin. Antimicrob Agents Chemother 2020; 64:AAC.02033-19. [PMID: 31964794 DOI: 10.1128/aac.02033-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/13/2020] [Indexed: 12/29/2022] Open
Abstract
The intrinsic resistance of Pseudomonas aeruginosa to polymyxins in part relies on the addition of 4-amino-4-deoxy-l-arabinose (Ara4N) molecules to the lipid A of lipopolysaccharide (LPS), through induction of operon arnBCADTEF-ugd (arn) expression. As demonstrated previously, at least three two-component regulatory systems (PmrAB, ParRS, and CprRS) are able to upregulate this operon when bacteria are exposed to colistin. In the present study, gene deletion experiments with the bioluminescent strain PAO1::lux showed that ParRS is a key element in the tolerance of P. aeruginosa to this last-resort antibiotic (i.e., resistance to early drug killing). Other loci of the ParR regulon, such as those encoding the efflux proteins MexXY (mexXY), the polyamine biosynthetic pathway PA4773-PA4774-PA4775, and Ara4N LPS modification process (arnBCADTEF-ugd), also contribute to the bacterial tolerance in an intricate way with ParRS. Furthermore, we found that both stable upregulation of the arn operon and drug-induced ParRS-dependent overexpression of the mexXY genes accounted for the elevated resistance of pmrB mutants to colistin. Deletion of the mexXY genes in a constitutively activated ParR mutant of PAO1 was associated with significantly increased expression of the genes arnA, PA4773, and pmrA in the absence of colistin exposure, thereby highlighting a functional link between the MexXY/OprM pump, the PA4773-PA4774-PA4775 pathway, and Ara4N-based modification of LPS. The role played by MexXY/OprM in the adaptation of P. aeruginosa to polymyxins opens new perspectives for restoring the susceptibility of resistant mutants through the use of efflux inhibitors.
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11
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Production of Norspermidine Contributes to Aminoglycoside Resistance in pmrAB Mutants of Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019; 63:AAC.01044-19. [PMID: 31383668 DOI: 10.1128/aac.01044-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/25/2019] [Indexed: 12/18/2022] Open
Abstract
Emergence of resistance to polymyxins in Pseudomonas aeruginosa is mainly due to mutations in two-component systems that promote the addition of 4-amino-4-deoxy-l-arabinose to the lipopolysaccharide (LPS) through upregulation of operon arnBCADTEF-ugd (arn) expression. Here, we demonstrate that mutations occurring in different domains of histidine kinase PmrB or in response regulator PmrA result in coresistance to aminoglycosides and colistin. All seventeen clinical strains tested exhibiting such a cross-resistance phenotype were found to be pmrAB mutants. As shown by gene deletion experiments, the decreased susceptibility of the mutants to aminoglycosides was independent from operon arn but required the efflux system MexXY-OprM and the products of three genes, PA4773-PA4774-PA4775, that are cotranscribed and activated with genes pmrAB Gene PA4773 (annotated as speD2 in the PAO1 genome) and PA4774 (speE2) are predicted to encode enzymes involved in biosynthesis of polyamines. Comparative analysis of cell surface extracts of an in vitro selected pmrAB mutant, called AB16.2, and derivatives lacking PA4773, PA4774, and PA4775 revealed that these genes were needed for norspermidine production via a pathway that likely uses 1,3-diaminopropane, a precursor of polyamines. Altogether, our results suggest that norspermidine decreases the self-promoted uptake pathway of aminoglycosides across the outer membrane and, thereby, potentiates the activity of efflux pump MexXY-OprM.
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12
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Fong K, Tremblay DM, Delaquis P, Goodridge L, Levesque RC, Moineau S, Suttle CA, Wang S. Diversity and Host Specificity Revealed by Biological Characterization and Whole Genome Sequencing of Bacteriophages Infecting Salmonella enterica. Viruses 2019; 11:v11090854. [PMID: 31540091 PMCID: PMC6783827 DOI: 10.3390/v11090854] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022] Open
Abstract
Phages infecting members of the opportunistic human pathogen, Salmonella enterica, are widespread in natural environments and offer a potential source of agents that could be used for controlling populations of this bacterium; yet, relatively little is known about these phages. Here we describe the isolation and characterization of 45 phages of Salmonella enterica from disparate geographic locations within British Columbia, Canada. Host-range profiling revealed host-specific patterns of susceptibility and resistance, with several phages identified that have a broad-host range (i.e., able to lyse >40% of bacterial hosts tested). One phage in particular, SE13, is able to lyse 51 out of the 61 Salmonella strains tested. Comparative genomic analyses also revealed an abundance of sequence diversity in the sequenced phages. Alignment of the genomes grouped the phages into 12 clusters with three singletons. Phages within certain clusters exhibited extraordinarily high genome homology (>98% nucleotide identity), yet between clusters, genomes exhibited a span of diversity (<50% nucleotide identity). Alignment of the major capsid protein also supported the clustering pattern observed with alignment of the whole genomes. We further observed associations between genomic relatedness and the site of isolation, as well as genetic elements related to DNA metabolism and host virulence. Our data support the knowledge framework for phage diversity and phage-host interactions that are required for developing phage-based applications for various sectors, including biocontrol, detection and typing.
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Affiliation(s)
- Karen Fong
- Food, Nutrition and Health, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Denise M Tremblay
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC G1V 0A6, Canada.
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC G1V 0A6, Canada.
| | - Pascal Delaquis
- Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada.
| | - Lawrence Goodridge
- Food Science Department, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada.
| | - Sylvain Moineau
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC G1V 0A6, Canada.
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC G1V 0A6, Canada.
