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Duffey M, Jumde RP, da Costa RM, Ropponen HK, Blasco B, Piddock LJ. Extending the Potency and Lifespan of Antibiotics: Inhibitors of Gram-Negative Bacterial Efflux Pumps. ACS Infect Dis 2024; 10:1458-1482. [PMID: 38661541 PMCID: PMC11091901 DOI: 10.1021/acsinfecdis.4c00091] [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: 02/02/2024] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Efflux is a natural process found in all prokaryotic and eukaryotic cells that removes a diverse range of substrates from inside to outside. Many antibiotics are substrates of bacterial efflux pumps, and modifications to the structure or overexpression of efflux pumps are an important resistance mechanism utilized by many multidrug-resistant bacteria. Therefore, chemical inhibition of bacterial efflux to revitalize existing antibiotics has been considered a promising approach for antimicrobial chemotherapy over two decades, and various strategies have been employed. In this review, we provide an overview of bacterial multidrug resistance (MDR) efflux pumps, of which the resistance nodulation division (RND) efflux pumps are considered the most clinically relevant in Gram-negative bacteria, and describe over 50 efflux inhibitors that target such systems. Although numerous efflux inhibitors have been identified to date, none have progressed into clinical use because of formulation, toxicity, and pharmacokinetic issues or a narrow spectrum of inhibition. For these reasons, the development of efflux inhibitors has been considered a difficult and complex area of research, and few active preclinical studies on efflux inhibitors are in progress. However, recently developed tools, including but not limited to computational tools including molecular docking models, offer hope that further research on efflux inhibitors can be a platform for research and development of new bacterial efflux inhibitors.
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Affiliation(s)
- Maëlle Duffey
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Ravindra P. Jumde
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Renata M.A. da Costa
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Henni-Karoliina Ropponen
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Benjamin Blasco
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Laura J.V. Piddock
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
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2
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Johnson CN, Wilde S, Tuomanen E, Rosch JW. Convergent impact of vaccination and antibiotic pressures on pneumococcal populations. Cell Chem Biol 2024; 31:195-206. [PMID: 38052216 PMCID: PMC10938186 DOI: 10.1016/j.chembiol.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/08/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
Streptococcus pneumoniae is a remarkably adaptable and successful human pathogen, playing dual roles of both asymptomatic carriage in the nasopharynx and invasive disease including pneumonia, bacteremia, and meningitis. Efficacious vaccines and effective antibiotic therapies are critical to mitigating morbidity and mortality. However, clinical interventions can be rapidly circumvented by the pneumococcus by its inherent proclivity for genetic exchange. This leads to an underappreciated interplay between vaccine and antibiotic pressures on pneumococcal populations. Circulating populations have undergone dramatic shifts due to the introduction of capsule-based vaccines of increasing valency imparting strong selective pressures. These alterations in population structure have concurrent consequences on the frequency of antibiotic resistance profiles in the population. This review will discuss the interactions of these two selective forces. Understanding and forecasting the drivers of antibiotic resistance and capsule switching are of critical importance for public health, particularly for such a genetically promiscuous pathogen as S. pneumoniae.
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Affiliation(s)
- Cydney N Johnson
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shyra Wilde
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elaine Tuomanen
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Jason W Rosch
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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3
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Cheema HS, Maurya A, Kumar S, Pandey VK, Singh RM. Antibiotic Potentiation Through Phytochemical-Based Efflux Pump Inhibitors to Combat Multidrug Resistance Bacteria. Med Chem 2024; 20:557-575. [PMID: 37907487 DOI: 10.2174/0115734064263586231022135644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND Antimicrobial resistance development poses a significant danger to the efficacy of antibiotics, which were once believed to be the most efficient method for treating infections caused by bacteria. Antimicrobial resistance typically involves various mechanisms, such as drug inactivation or modification, drug target modification, drug uptake restriction, and drug efflux, resulting in decreased antibiotic concentrations within the cell. Antimicrobial resistance has been associated with efflux Pumps, known for their capacity to expel different antibiotics from the cell non-specifically. This makes EPs fascinating targets for creating drugs to combat antimicrobial resistance (AMR). The varied structures of secondary metabolites (phytomolecules) found in plants have positioned them as a promising reservoir of efflux pump inhibitors. These inhibitors act as modifiers of bacterial resistance and facilitate the reintroduction of antibiotics that have lost clinical effectiveness. Additionally, they may play a role in preventing the emergence of multidrug resistant strains. OBJECTIVE The objective of this review article is to discuss the latest studies on plant-based efflux pump inhibitors such as terpenoids, alkaloids, flavonoids, glycosides, and tetralones. It highlighted their potential in enhancing the effectiveness of antibiotics and combating the development of multidrug resistance. RESULTS Efflux pump inhibitors (EPIs) derived from botanical sources, including compounds like lysergol, chanaoclavine, niazrin, 4-hydroxy-α-tetralone, ursolic acid, phytol, etc., as well as their partially synthesized forms, have shown significant potential as practical therapeutic approaches in addressing antimicrobial resistance caused by efflux pumps. Further, several phyto-molecules and their analogs demonstrated superior potential for reversing drug resistance, surpassing established agents like reserpine, niaziridin, etc. Conclusion: This review found that while the phyto-molecules and their derivatives did not possess notable antimicrobial activity, their combination with established antibiotics significantly reduced their minimum inhibitory concentration (MIC). Specific molecules, such as chanaoclavine and niaziridin, exhibited noteworthy potential in reversing the effectiveness of drugs, resulting in a reduction of the MIC of tetracycline by up to 16 times against the tested strain of bacteria. These molecules inhibited the efflux pumps responsible for drug resistance and displayed a stronger affinity for membrane proteins. By employing powerful EPIs, these molecules can selectively target and obstruct drug efflux pumps. This targeted approach can significantly augment the strength and efficacy of older antibiotics against various drug resistant bacteria, given that active drug efflux poses a susceptibility for nearly all antibiotics.
