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Collins J, Osheroff N. Gyrase and Topoisomerase IV: Recycling Old Targets for New Antibacterials to Combat Fluoroquinolone Resistance. ACS Infect Dis 2024; 10:1097-1115. [PMID: 38564341 PMCID: PMC11019561 DOI: 10.1021/acsinfecdis.4c00128] [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: 02/16/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Beyond their requisite functions in many critical DNA processes, the bacterial type II topoisomerases, gyrase and topoisomerase IV, are the targets of fluoroquinolone antibacterials. These drugs act by stabilizing gyrase/topoisomerase IV-generated DNA strand breaks and by robbing the cell of the catalytic activities of these essential enzymes. Since their clinical approval in the mid-1980s, fluoroquinolones have been used to treat a broad spectrum of infectious diseases and are listed among the five "highest priority" critically important antimicrobial classes by the World Health Organization. Unfortunately, the widespread use of fluoroquinolones has been accompanied by a rise in target-mediated resistance caused by specific mutations in gyrase and topoisomerase IV, which has curtailed the medical efficacy of this drug class. As a result, efforts are underway to identify novel antibacterials that target the bacterial type II topoisomerases. Several new classes of gyrase/topoisomerase IV-targeted antibacterials have emerged, including novel bacterial topoisomerase inhibitors, Mycobacterium tuberculosis gyrase inhibitors, triazaacenaphthylenes, spiropyrimidinetriones, and thiophenes. Phase III clinical trials that utilized two members of these classes, gepotidacin (triazaacenaphthylene) and zoliflodacin (spiropyrimidinetrione), have been completed with positive outcomes, underscoring the potential of these compounds to become the first new classes of antibacterials introduced into the clinic in decades. Because gyrase and topoisomerase IV are validated targets for established and emerging antibacterials, this review will describe the catalytic mechanism and cellular activities of the bacterial type II topoisomerases, their interactions with fluoroquinolones, the mechanism of target-mediated fluoroquinolone resistance, and the actions of novel antibacterials against wild-type and fluoroquinolone-resistant gyrase and topoisomerase IV.
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Affiliation(s)
- Jessica
A. Collins
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Medicine (Hematology/Oncology), Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
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2
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Zhang J, Tan YM, Li SR, Battini N, Zhang SL, Lin JM, Zhou CH. Discovery of benzopyridone cyanoacetates as new type of potential broad-spectrum antibacterial candidates. Eur J Med Chem 2024; 265:116107. [PMID: 38171147 DOI: 10.1016/j.ejmech.2023.116107] [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: 11/23/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024]
Abstract
Unique benzopyridone cyanoacetates (BCs) as new type of promising broad-spectrum antibacterial candidates were discovered with large potential to combat the lethal multidrug-resistant bacterial infections. Many prepared BCs showed broad antibacterial spectrum with low MIC values against the tested strains. Some highly active BCs exhibited rapid sterilization capacity, low resistant trend and good predictive pharmacokinetic properties. Furthermore, the highly active sodium BCs (NaBCs) displayed low hemolysis and cytotoxicity, and especially octyl NaBC 5g also showed in vivo potent anti-infective potential and appreciable pharmacokinetic profiles. A series of preliminary mechanistic explorations indicated that these active BCs could effectively eliminate bacterial biofilm and destroy membrane integrity, thus resulting in the leakage of bacterial cytoplasm. Moreover, their unique structures might further bind to intracellular DNA, DNA gyrase and topoisomerase IV through various direct noncovalent interactions to hinder bacterial reproduction. Meanwhile, the active BCs also induced bacterial oxidative stress and metabolic disturbance, thereby accelerating bacterial apoptosis. These results provided a bright hope for benzopyridone cyanoacetates as potential novel multitargeting broad-spectrum antibacterial candidates to conquer drug resistance.
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Affiliation(s)
- Jing Zhang
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yi-Min Tan
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Shu-Rui Li
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Narsaiah Battini
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Shao-Lin Zhang
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, China.
| | - Jian-Mei Lin
- Department of Infections, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
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3
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Singh S, Verma T, Khamari B, Bulagonda EP, Nandi D, Umapathy S. Antimicrobial Resistance Studies Using Raman Spectroscopy on Clinically Relevant Bacterial Strains. Anal Chem 2023. [PMID: 37463121 DOI: 10.1021/acs.analchem.3c01453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
There has been a steep rise in the emergence of antibiotic-resistant bacteria in the past few years. A timely diagnosis can help in initiating appropriate antibiotic therapy. However, conventional techniques for diagnosing antibiotic resistance are time-consuming and labor-intensive. Therefore, we investigated the potential of Raman spectroscopy as a rapid surveillance technology for tracking the emergence of antibiotic resistance. In this study, we used Raman spectroscopy to differentiate clinical isolates of antibiotic-resistant and -sensitive bacteria of Escherichia coli, Acinetobacter baumannii, and Enterobacter species. The spectra were collected with or without exposure to various antibiotics (ciprofloxacin, gentamicin, meropenem, and nitrofurantoin), each having a distinct mechanism of action. Ciprofloxacin- and meropenem-treated sensitive strains showed a decrease in the intensity of Raman bands associated with DNA (667, 724, 785, 1378, 1480, and 1575 cm-1) and proteins (640 and 1662 cm-1), coupled with an increase in the intensity of lipid bands (891, 960, and 1445 cm-1). Gentamicin- and nitrofurantoin-treated sensitive strains showed an increase in the intensity of nucleic acid bands (668, 724, 780, 810, 1378, 1480, and 1575 cm-1) while a decrease in the intensity of protein bands (640, 1003, 1606, and 1662 cm-1) and the lipid band (1445 cm-1). The Raman spectral changes observed in the antibiotic-resistant strains were opposite to that of antibiotic-sensitive strains. The Raman spectral data correlated well with the antimicrobial susceptibility test results. The Raman spectral dataset was used for partial least-squares (PLS) analysis to validate the biomarkers obtained from the univariate analysis. Overall, this study showcases the potential of Raman spectroscopy for detecting antibiotic-resistant and -sensitive bacteria.
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Affiliation(s)
- Saumya Singh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Taru Verma
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Balaram Khamari
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Eswarappa Pradeep Bulagonda
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Dipankar Nandi
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, Karnataka, India
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4
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Osorio Garcia MA, Wood EA, Keck JL, Cox MM. Interaction with single-stranded DNA-binding protein (SSB) modulates Escherichia coli RadD DNA repair activities. J Biol Chem 2023; 299:104773. [PMID: 37142225 DOI: 10.1016/j.jbc.2023.104773] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
The bacterial RadD enzyme is important for multiple genome maintenance pathways, including RecA DNA strand exchange and RecA-independent suppression of DNA crossover template switching. However, much remains unknown about the precise roles of RadD. One potential clue into RadD mechanisms is its direct interaction with the single-stranded DNA binding protein (SSB), which coats single-stranded DNA exposed during genome maintenance reactions in cells. Interaction with SSB stimulates the ATPase activity of RadD. To probe the mechanism and importance of RadD:SSB complex formation, we identified a pocket on RadD that is essential for binding SSB. In a mechanism shared with many other SSB-interacting proteins, RadD uses a hydrophobic pocket framed by basic residues to bind the C-terminal end of SSB. We found that RadD variants that substitute acidic residues for basic residues in the SSB binding site impair RadD:SSB complex formation and eliminate SSB stimulation of RadD ATPase activity in vitro. Additionally, mutant E. coli strains carrying charge reversal radD changes display increased sensitivity to DNA damaging agents synergistically with deletions of radA and recG, although the phenotypes of the SSB-binding radD mutants are not as severe as a full radD deletion. This suggests that cellular RadD requires an intact the interaction with SSB for full RadD function.
