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Chebotar I, Savinova T, Bocharova J, Korostin D, Evseev P, Mayanskiy N. Genetic Alternatives for Experimental Adaptation to Colistin in Three Pseudomonas aeruginosa Lineages. Antibiotics (Basel) 2024; 13:452. [PMID: 38786180 PMCID: PMC11117860 DOI: 10.3390/antibiotics13050452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Pseudomonas aeruginosa is characterized by a high adaptive potential, developing resistance in response to antimicrobial pressure. We employed a spatiotemporal evolution model to disclose the pathways of adaptation to colistin, a last-resort polymyxin antimicrobial, among three unrelated P. aeruginosa lineages. The P. aeruginosa ATCC-27833 reference strain (Pa_ATCC), an environmental P. aeruginosa isolate (Pa_Environment), and a clinical isolate with multiple drug resistance (Pa_MDR) were grown over an increasing 5-step colistin concentration gradient from 0 to 400 mg/L. Pa_Environment demonstrated the highest growth pace, achieving the 400 mg/L band in 15 days, whereas it took 37 and 60 days for Pa_MDR and Pa_ATCC, respectively. To identify the genome changes that occurred during adaptation to colistin, the isolates selected during the growth of the bacteria (n = 185) were subjected to whole genome sequencing. In total, 17 mutation variants in eight lipopolysaccharide-synthesis-associated genes were detected. phoQ and lpxL/PA0011 were affected in all three lineages, whereas changes in pmrB were found in Pa_Environment and Pa_MDR but not in Pa_ATCC. In addition, mutations were detected in 34 general metabolism genes, and each lineage developed mutations in a unique set of such genes. Thus, the three examined distinct P. aeruginosa strains demonstrated different capabilities and genetic pathways of colistin adaptation.
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Affiliation(s)
- Igor Chebotar
- Laboratory of Molecular Microbiology, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia (J.B.); (D.K.); (N.M.)
| | | | | | | | - Peter Evseev
- Laboratory of Molecular Microbiology, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia (J.B.); (D.K.); (N.M.)
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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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Vaňková E, Julák J, Machková A, Obrová K, Klančnik A, Smole Možina S, Scholtz V. Overcoming antibiotic resistance: non-thermal plasma and antibiotics combination inhibits important pathogens. Pathog Dis 2024; 82:ftae007. [PMID: 38730561 PMCID: PMC11094553 DOI: 10.1093/femspd/ftae007] [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: 12/17/2023] [Revised: 03/27/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
Antibiotic resistance (ATBR) is increasing every year as the overuse of antibiotics (ATBs) and the lack of newly emerging antimicrobial agents lead to an efficient pathogen escape from ATBs action. This trend is alarming and the World Health Organization warned in 2021 that ATBR could become the leading cause of death worldwide by 2050. The development of novel ATBs is not fast enough considering the situation, and alternative strategies are therefore urgently required. One such alternative may be the use of non-thermal plasma (NTP), a well-established antimicrobial agent actively used in a growing number of medical fields. Despite its efficiency, NTP alone is not always sufficient to completely eliminate pathogens. However, NTP combined with ATBs is more potent and evidence has been emerging over the last few years proving this is a robust and highly effective strategy to fight resistant pathogens. This minireview summarizes experimental research addressing the potential of the NTP-ATBs combination, particularly for inhibiting planktonic and biofilm growth and treating infections in mouse models caused by methicillin-resistant Staphylococcus aureus or Pseudomonas aeruginosa. The published studies highlight this combination as a promising solution to emerging ATBR, and further research is therefore highly desirable.
