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García-Villada L, Degtyareva NP, Brooks AM, Goldberg JB, Doetsch PW. A role for the stringent response in ciprofloxacin resistance in Pseudomonas aeruginosa. Sci Rep 2024; 14:8598. [PMID: 38615146 PMCID: PMC11016087 DOI: 10.1038/s41598-024-59188-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024] Open
Abstract
Pseudomonas aeruginosa is a major cause of nosocomial infections and the leading cause of chronic lung infections in cystic fibrosis and chronic obstructive pulmonary disease patients. Antibiotic treatment remains challenging because P. aeruginosa is resistant to high concentrations of antibiotics and has a remarkable ability to acquire mutations conferring resistance to multiple groups of antimicrobial agents. Here we report that when P. aeruginosa is plated on ciprofloxacin (cipro) plates, the majority of cipro-resistant (ciproR) colonies observed at and after 48 h of incubation carry mutations in genes related to the Stringent Response (SR). Mutations in one of the major SR components, spoT, were present in approximately 40% of the ciproR isolates. Compared to the wild-type strain, most of these isolates had decreased growth rate, longer lag phase and altered intracellular ppGpp content. Also, 75% of all sequenced mutations were insertions and deletions, with short deletions being the most frequently occurring mutation type. We present evidence that most of the observed mutations are induced on the selective plates in a subpopulation of cells that are not instantly killed by cipro. Our results suggests that the SR may be an important contributor to antibiotic resistance acquisition in P. aeruginosa.
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Affiliation(s)
| | | | - Ashley M Brooks
- Integrative Bioinformatics, Biostatistics and Computational Biology Branch, NIEHS, Durham, NC, USA
| | - Joanna B Goldberg
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul W Doetsch
- Genomic Integrity and Structural Biology Laboratory, NIEHS, Durham, NC, USA.
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2
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Wu YL, Hu SF, Zhang XL, Wang HM, Pan HY, Liu GH, Deng YP. Complete bacterial profile and potential pathogens of cat fleas Ctenocephalides felis. Acta Trop 2023; 243:106923. [PMID: 37080265 DOI: 10.1016/j.actatropica.2023.106923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/23/2023] [Accepted: 04/07/2023] [Indexed: 04/22/2023]
Abstract
Fleas are important ectoparasites and vectors associated with a wide range of pathogenic diseases, posing threats to public health concerns, especially cat fleas that spread worldwide. Understanding the microbial components is essential due to cat fleas are capable of transmitting pathogens to humans, causing diseases like plague and murine typhus. In the present study, metagenomic next-generation sequencing was applied to obtain the complete microbiota and related functions in the gut of Ctenocephalides felis. A total of 1,870 species was taxonomically recognized including 1,407 bacteria, 365 eukaryotes, 69 viruses, and 29 archaea. Proteobacteria was the dominant phylum among the six samples. Pathogens Rickettsia felis, Acinetobacter baumannii, Coxiella burnetii, and Anaplasma phagocytophilum were taxonomically identified and had high abundances in all samples. The resistance gene MexD was predominant in microbial communities of all cat fleas. We also performed epidemiological surveys of pathogens R. felis, A. baumannii, C. burnetii, and A. phagocytophilum among 165 cat fleas collected from seven provinces in China, while only the DNAs of R. felis (38/165, 23.03%) and C. burnetii (2/165, 1.21%) were obtained. The data provide new insight and understanding of flea intestinal microbiota and provided novel information for preventing and controlling fleas and their transmitted diseases.
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Affiliation(s)
- Ya-Li Wu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Shi-Feng Hu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Xue-Ling Zhang
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Hui-Mei Wang
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Hai-Yu Pan
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Guo-Hua Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China.
| | - Yuan-Ping Deng
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China.