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Affiliation(s)
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin, Madison, Madison, WI 53706
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA.
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin, Madison, Madison, WI 53706.
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McKenzie AM, Henry C, Myers KS, Place MM, Keck JL. Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli. G3 (BETHESDA, MD.) 2022; 12:jkac295. [PMID: 36326440 PMCID: PMC9713433 DOI: 10.1093/g3journal/jkac295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 11/30/2023]
Abstract
Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in Escherichia coli. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in E. coli and other bacteria. Three replication restart pathways have been identified in E. coli: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon-insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the priB replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel priB interactions were discovered. Targeted genetic and imaging-based experiments with priB and its genetic partners revealed significant double-strand DNA break accumulation in strains with mutations in dam, rep, rdgC, lexA, or polA. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of rdgC or lexA mutations in ΔpriB cells. Taken together, our results highlight roles for several genes in double-strand DNA break homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in E. coli.
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Affiliation(s)
- Aidan M McKenzie
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Camille Henry
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kevin S Myers
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Michael M Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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6
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Singh S, Verma T, Nandi D, Umapathy S. Herbicides 2,4-Dichlorophenoxy Acetic Acid and Glyphosate Induce Distinct Biochemical Changes in E. coli during Phenotypic Antibiotic Resistance: A Raman Spectroscopic Study. J Phys Chem B 2022; 126:8140-8154. [PMID: 36205931 DOI: 10.1021/acs.jpcb.2c04151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Antibiotic resistance is a major global health concern. The increased use of herbicides may lead to multiple antibiotic resistance in bacteria. Conventional techniques for diagnosing antibiotic resistance are laborious, time-intensive, expensive, and lack information about antibiotic susceptibility. On the other hand, Raman spectroscopy is a rapid, label-free, noninvasive alternative to traditional techniques to detect antibiotic resistance. In this study, two popular herbicides 2,4-dichlorophenoxy acetic acid (2,4-D) and N-(phosphonomethyl)glycine (glyphosate) were used to study their effects on the emergence of antibiotic resistance. The Escherichia coli wild-type (WT) MG1655 strain and two isogenic mutants, Δlon and ΔacrB, were used together with Raman spectroscopy. The WT E. coli is sensitive to antibiotics, but exposure to both herbicides induces antibiotic resistance. Using an excitation wavelength of 785 nm, the intensity ratios (e.g., I740/I785, I740/I1003, I1480/I1445, I2934/I2868, and I2934/I2845) were identified as biomarkers to study the induction of antibiotic resistance in bacteria but not NaCl-mediated stress. Using an excitation wavelength of 633 nm, the peak intensity at 740 cm-1 assigned to cytochrome bd decreases under antibiotic stress but increases upon exposure to both herbicides and antibiotics, indicating the development of resistance. Thus, this study can be applied to monitor antibiotic resistance using Raman spectroscopy.
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Affiliation(s)
- Saumya Singh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Taru Verma
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore560012, India
| | - Dipankar Nandi
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore560012, India.,Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore560012, India.,Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, India
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7
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Aminipoya H, Bagheri GH A. Ciprofloxacin: Binding Efficacy with DNA and Enhanced Photocatalytic Degradation by ZrO 2 Synthesized Using Coffee Extract. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2102665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Hana Aminipoya
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Azar Bagheri GH
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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8
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Jaramillo‐Riveri S, Broughton J, McVey A, Pilizota T, Scott M, El Karoui M. Growth-dependent heterogeneity in the DNA damage response in Escherichia coli. Mol Syst Biol 2022; 18:e10441. [PMID: 35620827 PMCID: PMC9136515 DOI: 10.15252/msb.202110441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 04/13/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
In natural environments, bacteria are frequently exposed to sub-lethal levels of DNA damage, which leads to the induction of a stress response (the SOS response in Escherichia coli). Natural environments also vary in nutrient availability, resulting in distinct physiological changes in bacteria, which may have direct implications on their capacity to repair their chromosomes. Here, we evaluated the impact of varying the nutrient availability on the expression of the SOS response induced by chronic sub-lethal DNA damage in E. coli. We found heterogeneous expression of the SOS regulon at the single-cell level in all growth conditions. Surprisingly, we observed a larger fraction of high SOS-induced cells in slow growth as compared with fast growth, despite a higher rate of SOS induction in fast growth. The result can be explained by the dynamic balance between the rate of SOS induction and the division rates of cells exposed to DNA damage. Taken together, our data illustrate how cell division and physiology come together to produce growth-dependent heterogeneity in the DNA damage response.
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Affiliation(s)
| | - James Broughton
- Institute of Cell Biology and SynthSysUniversity of EdinburghEdinburghUK
| | - Alexander McVey
- Institute of Cell Biology and SynthSysUniversity of EdinburghEdinburghUK
- Present address:
OGI Bio LtdEdinburghUK
| | - Teuta Pilizota
- Institute of Cell Biology and SynthSysUniversity of EdinburghEdinburghUK
| | - Matthew Scott
- Department of Applied MathematicsUniversity of WaterlooWaterlooONCanada
| | - Meriem El Karoui
- Institute of Cell Biology and SynthSysUniversity of EdinburghEdinburghUK
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9
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Rapid antimicrobial susceptibility profiling using impedance spectroscopy. Biosens Bioelectron 2022; 200:113876. [PMID: 34974262 DOI: 10.1016/j.bios.2021.113876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/29/2021] [Accepted: 11/18/2021] [Indexed: 11/20/2022]
Abstract
The present antibiotic susceptibility testing (AST) techniques based on bacterial culture, gene amplification and mass spectrometry are highly time consuming, labour intensive or expensive. Impedance spectroscopy is an emerging tool for rapid bacterial analysis as it is label-free, real-time, affordable and high-throughput. The over-reliance of this technique on complex chip designs and cell enrichment strategies has, however, slowed its foray into clinical AST. We demonstrate a label-free approach in which a low conductivity zwitterionic buffer is used for boosting impedance sensitivity in simple interdigitated electrodes (IDEs) allowing rapid AST in just 20 min without any liquid flow, biofunctionalization or cell enrichment steps. The detection principle relies on measuring changes in solution resistance due to antibiotic-induced bacterial cell death or growth. While the death-based approach is faster (20 min), it's restricted to surface-acting bactericidal antibiotics. The cell growth approach is longer (60-80 min) but more versatile as it applies to all drug types. Results for antibiotic sensitivity analysis and minimum inhibitory concentration (MIC) determination are illustrated for Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus against a wide class of antibiotics (penicillins, cephalosporins, polymyxins, carbapenems etc.).