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Affiliation(s)
- Eva Vaňková
- Department of Physics and Measurements, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
- Department of Biotechnology, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
| | - Jaroslav Julák
- Department of Physics and Measurements, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University in Prague, 160 00 Prague, Czech Republic
| | - Anna Machková
- Department of Physics and Measurements, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
| | - Klára Obrová
- Department of Physics and Measurements, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Sonja Smole Možina
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Vladimír Scholtz
- Department of Physics and Measurements, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
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Chagas MDS, Trindade dos Santos M, Argollo de Menezes M, da Silva FAB. Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851. Front Microbiol 2023; 14:1274740. [PMID: 38152377 PMCID: PMC10752298 DOI: 10.3389/fmicb.2023.1274740] [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: 08/08/2023] [Accepted: 10/31/2023] [Indexed: 12/29/2023] Open
Abstract
Introduction Pseudomonas aeruginosa infections are one of the leading causes of death in immunocompromised patients with cystic fibrosis, diabetes, and lung diseases such as pneumonia and bronchiectasis. Furthermore, P. aeruginosa is one of the main multidrug-resistant bacteria responsible for nosocomial infections worldwide, including the multidrug-resistant CCBH4851 strain isolated in Brazil. Methods One way to analyze their dynamic cellular behavior is through computational modeling of the gene regulatory network, which represents interactions between regulatory genes and their targets. For this purpose, Boolean models are important predictive tools to analyze these interactions. They are one of the most commonly used methods for studying complex dynamic behavior in biological systems. Results and discussion Therefore, this research consists of building a Boolean model of the gene regulatory network of P. aeruginosa CCBH4851 using data from RNA-seq experiments. Next, the basins of attraction are estimated, as these regions and the transitions between them can help identify the attractors, representing long-term behavior in the Boolean model. The essential genes of the basins were associated with the phenotypes of the bacteria for two conditions: biofilm formation and polymyxin B treatment. Overall, the Boolean model and the analysis method proposed in this work can identify promising control actions and indicate potential therapeutic targets, which can help pinpoint new drugs and intervention strategies.
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Peng H, Wu H, Gu W, Lu Y, Qin H, You Y, Zhou D, Wang D, Sun L, Zhou C, Zheng Y. Exploring the Application Potential of Aquaculture Sewage Treatment of Pseudomonas chengduensis Strain WD211 Based on Its Complete Genome. Genes (Basel) 2023; 14:2107. [PMID: 38136929 PMCID: PMC10743257 DOI: 10.3390/genes14122107] [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: 10/08/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Pseudomonas chengduensis is a new species of Pseudomonas discovered in 2014, and currently, there is a scarcity of research on this bacterium. The P. chengduensis strain WD211 was isolated from a fish pond. This study investigated the purification capability and environmental adaptability of strain WD211 in wastewater and described the basic features and functional genes of its complete genome. According to the results, the sewage treated with strain WD211 showed a decrease in concentration of 18.12% in total nitrogen, 89.39% in NH4+, 62.16% in NO3-, 79.97% in total phosphorus, and 71.41% in COD after 24 h. Strain WD211 is able to survive in a pH range of 6-11. It shows resistance to 7% sodium chloride and different types of antibiotics. Genomic analysis showed that strain WD211 may remove nitrogen and phosphorus through the metabolic pathway of nitrogen assimilation and phosphorus accumulation, and that it can promote organic decomposition through oxygenase. Strain WD211 possesses genes for producing betaine, trehalose, and sodium ion transport, which provide it with salt tolerance. It also has genes for antibiotic efflux and multiple oxidases, which give it antibiotic resistance. This study contributes to the understanding of the sewage treatment ability and potential applications of P. chengduensis.
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Affiliation(s)
- Huanlong Peng
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Hangtao Wu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Wenjie Gu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Yusheng Lu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Hongjie Qin
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yi You
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Donglai Zhou
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510610, China
| | - Dan Wang
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Lili Sun
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Changmin Zhou
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Yanling Zheng
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
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Zhao NL, Zhu ZQ, Feng HZ, Song YJ, Huang Q, Mou XY, Nong C, He YX, Bao R. Host-derived peptide signals regulate Pseudomonas aeruginosa virulence stress via the ParRS and CprRS two-component systems. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132512. [PMID: 37703740 DOI: 10.1016/j.jhazmat.2023.132512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023]
Abstract
Pseudomonas aeruginosa, a versatile bacterium, has dual significance because of its beneficial roles in environmental soil processes and its detrimental effects as a nosocomial pathogen that causes clinical infections. Understanding adaptability to environmental stress is essential. This investigation delves into the complex interplay of two-component system (TCS), specifically ParRS and CprRS, as P. aeruginosa interprets host signals and navigates stress challenges. In this study, through phenotypic and proteomic analyses, the nuanced contributions of ParRS and CprRS to the pathogenesis and resilience mechanisms were elucidated. Furthermore, the indispensable roles of the ParS and CprS extracellular sensor domains in orchestrating signal perception remain unknown. Structural revelations imply a remarkable convergence of TCS sensors in interacting with host peptides, suggesting evolutionary strategies for bacterial adaptation. This pioneering work not only established links between cationic antimicrobial peptide (CAMP) resistance-associated TCSs and virulence modulation in nosocomial bacteria, but also transcended conventional boundaries. These implications extend beyond clinical resistance, permeating into the realm of soil revitalization and environmental guardianship. As it unveils P. aeruginosa intricacies, this study assumes a mantle of guiding strategies to mitigate clinical hazards, harness environmental advantages, and propel sustainable solutions forward.