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC G1V 0A6, Canada.
| | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Siyun Wang
- Food, Nutrition and Health, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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The Essential Role of Hypermutation in Rapid Adaptation to Antibiotic Stress. Antimicrob Agents Chemother 2019; 63:AAC.00744-19. [PMID: 31036684 DOI: 10.1128/aac.00744-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 04/19/2019] [Indexed: 12/22/2022] Open
Abstract
A common outcome of antibiotic exposure in patients and in vitro is the evolution of a hypermutator phenotype that enables rapid adaptation by pathogens. While hypermutation is a robust mechanism for rapid adaptation, it requires trade-offs between the adaptive mutations and the more common "hitchhiker" mutations that accumulate from the increased mutation rate. Using quantitative experimental evolution, we examined the role of hypermutation in driving the adaptation of Pseudomonas aeruginosa to colistin. Metagenomic deep sequencing revealed 2,657 mutations at ≥5% frequency in 1,197 genes and 761 mutations in 29 endpoint isolates. By combining genomic information, phylogenetic analyses, and statistical tests, we showed that evolutionary trajectories leading to resistance could be reliably discerned. In addition to known alleles such as pmrB, hypermutation allowed identification of additional adaptive alleles with epistatic relationships. Although hypermutation provided a short-term fitness benefit, it was detrimental to overall fitness. Alarmingly, a small fraction of the colistin-adapted population remained colistin susceptible and escaped hypermutation. In a clinical population, such cells could play a role in reestablishing infection upon withdrawal of colistin. We present here a framework for evaluating the complex evolutionary trajectories of hypermutators that applies to both current and emerging pathogen populations.
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Widely Used Benzalkonium Chloride Disinfectants Can Promote Antibiotic Resistance. Appl Environ Microbiol 2018; 84:AEM.01201-18. [PMID: 29959242 DOI: 10.1128/aem.01201-18] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/23/2018] [Indexed: 01/15/2023] Open
Abstract
While the misuse of antibiotics has clearly contributed to the emergence and proliferation of resistant bacterial pathogens, with major health consequences, it remains less clear if the widespread use of disinfectants, such as benzalkonium chlorides (BAC), a different class of biocides than antibiotics, has contributed to this problem. Here, we provide evidence that exposure to BAC coselects for antibiotic-resistant bacteria and describe the underlying genetic mechanisms. After inoculation with river sediment, BAC-fed bioreactors selected for several bacterial taxa, including the opportunistic pathogen Pseudomonas aeruginosa, that were more resistant to several antibiotics than their counterparts in a control (no BAC) bioreactor. A metagenomic analysis of the bioreactor microbial communities, confirmed by gene cloning experiments with the derived isolates, suggested that integrative and conjugative elements encoding a BAC efflux pump together with antibiotic resistance genes were responsible for these results. Furthermore, the exposure of the P. aeruginosa isolates to increasing concentrations of BAC selected for mutations in pmrB (polymyxin resistance) and physiological adaptations that contributed to a higher tolerance to polymyxin B and other antibiotics. The physiological adaptations included the overexpression of mexCD-oprJ multidrug efflux pump genes when BAC was added in the growth medium at subinhibitory concentrations. Collectively, our results demonstrated that disinfectants promote antibiotic resistance via several mechanisms and highlight the need to remediate (degrade) disinfectants in nontarget environments to further restrain the spread of antibiotic-resistant bacteria.IMPORTANCE Benzalkonium chlorides (BAC) are biocides broadly used in disinfectant solutions. Disinfectants are widely used in food processing lines, domestic households, and pharmaceutical products and are typically designed to have a different mode of action than antibiotics to avoid interfering with the use of the latter. Whether exposure to BAC makes bacteria more resistant to antibiotics remains an unresolved issue of obvious practical consequences for public health. Using an integrated approach that combines metagenomics of natural microbial communities with gene cloning experiments with isolates and experimental evolution assays, we show that the widely used benzalkonium chloride disinfectants promote clinically relevant antibiotic resistance. Therefore, more attention should be given to the usage of these disinfectants, and their fate in nontarget environments should be monitored more tightly.
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Polymyxins: Antibacterial Activity, Susceptibility Testing, and Resistance Mechanisms Encoded by Plasmids or Chromosomes. Clin Microbiol Rev 2017; 30:557-596. [PMID: 28275006 DOI: 10.1128/cmr.00064-16] [Citation(s) in RCA: 924] [Impact Index Per Article: 132.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Polymyxins are well-established antibiotics that have recently regained significant interest as a consequence of the increasing incidence of infections due to multidrug-resistant Gram-negative bacteria. Colistin and polymyxin B are being seriously reconsidered as last-resort antibiotics in many areas where multidrug resistance is observed in clinical medicine. In parallel, the heavy use of polymyxins in veterinary medicine is currently being reconsidered due to increased reports of polymyxin-resistant bacteria. Susceptibility testing is challenging with polymyxins, and currently available techniques are presented here. Genotypic and phenotypic methods that provide relevant information for diagnostic laboratories are presented. This review also presents recent works in relation to recently identified mechanisms of polymyxin resistance, including chromosomally encoded resistance traits as well as the recently identified plasmid-encoded polymyxin resistance determinant MCR-1. Epidemiological features summarizing the current knowledge in that field are presented.
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Using experimental evolution to identify druggable targets that could inhibit the evolution of antimicrobial resistance. J Antibiot (Tokyo) 2017; 71:279-286. [PMID: 28928474 PMCID: PMC5788704 DOI: 10.1038/ja.2017.108] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/27/2017] [Accepted: 08/05/2017] [Indexed: 02/05/2023]
Abstract
With multi-drug and pan-drug-resistant bacteria becoming increasingly common in hospitals, antibiotic resistance has threatened to return us to a pre-antibiotic era that would completely undermine modern medicine. There is an urgent need to develop new antibiotics and strategies to combat resistance that are substantially different from earlier drug discovery efforts. One such strategy that would complement current and future antibiotics would be a class of co-drugs that target the evolution of resistance and thereby extend the efficacy of specific classes of antibiotics. A critical step in the development of such strategies lies in understanding the critical evolutionary trajectories responsible for resistance and which proteins or biochemical pathways within those trajectories would be good candidates for co-drug discovery. We identify the most important steps in the evolution of resistance for a specific pathogen and antibiotic combination by evolving highly polymorphic populations of pathogens to resistance in a novel bioreactor that favors biofilm development. As the populations evolve to increasing drug concentrations, we use deep sequencing to elucidate the network of genetic changes responsible for resistance and subsequent in vitro biochemistry and often structure determination to determine how the adaptive mutations produce resistance. Importantly, the identification of the molecular steps, their frequency within the populations and their chronology within the evolutionary trajectory toward resistance is critical to assessing their relative importance. In this work, we discuss findings from the evolution of the ESKAPE pathogen, Pseudomonas aeruginosa to the drug of last resort, colistin to illustrate the power of this approach.