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10
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Unique physiological and genetic features of ofloxacin-resistant Streptomyces mutants. Appl Environ Microbiol 2021; 88:e0232721. [PMID: 34936843 DOI: 10.1128/aem.02327-21] [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
New antimicrobial agents are urgently needed to combat the emergence and spread of multidrug-resistant bacteria. Activating the cryptic biosynthetic gene clusters for actinomycete secondary metabolites can provide essential clues for research into new antimicrobial agents. An effective method for this purpose is based on drug resistance selection. This report describes interesting results for drug resistance selection using antibiotics that target DNA replication can effectively potentiate secondary metabolite production by actinomycetes. Ofloxacin-resistant mutants were isolated from five different streptomycetes. Ofloxacin is an antibiotic that binds to DNA complexes and type II topoisomerase, causing double-stranded breaks in bacterial chromosomes. Physiological and genetic characterization of the mutants revealed that the development of ofloxacin resistance in streptomycetes leads to the emergence of various types of secondary metabolite-overproducing strains. In Streptomyces coelicolor A3(2), ofloxacin-resistant mutants that overproduced actinorhodin, undecylprodigiosin, or carotenoid were identified. Also, an ofloxacin-resistant mutant that overproduces methylenomycin A, whose biosynthetic gene cluster is located on the endogenous plasmid, SCP1, was isolated. These observations indicate that ofloxacin resistance might activate biosynthetic genes on both chromosomes and on endogenous plasmids. We also identified the mutations that are probably involved in the phenotype of ofloxacin resistance and secondary metabolite overproduction in S. coelicolor A3(2). Furthermore, we observed an interesting phenomenon in which several ofloxacin-resistant mutants overproduced antibiotics in the presence of ofloxacin. Based on these results, we present the unique physiological and genetic characteristics of ofloxacin-resistant Streptomyces mutants and discuss the importance and potential development of the new findings. IMPORTANCE The abuse or overuse of antibacterial agents for therapy and animal husbandry has caused an increased population of antimicrobial-resistant bacteria in the environment. Consequently, there are now fewer effective antimicrobials available. Due to the depleted antibiotic pipeline, pandemic outbreaks caused by antimicrobial-resistant bacteria are deeply concerned, and the development of new antibiotics is now an urgent issue. Promising sources of antimicrobial agents include cryptic biosynthetic gene clusters for secondary metabolites in streptomycetes and rare actinomycetes. This study's significance is an unprecedented activation method to accelerate drug discovery research on a global scale. The technique developed in this study could allow for simultaneous drug discovery in different countries, maximizing the world's microbial resources.
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11
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Azithromycin and Ciprofloxacin Can Promote Antibiotic Resistance in Biosolids and Biosolids-Amended Soils. Appl Environ Microbiol 2021; 87:e0037321. [PMID: 34085858 DOI: 10.1128/aem.00373-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spread of biosolids-borne antibiotic resistance is a growing public and environmental health concern. Herein, we conducted incubation experiments involving biosolids, which are byproducts of sewage treatment processes, and biosolids-amended soil. Quantitative reverse transcription-PCR (RT-qPCR) was employed to assess responses of select antibiotic resistance genes (ARGs) and mobile elements to environmentally relevant concentrations of two biosolids-borne antibiotics, azithromycin (AZ) and ciprofloxacin (CIP). Additionally, we examined sequence distribution of gyrA (encoding DNA gyrase; site of action of CIP) to assess potential shifts in genotype. Increasing antibiotic concentrations generally increased the transcriptional activities of qnrS (encoding CIP resistance) and ermB and mefE (encoding AZ resistance). The transcriptional activity of intl1, a marker of class 1 integrons, was unaffected by CIP or AZ concentrations, but biosolids amendment increased intl1 activity in the soil by 4 to 5 times, which persisted throughout incubation. While the dominant gyrA sequences found herein were unrelated to known CIP-resistant genotypes, the increasing CIP concentrations significantly decreased the diversity of genes encoding the DNA gyrase A subunit, suggesting changes in microbial community structures. This study suggests that biosolids harbor transcriptionally active ARGs and mobile elements that could survive and spread in biosolids-amended soils. However, more research is warranted to investigate these trends under field conditions. IMPORTANCE Although previous studies have indicated that biosolids may be important spreaders of antibiotics and antibiotic resistance genes (ARGs) in environments, the potential activities of ARGs or their responses to environmental parameters have been understudied. This study highlights that certain biosolids-borne antibiotics can induce transcriptional activities of ARGs and mobile genetic elements in biosolids and biosolids-amended soil, even when present at environmentally relevant concentrations. Furthermore, these antibiotics can alter the structure of microbial populations expressing ARGs. Our findings indicate the bioavailability of the antibiotics in biosolids and provide evidence that biosolids can promote the activities and dissemination of ARGs and mobile genes in biosolids and soils that receive contaminated biosolids, thus, underscoring the importance of investigating anthropogenically induced antibiotic resistance in the environment under real-world scenarios.
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12
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Zhou L, Alcalde RE, Deng J, Zuniga B, Sanford RA, Fouke BW, Werth CJ. Impact of antibiotic concentration gradients on nitrate reduction and antibiotic resistance in a microfluidic gradient chamber. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146503. [PMID: 34030234 DOI: 10.1016/j.scitotenv.2021.146503] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
In order to explore the impact of antibiotics on the bacterial metabolic cycling of nitrate within contaminated soil and groundwater environments, we compared the effects of polymyxin B (PMB) and ciprofloxacin (CIP) concentration gradients on the distribution and activity of a wild type (WT) and a flagella deficient mutant (Δflag) of Shewanella oneidensis MR-1 in a microfluidic gradient chamber (MGC). Complementary batch experiments were performed to measure bacteriostatic versus bactericidal concentrations of the two antibiotics, as well as their effect on nitrate reduction. Prior work demonstrated that PMB disrupts cell membranes while CIP inhibits DNA synthesis. Consistent with these modes of action, batch results from this work show that PMB is bactericidal at lower concentrations than CIP relative to their respective minimum inhibitory concentrations (MICs) (≥5× MICPMB vs. ≥20× MICCIP). Concentration gradients from 0 to 50× the MIC of both antibiotics were established in the MGC across a 2-cm interconnected pore network, with nutrients injected at both concentration boundaries. The WT cells could only access and reduce nitrate in regions of the MGC with PMB at <18× MICPMB, whereas this occurred with CIP up to 50× MICCIP; and cells extracted from these MGCs showed no antibiotic resistance. The distribution of Δflag cells was further limited to lower antibiotic concentrations (≤1× MICPMB, ≤43× MICCIP) due to inability of movement. These results indicate that S. oneidensis access and reduce nitrate in bactericidal regions via chemotactic migration without development of antibiotic resistance, and that this migration is inhibited by acutely lethal bactericidal levels of antibiotics.
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Affiliation(s)
- Lang Zhou
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Reinaldo E Alcalde
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Jinzi Deng
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Baltazar Zuniga
- College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Bruce W Fouke
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Charles J Werth
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA.
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Murawski AM, Brynildsen MP. Ploidy is an important determinant of fluoroquinolone persister survival. Curr Biol 2021; 31:2039-2050.e7. [PMID: 33711253 PMCID: PMC8183807 DOI: 10.1016/j.cub.2021.02.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 02/04/2023]
Abstract
Genetic mutants have demonstrated the importance of homologous recombination (HR) to fluoroquinolone (FQ) persistence, which suggests that single-cell chromosome (Chr) abundance might be a phenotypic variable of importance to persisters. Here, we sorted stationary-phase E. coli based on ploidy and subjected the subpopulations to tolerance assays. Subpopulations sorted to contain diploid cells harbored up to ∼40-fold more FQ persisters than those sorted to contain monoploid cells. This association was observed with distinct FQs, in independent environmental conditions, and with more than one strain of E. coli (MG1655; uropathogenic CFT073) but was abolished in HR-deficient strains (ΔrecA and ΔrecB). It was observed that the persister level of monoploid subpopulations exceeded those of ΔrecA and ΔrecB by 10-fold or more, and subsequent high-purity sorting confirmed that observation. Those data suggested the existence of distinct FQ persister subtypes: those that are and are not proficient with HR. Time-lapse microscopy revealed significant differences in initial size and growth dynamics during the post-antibiotic recovery period for persisters from monoploid- and diploid-enriched subpopulations. In addition, non-persisters in monoploid-enriched subpopulations elongated minimally following FQ treatment, resembling previous observations of HR-deficient strains, whereas non-persisters in diploid-enriched subpopulations on average filamented extensively. Together, these results identify a phenotypic variable with a significant impact on FQ persistence, establish the existence of more than one type of persister to the same antibiotic in an isogenic culture, and reveal roles for RecA and RecB in FQ persistence, even in the absence of homologous chromosomes.