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Affiliation(s)
- Ning-Lin Zhao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zi-Qi Zhu
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Han-Zhong Feng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ying-Jie Song
- College of Life Science, Sichuan Normal University, Chengdu 610101, China
| | - Qin Huang
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xing-Yu Mou
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Cheng Nong
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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He Y, Wu Q, Cui C, Tian Q, Zhang D, Zhang Y. ChIP-Seq Analysis of SlAREB1 Downstream Regulatory Network during Tomato Ripening. Foods 2023; 12:2357. [PMID: 37372568 DOI: 10.3390/foods12122357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
SlAREB1, a member of the abscisic acid (ABA) response element-binding factors (AREB/ABFs) family, was reported to play a crucial role in the expression of ABA-regulated downstream genes and affect the ripening of tomato fruit. However, the downstream genes of SlAREB1 are still unclear. Chromatin immunoprecipitation (ChIP) is a powerful tool and a standard method for studying the interactions between DNA and proteins at the genome-wide level. In the present study, SlAREB1 was proved to continually increase until the mature green stage and then decrease during the ripening period, and a total of 972 gene peaks were identified downstream of SlAREB1 by ChIP-seq analysis, mainly located in the intergenic and promoter regions. Further gene ontology (GO) annotation analysis revealed that the target sequence of SlAREB1 was the most involved in biological function. Kyoto Encylopaedia of Genes and Genomes (KEGG) pathway analysis showed that the identified genes were mainly involved in the oxidative phosphorylation and photosynthesis pathways, and some of them were associated with tomato phytohormone synthesis, the cell wall, pigment, and the antioxidant characteristic of the fruit as well. Based on these results, an initial model of SlAREB1 regulation on tomato fruit ripening was constructed, which provided a theoretical basis for further exploring the effects of the regulation mechanism of SlAREB1 and ABA on tomato fruit ripening.
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Affiliation(s)
- Yanan He
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Qiong Wu
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Chunxiao Cui
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Qisheng Tian
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Dongdong Zhang
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Yurong Zhang
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
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Liang Y, Li J, Xu Y, He Y, Jiang B, Wu C, Shan B, Shi H, Song G. Genomic variations in polymyxin-resistant Pseudomonas aeruginosa clinical isolates and their effects on polymyxin resistance. Braz J Microbiol 2023; 54:655-664. [PMID: 36930447 PMCID: PMC10234930 DOI: 10.1007/s42770-023-00933-3] [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: 10/30/2022] [Accepted: 02/13/2023] [Indexed: 03/18/2023] Open
Abstract
Infection with P. aeruginosa, one of the most relevant opportunistic pathogens in hospital-acquired infections, can lead to high mortality due to its low antibiotic susceptibility to limited choices of antibiotics. Polymyxin as last-resort antibiotics is used in the treatment of systemic infections caused by multidrug-resistant P. aeruginosa strains, so studying the emergence of polymyxin-resistant was a must. The present study was designed to define genomic differences between paired polymyxin-susceptible and polymyxin-resistant P. aeruginosa strains and established polymyxin resistance mechanisms, and common chromosomal mutations that may confer polymyxin resistance were characterized. A total of 116 CRPA clinical isolates from patients were collected from three tertiary care hospitals in China during 2017-2021. Our study found that polymyxin B resistance represented 3.45% of the isolated carbapenem-resistant P. aeruginosa (CRPA). No polymyxin-resistant isolates were positive for mcr (1-8 and 10) gene and efflux mechanisms. Key genetic variations identified in polymyxin-resistant isolates involved missense mutations in parR, parS, pmrB, pmrA, and phoP. The waaL and PA5005 substitutions related to LPS synthesis were detected in the highest levels of resistant strain (R1). The missense mutations H398R in ParS (4/4), Y345H in PmrB (4/4), and L71R in PmrA (3/4) were the predominant. Results of the PCR further confirmed that mutation of pmrA, pmrB, and phoP individually or simultaneously did affect the expression level of resistant populations and can directly increase the expression of arnBCADTEF operon to contribute to polymyxin resistance. In addition, we reported 3 novel mutations in PA1945 (2129872_A < G, 2130270_A < C, 2130272_T < G) that may confer polymyxin resistance in P. aeruginosa. Our findings enriched the spectrum of chromosomal mutations, highlighted the complexity at the molecular level, and multifaceted interplay mechanisms underlying polymyxin resistance in P. aeruginosa.