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3
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Karlowsky JA, Hackel MA, Wise MG, Six DA, Uehara T, Daigle DM, Cusick SM, Pevear DC, Moeck G, Sahm DF. In Vitro Activity of Cefepime-Taniborbactam and Comparators against Clinical Isolates of Gram-Negative Bacilli from 2018 to 2020: Results from the Global Evaluation of Antimicrobial Resistance via Surveillance (GEARS) Program. Antimicrob Agents Chemother 2023; 67:e0128122. [PMID: 36541767 PMCID: PMC9872668 DOI: 10.1128/aac.01281-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Taniborbactam is a novel cyclic boronate β-lactamase inhibitor in clinical development in combination with cefepime. We assessed the in vitro activity of cefepime-taniborbactam and comparators against a 2018-2020 collection of Enterobacterales (n = 13,731) and Pseudomonas aeruginosa (n = 4,619) isolates cultured from infected patients attending hospitals in 56 countries. MICs were determined by CLSI broth microdilution. Taniborbactam was tested at a fixed concentration of 4 μg/mL. Isolates with cefepime-taniborbactam MICs of ≥16 μg/mL underwent whole-genome sequencing. β-lactamase genes were identified in meropenem-resistant isolates by PCR/Sanger sequencing. Against Enterobacterales, taniborbactam reduced the cefepime MIC90 value by >64-fold (from >16 to 0.25 μg/mL). At ≤16 μg/mL, cefepime-taniborbactam inhibited 99.7% of all Enterobacterales isolates; >97% of isolates with multidrug-resistant (MDR) and ceftolozane-tazobactam-resistant phenotypes; ≥90% of isolates with meropenem-resistant, difficult-to-treat-resistant (DTR), meropenem-vaborbactam-resistant, and ceftazidime-avibactam-resistant phenotypes; 100% of VIM-positive, AmpC-positive, and KPC-positive isolates; 98.7% of extended-spectrum β-lactamase (ESBL)-positive; 98.8% of OXA-48-like-positive; and 84.6% of NDM-positive isolates. Against P. aeruginosa, taniborbactam reduced the cefepime MIC90 value by 4-fold (from 32 to 8 μg/mL). At ≤16 μg/mL, cefepime-taniborbactam inhibited 97.4% of all P. aeruginosa isolates; ≥85% of isolates with meropenem-resistant, MDR, and meropenem-vaborbactam-resistant phenotypes; >75% of isolates with DTR, ceftazidime-avibactam-resistant, and ceftolozane-tazobactam-resistant phenotypes; and 87.4% of VIM-positive isolates. Multiple potential mechanisms, including carriage of IMP, certain alterations in PBP3, permeability (porin) defects, and possibly, upregulation of efflux were present in most isolates with cefepime-taniborbactam MICs of ≥16 μg/mL. We conclude that cefepime-taniborbactam exhibited potent in vitro activity against Enterobacterales and P. aeruginosa and inhibited most carbapenem-resistant isolates, including those carrying serine carbapenemases or NDM/VIM metallo-β-lactamases (MBLs).
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Affiliation(s)
- James A. Karlowsky
- IHMA, Schaumburg, Illinois, USA
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | | | - David A. Six
- Venatorx Pharmaceuticals, Inc., Malvern, Pennsylvania, USA
| | | | | | | | | | - Greg Moeck
- Venatorx Pharmaceuticals, Inc., Malvern, Pennsylvania, USA
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Parallel Evolution to Elucidate the Contributions of PA0625 and parE to Ciprofloxacin Sensitivity in Pseudomonas aeruginosa. Microorganisms 2022; 11:microorganisms11010013. [PMID: 36677304 PMCID: PMC9860795 DOI: 10.3390/microorganisms11010013] [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: 11/27/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous pathogen that causes a wide range of acute and chronic infections. Ciprofloxacin, one of the first-line fluoroquinolone class antibiotics, is commonly used for the treatment of P. aeruginosa infections. However, ciprofloxacin-resistant P. aeruginosa is increasingly reported worldwide, making treatment difficult. To determine resistance-related mutations, we conducted an experimental evolution using a previously identified ciprofloxacin-resistant P. aeruginosa clinical isolate, CRP42. The evolved mutants could tolerate a 512-fold higher concentration of ciprofloxacin than CRP42. Genomic DNA reference mapping was performed, which revealed mutations in genes known to be associated with ciprofloxacin resistance as well as in those not previously linked to ciprofloxacin resistance, including the ParER586W substitution and PA0625 frameshift insertion. Simulation of the ParER586W substitution and PA0625 frameshift insertion by gene editing in CRP42 and the model strain PAO1 demonstrated that while the PA0625 mutation does contribute to resistance, mutation in the ParER586W does not contribute to resistance but rather affects tolerance against ciprofloxacin. These findings advance our understanding of ciprofloxacin resistance in P. aeruginosa.