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Affiliation(s)
- Allison M Murawski
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA.
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14
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Swami P, Sharma A, Anand S, Gupta S. DEPIS: A combined dielectrophoresis and impedance spectroscopy platform for rapid cell viability and antimicrobial susceptibility analysis. Biosens Bioelectron 2021; 182:113190. [PMID: 33866070 DOI: 10.1016/j.bios.2021.113190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/11/2021] [Accepted: 03/18/2021] [Indexed: 10/21/2022]
Abstract
Antimicrobial resistance (AMR) is caused by inappropriate or excessive antibiotic consumption. Early diagnosis of bacterial infections can greatly curb empirical treatment and thus AMR. Current diagnostic procedures are time-consuming as they rely on gene amplification and cell culture techniques that are inherently limited by the doubling rate of the involved species. Further, biochemical methods for species identification and antibiotic susceptibility testing for drug/dose effectiveness take several days and are non-scalable. We report a real-time, label-free approach called DEPIS that combines dielectrophoresis (DEP) for bacterial enrichment and impedance spectroscopy (IS) for cell viability analysis under 60 min. Target bacteria are captured on interdigitated electrodes using DEP (30 min) and their antibiotic-induced stress response is measured using IS (another 30 min). This principle is used to generate minimum bactericidal concentration (MBC) plots by measuring impedance change due to ionic release by dying bacteria in a low conductivity buffer. The results are rapid since they rely on cell death rather than cell growth which is an intrinsically slower process. The results are also highly specific and work across all bactericidal antibiotics studied, irrespective of their cellular target or drug action mechanism. More importantly, preliminary results with clinical isolates show that methicillin-susceptible Staphylococcus aureus (MSSA) can easily be differentiated from methicillin-resistant S. aureus (MRSA) under 1 h. This rapid cell analyses approach can aid in faster diagnosis of bacterial infections and benefit the clinical decision-making process for antibiotic treatment, addressing the critical issue of AMR.
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Affiliation(s)
- Pragya Swami
- Dept. of Chemical Engineering, Indian Institute of Technology, Delhi, 110016, India
| | - Ayush Sharma
- Dept. of Chemical Engineering, Indian Institute of Technology, Delhi, 110016, India
| | - Satyam Anand
- Dept. of Chemical Engineering, Indian Institute of Technology, Delhi, 110016, India
| | - Shalini Gupta
- Dept. of Chemical Engineering, Indian Institute of Technology, Delhi, 110016, India.
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15
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Verma T, Annappa H, Singh S, Umapathy S, Nandi D. Profiling antibiotic resistance in Escherichia coli strains displaying differential antibiotic susceptibilities using Raman spectroscopy. JOURNAL OF BIOPHOTONICS 2021; 14:e202000231. [PMID: 32981183 DOI: 10.1002/jbio.202000231] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/22/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
The rapid identification of antibiotic resistant bacteria is important for public health. In the environment, bacteria are exposed to sub-inhibitory antibiotic concentrations which has implications in the generation of multi-drug resistant strains. To better understand these issues, Raman spectroscopy was employed coupled with partial least squares-discriminant analysis to profile Escherichia coli strains treated with sub-inhibitory concentrations of antibiotics. Clear differences were observed between cells treated with bacteriostatic (tetracycline and rifampicin) and bactericidal (ampicillin, ciprofloxacin, and ceftriaxone) antibiotics for 6 hr: First, atomic force microscopy revealed that bactericidal antibiotics cause extensive cell elongation whereas short filaments are observed with bacteriostatic antibiotics. Second, Raman spectral analysis revealed that bactericidal antibiotics lower nucleic acid to protein (I812 /I830 ) and nucleic acid to lipid ratios (I1483 /I1452 ) whereas the opposite is seen with bacteriostatic antibiotics. Third, the protein to lipid ratio (I2936 /I2885 and I2936 /I2850 ) is a Raman stress signature common to both the classes. These signatures were validated using two mutants, Δlon and ΔacrB, that exhibit relatively high and low resistance towards antibiotics, respectively. In addition, these spectral markers correlated with the emergence of phenotypic antibiotic resistance. Overall, this study demonstrates the efficacy of Raman spectroscopy to identify resistance in bacteria to sub-lethal concentrations of antibiotics.
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Affiliation(s)
- Taru Verma
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Harshitha Annappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Saumya Singh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
| | - Siva Umapathy
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
| | - Dipankar Nandi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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16
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Bush NG, Diez-Santos I, Abbott LR, Maxwell A. Quinolones: Mechanism, Lethality and Their Contributions to Antibiotic Resistance. Molecules 2020; 25:E5662. [PMID: 33271787 PMCID: PMC7730664 DOI: 10.3390/molecules25235662] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/05/2022] Open
Abstract
Fluoroquinolones (FQs) are arguably among the most successful antibiotics of recent times. They have enjoyed over 30 years of clinical usage and become essential tools in the armoury of clinical treatments. FQs target the bacterial enzymes DNA gyrase and DNA topoisomerase IV, where they stabilise a covalent enzyme-DNA complex in which the DNA is cleaved in both strands. This leads to cell death and turns out to be a very effective way of killing bacteria. However, resistance to FQs is increasingly problematic, and alternative compounds are urgently needed. Here, we review the mechanisms of action of FQs and discuss the potential pathways leading to cell death. We also discuss quinolone resistance and how quinolone treatment can lead to resistance to non-quinolone antibiotics.
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Affiliation(s)
| | | | | | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (N.G.B.); (I.D.-S.); (L.R.A.)
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17
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Sun L, Ashcroft P, Ackermann M, Bonhoeffer S. Stochastic Gene Expression Influences the Selection of Antibiotic Resistance Mutations. Mol Biol Evol 2020; 37:58-70. [PMID: 31504754 PMCID: PMC6984361 DOI: 10.1093/molbev/msz199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteria can resist antibiotics by expressing enzymes that remove or deactivate drug molecules. Here, we study the effects of gene expression stochasticity on efflux and enzymatic resistance. We construct an agent-based model that stochastically simulates multiple biochemical processes in the cell and we observe the growth and survival dynamics of the cell population. Resistance-enhancing mutations are introduced by varying parameters that control the enzyme expression or efficacy. We find that stochastic gene expression can cause complex dynamics in terms of survival and extinction for these mutants. Regulatory mutations, which augment the frequency and duration of resistance gene transcription, can provide limited resistance by increasing mean expression. Structural mutations, which modify the enzyme or efflux efficacy, provide most resistance by improving the binding affinity of the resistance protein to the antibiotic; increasing the enzyme's catalytic rate alone may contribute to resistance if drug binding is not rate limiting. Overall, we identify conditions where regulatory mutations are selected over structural mutations, and vice versa. Our findings show that stochastic gene expression is a key factor underlying efflux and enzymatic resistances and should be taken into consideration in future antibiotic research.