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Affiliation(s)
- Yuan Liang
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China
- Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, 650032, China
| | - Jie Li
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China
- Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, 650032, China
| | - Yunmin Xu
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China
- Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, 650032, China
| | - Yuan He
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China
- Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, 650032, China
| | - Bo Jiang
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China
- Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, 650032, China
| | - Chunyan Wu
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China
- Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, 650032, China
| | - Bin Shan
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China
- Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, 650032, China
| | - Hongqiong Shi
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China.
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China.
- Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, 650032, China.
| | - Guibo Song
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China.
- Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China.
- Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, 650032, China.
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Hu M, Zhang Y, Huang X, He M, Zhu J, Zhang Z, Cui Y, He S, Shi X. PhoPQ Regulates Quinolone and Cephalosporin Resistance Formation in Salmonella Enteritidis at the Transcriptional Level. mBio 2023:e0339522. [PMID: 37184399 DOI: 10.1128/mbio.03395-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
The two-component system (TCS) PhoPQ has been demonstrated to be crucial for the formation of resistance to quinolones and cephalosporins in Salmonella Enteritidis (S. Enteritidis). However, the mechanism underlying PhoPQ-mediated antibiotic resistance formation remains poorly understood. Here, it was shown that PhoP transcriptionally regulated an assortment of genes associated with envelope homeostasis, the osmotic stress response, and the redox balance to confer resistance to quinolones and cephalosporins in S. Enteritidis. Specifically, cells lacking the PhoP regulator, under nalidixic acid and ceftazidime stress, bore a severely compromised membrane on the aspects of integrity, fluidity, and permeability, with deficiency to withstand osmolarity stress, an increased accumulation of intracellular reactive oxygen species, and dysregulated redox homeostasis, which are unfavorable for bacterial survival. The phosphorylated PhoP elicited transcriptional alterations of resistance-associated genes, including the outer membrane porin ompF and the aconitate hydratase acnA, by directly binding to their promoters, leading to a limited influx of antibiotics and a well-maintained intracellular metabolism. Importantly, it was demonstrated that the cavity of the PhoQ sensor domain bound to and sensed quinolones/cephalosporins via the crucial surrounding residues, as their mutations abrogated the binding and PhoQ autophosphorylation. This recognition mode promoted signal transduction that activated PhoP, thereby modulating the transcription of downstream genes to accommodate cells to antibiotic stress. These findings have revealed how bacteria employ a specific TCS to sense antibiotics and combat them, suggesting PhoPQ as a potential drug target with which to surmount S. Enteritidis. IMPORTANCE The prevalence of quinolone and cephalosporin-resistant S. Enteritidis is of increasing clinical concern. Thus, it is imperative to identify novel therapeutic targets with which to treat S. Enteritidis-associated infections. The PhoPQ two-component system is conserved across a variety of Gram-negative pathogens, by which bacteria adapt to a range of environmental stimuli. Our earlier work has demonstrated the importance of PhoPQ in the resistance formation in S. Enteritidis to quinolones and cephalosporins. In the current work, we identified a global profile of genes that are regulated by PhoP under antibiotic stresses, with a focus on how PhoP regulated downstream genes, either positively or negatively. Additionally, we established that PhoQ sensed quinolones and cephalosporins in a manner of directly binding to them. These identified genes and pathways that are mediated by PhoPQ represent promising targets for the development of a drug potentiator with which to neutralize antibiotic resistance in S. Enteritidis.