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Jeannot K, Bolard A, Plésiat P. Resistance to polymyxins in Gram-negative organisms. Int J Antimicrob Agents 2017; 49:526-535. [PMID: 28163137 DOI: 10.1016/j.ijantimicag.2016.11.029] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/10/2016] [Accepted: 11/25/2016] [Indexed: 12/30/2022]
Abstract
Polymyxins have recently been re-introduced into the therapeutic arsenal to combat infections caused by multidrug-resistant Gram-negative bacteria. However, the emergence of strains resistant to these last-resort drugs is becoming a critical issue in a growing number of countries. Both intrinsic and transferable mechanisms of polymyxin resistance have been characterised. These mechanisms as well as the epidemiological data regarding four relevant bacterial pathogens (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa) are considered in this review. A special focus is made on plasmid-mediated resistance and the spread of mcr genes.
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Affiliation(s)
- Katy Jeannot
- Laboratoire de bactériologie, Centre national de référence (CNR) de la résistance aux antibiotiques, Centre hospitalier universitaire (CHRU) de Besançon, boulevard Fleming, 25000 Besançon, France.
| | - Arnaud Bolard
- Laboratoire de bactériologie, Centre national de référence (CNR) de la résistance aux antibiotiques, Centre hospitalier universitaire (CHRU) de Besançon, boulevard Fleming, 25000 Besançon, France
| | - Patrick Plésiat
- Laboratoire de bactériologie, Centre national de référence (CNR) de la résistance aux antibiotiques, Centre hospitalier universitaire (CHRU) de Besançon, boulevard Fleming, 25000 Besançon, France
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18
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The dlt genes play a role in antimicrobial tolerance of Streptococcus mutans biofilms. Int J Antimicrob Agents 2016; 48:298-304. [DOI: 10.1016/j.ijantimicag.2016.06.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/27/2016] [Accepted: 06/05/2016] [Indexed: 11/23/2022]
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Evolved resistance to colistin and its loss due to genetic reversion in Pseudomonas aeruginosa. Sci Rep 2016; 6:25543. [PMID: 27150578 PMCID: PMC4858706 DOI: 10.1038/srep25543] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 04/20/2016] [Indexed: 11/17/2022] Open
Abstract
The increased reliance on colistin for treating multidrug-resistant Gram-negative bacterial infections has resulted in the emergence of colistin-resistant Pseudomonas aeruginosa. We attempted to identify genetic contributors to colistin resistance in vitro evolved isogenic colistin-resistant and -susceptible strains of two P. aeruginosa lineages (P5 and P155). Their evolutionary paths to acquisition and loss of colistin resistance were also tracked. Comparative genomic analysis revealed 13 and five colistin resistance determinants in the P5 and P155 lineages, respectively. Lipid A in colistin-resistant mutants was modified through the addition of 4-amino-L-arabinose; this modification was absent in colistin-susceptible revertant strains. Many amino acid substitutions that emerged during the acquisition of colistin resistance were reversed in colistin-susceptible revertants. We demonstrated that evolved colistin resistance in P. aeruginosa was mediated by a complicated regulatory network that likely emerges through diverse genetic alterations. Colistin-resistant P. aeruginosa became susceptible to the colistin upon its withdrawal because of genetic reversion. The mechanisms through which P. aeruginosa acquires and loses colistin resistance have implications on the treatment options that can be applied against P. aeruginosa infections, with respect to improving bactericidal efficacy and preventing further resistance to antibiotics.
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Functional Genome Screening to Elucidate the Colistin Resistance Mechanism. Sci Rep 2016; 6:23156. [PMID: 26988670 PMCID: PMC4796810 DOI: 10.1038/srep23156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/25/2016] [Indexed: 12/17/2022] Open
Abstract
Antibiogram profile of 1590 clinical bacterial isolates based on thirteen different antimicrobial compounds showed that 1.6% of the bacterial isolates are multidrug resistant. Distribution pattern based on 16S rRNA sequence analysis showed that Pseudomonas aeruginosa constituted the largest group (83.6%) followed by Burkholderia pseudomallei sp. A191 (5.17%), Staphylococcus sp. A261 (3.45%). Among the various antibiotics used, colistin appeared to be the most effective against the Gram negative bacteria. Burkholderia pseudomallei sp. A191 and Pseudomonas aeruginosa sp. A111 showed resistance to 1500 μg/ml and 750 μg/ml of colistin respectively which constitutes 7.7% of the bacterial population. A functional genomics strategy was employed to discover the molecular support for colistin resistance in Burkholderia pseudomallei sp. A191. A pUC plasmid-based genomic expression library was constructed with an estimated library size of 2.1 × 107bp. Five colistin resistant clones were obtained after functional screening of the library. Analysis of DNA sequence of five colistin resistant clones showed homology to two component regularity systems (TCRS) encoding for a histidine kinase (mrgS) and its regulatory component (mrgR). Cross complementation assay showed that mutations in mrgS were sufficient enough to confer colistin resistant phenotype in a sensitive strain.