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Affiliation(s)
- Lei Sun
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Peter Ashcroft
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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18
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Willcocks S, Huse KK, Stabler R, Oyston PCF, Scott A, Atkins HS, Wren BW. Genome-wide assessment of antimicrobial tolerance in Yersinia pseudotuberculosis under ciprofloxacin stress. Microb Genom 2019; 5. [PMID: 31580793 PMCID: PMC6927301 DOI: 10.1099/mgen.0.000304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Yersinia pseudotuberculosis is a Gram-negative bacterium capable of causing gastrointestinal infection and is closely related to the highly virulent plague bacillus Yersinia pestis. Infections by both species are currently treatable with antibiotics such as ciprofloxacin, a quinolone-class drug of major clinical importance in the treatment of many other infections. Our current understanding of the mechanism of action of ciprofloxacin is that it inhibits DNA replication by targeting DNA gyrase, and that resistance is primarily due to mutation of this target site, along with generic efflux and detoxification strategies. We utilized transposon-directed insertion site sequencing (TraDIS or TnSeq) to identify the non-essential chromosomal genes in Y. pseudotuberculosis that are required to tolerate sub-lethal concentrations of ciprofloxacin in vitro. As well as highlighting recognized antibiotic resistance genes, we provide evidence that multiple genes involved in regulating DNA replication and repair are central in enabling Y. pseudotuberculosis to tolerate the antibiotic, including DksA (yptb0734), a regulator of RNA polymerase, and Hda (yptb2792), an inhibitor of DNA replication initiation. We furthermore demonstrate that even at sub-lethal concentrations, ciprofloxacin causes severe cell-wall stress, requiring lipopolysaccharide lipid A, O-antigen and core biosynthesis genes to resist the sub-lethal effects of the antibiotic. It is evident that coping with the consequence(s) of antibiotic-induced stress requires the contribution of scores of genes that are not exclusively engaged in drug resistance.
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Affiliation(s)
- Samuel Willcocks
- The London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Kristin K Huse
- The London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Richard Stabler
- The London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Petra C F Oyston
- Microbiology, CBR Division, DSTL Porton Down, Salisbury SP4 0JQ, UK
| | - Andrew Scott
- Microbiology, CBR Division, DSTL Porton Down, Salisbury SP4 0JQ, UK
| | - Helen S Atkins
- University of Exeter, Exeter, Devon EX4 4SB, UK.,Microbiology, CBR Division, DSTL Porton Down, Salisbury SP4 0JQ, UK
| | - Brendan W Wren
- The London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
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19
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Cabral DJ, Penumutchu S, Reinhart EM, Zhang C, Korry BJ, Wurster JI, Nilson R, Guang A, Sano WH, Rowan-Nash AD, Li H, Belenky P. Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome. Cell Metab 2019; 30:800-823.e7. [PMID: 31523007 PMCID: PMC6948150 DOI: 10.1016/j.cmet.2019.08.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/24/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Although antibiotics disturb the structure of the gut microbiota, factors that modulate these perturbations are poorly understood. Bacterial metabolism is an important regulator of susceptibility in vitro and likely plays a large role within the host. We applied a metagenomic and metatranscriptomic approach to link antibiotic-induced taxonomic and transcriptional responses within the murine microbiome. We found that antibiotics significantly alter the expression of key metabolic pathways at the whole-community and single-species levels. Notably, Bacteroides thetaiotaomicron, which blooms in response to amoxicillin, upregulated polysaccharide utilization. In vitro, we found that the sensitivity of this bacterium to amoxicillin was elevated by glucose and reduced by polysaccharides. Accordingly, we observed that dietary composition affected the abundance and expansion of B. thetaiotaomicron, as well as the extent of microbiome disruption with amoxicillin. Our work indicates that the metabolic environment of the microbiome plays a role in the response of this community to antibiotics.
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Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Elizabeth M Reinhart
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Rachael Nilson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - August Guang
- Center for Computation & Visualization, Brown University, Brown University, Providence, RI 02906, USA; Center for Computational Biology of Human Disease, Brown University, Providence, RI 02906, USA
| | - William H Sano
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA.
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20
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Watching DNA Replication Inhibitors in Action: Exploiting Time-Lapse Microfluidic Microscopy as a Tool for Target-Drug Interaction Studies in Mycobacterium. Antimicrob Agents Chemother 2019; 63:AAC.00739-19. [PMID: 31383667 PMCID: PMC6761567 DOI: 10.1128/aac.00739-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023] Open
Abstract
Spreading resistance to antibiotics and the emergence of multidrug-resistant strains have become frequent in many bacterial species, including mycobacteria, which are the causative agents of severe diseases and which have profound impacts on global health. Here, we used a system of microfluidics, fluorescence microscopy, and target-tagged fluorescent reporter strains of Mycobacterium smegmatis to perform real-time monitoring of replisome and chromosome dynamics following the addition of replication-altering drugs (novobiocin, nalidixic acid, and griselimycin) at the single-cell level. We found that novobiocin stalled replication forks and caused relaxation of the nucleoid and that nalidixic acid triggered rapid replisome collapse and compaction of the nucleoid, while griselimycin caused replisome instability, with the subsequent overinitiation of chromosome replication and overrelaxation of the nucleoid. In addition to study target-drug interactions, our system also enabled us to observe how the tested antibiotics affected the physiology of mycobacterial cells (i.e., growth, chromosome segregation, etc.).
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21
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Our Evolving Understanding of the Mechanism of Quinolones. Antibiotics (Basel) 2018; 7:antibiotics7020032. [PMID: 29642475 PMCID: PMC6023003 DOI: 10.3390/antibiotics7020032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/30/2018] [Accepted: 04/04/2018] [Indexed: 12/16/2022] Open
Abstract
The maintenance of DNA supercoiling is essential for the proper regulation of a plethora of biological processes. As a consequence of this mode of regulation, ahead of the replication fork, DNA replication machinery is prone to introducing supercoiled regions into the DNA double helix. Resolution of DNA supercoiling is essential to maintain DNA replication rates that are amenable to life. This resolution is handled by evolutionarily conserved enzymes known as topoisomerases. The activity of topoisomerases is essential, and therefore constitutes a prime candidate for targeting by antibiotics. In this review, we present hallmark investigations describing the mode of action of quinolones, one of the antibacterial classes targeting the function of topoisomerases in bacteria. By chronologically analyzing data gathered on the mode of action of this imperative antibiotic class, we highlight the necessity to look beyond primary drug-target interactions towards thoroughly understanding the mechanism of quinolones at the level of the cell.
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22
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The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives. Infect Dis Clin North Am 2017; 30:323-345. [PMID: 27208762 DOI: 10.1016/j.idc.2016.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens.
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23
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Bodine TJ, Evangelista MA, Chang HT, Ayoub CA, Samuel BS, Sucgang R, Zechiedrich L. Escherichia coli DNA ligase B may mitigate damage from oxidative stress. PLoS One 2017; 12:e0180800. [PMID: 28700629 PMCID: PMC5507437 DOI: 10.1371/journal.pone.0180800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 06/21/2017] [Indexed: 01/02/2023] Open
Abstract
Escherichia coli encodes two DNA ligases, ligase A, which is essential under normal laboratory growth conditions, and ligase B, which is not. Here we report potential functions of ligase B. We found that across the entire Enterobacteriaceae family, ligase B is highly conserved in both amino acid identity and synteny with genes associated with oxidative stress. Deletion of ligB sensitized E. coli to specific DNA damaging agents and antibiotics resulted in a weak mutator phenotype, and decreased biofilm formation. Overexpression of ligB caused a dramatic extension of lag phase that eventually resumed normal growth. The ligase function of ligase B was not required to mediate the extended lag phase, as overexpression of a ligase-deficient ligB mutant also blocked growth. Overexpression of ligB during logarithmic growth caused an immediate block of cell growth and DNA replication, and death of about half of cells. These data support a potential role for ligase B in the base excision repair pathway or the mismatch repair pathway.