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Affiliation(s)
| | - Anupam Maurya
- Chemistry Section, Pharmacopoeia Commission for Indian Medicine, and Homoeopathy (PCIM&H), Ministry of Ayush, Ghaziabad, 201002, (U.P.), India
| | - Sandeep Kumar
- Department of Botany, Meerut College, Meerut, 250003 (U.P.), India
| | - Vineet Kumar Pandey
- Chemistry Section, Pharmacopoeia Commission for Indian Medicine, and Homoeopathy (PCIM&H), Ministry of Ayush, Ghaziabad, 201002, (U.P.), India
| | - Raman Mohan Singh
- Chemistry Section, Pharmacopoeia Commission for Indian Medicine, and Homoeopathy (PCIM&H), Ministry of Ayush, Ghaziabad, 201002, (U.P.), India
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4
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Zhang S, Wang J, Ahn J. Advances in the Discovery of Efflux Pump Inhibitors as Novel Potentiators to Control Antimicrobial-Resistant Pathogens. Antibiotics (Basel) 2023; 12:1417. [PMID: 37760714 PMCID: PMC10525980 DOI: 10.3390/antibiotics12091417] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The excessive use of antibiotics has led to the emergence of multidrug-resistant (MDR) pathogens in clinical settings and food-producing animals, posing significant challenges to clinical management and food control. Over the past few decades, the discovery of antimicrobials has slowed down, leading to a lack of treatment options for clinical infectious diseases and foodborne illnesses. Given the increasing prevalence of antibiotic resistance and the limited availability of effective antibiotics, the discovery of novel antibiotic potentiators may prove useful for the treatment of bacterial infections. The application of antibiotics combined with antibiotic potentiators has demonstrated successful outcomes in bench-scale experiments and clinical settings. For instance, the use of efflux pump inhibitors (EPIs) in combination with antibiotics showed effective inhibition of MDR pathogens. Thus, this review aims to enable the possibility of using novel EPIs as potential adjuvants to effectively control MDR pathogens. Specifically, it provides a comprehensive summary of the advances in novel EPI discovery and the underlying mechanisms that restore antimicrobial activity. In addition, we also characterize plant-derived EPIs as novel potentiators. This review provides insights into current challenges and potential strategies for future advancements in fighting antibiotic resistance.
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Affiliation(s)
- Song Zhang
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Jun Wang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea;
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
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5
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De Gaetano GV, Lentini G, Famà A, Coppolino F, Beninati C. Antimicrobial Resistance: Two-Component Regulatory Systems and Multidrug Efflux Pumps. Antibiotics (Basel) 2023; 12:965. [PMID: 37370284 DOI: 10.3390/antibiotics12060965] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The number of multidrug-resistant bacteria is rapidly spreading worldwide. Among the various mechanisms determining resistance to antimicrobial agents, multidrug efflux pumps play a noteworthy role because they export extraneous and noxious substrates from the inside to the outside environment of the bacterial cell contributing to multidrug resistance (MDR) and, consequently, to the failure of anti-infective therapies. The expression of multidrug efflux pumps can be under the control of transcriptional regulators and two-component systems (TCS). TCS are a major mechanism by which microorganisms sense and reply to external and/or intramembrane stimuli by coordinating the expression of genes involved not only in pathogenic pathways but also in antibiotic resistance. In this review, we describe the influence of TCS on multidrug efflux pump expression and activity in some Gram-negative and Gram-positive bacteria. Taking into account the strict correlation between TCS and multidrug efflux pumps, the development of drugs targeting TCS, alone or together with already discovered efflux pump inhibitors, may represent a beneficial strategy to contribute to the fight against growing antibiotic resistance.
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Affiliation(s)
| | - Germana Lentini
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
| | - Agata Famà
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
| | - Francesco Coppolino
- Department of Biomedical, Dental and Imaging Sciences, University of Messina, 98124 Messina, Italy
| | - Concetta Beninati
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
- Scylla Biotech Srl, 98124 Messina, Italy
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6
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Chetri S. The culmination of multidrug-resistant efflux pumps vs. meager antibiotic arsenal era: Urgent need for an improved new generation of EPIs. Front Microbiol 2023; 14:1149418. [PMID: 37138605 PMCID: PMC10149990 DOI: 10.3389/fmicb.2023.1149418] [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: 01/21/2023] [Accepted: 03/13/2023] [Indexed: 05/05/2023] Open
Abstract
Efflux pumps function as an advanced defense system against antimicrobials by reducing the concentration of drugs inside the bacteria and extruding the substances outside. Various extraneous substances, including antimicrobials, toxic heavy metals, dyes, and detergents, have been removed by this protective barrier composed of diverse transporter proteins found in between the cell membrane and the periplasm within the bacterial cell. In this review, multiple efflux pump families have been analytically and widely outlined, and their potential applications have been discussed in detail. Additionally, this review also discusses a variety of biological functions of efflux pumps, including their role in the formation of biofilms, quorum sensing, their survivability, and the virulence in bacteria, and the genes/proteins associated with efflux pumps have also been explored for their potential relevance to antimicrobial resistance and antibiotic residue detection. A final discussion centers around efflux pump inhibitors, particularly those derived from plants.
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Amblar M, Zaballos Á, de la Campa AG. Role of PatAB Transporter in Efflux of Levofloxacin in Streptococcus pneumoniae. Antibiotics (Basel) 2022; 11:antibiotics11121837. [PMID: 36551495 PMCID: PMC9774293 DOI: 10.3390/antibiotics11121837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
PatAB is an ABC bacterial transporter that facilitates the export of antibiotics and dyes. The overexpression of patAB genes conferring efflux-mediated fluoroquinolone resistance has been observed in several laboratory strains and clinical isolates of Streptococcus pneumoniae. Using transformation and whole-genome sequencing, we characterized the fluoroquinolone-resistance mechanism of one S. pneumoniae clinical isolate without mutations in the DNA topoisomerase genes. We identified the PatAB fluoroquinolone efflux-pump as the mechanism conferring a low-level resistance to ciprofloxacin (8 µg/mL) and levofloxacin (4 µg/mL). Genetic transformation experiments with different amplimers revealed that the entire patA plus the 5'-terminus of patB are required for levofloxacin-efflux. By contrast, only the upstream region of the patAB operon, plus the region coding the N-terminus of PatA containing the G39D, T43A, V48A and D100N amino acid changes, are sufficient to confer a ciprofloxacin-efflux phenotype, thus suggesting differences between fluoroquinolones in their binding and/or translocation pathways. In addition, we identified a novel single mutation responsible for the constitutive and ciprofloxacin-inducible upregulation of patAB. This mutation is predicted to destabilize the putative rho-independent transcriptional terminator located upstream of patA, increasing transcription of downstream genes. This is the first report demonstrating the role of the PatAB transporter in levofloxacin-efflux in a pneumoccocal clinical isolate.