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5
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On YY, Welch M. The methylation-independent mismatch repair machinery in Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34882086 PMCID: PMC8744996 DOI: 10.1099/mic.0.001120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the last 70 years, we've all gotten used to an Escherichia coli-centric view of the microbial world. However, genomics, as well as the development of improved tools for genetic manipulation in other species, is showing us that other bugs do things differently, and that we cannot simply extrapolate from E. coli to everything else. A particularly good example of this is encountered when considering the mechanism(s) involved in DNA mismatch repair by the opportunistic human pathogen, Pseudomonas aeruginosa (PA). This is a particularly relevant phenotype to examine in PA, since defects in the mismatch repair (MMR) machinery often give rise to the property of hypermutability. This, in turn, is linked with the vertical acquisition of important pathoadaptive traits in the organism, such as antimicrobial resistance. But it turns out that PA lacks some key genes associated with MMR in E. coli, and a closer inspection of what is known (or can be inferred) about the MMR enzymology reveals profound differences compared with other, well-characterized organisms. Here, we review these differences and comment on their biological implications.
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Affiliation(s)
- Yue Yuan On
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Downing Site, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Martin Welch
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Downing Site, University of Cambridge, Cambridge, CB2 1QW, UK
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6
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Korry BJ, Lee SYE, Chakrabarti AK, Choi AH, Ganser C, Machan JT, Belenky P. Genotoxic Agents Produce Stressor-Specific Spectra of Spectinomycin Resistance Mutations Based on Mechanism of Action and Selection in Bacillus subtilis. Antimicrob Agents Chemother 2021; 65:e0089121. [PMID: 34339280 PMCID: PMC8448107 DOI: 10.1128/aac.00891-21] [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: 04/29/2021] [Accepted: 07/23/2021] [Indexed: 11/20/2022] Open
Abstract
Mutagenesis is integral for bacterial evolution and the development of antibiotic resistance. Environmental toxins and stressors are known to elevate the rate of mutagenesis through direct DNA toxicity, known as stress-associated mutagenesis, or via a more general stress-induced process that relies on intrinsic bacterial pathways. Here, we characterize the spectra of mutations induced by an array of different stressors using high-throughput sequencing to profile thousands of spectinomycin-resistant colonies of Bacillus subtilis. We found 69 unique mutations in the rpsE and rpsB genes, and that each stressor leads to a unique and specific spectrum of antibiotic-resistance mutations. While some mutations clearly reflected the DNA damage mechanism of the stress, others were likely the result of a more general stress-induced mechanism. To determine the relative fitness of these mutants under a range of antibiotic selection pressures, we used multistrain competitive fitness experiments and found an additional landscape of fitness and resistance. The data presented here support the idea that the environment in which the selection is applied (mutagenic stressors that are present), as well as changes in local drug concentration, can significantly alter the path to spectinomycin resistance in B. subtilis.