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Affiliation(s)
- Truston J. Bodine
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States of America
| | - Michael A. Evangelista
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Huan Ting Chang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
- Department of BioSciences, Rice University, Houston, TX, United States of America
| | - Christopher A. Ayoub
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Buck S. Samuel
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States of America
| | - Richard Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Lynn Zechiedrich
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, United States of America
- * E-mail:
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24
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Peptoids successfully inhibit the growth of gram negative E. coli causing substantial membrane damage. Sci Rep 2017; 7:42332. [PMID: 28195195 PMCID: PMC5307948 DOI: 10.1038/srep42332] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 01/10/2017] [Indexed: 02/05/2023] Open
Abstract
Peptoids are an alternative approach to antimicrobial peptides that offer higher stability towards enzymatic degradation. It is essential when developing new types of peptoids, that mimic the function of antimicrobial peptides, to understand their mechanism of action. Few studies on the specific mechanism of action of antimicrobial peptoids have been described in the literature, despite the plethora of studies on the mode of action of antimicrobial peptides. Here, we investigate the mechanism of action of two short cationic peptoids, rich in lysine and tryptophan side chain functionalities. We demonstrate that both peptoids are able to cause loss of viability in E. coli susceptible cells at their MIC (16–32 μg/ml) concentrations. Dye leakage assays demonstrate slow and low membrane permeabilization for peptoid 1, that is still higher for lipid compositions mimicking bacterial membranes than lipid compositions containing Cholesterol. At concentrations of 4 × MIC (64–128 μg/ml), pore formation, leakage of cytoplasmic content and filamentation were the most commonly observed morphological changes seen by SEM in E. coli treated with both peptoids. Flow cytometry data supports the increase of cell size as observed in the quantification analysis from the SEM images and suggests overall decrease of DNA per cell mass over time.
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25
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Smirnova GV, Tyulenev AV, Muzyka NG, Peters MA, Oktyabrsky ON. Ciprofloxacin provokes SOS-dependent changes in respiration and membrane potential and causes alterations in the redox status of Escherichia coli. Res Microbiol 2016; 168:64-73. [PMID: 27498196 DOI: 10.1016/j.resmic.2016.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 10/21/2022]
Abstract
An in-depth understanding of the physiological response of bacteria to antibiotic-induced stress is needed for development of new approaches to combatting microbial infections. Fluoroquinolone ciprofloxacin causes phase alterations in Escherichia coli respiration and membrane potential that strongly depend on its concentration. Concentrations lower than the optimal bactericidal concentration (OBC) do not inhibit respiration during the first phase. A dose higher than the OBC provokes immediate SOS-independent inhibition of respiration and growth that can contribute to a decreased SOS response and lowered susceptibility to high concentrations of ciprofloxacin. Cells retain their metabolic activity, membrane potential and accelerated K+ uptake and produce low levels of superoxide and H2O2 during the first phase. The time before initiation of the second phase is inversely correlated with the ciprofloxacin concentration. The second phase is SOS-dependent and characterized by respiratory inhibition, membrane depolarization, K+ and glutathione leakage and cessation of glucose consumption and may be considered as cell death. atpA, gshA and kefBkefC knockouts, which perturb fluxes of protons and K+, can modify the degree and duration of respiratory inhibition and potassium retention. Loss of K+ efflux channels KefB and KefC enhances the susceptibility of E. coli to ciprofloxacin.
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Affiliation(s)
- Galina V Smirnova
- Institute of Ecology and Genetics of Microorganisms, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia.
| | - Aleksey V Tyulenev
- Institute of Ecology and Genetics of Microorganisms, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia.
| | - Nadezda G Muzyka
- Institute of Ecology and Genetics of Microorganisms, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia.
| | - Mikhail A Peters
- Institute of Ecology and Genetics of Microorganisms, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia.
| | - Oleg N Oktyabrsky
- Institute of Ecology and Genetics of Microorganisms, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia; Department of Chemistry and Biotechnology, Perm National Research Polytechnic University, Komsomolsky pr., 29, Perm, 614990, Russia.
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26
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Rodríguez-Martínez JM, Santiso R, Machuca J, Bou G, Pascual Á, Fernández JL. Assessment of Chromosomal DNA Fragmentation by Quinolones in an Isogenic Collection of Escherichia coli with Defined Resistance Mechanisms. Microb Drug Resist 2016; 22:354-9. [PMID: 26890225 DOI: 10.1089/mdr.2015.0298] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aim of this study was to investigate the potential usefulness of DNA fragmentation as a quick and simple procedure for detecting resistance to fluoroquinolones (FQ) in isogenic Escherichia coli strains harboring defined and multiple quinolone resistance mechanisms, including low-level quinolone resistance (LLQR) phenotypes. DNA fragmentation assay (Micromax(®)) was evaluated for detecting resistance to FQ in 71 isogenic strains of E. coli harboring specific quinolone resistance mechanisms frequently found in clinical isolates. These isogenic strains represent a consistent and reliable model of increasing minimum inhibitory concentrations (MICs) of ciprofloxacin (CIP), ranging from 0.004 to 16 mg/L. According to CLSI criteria, the assay correctly identified all CIP-resistant strains (MIC ≥4 mg/L). As regards susceptible strains, 96% of bacterial strains were correctly assigned as susceptible to CIP. Moreover, the procedure enabled LLQR phenotypes to be efficiently identified; this subset may show different levels of DNA damage depending on the strain, even with similar MIC. Interestingly, despite increasing the dose according to the MIC, a lower response to quinolones occurs in strains with higher MIC values. This is a simple, rapid, and reliable test for evaluating susceptibility to FQ of E. coli, including the detection of strains harboring LLQR mechanisms.
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Affiliation(s)
- José-Manuel Rodríguez-Martínez
- 1 Department of Microbiology, University of Seville , Seville, Spain .,2 Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III , Madrid, Spain
| | - Rebeca Santiso
- 3 INIBIC-Complejo Hospitalario Universitario A Coruña , Unidad de Genética, A Coruña, Spain .,4 Laboratorio de Genética Molecular y Radiobiología, Centro Oncológico de Galicia , A Coruña, Spain
| | - Jesús Machuca
- 2 Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III , Madrid, Spain .,5 Infectious Diseases and Clinical Microbiology Unit, University Hospital Virgen Macarena , Seville, Spain
| | - Germán Bou
- 2 Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III , Madrid, Spain .,6 INIBIC-Complejo Hospitalario Universitario A Coruña , Servicio de Microbiología, A Coruña, Spain
| | - Álvaro Pascual
- 1 Department of Microbiology, University of Seville , Seville, Spain .,2 Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III , Madrid, Spain .,5 Infectious Diseases and Clinical Microbiology Unit, University Hospital Virgen Macarena , Seville, Spain
| | - José Luis Fernández
- 2 Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III , Madrid, Spain .,3 INIBIC-Complejo Hospitalario Universitario A Coruña , Unidad de Genética, A Coruña, Spain .,4 Laboratorio de Genética Molecular y Radiobiología, Centro Oncológico de Galicia , A Coruña, Spain
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Antibiograma rápido en Microbiología Clínica. Enferm Infecc Microbiol Clin 2016; 34:61-8. [DOI: 10.1016/j.eimc.2014.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/25/2014] [Accepted: 11/15/2014] [Indexed: 11/22/2022]
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Rajendram M, Hurley KA, Foss MH, Thornton KM, Moore JT, Shaw JT, Weibel DB. Gyramides prevent bacterial growth by inhibiting DNA gyrase and altering chromosome topology. ACS Chem Biol 2014; 9:1312-9. [PMID: 24712739 PMCID: PMC4068256 DOI: 10.1021/cb500154m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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Antibiotics targeting DNA gyrase
have been a clinical success story
for the past half-century, and the emergence of bacterial resistance
has fueled the search for new gyrase inhibitors. In this paper we
demonstrate that a new class of gyrase inhibitors, the gyramides,
are bacteriostatic agents that competitively inhibit the ATPase activity
of Escherichia coli gyrase and produce supercoiled
DNA in vivo. E. coli cells treated with gyramide
A have abnormally localized, condensed chromosomes that blocks DNA
replication and interrupts chromosome segregation. The resulting alterations
in DNA topology inhibit cell division through a mechanism that involves
the SOS pathway. Importantly, gyramide A is a specific inhibitor of
gyrase and does not inhibit the closely related E. coli enzyme topoisomerase IV. E. coli mutants with reduced
susceptibility to gyramide A do not display cross-resistance to ciprofloxacin
and novobiocin. The results demonstrate that the gyramides prevent
bacterial growth by a mechanism in which the topological state of
chromosomes is altered and halts DNA replication and segregation.