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Affiliation(s)
- Mónica Amblar
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo Km 2.200, Majadahonda, 28220 Madrid, Spain
- Correspondence: (M.A.); (A.G.d.l.C.); Tel.: +34-91448283 (M.A.); +34-91448944 (A.G.d.l.C.)
| | - Ángel Zaballos
- Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo Km 2.200, Majadahonda, 28220 Madrid, Spain
| | - Adela G de la Campa
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo Km 2.200, Majadahonda, 28220 Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
- Correspondence: (M.A.); (A.G.d.l.C.); Tel.: +34-91448283 (M.A.); +34-91448944 (A.G.d.l.C.)
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8
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Seukep AJ, Mbuntcha HG, Kuete V, Chu Y, Fan E, Guo MQ. What Approaches to Thwart Bacterial Efflux Pumps-Mediated Resistance? Antibiotics (Basel) 2022; 11:antibiotics11101287. [PMID: 36289945 PMCID: PMC9598416 DOI: 10.3390/antibiotics11101287] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 12/03/2022] Open
Abstract
An effective response that combines prevention and treatment is still the most anticipated solution to the increasing incidence of antimicrobial resistance (AMR). As the phenomenon continues to evolve, AMR is driving an escalation of hard-to-treat infections and mortality rates. Over the years, bacteria have devised a variety of survival tactics to outwit the antibiotic’s effects, yet given their great adaptability, unexpected mechanisms are still to be discovered. Over-expression of efflux pumps (EPs) constitutes the leading strategy of bacterial resistance, and it is also a primary driver in the establishment of multidrug resistance (MDR). Extensive efforts are being made to develop antibiotic resistance breakers (ARBs) with the ultimate goal of re-sensitizing bacteria to medications to which they have become unresponsive. EP inhibitors (EPIs) appear to be the principal group of ARBs used to impair the efflux system machinery. Due to the high toxicity of synthetic EPIs, there is a growing interest in natural, safe, and innocuous ones, whereby plant extracts emerge to be excellent candidates. Besides EPIs, further alternatives are being explored including the development of nanoparticle carriers, biologics, and phage therapy, among others. What roles do EPs play in the occurrence of MDR? What weapons do we have to thwart EP-mediated resistance? What are the obstacles to their development? These are some of the core questions addressed in the present review.
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Affiliation(s)
- Armel Jackson Seukep
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 437004, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea P.O. Box 63, Cameroon
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 437004, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
| | - Helene Gueaba Mbuntcha
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon
| | - Victor Kuete
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon
| | - Yindi Chu
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Enguo Fan
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- College of Life Sciences, Linyi University, Linyi 276005, China
- Correspondence: (E.F.); (M.-Q.G.)
| | - Ming-Quan Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 437004, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 437004, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
- Correspondence: (E.F.); (M.-Q.G.)
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9
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Guffick C, Hsieh PY, Ali A, Shi W, Howard J, Chinthapalli DK, Kong AC, Salaa I, Crouch LI, Ansbro MR, Isaacson SC, Singh H, Barrera NP, Nair AV, Robinson CV, Deery MJ, van Veen HW. Drug-dependent inhibition of nucleotide hydrolysis in the heterodimeric ABC multidrug transporter PatAB from Streptococcus pneumoniae. FEBS J 2022; 289:3770-3788. [PMID: 35066976 PMCID: PMC9541285 DOI: 10.1111/febs.16366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 02/02/2023]
Abstract
The bacterial heterodimeric ATP‐binding cassette (ABC) multidrug exporter PatAB has a critical role in conferring antibiotic resistance in multidrug‐resistant infections by Streptococcus pneumoniae. As with other heterodimeric ABC exporters, PatAB contains two transmembrane domains that form a drug translocation pathway for efflux and two nucleotide‐binding domains that bind ATP, one of which is hydrolysed during transport. The structural and functional elements in heterodimeric ABC multidrug exporters that determine interactions with drugs and couple drug binding to nucleotide hydrolysis are not fully understood. Here, we used mass spectrometry techniques to determine the subunit stoichiometry in PatAB in our lactococcal expression system and investigate locations of drug binding using the fluorescent drug‐mimetic azido‐ethidium. Surprisingly, our analyses of azido‐ethidium‐labelled PatAB peptides point to ethidium binding in the PatA nucleotide‐binding domain, with the azido moiety crosslinked to residue Q521 in the H‐like loop of the degenerate nucleotide‐binding site. Investigation into this compound and residue’s role in nucleotide hydrolysis pointed to a reduction in the activity for a Q521A mutant and ethidium‐dependent inhibition in both mutant and wild type. Most transported drugs did not stimulate or inhibit nucleotide hydrolysis of PatAB in detergent solution or lipidic nanodiscs. However, further examples for ethidium‐like inhibition were found with propidium, novobiocin and coumermycin A1, which all inhibit nucleotide hydrolysis by a non‐competitive mechanism. These data cast light on potential mechanisms by which drugs can regulate nucleotide hydrolysis by PatAB, which might involve a novel drug binding site near the nucleotide‐binding domains.