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Rosales-Reyes R, Alcántar-Curiel MD, Jarillo-Quijada MD, Gayosso-Vázquez C, Morfin-Otero MDR, Rodríguez-Noriega E, Santos-Preciado JI. Biofilm Formation and Susceptibility to Polymyxin B by a Highly Prevalent Clone of Multidrug-Resistant Acinetobacter baumannii from a Mexican Tertiary Care Hospital. Chemotherapy 2015; 61:8-14. [PMID: 26536333 DOI: 10.1159/000440605] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 08/24/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Acinetobacter baumannii has emerged as a major cause of hospital-associated infections with increased morbidity and mortality among those affected. METHODS A total of 85 isolates of a highly prevalent multidrug-resistant clone, identified during the period 2007-2011, were analyzed for biofilm formation on a polystyrene surface. The minimal inhibitory concentration was determined by the Sensititre System, the agar disk diffusion method and then read by means of the BIOMIC system and serial dilutions on Müller-Hinton agar. RESULTS In this study, covering a period of 5 years (2007-2011), we demonstrate that a particular clone emerged as the most prevalent, with an associated lethality of 28.2%. We demonstrate that 92.9% of strains corresponding to this clone are biofilm producers. Our results also demonstrate that all isolates were 100% susceptible to polymyxin B. CONCLUSION Our study suggests that the high prevalence and lethality of this multidrug-resistant clone of A. baumannii and its persistence over close to 5 years in a Mexican tertiary hospital environment can be explained in part by the ability of these clinical isolates of A. baumannii to form biofilms.
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Ubagai T, Nakano R, Nakano A, Kamoshida G, Ono Y. Gene expression analysis in human polymorphonuclear leukocytes stimulated by LPSs from nosocomial opportunistic pathogens. Innate Immun 2015; 21:802-12. [PMID: 26376669 DOI: 10.1177/1753425915605892] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 08/23/2015] [Indexed: 12/29/2022] Open
Abstract
Innate immunity coordinates LPS detection via TLR4 on polymorphonuclear leukocytes (PMNs) to elicit responses to many Gram-negative bacteria. In this study, we describe the effects of five subtypes of LPS [isolated from Escherichia coli B4, Pseudomonas aeruginosa PAO1, multidrug-resistant P. aeruginosa (MDRP), Acinetobacter baumannii and multidrug-resistant A. baumannii (MDRA)] on gene expression in PMNs. LPS isolated from B4, PAO1, and A. baumannii did not significantly alter TLR2 expression. However, LPS from MDRP and MDRA caused a 0.6-fold decrease and 2.7-fold increase, respectively, in TLR2 expression. Similarly, TLR4 expression was not significantly altered by LPS isolated from B4, PAO1 and A. baumannii but was down-regulated by LPS isolated from MDRP and MDRA by 0.1- and 0.6-fold, respectively. All LPS subtypes, excluding PAO1, down-regulated CD14 expression in PMNs. However, all five LPS subtypes up-regulated TNFA, IL1B, IL6, IL10 and TREM1 expression in a concentration-dependent manner, with the most substantial responses observed following exposure to LPS from MDRP and MDRA. These different effects on the gene expression in PMNs may depend on variation in LPS structural modifications related to acquired drug resistance, such as acylation and/or glycosylation.
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Affiliation(s)
- Tsuneyuki Ubagai
- Department of Microbiology and Immunology, Teikyo University School of Medicine, Tokyo, Japan
| | - Ryuichi Nakano
- Department of Microbiology and Immunology, Teikyo University School of Medicine, Tokyo, Japan
| | - Akiyo Nakano
- Department of Microbiology and Immunology, Teikyo University School of Medicine, Tokyo, Japan
| | - Go Kamoshida
- Department of Microbiology and Immunology, Teikyo University School of Medicine, Tokyo, Japan
| | - Yasuo Ono
- Department of Microbiology and Immunology, Teikyo University School of Medicine, Tokyo, Japan
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Pseudomonas aeruginosa high-level resistance to polymyxins and other antimicrobial peptides requires cprA, a gene that is disrupted in the PAO1 strain. Antimicrob Agents Chemother 2015; 59:5377-87. [PMID: 26100714 DOI: 10.1128/aac.00904-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 06/11/2015] [Indexed: 11/20/2022] Open
Abstract
The arn locus, found in many Gram-negative bacterial pathogens, mediates resistance to polymyxins and other cationic antimicrobial peptides through 4-amino-l-arabinose modification of the lipid A moiety of lipopolysaccharide. In Pseudomonas aeruginosa, several two-component regulatory systems (TCSs) control the arn locus, which is necessary but not sufficient for these resistance phenotypes. A previous transposon mutagenesis screen to identify additional polymyxin resistance genes that these systems regulate implicated an open reading frame designated PA1559 in the genome of the P. aeruginosa PAO1 strain. Resequencing of this chromosomal region and bioinformatics analysis for a variety of P. aeruginosa strains revealed that in the sequenced PAO1 strain, a guanine deletion at the end of PA1559 results in a frameshift and truncation of a full-length open reading frame that also encompasses PA1560 in non-PAO1 strains, such as P. aeruginosa PAK. Deletion analysis in the PAK strain showed that this full-length open reading frame, designated cprA, is necessary for polymyxin resistance conferred by activating mutations in the PhoPQ, PmrAB, and CprRS TCSs. The cprA gene was also required for PmrAB-mediated resistance to other cationic antimicrobial peptides in the PAK strain. Repair of the mutated cprA allele in the PAO1 strain restored polymyxin resistance conferred by an activating TCS mutation. The deletion of cprA did not affect the arn-mediated lipid A modification, indicating that the CprA protein is necessary for a different aspect of polymyxin resistance. This protein has a domain structure with a strong similarity to the extended short-chain dehydrogenase/reductase family that comprises isomerases, lyases, and oxidoreductases. These results suggest a new avenue through which to pursue targeted inhibition of polymyxin resistance.