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Affiliation(s)
- Mengjun Hu
- Department of Food Science & Technology, School of Agriculture & Biology, and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yuyan Zhang
- Department of Food Science & Technology, School of Agriculture & Biology, and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaozhen Huang
- Department of Food Science & Technology, School of Agriculture & Biology, and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Mu He
- Department of Food Science & Technology, School of Agriculture & Biology, and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Jinyu Zhu
- Department of Food Science & Technology, School of Agriculture & Biology, and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Zengfeng Zhang
- Department of Food Science & Technology, School of Agriculture & Biology, and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Cui
- Department of Food Science & Technology, School of Agriculture & Biology, and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Shoukui He
- Department of Food Science & Technology, School of Agriculture & Biology, and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xianming Shi
- Department of Food Science & Technology, School of Agriculture & Biology, and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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10
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Han X, Cui AL, Yang HX, Wu L, Wei R, Liu Q, Li ZR, Hu HY. Polymyxin-based fluorescent probes to combat Gram-negative antimicrobial resistance. Talanta 2023; 260:124576. [PMID: 37148689 DOI: 10.1016/j.talanta.2023.124576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
Reliable diagnostic approaches especially those targeting critical Gram-negative bacteria are urgently needed for the prevention of antimicrobial resistance. Polymyxin B (PMB) which specifically targets the outer membrane of Gram-negative bacteria is the last-line antibiotic against life-threatening multidrug-resistant Gram-negative bacteria. However, increasing number of studies have reported the spread of PMB-resistant strains. With the aim to specifically detect Gram-negative bacteria and potentially reduce the irrational use of antibiotics, we herein rationally designed two Gram-negative bacteria specific fluorescent probes based on our previous activity-toxicity optimization of PMB. The in vitro probe PMS-Dns showed fast and selective labeling of Gram-negative pathogens in complex biological cultures. Subsequently, we constructed the caged in vivo fluorescent probe PMS-Cy-NO2 by conjugating bacterial nitroreductase (NTR)-activatable positive charged hydrophobic near-infrared (NIR) fluorophore with polymyxin scaffold. Significantly, PMS-Cy-NO2 exhibited excellent Gram-negative bacterial detection capability with the differentiation between Gram-positive and Gram-negative in a mouse skin infection model.
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Affiliation(s)
- Xiaowan Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - A-Long Cui
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - He-Xian Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Lingling Wu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Rao Wei
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Qian Liu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Zhuo-Rong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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11
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Special Issue: “Antimicrobial Resistance in Pseudomonas aeruginosa”. Microorganisms 2023; 11:microorganisms11030744. [PMID: 36985317 PMCID: PMC10056382 DOI: 10.3390/microorganisms11030744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023] Open
Abstract
Pseudomonas aeruginosa is one of the most prevalent pathogens causing nosocomial infections, mainly in patients presenting with basal pathologies or those who are immunocompromised [...]
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12
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Proteomic Profiling Reveals Distinct Bacterial Extracellular Vesicle Subpopulations with Possibly Unique Functionality. Appl Environ Microbiol 2023; 89:e0168622. [PMID: 36533919 PMCID: PMC9888257 DOI: 10.1128/aem.01686-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial outer membrane vesicles (OMVs) are 20- to 200-nm secreted packages of lipids, small molecules, and proteins that contribute to diverse bacterial processes. In plant systems, OMVs from pathogenic and beneficial strains elicit plant immune responses that inhibit seedling growth and protect against future pathogen challenge. Previous studies of OMV-plant interactions suggest functionally important differences in the protein composition of Pseudomonas syringae and Pseudomonas fluorescens OMVs, and that their composition and activity differ as a result of medium culture conditions. Here, we show that plant apoplast-mimicking minimal medium conditions impact OMV protein content dramatically in P. syringae but not in P. fluorescens relative to complete medium conditions. Comparative, 2-way analysis of the four conditions reveals subsets of proteins that may contribute to OMV-mediated bacterial virulence and plant immune activation as well as those involved in bacterial stress tolerance or adaptation to a beneficial relationship with plants. Additional localization enrichment analysis of these subsets suggests the presence of outer-inner membrane vesicles (OIMVs). Collectively, these results reveal distinct differences in bacterial extracellular vesicle cargo and biogenesis routes from pathogenic and beneficial plant bacteria in different medium conditions and point to distinct populations of vesicles with diverse functional roles. IMPORTANCE Recent publications have shown that bacterial vesicles play important roles in interkingdom communication between bacteria and plants. Indeed, our recently published data reveal that bacterial vesicles from pathogenic and beneficial strains elicit immune responses in plants that protect against future pathogen challenge. However, the molecules underlying these striking phenomena remain unknown. Our recent work indicated that proteins packaged in vesicles are critically important for vesicle-mediated seedling growth inhibition, often considered an indirect measure of plant immune activation. In this study, we characterize the protein cargo of vesicles from Pseudomonas syringae pathovar tomato DC3000 and Pseudomonas fluorescens from two different medium conditions and show that distinct subpopulations of vesicles contribute to bacterial virulence and stress tolerance. Furthermore, we reveal differences in how beneficial and pathogenic bacterial species respond to harsh environmental conditions through vesicle packaging. Importantly, we find that protein cargo implicates outer-inner membrane vesicles in bacterial stress responses, while outer membrane vesicles are packaged for virulence.