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Affiliation(s)
- Benjamin J. Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Stella Ye Eun Lee
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Amit K. Chakrabarti
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Ashley H. Choi
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Collin Ganser
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Jason T. Machan
- Department of Orthopedics, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Surgery, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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Rada AM, De La Cadena E, Agudelo CA, Pallares C, Restrepo E, Correa A, Villegas MV, Capataz C. Genetic Diversity of Multidrug-Resistant Pseudomonas aeruginosa Isolates Carrying bla VIM-2 and bla KPC-2 Genes That Spread on Different Genetic Environment in Colombia. Front Microbiol 2021; 12:663020. [PMID: 34512563 PMCID: PMC8432936 DOI: 10.3389/fmicb.2021.663020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/19/2021] [Indexed: 01/15/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen with an increase in the frequency of infections caused by multidrug resistant (MDR) and extensively drug resistant (XDR) strains, limiting the available therapeutic options. The most troublesome resistance is the acquisition and production of carbapenemases such as Verona integron-encoded metallo-β-lactamases (VIM), the most frequent and widespread, and the Klebsiella pneumoniae carbapenemases (KPC), which has continuously spread in the last decade. Its dissemination is linked to their location on mobile genetic elements (MGEs). In Colombia, VIM and KPC have been increasing in its frequency showing major successful dissemination. In this article, we molecularly characterized and analyzed the genetic context of bla VIM and bla KPC in carbapenem-resistant P. aeruginosa (CRPA) isolates from infected and colonized patients in two tertiary-care hospitals, one in Medellín and the other in a municipality close to Medellín, both areas with high carbapenemase endemicity in Colombia (2013-2015). Using whole-genome sequencing (WGS), we identified a remarkable variety of genetic backgrounds in these MDR P. aeruginosa isolates carrying bla KPC- 2 and bla VIM- 2. There were a diversity of class 1 integron and variations in the gene cassettes associated to bla VIM- 2, as well as a possible event of spread of bla KPC- 2 mediated by a plasmid that contained part of Tn4401b in one infection case. The dissemination of bla VIM- 2 and bla KPC- 2 in P. aeruginosa in this area in Colombia has been strongly influenced by successful international clones, carrying these genes and additional determinants of resistance on MGEs, accompanied by gene rearrangement under an antimicrobial selection pressure. These findings emphasize the need to implement control strategies based on rational antibiotic use.
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Affiliation(s)
- Ana M Rada
- Department of Microbiology and Parasitology, Bacteria and Cancer Group, Universidad de Antioquia, Medellín, Colombia.,Faculad de Ciencias de la Salud, Biociencias Group, Institución Universitaria Colegio Mayor de Antioquia, Medellín, Colombia
| | - Elsa De La Cadena
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Bogotá, Colombia
| | - Carlos A Agudelo
- Clinica Universitaria Bolivariana, Medellín, Colombia.,School of Health Sciences, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Christian Pallares
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Bogotá, Colombia
| | - Eliana Restrepo
- Department of Microbiology and Parasitology, Bacteria and Cancer Group, Universidad de Antioquia, Medellín, Colombia
| | - Adriana Correa
- Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali, Colombia
| | - María V Villegas
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Bogotá, Colombia
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8
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Zhang W, Yuan Y, Li S, Deng B, Zhang J, Li Z. Comparative transcription analysis of resistant mutants against four different antibiotics in Pseudomonas aeruginosa. Microb Pathog 2021; 160:105166. [PMID: 34480983 DOI: 10.1016/j.micpath.2021.105166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/26/2021] [Accepted: 08/29/2021] [Indexed: 11/28/2022]
Abstract
The emergence of antibiotic resistance has severely impaired the treatment of infections caused by Pseudomonas aeruginosa. There are few studies related to comparing the antibiotics resistance mechanisms of P. aeruginosa against different antibiotics. In this study, RNA sequencing was used to investigate the differences of transcriptome between wild strain and four antibiotics resistant strains of P. aeruginosa PAO1 (polymyxin B, ciprofloxacin, doxycycline, and ceftriaxone). Compared to the wild strain, 1907, 495, 2402, and 116 differentially expressed genes (DEGs) were identified in polymyxin B, ciprofloxacin, doxycycline, and ceftriaxone resistant PAO1, respectively. After analysis of genes related to antimicrobial resistance, we found genes implicated in biofilm formation (pelB, pelC, pelD, pelE, pelF, pelG, algA, algF, and