The specificity and activity of the gyramides for inhibiting gyrase
makes these compounds important chemical tools for studying the mechanism
of gyrase and the connection between DNA topology and bacterial cell
division.
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Affiliation(s)
| | | | | | | | - Jared T. Moore
- Department
of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Jared T. Shaw
- Department
of Chemistry, University of California-Davis, Davis, California 95616, United States
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Rapid determination of colistin resistance in clinical strains of Acinetobacter baumannii by use of the micromax assay. J Clin Microbiol 2013; 51:3675-82. [PMID: 23985913 DOI: 10.1128/jcm.01787-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Colistin is an old antibiotic which has been used as a therapeutic option for carbapenem- and multidrug-resistant Gram-negative bacteria, like Acinetobacter baumannii. This pathogen produces life-threatening infections, mainly in patients admitted to intensive care units. Rapid detection of resistance to colistin may improve patient outcomes and prevent the spread of resistance. For this purpose, Micromax technology was evaluated in four isogenic A. baumannii strains with known mechanisms of resistance to colistin and in 66 isolates (50 susceptible and 16 resistant). Two parameters were determined, DNA fragmentation and cell wall damage. To assess DNA fragmentation, cells trapped in a microgel were incubated with a lysing solution to remove the cell wall, and the released nucleoids were visualized under fluorescence microscopy. Fragmented DNA was observed as spots that diffuse from the nucleoid. To assess cell wall integrity, cells were incubated with a lysis solution which removes only weakened cell walls, resulting in nucleoid release exclusively in affected cells. A dose-response relationship was demonstrated between colistin concentrations and the percentages of bacteria with DNA fragmentation and cell wall damage, antibiotic effects that were delayed and less frequent in resistant strains. Receiver operating characteristic (ROC) curves demonstrated that both DNA fragmentation and cell wall damage were excellent parameters for identifying resistant strains. Obtaining ≤11% of bacteria with cell wall damage after incubation with 0.5 μg/ml colistin identified resistant strains of A. baumannii with 100% sensitivity and 96% specificity. Results were obtained in 3 h 30 min. This is a simple, rapid, and accurate assay for detecting colistin resistance in A. baumannii, with strong potential value in critical clinical situations.
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Pulido MR, Garcia-Quintanilla M, Martin-Pena R, Cisneros JM, McConnell MJ. Progress on the development of rapid methods for antimicrobial susceptibility testing. J Antimicrob Chemother 2013; 68:2710-7. [DOI: 10.1093/jac/dkt253] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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31
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Li H, Bu X, Lu J, Xu C, Wang X, Yang X. Interaction study of ciprofloxacin with human telomeric DNA by spectroscopy and molecular docking. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 107:227-234. [PMID: 23434548 DOI: 10.1016/j.saa.2013.01.069] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/23/2013] [Accepted: 01/24/2013] [Indexed: 06/01/2023]
Abstract
The interaction of ciprofloxacin (CIP) with human telomeric DNA was studied in vitro using multi-spectroscopy and molecular modeling methods. The hypochromic effect with a red shift in ultraviolet (UV) absorption indicated the occurrence of the interaction between CIP and DNA. The fluorescence quenching of CIP was observed with the addition of DNA and was proved to be the static quenching. The binding constant was found to be 9.62×10(4) L mol(-1). Electrospray ionization mass spectrometry (ESI-MS) result further confirmed the formation of 1:1 non-covalent complex between DNA and CIP. Combined with the UV melting results, circular dichroism (CD) results confirmed the existence of groove binding mode, as well as conformational changes of DNA. Molecular docking studies illustrated the visual display of the CIP binding to the GC region in the minor groove of DNA. Specific hydrogen bonds and van der Waals forces were demonstrated as main acting forces between CIP and guanine bases of DNA.
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Affiliation(s)
- Huihui Li
- Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, China.
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Park S, Park M, Rafii F. Comparative transcription analysis and toxin production of two fluoroquinolone-resistant mutants of Clostridium perfringens. BMC Microbiol 2013; 13:50. [PMID: 23452396 PMCID: PMC3599539 DOI: 10.1186/1471-2180-13-50] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 02/18/2013] [Indexed: 11/10/2022] Open
Abstract
Background Fluoroquinolone use has been listed as a risk factor for the emergence of virulent clinical strains of some bacteria. The aim of our study was to evaluate the effect of fluoroquinolone (gatifloxacin) resistance selection on differential gene expression, including the toxin genes involved in virulence, in two fluoroquinolone-resistant strains of Clostridium perfringens by comparison with their wild-type isogenic strains. Results DNA microarray analyses were used to compare the gene transcription of two wild types, NCTR and ATCC 13124, with their gatifloxacin-resistant mutants, NCTRR and 13124R. Transcription of a variety of genes involved in bacterial metabolism was either higher or lower in the mutants than in the wild types. Some genes, including genes for toxins and regulatory genes, were upregulated in NCTRR and downregulated in 13124R. Transcription analysis by quantitative real-time PCR (qRT-PCR) confirmed the altered expression of many of the genes that were affected differently in the fluoroquinolone-resistant mutants and wild types. The levels of gene expression and enzyme production for the toxins phospholipase C, perfringolysin O, collagenase and clostripain had decreased in 13124R and increased in NCTRR in comparison with the wild types. After centrifugation, the cytotoxicity of the supernatants of NCTRR and 13224R cultures for mouse peritoneal macrophages confirmed the increased cytotoxicity of NCTRR and the decreased cytotoxicity of 13124R in comparison with the respective wild types. Fluoroquinolone resistance selection also affected cell shape and colony morphology in both strains. Conclusion Our results indicate that gatifloxacin resistance selection was associated with altered gene expression in two C. perfringens strains and that the effect was strain-specific. This study clearly demonstrates that bacterial exposure to fluoroquinolones may affect virulence (toxin production) in addition to drug resistance.
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Affiliation(s)
- Sunny Park
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
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33
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Fast assessment of resistance to carbapenems and ciprofloxacin of clinical strains of Acinetobacter baumannii. J Clin Microbiol 2012; 50:3609-13. [PMID: 22933604 DOI: 10.1128/jcm.01675-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infections caused by multidrug-resistant Acinetobacter baumannii constitute a major life-threatening problem worldwide, and early adequate antibiotic therapy is decisive for success. For these reasons, rapid detection of antibiotic susceptibility in this pathogen is a clinical challenge. Two variants of the Micromax kit were evaluated for a rapid detection in situ of susceptibility or resistance to meropenem or ciprofloxacin, separately, in 322 clinical isolates. Release of the nucleoid is the criterion of susceptibility to the beta-lactams (carbapenems), whereas diffusion of DNA fragments emerging from the nucleoid characterizes the quinolone activity. All the susceptible and resistant strains were correctly categorized in 100 min according to the MIC results and CLSI criteria. Thus, our technology is a promising tool for rapid identification of carbapenem and quinolone resistance of A. baumannii strains in hospital settings.