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Affiliation(s)
| | - Pei-Yu Hsieh
- Department of Pharmacology, University of Cambridge, UK
| | - Anam Ali
- Department of Pharmacology, University of Cambridge, UK
| | - Wilma Shi
- Department of Pharmacology, University of Cambridge, UK
| | - Julie Howard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
| | | | - Alex C Kong
- Department of Pharmacology, University of Cambridge, UK
| | - Ihsene Salaa
- Department of Pharmacology, University of Cambridge, UK
| | - Lucy I Crouch
- Department of Pharmacology, University of Cambridge, UK
| | | | | | | | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Asha V Nair
- Department of Pharmacology, University of Cambridge, UK
| | | | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
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10
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Yang X, Peng W, Wang N, Dou B, Yang F, Chen H, Yuan F, Bei W. Role of the Two-Component System CiaRH in the Regulation of Efflux Pump SatAB and Its Correlation with Fluoroquinolone Susceptibility. Microbiol Spectr 2022; 10:e0041722. [PMID: 35638854 PMCID: PMC9241815 DOI: 10.1128/spectrum.00417-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022] Open
Abstract
Streptococcus suis is an important pathogen in both pigs and humans. Although the diseases associated with S. suis can typically be treated with antibiotics, such use has resulted in a sustained increase in drug resistance. Bacteria can sense and respond to antibiotics via two-component systems (TCSs). In this study, the TCS CiaRH was identified as playing an important role in the susceptibility of S. suis to fluoroquinolones (FQs). We found that a ΔciaRH mutant possessed lower susceptibility to FQs than the wild-type strain, with no observed growth defects at the tested concentrations and lower levels of intracellular drugs and dye. Proteomic data revealed that the levels of SatA and SatB expression were upregulated in the ΔciaRH mutant compared with their levels in the wild-type strain. The satA and satB genes encode a narrow-spectrum FQ efflux pump. The phenomena associated with combined ciaRH-and-satAB deletion mutations almost returned the ΔciaRH ΔsatAB mutant to the phenotype of the wild-type strain compared to the phenotype of the ΔciaRH mutant, suggesting that the resistance of the ΔciaRH strain to FQs could be attributed to satAB overexpression. Moreover, SatAB expression was regulated by CiaR (a response regulator of CiaRH) and SatR (a regulator of the MarR family). The ciaRH genes were consistently downregulated in response to antibiotic stress. The results of electrophoretic mobility shift assays (EMSAs) and affinity assays revealed that both regulator proteins directly controlled the ABC transporter proteins SatAB. Together, the results show that cascade-mediated regulation of antibiotic export by CiaRH is crucial for the ability of S. suis to adapt to conditions of antibiotic pressure. Our study may provide a new target for future antibiotic research and development. IMPORTANCE Streptococcus suis is a zoonotic pathogen with high incidence and mortality rates in both swine and humans. Following antibiotic treatment, the organism has evolved many resistance mechanisms, among which efflux pump overexpression can promote drug extrusion from the cell. This study clarified the role of CiaRH in fluoroquinolone resistance. A mutant with the ciaRH genes deleted showed decreased susceptibility to the antibiotics tested, an invariant growth rate, and reduced intracellular efflux pump substrates. This research also demonstrated that overexpression of the efflux pump SatAB was the main cause of ΔciaRH resistance. In addition, CiaR could combine with the promoter region of satAB to further directly suppress target gene transcription. Simultaneously, satAB was also directly regulated by SatR. Our findings may provide novel insights for the development of drug targets and help to exploit corresponding inhibitors to combat bacterial multidrug resistance.
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Affiliation(s)
- Xia Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Wei Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Ningning Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Beibei Dou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Fengming Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Fangyan Yuan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Weicheng Bei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- Guangxi Yangxiang Co., Ltd., Guigang, China
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11
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López-Siles M, McConnell MJ, Martín-Galiano AJ. Identification of Promoter Region Markers Associated With Altered Expression of Resistance-Nodulation-Division Antibiotic Efflux Pumps in Acinetobacter baumannii. Front Microbiol 2022; 13:869208. [PMID: 35663863 PMCID: PMC9161033 DOI: 10.3389/fmicb.2022.869208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic alterations leading to the constitutive upregulation of specific efflux pumps contribute to antibacterial resistance in multidrug resistant bacteria. The identification of such resistance markers remains one of the most challenging tasks of genome-level resistance predictors. In this study, 487 non-redundant genetic events were identified in upstream zones of three operons coding for resistance-nodulation-division (RND) efflux pumps of 4,130 Acinetobacter baumannii isolates. These events included insertion sequences, small indels, and single nucleotide polymorphisms. In some cases, alterations explicitly modified the expression motifs described for these operons, such as the promoter boxes, operators, and Shine-Dalgarno sequences. In addition, changes in DNA curvature and mRNA secondary structures, which are structural elements that regulate expression, were also calculated. According to their influence on RND upregulation, the catalog of upstream modifications were associated with “experimentally verified,” “presumed,” and “probably irrelevant” degrees of certainty. For experimental verification, DNA of upstream sequences independently carrying selected markers, three for each RND operon, were fused to a luciferase reporter plasmid system. Five out of the nine selected markers tested showed significant increases in expression with respect to the wild-type sequence control. In particular, a 25-fold expression increase was observed with the ISAba1 insertion sequence upstream the adeABC pump. Next, overexpression of each of the three multi-specific RND pumps was linked to their respective antibacterial substrates by a deep A. baumannii literature screen. Consequently, a data flow framework was then developed to link genomic upregulatory RND determinants to potential antibiotic resistance. Assignment of potential increases in minimal inhibitory concentrations at the “experimentally verified” level was permitted for 42 isolates to 7–8 unrelated antibacterial agents including tigecycline, which is overlooked by conventional resistome predictors. Thus, our protocol may represent a time-saving filter step prior to laborious confirmation experiments for efflux-driven resistance. Altogether, a computational-experimental pipeline containing all components required for identifying the upstream regulatory resistome is proposed. This schema may provide the foundational stone for the elaboration of tools approaching antibiotic efflux that complement routine resistome predictors for preventing antimicrobial therapy failure against difficult-to-threat bacteria.
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Huang L, Wu C, Gao H, Xu C, Dai M, Huang L, Hao H, Wang X, Cheng G. Bacterial Multidrug Efflux Pumps at the Frontline of Antimicrobial Resistance: An Overview. Antibiotics (Basel) 2022; 11:antibiotics11040520. [PMID: 35453271 PMCID: PMC9032748 DOI: 10.3390/antibiotics11040520] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 02/06/2023] Open
Abstract
Multidrug efflux pumps function at the frontline to protect bacteria against antimicrobials by decreasing the intracellular concentration of drugs. This protective barrier consists of a series of transporter proteins, which are located in the bacterial cell membrane and periplasm and remove diverse extraneous substrates, including antimicrobials, organic solvents, toxic heavy metals, etc., from bacterial cells. This review systematically and comprehensively summarizes the functions of multiple efflux pumps families and discusses their potential applications. The biological functions of efflux pumps including their promotion of multidrug resistance, biofilm formation, quorum sensing, and survival and pathogenicity of bacteria are elucidated. The potential applications of efflux pump-related genes/proteins for the detection of antibiotic residues and antimicrobial resistance are also analyzed. Last but not least, efflux pump inhibitors, especially those of plant origin, are discussed.