alg44) were significantly upregulated in polymyxin B-resistant PAO1, efflux pump genes (mexA, mexB, oprM) and biofilm formation genes (pslJ, pslK and pslN) were upregulated in ciprofloxacin-resistant PAO1; other efflux pump genes (mexC, mexD, oprJ) were upregulated in doxycycline-resistant PAO1; ampC were upregulated in ceftriaxone-resistant PAO1. As a consequence of antibiotic resistance, genes related to virulence factors such as type Ⅱ secretion system (lasA, lasB and piv) were significantly upregulated in polymyxin B-resistant PAO1, and type Ⅲ secretion system (exoS, exoT, exoY, exsA, exsB, exsC, exsD, pcrV, popB, popD, pscC, pscE, pscG, and pscJ) were upregulated in doxycycline-resistant PAO1. While, ampC were upregulated in ceftriaxone-resistant PAO1. In addition, variants were obtained in wild type and four antibiotics resistant PAO1. Our findings provide a comparative transcriptome analysis of antibiotic resistant mutants selected by different antibiotics, and might assist in identifying potential therapeutic strategies for P. aeruginosa infection.
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Affiliation(s)
- Wenlu Zhang
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China
| | - Yaping Yuan
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China
| | - Shasha Li
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China
| | - Bo Deng
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China
| | - Jiaming Zhang
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China
| | - Zhongjie Li
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471003, China.
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9
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Shared and Unique Evolutionary Trajectories to Ciprofloxacin Resistance in Gram-Negative Bacterial Pathogens. mBio 2021; 12:e0098721. [PMID: 34154405 PMCID: PMC8262867 DOI: 10.1128/mbio.00987-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Resistance to the broad-spectrum antibiotic ciprofloxacin is detected at high rates for a wide range of bacterial pathogens. To investigate the dynamics of ciprofloxacin resistance development, we applied a comparative resistomics workflow for three clinically relevant species of Gram-negative bacteria: Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. We combined experimental evolution in a morbidostat with deep sequencing of evolving bacterial populations in time series to reveal both shared and unique aspects of evolutionary trajectories. Representative clone characterization by sequencing and MIC measurements enabled direct assessment of the impact of mutations on the extent of acquired drug resistance. In all three species, we observed a two-stage evolution: (i) early ciprofloxacin resistance reaching 4- to 16-fold the MIC for the wild type, commonly as a result of single mutations in DNA gyrase target genes (gyrA or gyrB), and (ii) additional genetic alterations affecting the transcriptional control of the drug efflux machinery or secondary target genes (DNA topoisomerase parC or parE).
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10
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Rehman A, Jeukens J, Levesque RC, Lamont IL. Gene-Gene Interactions Dictate Ciprofloxacin Resistance in Pseudomonas aeruginosa and Facilitate Prediction of Resistance Phenotype from Genome Sequence Data. Antimicrob Agents Chemother 2021; 65:e0269620. [PMID: 33875431 PMCID: PMC8218647 DOI: 10.1128/aac.02696-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
Ciprofloxacin is one of the most widely used antibiotics for treating Pseudomonas aeruginosa infections. However, P. aeruginosa acquires mutations that confer ciprofloxacin resistance, making treatment more difficult. Resistance is multifactorial, with mutations in multiple genes influencing the resistance phenotype. However, the contributions of individual mutations and mutation combinations to the amounts of ciprofloxacin that P. aeruginosa can tolerate are not well understood. Engineering P. aeruginosa strain PAO1 to contain mutations in any one of the resistance-associated genes gyrA, nfxB, rnfC, parC, and parE showed that only gyrA mutations increased the MIC for ciprofloxacin. Mutations in parC and parE increased the MIC of a gyrA mutant, making the bacteria ciprofloxacin resistant. Mutations in nfxB and rnfC increased the MIC, conferring resistance, only if both were mutated in a gyrA background. Mutations in all of gyrA, nfxB, rnfC, and parC/E further increased the MIC. These findings reveal an epistatic network of gene-gene interactions in ciprofloxacin resistance. We used this information to predict ciprofloxacin resistance/susceptibility for 274 isolates of P. aeruginosa from their genome sequences. Antibiotic susceptibility profiles were predicted correctly for 84% of the isolates. The majority of isolates for which prediction was unsuccessful were ciprofloxacin resistant, demonstrating the involvement of additional as yet unidentified genes and mutations in resistance. Our data show that gene-gene interactions can play an important role in antibiotic resistance and can be successfully incorporated into models predicting resistance phenotype.