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25
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Poole K. Stress responses as determinants of antimicrobial resistance in Pseudomonas aeruginosa: multidrug efflux and more. Can J Microbiol 2015; 60:783-91. [PMID: 25388098 DOI: 10.1139/cjm-2014-0666] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pseudomonas aeruginosa is a notoriously antimicrobial-resistant organism that is increasingly refractory to antimicrobial chemotherapy. While the usual array of acquired resistance mechanisms contribute to resistance development in this organism a multitude of endogenous genes also play a role. These include a variety of multidrug efflux loci that contribute to both intrinsic and acquired antimicrobial resistance. Despite their roles in resistance, however, it is clear that these efflux systems function in more than just antimicrobial efflux. Indeed, recent data indicate that they are recruited in response to environmental stress and, therefore, function as components of the organism's stress responses. In fact, a number of endogenous resistance-promoting genes are linked to environmental stress, functioning as part of known stress responses or recruited in response to a variety of environmental stress stimuli. Stress responses are, thus, important determinants of antimicrobial resistance in P. aeruginosa. As such, they represent possible therapeutic targets in countering antimicrobial resistance in this organism.
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Affiliation(s)
- Keith Poole
- Department of Biomedical and Molecular Sciences, Botterell Hall, Queen's University, Kingston, ON K7L 3N6, Canada
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26
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Olaitan AO, Morand S, Rolain JM. Mechanisms of polymyxin resistance: acquired and intrinsic resistance in bacteria. Front Microbiol 2014; 5:643. [PMID: 25505462 PMCID: PMC4244539 DOI: 10.3389/fmicb.2014.00643] [Citation(s) in RCA: 927] [Impact Index Per Article: 92.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/07/2014] [Indexed: 01/06/2023] Open
Abstract
Polymyxins are polycationic antimicrobial peptides that are currently the last-resort antibiotics for the treatment of multidrug-resistant, Gram-negative bacterial infections. The reintroduction of polymyxins for antimicrobial therapy has been followed by an increase in reports of resistance among Gram-negative bacteria. Some bacteria, such as Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii, develop resistance to polymyxins in a process referred to as acquired resistance, whereas other bacteria, such as Proteus spp., Serratia spp., and Burkholderia spp., are naturally resistant to these drugs. Reports of polymyxin resistance in clinical isolates have recently increased, including acquired and intrinsically resistant pathogens. This increase is considered a serious issue, prompting concern due to the low number of currently available effective antibiotics. This review summarizes current knowledge concerning the different strategies bacteria employ to resist the activities of polymyxins. Gram-negative bacteria employ several strategies to protect themselves from polymyxin antibiotics (polymyxin B and colistin), including a variety of lipopolysaccharide (LPS) modifications, such as modifications of lipid A with phosphoethanolamine and 4-amino-4-deoxy-L-arabinose, in addition to the use of efflux pumps, the formation of capsules and overexpression of the outer membrane protein OprH, which are all effectively regulated at the molecular level. The increased understanding of these mechanisms is extremely vital and timely to facilitate studies of antimicrobial peptides and find new potential drugs targeting clinically relevant Gram-negative bacteria.
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Affiliation(s)
- Abiola O Olaitan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université Marseille, France
| | - Serge Morand
- Institut des Sciences de l'Evolution, CNRS-IRD-UM2, CC065, Université Montpellier 2 Montpellier, France
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université Marseille, France
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Lee JY, Ko KS. Mutations and expression of PmrAB and PhoPQ related with colistin resistance in Pseudomonas aeruginosa clinical isolates. Diagn Microbiol Infect Dis 2013; 78:271-6. [PMID: 24412662 DOI: 10.1016/j.diagmicrobio.2013.11.027] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 11/18/2013] [Accepted: 11/26/2013] [Indexed: 11/25/2022]
Abstract
To comprehend the resistance of colistin resistance, we investigated the relationships between amino acid alterations and expression of PmrAB and PhoPQ and colistin resistance in 16 colistin-nonsusceptible clinical Pseudomonas aeruginosa isolates. In addition, we obtained induced colistin-resistant mutants and their colistin-susceptible revertants. Expression levels of the pmrA, phoP, parR, cprR, and pmrH genes were determined for them. Nine amino acid substitutions unique to 10 colistin-nonsusceptible P. aeruginosa (CNPA) isolates were identified: 7 in PmrB and 1 each in PmrA and PhoQ. However, 6 CNPA isolates did not show amino acid substitutions compared with colistin-susceptible P. aeruginosa isolates. Among 16 CNPA isolates, 7 and 8 isolates displayed activated expression of pmrA and phoP, respectively. Activated expression of pmrA and/or phoP was identified in 13 isolates of CNPA isolates, but some had no noticeable PmrAB and PhoPQ amino acid substitutions. In addition, in vitro selected colistin-resistant mutants (P5R and P155R) showed higher expression level in pmrA, phoP, and pmrH than their parent strains (P5 and P155) and colistin-susceptible, revertant strains (P5R-rev and P155R-rev). However, expression of the parR and cprR genes was not consistent. Our data may indicate that amino acid substitutions of PmrAB or PhoPQ do not have an immediate connection with decreased susceptibility of colistin in P. aeruginosa isolates, although activated expression of pmrAB and/or phoPQ resulting in overexpression of pmrH may be required for colistin resistance. Expression of pmrAB or phoPQ related with colistin nonsusceptibility may not explained by a single mechanism, which may suggest that colistin resistance appears easily by diverse pathways in clinical settings as well as in laboratory.
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Affiliation(s)
- Ji-Young Lee
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, South Korea; Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, South Korea.