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13
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Ramsay KA, Rehman A, Wardell ST, Martin LW, Bell SC, Patrick WM, Winstanley C, Lamont IL. Ceftazidime resistance in Pseudomonas aeruginosa is multigenic and complex. PLoS One 2023; 18:e0285856. [PMID: 37192202 DOI: 10.1371/journal.pone.0285856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
Pseudomonas aeruginosa causes a wide range of severe infections. Ceftazidime, a cephalosporin, is a key antibiotic for treating infections but a significant proportion of isolates are ceftazidime-resistant. The aim of this research was to identify mutations that contribute to resistance, and to quantify the impacts of individual mutations and mutation combinations. Thirty-five mutants with reduced susceptibility to ceftazidime were evolved from two antibiotic-sensitive P. aeruginosa reference strains PAO1 and PA14. Mutations were identified by whole genome sequencing. The evolved mutants tolerated ceftazidime at concentrations between 4 and 1000 times that of the parental bacteria, with most mutants being ceftazidime resistant (minimum inhibitory concentration [MIC] ≥ 32 mg/L). Many mutants were also resistant to meropenem, a carbapenem antibiotic. Twenty-eight genes were mutated in multiple mutants, with dacB and mpl being the most frequently mutated. Mutations in six key genes were engineered into the genome of strain PAO1 individually and in combinations. A dacB mutation by itself increased the ceftazidime MIC by 16-fold although the mutant bacteria remained ceftazidime sensitive (MIC < 32 mg/L). Mutations in ampC, mexR, nalC or nalD increased the MIC by 2- to 4-fold. The MIC of a dacB mutant was increased when combined with a mutation in ampC, rendering the bacteria resistant, whereas other mutation combinations did not increase the MIC above those of single mutants. To determine the clinical relevance of mutations identified through experimental evolution, 173 ceftazidime-resistant and 166 sensitive clinical isolates were analysed for the presence of sequence variants that likely alter function of resistance-associated genes. dacB and ampC sequence variants occur most frequently in both resistant and sensitive clinical isolates. Our findings quantify the individual and combinatorial effects of mutations in different genes on ceftazidime susceptibility and demonstrate that the genetic basis of ceftazidime resistance is complex and multifactorial.
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Affiliation(s)
- Kay A Ramsay
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Attika Rehman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Samuel T Wardell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Lois W Martin
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia
- Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, Queensland, Australia
| | - Wayne M Patrick
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Craig Winstanley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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14
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Chiu S, Hancock AM, Schofner BW, Sniezek KJ, Soto-Echevarria N, Leon G, Sivaloganathan DM, Wan X, Brynildsen MP. Causes of polymyxin treatment failure and new derivatives to fill the gap. J Antibiot (Tokyo) 2022; 75:593-609. [PMID: 36123537 DOI: 10.1038/s41429-022-00561-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022]
Abstract
Polymyxins are a class of antibiotics that were discovered in 1947 from programs searching for compounds effective in the treatment of Gram-negative infections. Produced by the Gram-positive bacterium Paenibacillus polymyxa and composed of a cyclic peptide chain with a peptide-fatty acyl tail, polymyxins exert bactericidal effects through membrane disruption. Currently, polymyxin B and colistin (polymyxin E) have been developed for clinical use, where they are reserved as "last-line" therapies for multidrug-resistant (MDR) infections. Unfortunately, the incidences of strains resistant to polymyxins have been increasing globally, and polymyxin heteroresistance has been gaining appreciation as an important clinical challenge. These phenomena, along with bacterial tolerance to this antibiotic class, constitute important contributors to polymyxin treatment failure. Here, we review polymyxins and their mechanism of action, summarize the current understanding of how polymyxin treatment fails, and discuss how the next generation of polymyxins holds promise to invigorate this antibiotic class.