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Affiliation(s)
- Attika Rehman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Julie Jeukens
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Québec, Canada
| | - Roger C. Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Québec, Canada
| | - Iain L. Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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11
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Rehman A, Patrick WM, Lamont IL. Mechanisms of ciprofloxacin resistance in Pseudomonas aeruginosa: new approaches to an old problem. J Med Microbiol 2019; 68:1-10. [DOI: 10.1099/jmm.0.000873] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Attika Rehman
- 1Department of Biochemistry, University of Otago, New Zealand
| | - Wayne M. Patrick
- 1Department of Biochemistry, University of Otago, New Zealand
- 2School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Iain L. Lamont
- 1Department of Biochemistry, University of Otago, New Zealand
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12
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Martins-Pinheiro M, Oliveira AR, Valencia AO, Fernandez-Silva FS, Silva LG, Lopes-Kulishev CO, Italiani VCS, Marques MV, Menck CF, Galhardo RS. Molecular characterization of Caulobacter crescentus mutator strains. Gene 2017; 626:251-257. [PMID: 28533123 DOI: 10.1016/j.gene.2017.05.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/31/2017] [Accepted: 05/18/2017] [Indexed: 10/25/2022]
Abstract
Mutator strains were identified by screening random Tn5 insertion clones of Caulobacter crescentus. We identified clones with robust increases in mutation rates with Tn5 insertions in the mutY, mutS, mutL and uvrD genes, known to act in mutation-preventing pathways in Escherichia coli. Analysis of mutations in the rpoB gene revealed that in both the parental strain and mismatch repair-deficient mutants, A:T→G:C transitions predominate by a large margin over C:G→T:A. We have also investigated the role of the error-prone polymerase encoded by imuC (dnaE2) in spontaneous mutagenesis, and found that a imuC mutant strain shows mutation rates and sequences comparable to the parental strain. Our study characterizes for the first time mutator strains in a member of the alphaproteobacteria group. In spite of the limitations of using a single marker, possible reasons for the observed mutational bias are discussed in the light of the repertoire of DNA repair genes in this bacterium.
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Affiliation(s)
- Marinalva Martins-Pinheiro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Alice R Oliveira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Alexy O Valencia
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Frank S Fernandez-Silva
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Larissa G Silva
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Carina O Lopes-Kulishev
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Valeria C S Italiani
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Marilis V Marques
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Carlos F Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Rodrigo S Galhardo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.