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13
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Deng R, Yang K, Lin D. Pentachlorophenol and ciprofloxacin present dissimilar joint toxicities with carbon nanotubes to Bacillus subtilis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 270:116071. [PMID: 33218776 DOI: 10.1016/j.envpol.2020.116071] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
Discharged carbon nanotubes (CNTs) likely interact with co-existing organic contaminants (OCs) and pose joint toxicity to environmental microbes. Herein, hydrophobic pentachlorophenol (PCP) and hydrophilic ciprofloxacin (CIP) were used as representative OCs and their joint toxicities with CNTs to Bacillus subtilis were systematically investigated at cellular, biochemical, and omics levels. The 3-h bacterial growth half inhibitory concentrations of CNTs, PCP, and CIP were 12.5 ± 2.6, 3.5 ± 0.5, and 0.46 ± 0.03 mg/L, respectively, and they all could damage cell membrane, increase intracellular oxidative stress, and alter bacterial metabolomics and transcriptomics; while CNTs-PCP and CNTs-CIP binary exposures exhibited distinct additive and synergistic toxicities, respectively. CNTs increased bacterial bioaccumulation of PCP and CIP via destabilizing and damaging cell membrane. PCP reduced the bioaccumulation of CNTs, while CIP had no significant effect; this difference could be owing to the different effects of the two OCs on cell-surface hydrophobicity and CNTs electronegativity. The additive toxicity outcome upon CNTs-PCP co-exposure could be a result of the balance between the increased toxicity from increased PCP bioaccumulation and the decreased toxicity from decreased CNTs bioaccumulation. The increased bioaccumulation of CIP contributed to the synergistic toxicity upon CNTs-CIP co-exposure, as confirmed by the increased inhibition of topoisomerase Ⅳ activity and interference in gene expressions regulating ABC transporters and lysine biosynthesis. The findings provide novel insights into environmental risks of CNTs.
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Affiliation(s)
- Rui Deng
- Department of Environmental Science, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou, 310058, China; Joint International Research Laboratory of Green Buildings and Built Environments, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Kun Yang
- Department of Environmental Science, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou, 310058, China
| | - Daohui Lin
- Department of Environmental Science, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou, 310058, China.
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Deng R, Gao X, Hou J, Lin D. Multi-omics analyses reveal molecular mechanisms for the antagonistic toxicity of carbon nanotubes and ciprofloxacin to Escherichia coli. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 726:138288. [PMID: 32305750 DOI: 10.1016/j.scitotenv.2020.138288] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 05/05/2023]
Abstract
With the increasing production and application, engineered nanomaterials (ENMs) are being discharged into the environment, where they can interact with co-existing contaminants, causing complicated joint toxicity to organisms that needs to be studied. The case study of ENMs-contaminant joint toxicity and the understanding of relative mechanisms are very insufficient, particularly the mechanisms of molecular interactions and governing processes. Herein, a typical ENMs, carbon nanotubes (CNTs, 0-60 mg/L), and a common antibiotic, ciprofloxacin (CIP, 0-900 mg/L), were selected as the analytes. Their joint toxicity to a model microbe Escherichia coli was specifically investigated via biochemical, transcriptomics, and metabolomics approaches. The result revealed an antagonistic effect on growth inhibition between CNTs and CIP. Mitigations in cell membrane disruption and oxidative stress were involved in the antagonistic action. CIP (48.8-244 mg/L) decreased the bioaccumulation of CNTs (7.2 mg/L) via reducing cell-surface hydrophobicity and hindering the bio-nano interaction, which could attenuate the toxicity of CNTs to bacteria. CNTs (7.2 and 14.4 mg/L) alleviated the disturbance of CIP (122 and 244 mg/L) to gene expressions especially related to nitrogen compound metabolism, oxidoreductase activity, and iron-sulfur protein maturation, probably through relieving the CIP-induced inhibition of DNA gyrase activity. Further, CNTs (7.2 and 14.4 mg/L) offset the impact of CIP (122 and 244 mg/L) on bacterial metabolome via the regulation of biosynthesis of unsaturated fatty acids and metabolisms of some amino acids and glutathione. The findings shed new light on the molecular mechanisms by which ENMs present joint effect on contaminant toxicity, and provide important information for risk assessments of CNTs and fluoroquinolones in the environment.
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Affiliation(s)
- Rui Deng
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
| | - Xuan Gao
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
| | - Jie Hou
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
| | - Daohui Lin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China.
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15
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Multidrug ABC transporters in bacteria. Res Microbiol 2019; 170:381-391. [DOI: 10.1016/j.resmic.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
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16
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Mathieu K, Javed W, Vallet S, Lesterlin C, Candusso MP, Ding F, Xu XN, Ebel C, Jault JM, Orelle C. Functionality of membrane proteins overexpressed and purified from E. coli is highly dependent upon the strain. Sci Rep 2019; 9:2654. [PMID: 30804404 PMCID: PMC6390180 DOI: 10.1038/s41598-019-39382-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/22/2019] [Indexed: 11/24/2022] Open
Abstract
Overexpression of correctly folded membrane proteins is a fundamental prerequisite for functional and structural studies. One of the most commonly used expression systems for the production of membrane proteins is Escherichia coli. While misfolded proteins typically aggregate and form inclusions bodies, membrane proteins that are addressed to the membrane and extractable by detergents are generally assumed to be properly folded. Accordingly, GFP fusion strategy is often used as a fluorescent proxy to monitor their expression and folding quality. Here we investigated the functionality of two different multidrug ABC transporters, the homodimer BmrA from Bacillus subtilis and the heterodimer PatA/PatB from Streptococcus pneumoniae, when produced in several E. coli strains with T7 expression system. Strikingly, while strong expression in the membrane of several strains could be achieved, we observed drastic differences in the functionality of these proteins. Moreover, we observed a general trend in which mild detergents mainly extract the population of active transporters, whereas a harsher detergent like Fos-choline 12 could solubilize transporters irrespective of their functionality. Our results suggest that the amount of T7 RNA polymerase transcripts may indirectly but notably impact the structure and activity of overexpressed membrane proteins, and advise caution when using GFP fusion strategy.
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Affiliation(s)
- Khadija Mathieu
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Waqas Javed
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.,Université Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Sylvain Vallet
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Christian Lesterlin
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Marie-Pierre Candusso
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Feng Ding
- Department of Chemistry & Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Xiaohong Nancy Xu
- Department of Chemistry & Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Christine Ebel
- Université Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Jean-Michel Jault
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.
| | - Cédric Orelle
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.