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Rapid determination of colistin resistance in clinical strains of Acinetobacter baumannii by use of the micromax assay. J Clin Microbiol 2013; 51:3675-82. [PMID: 23985913 DOI: 10.1128/jcm.01787-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Colistin is an old antibiotic which has been used as a therapeutic option for carbapenem- and multidrug-resistant Gram-negative bacteria, like Acinetobacter baumannii. This pathogen produces life-threatening infections, mainly in patients admitted to intensive care units. Rapid detection of resistance to colistin may improve patient outcomes and prevent the spread of resistance. For this purpose, Micromax technology was evaluated in four isogenic A. baumannii strains with known mechanisms of resistance to colistin and in 66 isolates (50 susceptible and 16 resistant). Two parameters were determined, DNA fragmentation and cell wall damage. To assess DNA fragmentation, cells trapped in a microgel were incubated with a lysing solution to remove the cell wall, and the released nucleoids were visualized under fluorescence microscopy. Fragmented DNA was observed as spots that diffuse from the nucleoid. To assess cell wall integrity, cells were incubated with a lysis solution which removes only weakened cell walls, resulting in nucleoid release exclusively in affected cells. A dose-response relationship was demonstrated between colistin concentrations and the percentages of bacteria with DNA fragmentation and cell wall damage, antibiotic effects that were delayed and less frequent in resistant strains. Receiver operating characteristic (ROC) curves demonstrated that both DNA fragmentation and cell wall damage were excellent parameters for identifying resistant strains. Obtaining ≤11% of bacteria with cell wall damage after incubation with 0.5 μg/ml colistin identified resistant strains of A. baumannii with 100% sensitivity and 96% specificity. Results were obtained in 3 h 30 min. This is a simple, rapid, and accurate assay for detecting colistin resistance in A. baumannii, with strong potential value in critical clinical situations.
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29
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Chen HD, Groisman EA. The biology of the PmrA/PmrB two-component system: the major regulator of lipopolysaccharide modifications. Annu Rev Microbiol 2013; 67:83-112. [PMID: 23799815 DOI: 10.1146/annurev-micro-092412-155751] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ability of gram-negative bacteria to resist killing by antimicrobial agents and to avoid detection by host immune systems often entails modification to the lipopolysaccharide (LPS) in their outer membrane. In this review, we examine the biology of the PmrA/PmrB two-component system, the major regulator of LPS modifications in the enteric pathogen Salmonella enterica. We examine the signals that activate the sensor PmrB and the targets controlled by the transcriptional regulator PmrA. We discuss the PmrA/PmrB-dependent chemical decorations of the LPS and their role in resistance to antibacterial agents. We analyze the feedback mechanisms that modulate the activity and thus output of the PmrA/PmrB system, dictating when, where, and to what extent bacteria modify their LPS. Finally, we explore the qualitative and quantitative differences in gene expression outputs resulting from the distinct PmrA/PmrB circuit architectures in closely related bacteria, which may account for their differential survival in various ecological niches.
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Polymyxin resistance of Pseudomonas aeruginosa phoQ mutants is dependent on additional two-component regulatory systems. Antimicrob Agents Chemother 2013; 57:2204-15. [PMID: 23459479 DOI: 10.1128/aac.02353-12] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Pseudomonas aeruginosa can develop resistance to polymyxin as a consequence of mutations in the PhoPQ regulatory system, mediated by covalent lipid A modification. Transposon mutagenesis of a polymyxin-resistant phoQ mutant defined 41 novel loci required for resistance, including two regulatory systems, ColRS and CprRS. Deletion of the colRS genes, individually or in tandem, abrogated the polymyxin resistance of a ΔphoQ mutant, as did individual or tandem deletion of cprRS. Individual deletion of colR or colS in a ΔphoQ mutant also suppressed 4-amino-L-arabinose addition to lipid A, consistent with the known role of this modification in polymyxin resistance. Surprisingly, tandem deletion of colRS or cprRS in the ΔphoQ mutant or individual deletion of cprR or cprS failed to suppress 4-amino-L-arabinose addition to lipid A, indicating that this modification alone is not sufficient for PhoPQ-mediated polymyxin resistance in P. aeruginosa. Episomal expression of colRS or cprRS in tandem or of cprR individually complemented the Pm resistance phenotype in the ΔphoQ mutant, while episomal expression of colR, colS, or cprS individually did not. Highly polymyxin-resistant phoQ mutants of P. aeruginosa isolated from polymyxin-treated cystic fibrosis patients harbored mutant alleles of colRS and cprS; when expressed in a ΔphoQ background, these mutant alleles enhanced polymyxin resistance. These results define ColRS and CprRS as two-component systems regulating polymyxin resistance in P. aeruginosa, indicate that addition of 4-amino-L-arabinose to lipid A is not the only PhoPQ-regulated biochemical mechanism required for resistance, and demonstrate that colRS and cprS mutations can contribute to high-level clinical resistance.
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Poole K. Bacterial stress responses as determinants of antimicrobial resistance. J Antimicrob Chemother 2012; 67:2069-89. [PMID: 22618862 DOI: 10.1093/jac/dks196] [Citation(s) in RCA: 305] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacteria encounter a myriad of stresses in their natural environments, including, for pathogens, their hosts. These stresses elicit a variety of specific and highly regulated adaptive responses that not only protect bacteria from the offending stress, but also manifest changes in the cell that impact innate antimicrobial susceptibility. Thus exposure to nutrient starvation/limitation (nutrient stress), reactive oxygen and nitrogen species (oxidative/nitrosative stress), membrane damage (envelope stress), elevated temperature (heat stress) and ribosome disruption (ribosomal stress) all impact bacterial susceptibility to a variety of antimicrobials through their initiation of stress responses that positively impact recruitment of resistance determinants or promote physiological changes that compromise antimicrobial activity. As de facto determinants of antimicrobial, even multidrug, resistance, stress responses may be worthy of consideration as therapeutic targets.
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Affiliation(s)
- Keith Poole
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6.