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Affiliation(s)
- Selena Chiu
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Anna M Hancock
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Bob W Schofner
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Katherine J Sniezek
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | | | - Gabrielle Leon
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | | | - Xuanqing Wan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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15
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Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022; 10:microorganisms10061239. [PMID: 35744757 PMCID: PMC9228545 DOI: 10.3390/microorganisms10061239] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.
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16
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Pseudomonas aeruginosa
Oligoribonuclease Controls Susceptibility to Polymyxin B by Regulating Pel Exopolysaccharide Production. Antimicrob Agents Chemother 2022; 66:e0207221. [DOI: 10.1128/aac.02072-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polymyxins are considered as the last resort antibiotics to treat infections caused by multidrug-resistant Gram negative pathogens.
Pseudomonas aeruginosa
is an opportunistic pathogen that causes various infections in humans. Proteins involved in lipopolysaccharide modification and maintaining inner and outer membrane integrities have been found to contribute to the bacterial resistance to polymyxins. Oligoribonuclease (Orn) is an exonuclease that regulates the homeostasis of intracellular (3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), thereby regulating the production of extracellular polysaccharide in
P. aeruginosa
. Previously, we demonstrated that Orn affects the bacterial resistance to fluoroquinolone, β-lactam and aminoglycoside antibiotics. In this study, we found that mutation of
orn
increased the bacterial survival following polymyxin B treatment in a wild type
P. aeruginosa
strain PA14. Overexpression of c-di-GMP degradation enzymes in the
orn
mutant reduced the bacterial survival. By using a fluorescence labeled polymyxin B, we found that mutation of
orn
increased the bacterial surface bound polymyxin B. Deletion of the Pel synthesis genes or treatment with a Pel hydrolase reduced the surface bound polymyxin B and bacterial survival. We further demonstrated that Pel binds to extracellular DNA (eDNA), which traps polymyxin B and thus protects the bacterial cells. Collectively, our results revealed a novel defense mechanism against polymyxin in
P. aeruginosa
.
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17
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Cell Envelope Stress Response in Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:147-184. [DOI: 10.1007/978-3-031-08491-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Trouillon J, Imbert L, Villard AM, Vernet T, Attrée I, Elsen S. Determination of the two-component systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages. Nucleic Acids Res 2021; 49:11476-11490. [PMID: 34718721 PMCID: PMC8599809 DOI: 10.1093/nar/gkab928] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/24/2021] [Accepted: 09/28/2021] [Indexed: 01/01/2023] Open
Abstract
Pseudomonas aeruginosa possesses one of the most complex bacterial regulatory networks, which largely contributes to its success as a pathogen. However, most of its transcription factors (TFs) are still uncharacterized and the potential intra-species variability in regulatory networks has been mostly ignored so far. Here, we used DAP-seq to map the genome-wide binding sites of all 55 DNA-binding two-component systems (TCSs) response regulators (RRs) across the three major P. aeruginosa lineages. The resulting networks encompass about 40% of all genes in each strain and contain numerous new regulatory interactions across most major physiological processes. Strikingly, about half of the detected targets are specific to only one or two strains, revealing a previously unknown large functional diversity of TFs within a single species. Three main mechanisms were found to drive this diversity, including differences in accessory genome content, as exemplified by the strain-specific plasmid in IHMA87 outlier strain which harbors numerous binding sites of conserved chromosomally-encoded RRs. Additionally, most RRs display potential auto-regulation or RR-RR cross-regulation, bringing to light the vast complexity of this network. Overall, we provide the first complete delineation of the TCSs regulatory network in P. aeruginosa that will represent an important resource for future studies on this pathogen.
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Affiliation(s)
- Julian Trouillon
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, Team Bacterial Pathogenesis and Cellular Responses, 38044 Grenoble, France
| | - Lionel Imbert
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, EMBL, ISBG UAR 3518, 38044 Grenoble, France
| | - Anne-Marie Villard
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044 Grenoble, France
| | - Thierry Vernet
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044 Grenoble, France
| | - Ina Attrée
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, Team Bacterial Pathogenesis and Cellular Responses, 38044 Grenoble, France
| | - Sylvie Elsen
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, Team Bacterial Pathogenesis and Cellular Responses, 38044 Grenoble, France
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19
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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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