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Gain- and Loss-of-Function Screens Coupled to Next-Generation Sequencing for Antibiotic Mode of Action and Resistance Studies in Streptococcus pneumoniae. Antimicrob Agents Chemother 2019; 63:AAC.02381-18. [PMID: 30783004 DOI: 10.1128/aac.02381-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/08/2019] [Indexed: 12/23/2022] Open
Abstract
Two whole-genome screening approaches are described for studying the mode of action and the mechanisms of resistance to trimethoprim (TMP) in the Gram-positive Streptococcus pneumoniae The gain-of-function approach (Int-Seq) relies on a genomic library of DNA fragments integrated into a fucose-inducible cassette. The second approach, leading to both gain- and loss-of-function mutation, is based on chemical mutagenesis coupled to next-generation sequencing (Mut-Seq). Both approaches pointed at the drug target dihydrofolate reductase (DHFR) as a major resistance mechanism to TMP. Resistance was achieved by dhfr overexpression either through the addition of fucose (Int-Seq) or by mutations upstream of the gene (Mut-Seq). Three types of mutations increased expression by disrupting a predicted Rho-independent terminator upstream of dhfr Known and novel DHFR mutations were also detected by Mut-Seq, and these were functionally validated for TMP resistance. The two approaches also suggested that an increase in the metabolic flux from purine synthesis to GTP and then to folate can modulate the susceptibility to TMP. Finally, we provide evidence for a novel role of the ABC transporter PatAB in TMP susceptibility. Our genomic screens highlighted novel aspects on the mode of action and mechanisms of resistance to antibiotics.
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18
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In Vitro Activity of Lascufloxacin against Streptococcus pneumoniae with Mutations in the Quinolone Resistance-Determining Regions. Antimicrob Agents Chemother 2018; 62:AAC.01971-17. [PMID: 29439959 DOI: 10.1128/aac.01971-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/03/2018] [Indexed: 11/20/2022] Open
Abstract
Lascufloxacin showed potent activity against Streptococcus pneumoniae with a GyrA or ParC mutation (first-step mutant). The frequency of selecting resistant strains tended to be lower for lascufloxacin than for levofloxacin and garenoxacin after drug exposure in first-step mutants but was similar in the comparison between lascufloxacin and moxifloxacin. The increase in MIC was smaller for lascufloxacin than for levofloxacin, garenoxacin, and moxifloxacin when clinical strains with only ParC mutations were exposed to the corresponding drug.
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Alvarado M, Martín-Galiano AJ, Ferrándiz MJ, Zaballos Á, de la Campa AG. Upregulation of the PatAB Transporter Confers Fluoroquinolone Resistance to Streptococcus pseudopneumoniae. Front Microbiol 2017; 8:2074. [PMID: 29123510 PMCID: PMC5662624 DOI: 10.3389/fmicb.2017.02074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/10/2017] [Indexed: 11/27/2022] Open
Abstract
We characterized the mechanism of fluoroquinolone-resistance in two isolates of Streptococcus pseudopneumoniae having fluoroquinolone-efflux as unique mechanism of resistance. Whole genome sequencing and genetic transformation experiments were performed together with phenotypic determinations of the efflux mechanism. The PatAB pump was identified as responsible for efflux of ciprofloxacin (MIC of 4 μg/ml), ethidium bromide (MICs of 8-16 μg/ml) and acriflavine (MICs of 4-8 μg/ml) in both isolates. These MICs were at least 8-fold lower in the presence of the efflux inhibitor reserpine. Complete genome sequencing indicated that the sequence located between the promoter of the patAB operon and the initiation codon of patA, which putatively forms an RNA stem-loop structure, may be responsible for the efflux phenotype. RT-qPCR determinations performed on RNAs of cultures treated or not treated with subinhibitory ciprofloxacin concentrations were performed. While no significant changes were observed in wild-type Streptococcus pneumoniae R6 strain, increases in transcription were detected in the ciprofloxacin-efflux transformants obtained with DNA from efflux-positive isolates, in the ranges of 1.4 to 3.4-fold (patA) and 2.1 to 2.9-fold (patB). Ciprofloxacin-induction was related with a lower predicted free energy for the stem-loop structure in the RNA of S. pseudopneumoniae isolates (-13.81 and -8.58) than for R6 (-15.32 kcal/mol), which may ease transcription. The presence of these regulatory variations in commensal S. pseudopneumoniae isolates, and the possibility of its transfer to Streptococcus pneumoniae by genetic transformation, could increase fluoroquinolone resistance in this important pathogen.
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Affiliation(s)
- María Alvarado
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio J. Martín-Galiano
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María J. Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Ángel Zaballos
- Unidad de Genómica, Instituto de Salud Carlos III, Madrid, Spain
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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El Moujaber G, Osman M, Rafei R, Dabboussi F, Hamze M. Molecular mechanisms and epidemiology of resistance in Streptococcus pneumoniae in the Middle East region. J Med Microbiol 2017. [DOI: 10.1099/jmm.0.000503] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Grace El Moujaber
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
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Yılmaz Ç, Özcengiz G. Antibiotics: Pharmacokinetics, toxicity, resistance and multidrug efflux pumps. Biochem Pharmacol 2017; 133:43-62. [DOI: 10.1016/j.bcp.2016.10.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/14/2016] [Indexed: 02/03/2023]
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Mikalayeva V, Sakalauskaitė S, Daugelavičius R. Interaction of ethidium and tetraphenylphosphonium cations with Salmonella enterica cells. MEDICINA-LITHUANIA 2017; 53:122-130. [PMID: 28462872 DOI: 10.1016/j.medici.2017.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/01/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND AND OBJECTIVE One of the main causes of bacterial resistance to antimicrobials is multidrug resistance induced by the increased efficiency of the efflux pumps. In this study we analyzed how the conditions of assay affect the efflux of indicator substrates ethidium (Et+) and tetraphenylphosphonium (TPP+) in Salmonella enterica ser. Typhimurium cells. Impact of the outer membrane permeability barrier, composition and temperature of the medium on accumulation of the indicator compounds also was analyzed. MATERIALS AND METHODS The fluorescence of Et+ and Nile Red was measured using 96-well plates and a plate reader. In parallel to traditional studies of fluorescence we applied a constructed selective electrode to follow the accumulation of Et+ in S. enterica cells. Simultaneously with monitoring of Et+ concentration in the cell incubation medium, electrochemical measurements of TPP+ accumulation were performed. Furthermore, Et+ and TPP+ were used within the same sample as agents competing for the interaction with the efflux pumps. An inhibitor phenylalanyl-arginyl-β-naphtylamide (PAβN) was applied to evaluate the input of RND-family pumps in the total efflux of these indicator compounds. RESULTS S. enterica cells with the intact outer membrane (OM) bound very low amounts of Et+ or TPP+. Cells with the permeabilized OM accumulate considerably higher amounts of the indicator compounds at pH 8.0, but only Et+ was considerably accumulated at pH 6.5. At conditions of electrochemical monitoring accumulation of Et+ by the permeabilized cells at 37°C was considerably faster than at 23°C, but at the higher temperature most of the cell-accumulated Et+ was extruded back to the medium. The fluorescence of Et+ in suspension of cells incubated in 400mmol/L Tris buffer was about twice higher compared to 100mmol/L one. The inhibitory action of TPP+ on Et+ efflux was evident only in 400mmol/L Tris although PAβN effectively increased Et+ fluorescence at both buffer concentrations. CONCLUSIONS Results of our experiments indicate that ionic strength of the incubation medium influence the selectivity, the medium temperature and the assay conditions impact the kinetics of efflux. The lower accumulated amount and the weaker fluorescence of Et+ registered in slightly acidic medium indicate that ΔΨ plays a role in the accumulation of this indicator cation. The bound amount of Et+ to the de-energized or permeabilized cells considerably varies depending on the conditions and methods of de-energization or permeabilization of cells. Tris/EDTA permeabilization of the cells does not inhibit the efflux.