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Zaborskyte G, Andersen JB, Kragh KN, Ciofu O. Real-Time Monitoring of nfxB Mutant Occurrence and Dynamics in Pseudomonas aeruginosa Biofilm Exposed to Subinhibitory Concentrations of Ciprofloxacin. Antimicrob Agents Chemother 2017; 61:e02292-16. [PMID: 27993856 PMCID: PMC5328521 DOI: 10.1128/aac.02292-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/11/2016] [Indexed: 12/14/2022] Open
Abstract
Biofilm infections caused by Pseudomonas aeruginosa are frequently treated with ciprofloxacin (CIP); however, resistance rapidly develops. One of the primary resistance mechanisms is the overexpression of the MexCD-OprJ pump due to a mutation in nfxB, encoding the transcriptional repressor of this pump. The aim of this study was to investigate the effect of subinhibitory concentrations of CIP on the occurrence of nfxB mutants in the wild-type PAO1 flow cell biofilm model. For this purpose, we constructed fluorescent reporter strains (PAO1 background) with an mCherry tag for constitutive red fluorescence and chromosomal transcriptional fusion between the P mexCD promoter and gfp leading to green fluorescence upon mutation of nfxB We observed a rapid development of nfxB mutants by live confocal laser scanning microscopy (CLSM) imaging of the flow cell biofilm (reaching 80 to 90% of the whole population) when treated with 1/10 minimal biofilm inhibitory concentration of CIP for 24 h and 96 h. Based on the observed developmental stages, we propose that nfxB mutants emerged de novo in the biofilm during CIP treatment from filamentous cells, which might have arisen due to the stress responses induced by CIP. Identical nfxB mutations were found in fluorescent colonies from the same flow cell biofilm, especially in 24-h biofilms, suggesting selection and clonal expansion of the mutants during biofilm growth. Our findings point at the significant role of high-enough antibiotic dosages or appropriate combination therapy to avoid the emergence of resistant mutants in biofilms.
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Affiliation(s)
- Greta Zaborskyte
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bo Andersen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Nørskov Kragh
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Oana Ciofu
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
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14
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Peng J, Cao J, Ng FM, Hill J. Pseudomonas aeruginosa develops Ciprofloxacin resistance from low to high level with distinctive proteome changes. J Proteomics 2017; 152:75-87. [DOI: 10.1016/j.jprot.2016.10.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 10/08/2016] [Accepted: 10/17/2016] [Indexed: 12/12/2022]
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15
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Tagel M, Tavita K, Hõrak R, Kivisaar M, Ilves H. A novel papillation assay for the identification of genes affecting mutation rate in Pseudomonas putida and other pseudomonads. Mutat Res 2016; 790:41-55. [PMID: 27447898 DOI: 10.1016/j.mrfmmm.2016.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Formation of microcolonies (papillae) permits easy visual screening of mutational events occurring in single colonies of bacteria. In this study, we have established a novel papillation assay employable in a wide range of pseudomonads including Pseudomonas aeruginosa and Pseudomonas putida for monitoring mutation frequency in distinct colonies. With the aid of this assay, we conducted a genome-wide search for the factors affecting mutation frequency in P. putida. Screening ∼27,000 transposon mutants for increased mutation frequency allowed us to identify 34 repeatedly targeted genes. In addition to genes involved in DNA replication and repair, we identified genes participating in metabolism and transport of secondary metabolites, cell motility, and cell wall synthesis. The highest effect on mutant frequency was observed when truA (tRNA pseudouridine synthase), mpl (UDP-N-acetylmuramate-alanine ligase) or gacS (multi-sensor hybrid histidine kinase) were inactivated. Inactivation of truA elevated the mutant frequency only in growing cells, while the deficiency of gacS affected mainly stationary-phase mutagenesis. Thus, our results demonstrate the feasibility of the assay for isolating mutants with elevated mutagenesis in growing as well as stationary-phase bacteria.
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Affiliation(s)
- Mari Tagel
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Kairi Tavita
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Rita Hõrak
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Heili Ilves
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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16
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Margara LM, Fernández MM, Malchiodi EL, Argaraña CE, Monti MR. MutS regulates access of the error-prone DNA polymerase Pol IV to replication sites: a novel mechanism for maintaining replication fidelity. Nucleic Acids Res 2016; 44:7700-13. [PMID: 27257069 PMCID: PMC5027486 DOI: 10.1093/nar/gkw494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/20/2016] [Indexed: 12/02/2022] Open
Abstract
Translesion DNA polymerases (Pol) function in the bypass of template lesions to relieve stalled replication forks but also display potentially deleterious mutagenic phenotypes that contribute to antibiotic resistance in bacteria and lead to human disease. Effective activity of these enzymes requires association with ring-shaped processivity factors, which dictate their access to sites of DNA synthesis. Here, we show for the first time that the mismatch repair protein MutS plays a role in regulating access of the conserved Y-family Pol IV to replication sites. Our biochemical data reveals that MutS inhibits the interaction of Pol IV with the β clamp processivity factor by competing for binding to the ring. Moreover, the MutS–β clamp association is critical for controlling Pol IV mutagenic replication under normal growth conditions. Thus, our findings reveal important insights into a non-canonical function of MutS in the regulation of a replication activity.