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Repeated isolation of Pseudomonas aeruginosa isolates resistant to both polymyxins and carbapenems from 1 patient. Diagn Microbiol Infect Dis 2012; 72:267-71. [DOI: 10.1016/j.diagmicrobio.2011.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 11/17/2011] [Accepted: 11/20/2011] [Indexed: 01/01/2023]
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Moskowitz SM, Brannon MK, Dasgupta N, Pier M, Sgambati N, Miller AK, Selgrade SE, Miller SI, Denton M, Conway SP, Johansen HK, Høiby N. PmrB mutations promote polymyxin resistance of Pseudomonas aeruginosa isolated from colistin-treated cystic fibrosis patients. Antimicrob Agents Chemother 2012; 56:1019-30. [PMID: 22106224 PMCID: PMC3264203 DOI: 10.1128/aac.05829-11] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 11/16/2011] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa can develop resistance to polymyxin and other cationic antimicrobial peptides. Previous work has shown that mutations in the PmrAB and PhoPQ regulatory systems can confer low to moderate levels of colistin (polymyxin E) resistance in laboratory strains and clinical isolates of this organism (MICs of 8 to 64 mg/liter). To explore the role of PmrAB in high-level clinical polymyxin resistance, P. aeruginosa isolates from chronically colistin-treated cystic fibrosis patients, most with colistin MICs of >512 mg/liter, were analyzed. These cystic fibrosis isolates contained probable gain-of-function pmrB alleles that conferred polymyxin resistance to strains with a wild-type or pmrAB deletion background. Double mutant pmrB alleles that contained mutations in both the periplasmic and dimerization-phosphotransferase domains markedly augmented polymyxin resistance. Expression of mutant pmrB alleles induced transcription from the promoter of the arnB operon and stimulated addition of 4-amino-l-arabinose to lipid A, consistent with the known role of this lipid A modification in polymyxin resistance. For some highly polymyxin-resistant clinical isolates, repeated passage without antibiotic selection pressure resulted in loss of resistance, suggesting that secondary suppressors occur at a relatively high frequency and account for the instability of this phenotype. These results indicate that pmrB gain-of-function mutations can contribute to high-level polymyxin resistance in clinical strains of P. aeruginosa.
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Affiliation(s)
- Samuel M Moskowitz
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA.
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Owusu-Anim D, Kwon DH. Differential Role of Two-Component Regulatory Systems ( phoPQ and pmrAB) in Polymyxin B Susceptibility of Pseudomonas aeruginosa.. ACTA ACUST UNITED AC 2012; 2. [PMID: 24349887 DOI: 10.4236/aim.2012.21005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Polymyxins are often considered as a last resort to treat multidrug resistant P. aeruginosa but polymyxin resistance has been increasingly reported worldwide in clinical isolates. Polymyxin resistance in P. aeruginosa is known to be associated with alterations in either PhoQ or PmrB. In this study, mutant strains of P. aeruginosa carrying amino acid substitution, a single and/or dual inactivation of PhoQ and PmrB were constructed to further understand the roles of PhoQ and PmrB in polymyxin susceptibility. Polymyxin B resistance was caused by both inactivation and/or amino acid substitutions in PhoQ but by only amino acid substitutions of PmrB. Alterations of both PhoQ and PmrB resulted in higher levels of polymyxin B resistance than alteration of either PhoQ or PmrB alone. These results were confirmed by time-killing assays suggesting that high-level polymyxin resistance in P. aeruginosa is caused by alterations of both PhoQ and PmrB.
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Affiliation(s)
| | - Dong H Kwon
- Department of Biology, Long Island University, New York, USA ; Department of Medicine of Michael E DeBakey VA Medical Center, Baylor College of Medicine, Houston, USA
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Lee JY, Ko KS. Antimicrobial Resistance and Clones ofAcinetobacterSpecies andPseudomonas aeruginosa. ACTA ACUST UNITED AC 2012. [DOI: 10.4167/jbv.2012.42.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Ji-Young Lee
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
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Abstract
Pseudomonas aeruginosa is intrinsically resistant to a variety of antimicrobials and can develop resistance during anti-pseudomonal chemotherapy both of which compromise treatment of infections caused by this organism. Resistance to multiple classes of antimicrobials (multidrug resistance) in particular is increasingly common in P. aeruginosa, with a number of reports of pan-resistant isolates treatable with a single agent, colistin. Acquired resistance in this organism is multifactorial and attributable to chromosomal mutations and the acquisition of resistance genes via horizontal gene transfer. Mutational changes impacting resistance include upregulation of multidrug efflux systems to promote antimicrobial expulsion, derepression of ampC, AmpC alterations that expand the enzyme's substrate specificity (i.e., extended-spectrum AmpC), alterations to outer membrane permeability to limit antimicrobial entry and alterations to antimicrobial targets. Acquired mechanisms contributing to resistance in P. aeruginosa include β-lactamases, notably the extended-spectrum β-lactamases and the carbapenemases that hydrolyze most β-lactams, aminoglycoside-modifying enzymes, and 16S rRNA methylases that provide high-level pan-aminoglycoside resistance. The organism's propensity to grow in vivo as antimicrobial-tolerant biofilms and the occurrence of hypermutator strains that yield antimicrobial resistant mutants at higher frequency also compromise anti-pseudomonal chemotherapy. With limited therapeutic options and increasing resistance will the untreatable P. aeruginosa infection soon be upon us?
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Affiliation(s)
- Keith Poole
- Department of Microbiology and Immunology, Queen's University Kingston, ON, Canada
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Phosphoethanolamine modification of lipid A in colistin-resistant variants of Acinetobacter baumannii mediated by the pmrAB two-component regulatory system. Antimicrob Agents Chemother 2011; 55:3370-9. [PMID: 21576434 DOI: 10.1128/aac.00079-11] [Citation(s) in RCA: 285] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Colistin resistance is rare in Acinetobacter baumannii, and little is known about its mechanism. We investigated the role of PmrCAB in this trait, using (i) resistant and susceptible clinical strains, (ii) laboratory-selected mutants of the type strain ATCC 19606 and of the clinical isolate ABRIM, and (iii) a susceptible/resistant pair of isogenic clinical isolates, Ab15/133 and Ab15/132, isolated from the same patient. pmrAB sequences in all the colistin-susceptible isolates were identical to reference sequences, whereas resistant clinical isolates harbored one or two amino acid replacements variously located in PmrB. Single substitutions in PmrB were also found in resistant mutants of strains ATCC 19606 and ABRIM and in the resistant clinical isolate Ab15/132. No mutations in PmrA or PmrC were found. Reverse transcriptase (RT)-PCR identified increased expression of pmrA (4- to 13-fold), pmrB (2- to 7-fold), and pmrC (1- to 3-fold) in resistant versus susceptible organisms. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry showed the addition of phosphoethanolamine to the hepta-acylated form of lipid A in the resistant variants and in strain ATCC 19606 grown under low-Mg(2+) induction conditions. pmrB gene knockout mutants of the colistin-resistant ATCC 19606 derivative showed >100-fold increased susceptibility to colistin and 5-fold decreased expression of pmrC; they also lacked the addition of phosphoethanolamine to lipid A. We conclude that the development of a moderate level of colistin resistance in A. baumannii requires distinct genetic events, including (i) at least one point mutation in pmrB, (ii) upregulation of pmrAB, and (iii) expression of pmrC, which lead to addition of phosphoethanolamine to lipid A.