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Affiliation(s)
- Valeryia Mikalayeva
- Department of Biochemistry, Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania; Institute of Cardiology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Sandra Sakalauskaitė
- Department of Biochemistry, Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania
| | - Rimantas Daugelavičius
- Department of Biochemistry, Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania.
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Sharma A, Sharma R, Bhattacharyya T, Bhando T, Pathania R. Fosfomycin resistance in Acinetobacter baumannii is mediated by efflux through a major facilitator superfamily (MFS) transporter-AbaF. J Antimicrob Chemother 2016; 72:68-74. [PMID: 27650185 DOI: 10.1093/jac/dkw382] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVES To decipher the function of A1S_1331, named AbaF (Acinetobacter baumannii Fosfomycin efflux), one of the primary targets of AbsR25, a small RNA of A. baumannii. METHODS abaF was cloned in a multicopy plasmid and expressed from its native promoter in an efflux-deficient strain-Escherichia coli KAM32. Drug susceptibility, accumulation and efflux of ethidium bromide (EtBr) were determined in this strain. abaF was disrupted in A. baumannii using homologous recombination and its effect on drug susceptibility, biofilm formation and virulence was studied. Expression of abaF was followed by quantitative PCR in fosfomycin-challenged A. baumannii and fosfomycin-resistant mutants of A. baumannii. Expression of abaF in clinical strains of A. baumannii was determined by RT-PCR. RESULTS Expression of abaF in E. coli KAM32 resulted in increased resistance to fosfomycin. Lower accumulation and higher efflux of EtBr from this strain confirmed the role of AbaF as an efflux pump. Disruption of abaF in A. baumannii caused an increase in fosfomycin susceptibility and a decrease in biofilm formation and virulence. The expression of abaF was higher in A. baumannii cells exposed to fosfomycin and in cells resistant to higher concentrations of fosfomycin. The clinically relevant strains of A. baumannii also tested positive for the expression of abaF. CONCLUSIONS The results of this study suggest that efflux is an important mechanism of fosfomycin resistance and AbaF is involved in fosfomycin resistance in A. baumannii. AbaF also seems to play a role in biofilm formation and virulence of A. baumannii.
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Affiliation(s)
- Atin Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Rajnikant Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Tapas Bhattacharyya
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Timsy Bhando
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ranjana Pathania
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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25
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Schindler BD, Kaatz GW. Multidrug efflux pumps of Gram-positive bacteria. Drug Resist Updat 2016; 27:1-13. [DOI: 10.1016/j.drup.2016.04.003] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/28/2016] [Accepted: 04/22/2016] [Indexed: 11/16/2022]
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26
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Ceyssens PJ, Van Bambeke F, Mattheus W, Bertrand S, Fux F, Van Bossuyt E, Damée S, Nyssen HJ, De Craeye S, Verhaegen J, Tulkens PM, Vanhoof R. Molecular Analysis of Rising Fluoroquinolone Resistance in Belgian Non-Invasive Streptococcus pneumoniae Isolates (1995-2014). PLoS One 2016; 11:e0154816. [PMID: 27227336 PMCID: PMC4881901 DOI: 10.1371/journal.pone.0154816] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/19/2016] [Indexed: 11/25/2022] Open
Abstract
We present the results of a longitudinal surveillance study (1995–2014) on fluoroquinolone resistance (FQ-R) among Belgian non-invasive Streptococcus pneumoniae isolates (n = 5,602). For many years, the switch to respiratory fluoroquinolones for the treatment of (a)typical pneumonia had no impact on FQ-R levels. However, since 2011 we observed a significant decrease in susceptibility towards ciprofloxacin, ofloxacin and levofloxacin with peaks of 9.0%, 6.6% and 3.1% resistant isolates, respectively. Resistance to moxifloxacin arised sporadically, and remained <1% throughout the entire study period. We observed classical topoisomerase mutations in gyrA (n = 25), parC (n = 46) and parE (n = 3) in varying combinations, arguing against clonal expansion of FQ-R. The impact of recombination with co-habiting commensal streptococci on FQ-R remains marginal (10.4%). Notably, we observed that a rare combination of DNA Gyrase mutations (GyrA_S81L/GyrB_P454S) suffices for high-level moxifloxacin resistance, contrasting current model. Interestingly, 85/422 pneumococcal strains display MICCIP values which were lowered by at least four dilutions by reserpine, pointing at involvement of efflux pumps in FQ-R. In contrast to susceptible strains, isolates resistant to ciprofloxacin significantly overexpressed the ABC pump PatAB in comparison to reference strain S. pneumoniae ATCC 49619, but this could only be linked to disruptive terminator mutations in a fraction of these. Conversely, no difference in expression of the Major Facilitator PmrA, unaffected by reserpine, was noted between susceptible and resistant S. pneumoniae strains. Finally, we observed that four isolates displayed intermediate to high-level ciprofloxacin resistance without any known molecular resistance mechanism. Focusing future molecular studies on these isolates, which are also commonly found in other studies, might greatly assist in the battle against rising pneumococcal drug resistance.