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Tamayo M, Santiso R, Gosálvez J, Bou G, Fernández MDC, Fernández JL. Cell wall active antibiotics reduce chromosomal DNA fragmentation by peptidoglycan hydrolysis in Staphylococcus aureus. Arch Microbiol 2012; 194:967-75. [PMID: 22797526 DOI: 10.1007/s00203-012-0831-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 06/27/2012] [Accepted: 06/29/2012] [Indexed: 11/30/2022]
Abstract
Lysostaphin digestion of peptidoglycan (PG) from Staphylococcus aureus resulted in chromosomal DNA fragmentation by released DNase, as directly visualized in situ on isolated nucleoids. Nevertheless, DNA digestion was partially prevented by previous incubation with antibiotics that inhibit PG synthesis. This inhibitory effect was much more remarkable with glycopeptides vancomycin and mainly teicoplanin than with beta-lactams cloxacillin and ceftazidime. Therefore, inhibition of PG chain elongation has a more significant inhibition of DNA degradation than inhibition of PG cross-linking, possibly due to a reduction in DNase storage at the cell wall.
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Affiliation(s)
- María Tamayo
- Genetics Unit, INIBIC-Complejo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
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Kicia M, Janeczko N, Lewicka J, Hendrich AB. Comparison of the effects of subinhibitory concentrations of ciprofloxacin and colistin on the morphology of cardiolipin domains in Escherichia coli membranes. J Med Microbiol 2011; 61:520-524. [PMID: 22160313 DOI: 10.1099/jmm.0.037788-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Membrane domains characterized by unique protein and lipid composition allow for compartmentalization and regulation of various biological processes. In Escherichia coli cardiolipin domains play a key role in the dynamic organization of bacterial membranes, and their distribution depends on the stage of the cell cycle. We studied the influence of subinhibitory concentrations of ciprofloxacin and colistin on the morphology and distribution of E. coli cardiolipin domains. Using the fluorescent dye 10-N-nonyl acridine orange we found that exposure of bacteria to ciprofloxacin significantly increased the percentage of filamentous cells with altered morphology of the cardiolipin domains, while colistin did not induce any significant changes. These results allow us to conclude that inhibition of DNA gyrase causes effects even at the bacterial membrane level and those changes can be easily visualized using 10-N-nonyl acridine orange.
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Affiliation(s)
- Marta Kicia
- Department of Medical Biology and Parasitology, Wrocław Medical University, ul. Mikulicza-Radeckiego 9, 50-367 Wrocław, Poland
| | - Natalia Janeczko
- Department of Medical Biology and Parasitology, Wrocław Medical University, ul. Mikulicza-Radeckiego 9, 50-367 Wrocław, Poland
| | - Jagoda Lewicka
- Department of Medical Biology and Parasitology, Wrocław Medical University, ul. Mikulicza-Radeckiego 9, 50-367 Wrocław, Poland
| | - Andrzej B Hendrich
- Department of Medical Biology and Parasitology, Wrocław Medical University, ul. Mikulicza-Radeckiego 9, 50-367 Wrocław, Poland
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Santiso R, Tamayo M, Gosálvez J, Bou G, Fernández MDC, Fernández JL. A rapid in situ procedure for determination of bacterial susceptibility or resistance to antibiotics that inhibit peptidoglycan biosynthesis. BMC Microbiol 2011; 11:191. [PMID: 21867549 PMCID: PMC3179955 DOI: 10.1186/1471-2180-11-191] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 08/25/2011] [Indexed: 11/10/2022] Open
Abstract
Background Antibiotics which inhibit bacterial peptidoglycan biosynthesis are the most widely used in current clinical practice. Nevertheless, resistant strains increase dramatically, with serious economic impact and effects on public health, and are responsible for thousands of deaths each year. Critical clinical situations should benefit from a rapid procedure to evaluate the sensitivity or resistance to antibiotics that act at the cell wall. We have adapted a kit for rapid determination of bacterial DNA fragmentation, to assess cell wall integrity. Results Cells incubated with the antibiotic were embedded in an agarose microgel on a slide, incubated in an adapted lysis buffer, stained with a DNA fluorochrome, SYBR Gold and observed under fluorescence microscopy. The lysis affects the cells differentially, depending on the integrity of the wall. If the bacterium is susceptible to the antibiotic, the weakened cell wall is affected by the lysing solution so the nucleoid of DNA contained inside the bacterium is released and spread. Alternatively, if the bacterium is resistant to the antibiotic, it is practically unaffected by the lysis solution and does not liberate the nucleoid, retaining its normal morphological appearance. In an initial approach, the procedure accurately discriminates susceptible, intermediate and resistant strains of Escherichia coli to amoxicillin/clavulanic acid. When the bacteria came from an exponentially growing liquid culture, the effect on the cell wall of the β-lactam was evident much earlier that when they came from an agar plate. A dose-response experiment with an E. coli strain susceptible to ampicillin demonstrated a weak effect before the MIC dose. The cell wall damage was not homogenous among the different cells, but the level of damage increased as dose increased with a predominant degree of effect for each dose. A microgranular-fibrilar extracellular background was evident in gram-negative susceptible strains after β-lactam treatment. This material was digested by DNase I, hybridised with a specific whole genome probe, and so recognized as DNA fragments released by the bacteria. Finally, 46 clinical strains from eight gram-negative and four gram-positive species were evaluated blind for susceptibility or resistance to one of four different β-lactams and vancomycin, confirming the applicability of the methodology. Conclusion The technique to assess cell wall integrity appears to be a rapid and simple procedure to identify resistant and susceptible strains to antibiotics that interfere with peptidoglycan biosynthesis.
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Affiliation(s)
- Rebeca Santiso
- INIBIC-Complejo Hospitalario Universitario A Coruña, Unidad de Genética, As Xubias 84, 15006- A Coruña, Spain
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Silva F, Lourenço O, Queiroz JA, Domingues FC. Bacteriostatic versus bactericidal activity of ciprofloxacin in Escherichia coli assessed by flow cytometry using a novel far-red dye. J Antibiot (Tokyo) 2011; 64:321-5. [DOI: 10.1038/ja.2011.5] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Release dynamics of ciprofloxacin from swellable nanocarriers of poly(2-hydroxyethyl methacrylate): an in vitro study. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2010; 6:453-62. [DOI: 10.1016/j.nano.2009.11.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 11/03/2009] [Accepted: 11/18/2009] [Indexed: 01/15/2023]
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Dörr T, Lewis K, Vulić M. SOS response induces persistence to fluoroquinolones in Escherichia coli. PLoS Genet 2009; 5:e1000760. [PMID: 20011100 PMCID: PMC2780357 DOI: 10.1371/journal.pgen.1000760] [Citation(s) in RCA: 336] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 11/09/2009] [Indexed: 01/12/2023] Open
Abstract
Bacteria can survive antibiotic treatment without acquiring heritable antibiotic resistance. We investigated persistence to the fluoroquinolone ciprofloxacin in Escherichia coli. Our data show that a majority of persisters to ciprofloxacin were formed upon exposure to the antibiotic, in a manner dependent on the SOS gene network. These findings reveal an active and inducible mechanism of persister formation mediated by the SOS response, challenging the prevailing view that persisters are pre-existing and formed purely by stochastic means. SOS-induced persistence is a novel mechanism by which cells can counteract DNA damage and promote survival to fluoroquinolones. This unique survival mechanism may be an important factor influencing the outcome of antibiotic therapy in vivo.
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Affiliation(s)
- Tobias Dörr
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Marin Vulić
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail:
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Rapid and simple determination of ciprofloxacin resistance in clinical strains of Escherichia coli. J Clin Microbiol 2009; 47:2593-5. [PMID: 19571026 DOI: 10.1128/jcm.00367-09] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We recently reported a simple new in situ diffusion assay, developed as a kit, to visualize DNA fragmentation in single bacterial cells. Use of this assay in a collection of 95 genetically unrelated Escherichia coli clinical strains resulted in correct identification of all of the isolates as resistant or susceptible to ciprofloxacin, consistent with the MIC results. This relevant information is obtained in 80 min.
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