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Park YK, Choi JY, Shin D, Ko KS. Correlation between overexpression and amino acid substitution of the PmrAB locus and colistin resistance in Acinetobacter baumannii. Int J Antimicrob Agents 2011; 37:525-30. [PMID: 21497062 DOI: 10.1016/j.ijantimicag.2011.02.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 02/07/2011] [Accepted: 02/07/2011] [Indexed: 11/17/2022]
Abstract
Relationships between the PmrAB two-component system and colistin resistance were investigated in Acinetobacter baumannii. The sequences of pmrA, pmrB and pmrC in 26 colistin-susceptible (ColS) and 7 colistin-resistant (ColR) A. baumannii isolates were determined. In addition, 30 ColR mutants (colistin minimum inhibitory concentration >64 mg/L) were selected in vitro from 10 ColS strains and the pmrA, pmrB and pmrC sequences of the in-vitro-selected ColR mutants were also determined. Expression of pmrA and pmrB was compared between the ColR mutants and their parent ColS strains using a quantitative real-time polymerase chain reaction method. Elevated expression of pmrA and pmrB genes was evident both in wild-type and in in-vitro-selected ColR strains. However, no amino acid differences in the pmrA, pmrB and pmrC genes were found between wild-type ColR and ColS isolates. Although six kinds of amino acid alterations in pmrB were identified in in-vitro-selected ColR mutants, no changes were found in some of the mutants. These findings indicate that increased expression of the PmrAB system is essential for colistin resistance in A. baumannii but that amino acid alterations might be only partially responsible for resistance.
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Affiliation(s)
- Young Kyoung Park
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, South Korea
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Poole K. Pseudomonas aeruginosa: resistance to the max. Front Microbiol 2011; 2:65. [PMID: 21747788 PMCID: PMC3128976 DOI: 10.3389/fmicb.2011.00065] [Citation(s) in RCA: 561] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 03/24/2011] [Indexed: 01/04/2023] Open
Abstract
Pseudomonas aeruginosa is intrinsically resistant to a variety of antimicrobials and can develop resistance during anti-pseudomonal chemotherapy both of which compromise treatment of infections caused by this organism. Resistance to multiple classes of antimicrobials (multidrug resistance) in particular is increasingly common in P. aeruginosa, with a number of reports of pan-resistant isolates treatable with a single agent, colistin. Acquired resistance in this organism is multifactorial and attributable to chromosomal mutations and the acquisition of resistance genes via horizontal gene transfer. Mutational changes impacting resistance include upregulation of multidrug efflux systems to promote antimicrobial expulsion, derepression of ampC, AmpC alterations that expand the enzyme's substrate specificity (i.e., extended-spectrum AmpC), alterations to outer membrane permeability to limit antimicrobial entry and alterations to antimicrobial targets. Acquired mechanisms contributing to resistance in P. aeruginosa include β-lactamases, notably the extended-spectrum β-lactamases and the carbapenemases that hydrolyze most β-lactams, aminoglycoside-modifying enzymes, and 16S rRNA methylases that provide high-level pan-aminoglycoside resistance. The organism's propensity to grow in vivo as antimicrobial-tolerant biofilms and the occurrence of hypermutator strains that yield antimicrobial resistant mutants at higher frequency also compromise anti-pseudomonal chemotherapy. With limited therapeutic options and increasing resistance will the untreatable P. aeruginosa infection soon be upon us?
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Affiliation(s)
- Keith Poole
- Department of Microbiology and Immunology, Queen's University Kingston, ON, Canada
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40
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Lee JY, Song JH, Ko KS. Identification of nonclonal Pseudomonas aeruginosa isolates with reduced colistin susceptibility in Korea. Microb Drug Resist 2011; 17:299-304. [PMID: 21381965 DOI: 10.1089/mdr.2010.0145] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The in vitro activity of colistin was evaluated against 215 nonduplicated Pseudomonas aeruginosa isolates, including 53 multidrug-resistant isolates, which were collected between 2006 and 2007 from nine tertiary care hospitals in Korea. Colistin-nonsusceptible P. aeruginosa (CNPA) isolates were genotyped using multilocus sequence typing. Sixteen (7.4%) CNPA isolates (minimum inhibitory concentration [MIC], >2 mg/l) were identified, including three resistant isolates. All but one of the MDR P. aeruginosa isolates was susceptible to colistin. Multilocus sequence typing analysis identified 12 sequence types (STs) among 16 CNPA isolates, indicating that colistin nonsusceptibility might arise independently. However, ST244 and ST292, which may be international clones, were found in multiple CNPA isolates. Our data indicate an increase of P. aeruginosa isolates with reduced colistin susceptibility, suggesting the need for continuous surveillance of P. aeruginosa.
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Affiliation(s)
- Ji-Young Lee
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, South Korea
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The PmrAB system in Erwinia amylovora renders the pathogen more susceptible to polymyxin B and more resistant to excess iron. Res Microbiol 2010; 161:153-7. [DOI: 10.1016/j.resmic.2009.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 12/07/2009] [Accepted: 12/07/2009] [Indexed: 11/23/2022]
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