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Affiliation(s)
- Pieter-Jan Ceyssens
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Françoise Van Bambeke
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Wesley Mattheus
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Sophie Bertrand
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Frédéric Fux
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Eddie Van Bossuyt
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Sabrina Damée
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Henry-Jean Nyssen
- Unit of Foodborne Pathogens, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Stéphane De Craeye
- Unit of Foodborne Pathogens, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Jan Verhaegen
- Laboratory of Clinical Bacteriology and Mycology, KULeuven, 3000 Leuven, Belgium
| | | | - Paul M. Tulkens
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Raymond Vanhoof
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
- * E-mail:
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Differences in antibiotic-induced oxidative stress responses between laboratory and clinical isolates of Streptococcus pneumoniae. Antimicrob Agents Chemother 2015; 59:5420-6. [PMID: 26100702 DOI: 10.1128/aac.00316-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 06/15/2015] [Indexed: 11/20/2022] Open
Abstract
Oxidants were shown to contribute to the lethality of bactericidal antibiotics in different bacterial species, including the laboratory strain Streptococcus pneumoniae R6. Resistance to penicillin among S. pneumoniae R6 mutants was further shown to protect against the induction of oxidants upon exposure to unrelated bactericidal compounds. In the work described here, we expanded on these results by studying the accumulation of reactive oxygen species in the context of antibiotic sensitivity and resistance by including S. pneumoniae clinical isolates. In S. pneumoniae R6, penicillin, ciprofloxacin, and kanamycin but not the bacteriostatic linezolid, erythromycin, or tetracycline induced the accumulation of reactive oxygen species. For the three bactericidal compounds, resistance to a single molecule prevented the accumulation of oxidants upon exposure to unrelated bactericidal antibiotics, and this was accompanied by a reduced lethality. This phenomenon does not involve target site mutations but most likely implicates additional mutations occurring early during the selection of resistance to increase survival while more efficient resistance mechanisms are being selected or acquired. Bactericidal antibiotics also induced oxidants in sensitive S. pneumoniae clinical isolates. The importance of oxidants in the lethality of bactericidal antibiotics was less clear than for S. pneumoniae R6, however, since ciprofloxacin induced oxidants even in ciprofloxacin-resistant S. pneumoniae clinical isolates. Our results provide a clear example of the complex nature of the mode of action of antibiotics. The adaptive approach to oxidative stress of S. pneumoniae is peculiar, and a better understanding of the mechanism implicated in response to oxidative injury should also help clarify the role of oxidants induced by antibiotics.
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Lupien A, Gingras H, Bergeron MG, Leprohon P, Ouellette M. Multiple mutations and increased RNA expression in tetracycline-resistant Streptococcus pneumoniae as determined by genome-wide DNA and mRNA sequencing. J Antimicrob Chemother 2015; 70:1946-59. [PMID: 25862682 DOI: 10.1093/jac/dkv060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/13/2015] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVES The objective of this study was to characterize chromosomal mutations associated with resistance to tetracycline in Streptococcus pneumoniae. METHODS Chronological appearance of mutations in two S. pneumoniae R6 mutants (R6M1TC-5 and R6M2TC-4) selected for resistance to tetracycline was determined by next-generation sequencing. A role for the mutations identified was confirmed by reconstructing resistance to tetracycline in a S. pneumoniae R6 WT background. RNA sequencing was performed on R6M1TC-5 and R6M2TC-4 and the relative expression of genes was reported according to R6. Differentially expressed genes were classified according to their ontology. RESULTS WGS of R6M1TC-5 and R6M2TC-4 revealed mutations in the gene rpsJ coding for the ribosomal protein S10 and in the promoter region and coding sequences of the ABC genes patA and patB. These cells were cross-resistant to ciprofloxacin. Resistance reconstruction confirmed a role in resistance for the mutations in rpsJ and patA. Overexpression of the ABC transporter PatA/PatB or mutations in the coding sequence of patA contributed to resistance to tetracycline, ciprofloxacin and ethidium bromide, and was associated with a decreased accumulation of [(3)H]tetracycline. Comparative transcriptome profiling of the resistant mutants further revealed that, in addition to the overexpression of patA and patB, several genes of the thiamine biosynthesis and salvage pathway were increased in the two mutants, but also in clinical isolates resistant to tetracycline. This overexpression most likely contributes to the tetracycline resistance phenotype. CONCLUSIONS The combination of genomic and transcriptomic analysis coupled to functional studies has allowed the discovery of novel tetracycline resistance mutations in S. pneumoniae.
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Affiliation(s)
- Andréanne Lupien
- Centre de recherche en Infectiologie du Centre de recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Hélène Gingras
- Centre de recherche en Infectiologie du Centre de recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Michel G Bergeron
- Centre de recherche en Infectiologie du Centre de recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Philippe Leprohon
- Centre de recherche en Infectiologie du Centre de recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Marc Ouellette
- Centre de recherche en Infectiologie du Centre de recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
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Baylay AJ, Ivens A, Piddock LJV. A novel gene amplification causes upregulation of the PatAB ABC transporter and fluoroquinolone resistance in Streptococcus pneumoniae. Antimicrob Agents Chemother 2015; 59:3098-108. [PMID: 25779578 PMCID: PMC4432121 DOI: 10.1128/aac.04858-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/01/2015] [Indexed: 01/14/2023] Open
Abstract
Overexpression of the ABC transporter genes patA and patB confers efflux-mediated fluoroquinolone resistance in Streptococcus pneumoniae and is also linked to pneumococcal stress responses. Although upregulation of patAB has been observed in many laboratory mutants and clinical isolates, the regulatory mechanisms controlling expression of these genes are unknown. In this study, we aimed to identify the cause of high-level constitutive overexpression of patAB in M184, a multidrug-resistant mutant of S. pneumoniae R6. Using a whole-genome transformation and sequencing approach, we identified a novel duplication of a 9.2-kb region of the M184 genome which included the patAB genes. This duplication did not affect growth and was semistable with a low segregation rate. The expression levels of patAB in M184 were much higher than those that could be fully explained by doubling of the gene dosage alone, and inactivation of the first copy of patA had no effect on multidrug resistance. Using a green fluorescent protein reporter system, increased patAB expression was ascribed to transcriptional read-through from a tRNA gene upstream of the second copy of patAB. This is the first report of a large genomic duplication causing antibiotic resistance in S. pneumoniae and also of a genomic duplication causing antibiotic resistance by a promoter switching mechanism.
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Affiliation(s)
- Alison J Baylay
- Antimicrobials Research Group, School of Immunity and Infection, Institute of Microbiology and Infection, and College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Alasdair Ivens
- Centre for Immunity, Infection and Evolution, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura J V Piddock
- Antimicrobials Research Group, School of Immunity and Infection, Institute of Microbiology and Infection, and College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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