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Affiliation(s)
- Lucía M Margara
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba X5000HUA, Argentina
| | - Marisa M Fernández
- Cátedra de Inmunología and Instituto de Estudios de la Inmunidad Humoral Profesor Ricardo A. Margni, CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires C1113AAD, Argentina
| | - Emilio L Malchiodi
- Cátedra de Inmunología and Instituto de Estudios de la Inmunidad Humoral Profesor Ricardo A. Margni, CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires C1113AAD, Argentina
| | - Carlos E Argaraña
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba X5000HUA, Argentina
| | - Mariela R Monti
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba X5000HUA, Argentina
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17
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Determinants of Genetic Diversity of Spontaneous Drug Resistance in Bacteria. Genetics 2016; 203:1369-80. [PMID: 27182949 DOI: 10.1534/genetics.115.185355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 05/04/2016] [Indexed: 01/05/2023] Open
Abstract
Any pathogen population sufficiently large is expected to harbor spontaneous drug-resistant mutants, often responsible for disease relapse after antibiotic therapy. It is seldom appreciated, however, that while larger populations harbor more mutants, the abundance distribution of these mutants is expected to be markedly uneven. This is because a larger population size allows early mutants to expand for longer, exacerbating their predominance in the final mutant subpopulation. Here, we investigate the extent to which this reduction in evenness can constrain the genetic diversity of spontaneous drug resistance in bacteria. Combining theory and experiments, we show that even small variations in growth rate between resistant mutants and the wild type result in orders-of-magnitude differences in genetic diversity. Indeed, only a slight fitness advantage for the mutant is enough to keep diversity low and independent of population size. These results have important clinical implications. Genetic diversity at antibiotic resistance loci can determine a population's capacity to cope with future challenges (i.e., second-line therapy). We thus revealed an unanticipated way in which the fitness effects of antibiotic resistance can affect the evolvability of pathogens surviving a drug-induced bottleneck. This insight will assist in the fight against multidrug-resistant microbes, as well as contribute to theories aimed at predicting cancer evolution.
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Solé M, Fàbrega A, Cobos-Trigueros N, Zamorano L, Ferrer-Navarro M, Ballesté-Delpierre C, Reustle A, Castro P, Nicolás JM, Oliver A, Martínez JA, Vila J. In vivo evolution of resistance of Pseudomonas aeruginosa strains isolated from patients admitted to an intensive care unit: mechanisms of resistance and antimicrobial exposure. J Antimicrob Chemother 2015; 70:3004-13. [PMID: 26260130 DOI: 10.1093/jac/dkv228] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/04/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The main objective of this study was to investigate the relationship among the in vivo acquisition of antimicrobial resistance in Pseudomonas aeruginosa clinical isolates, the underlying molecular mechanisms and previous exposure to antipseudomonal agents. METHODS PFGE was used to study the molecular relatedness of the strains. The MICs of ceftazidime, cefepime, piperacillin/tazobactam, imipenem, meropenem, ciprofloxacin and amikacin were determined. Outer membrane protein profiles were assessed to study OprD expression. RT-PCR was performed to analyse ampC, mexB, mexD, mexF and mexY expression. The presence of mutations was analysed through DNA sequencing. RESULTS We collected 17 clonally related paired isolates [including first positive samples (A) and those with MICs increased ≥4-fold (B)]. Most B isolates with increased MICs of imipenem, meropenem and ceftazidime became resistant to these drugs. The most prevalent resistance mechanisms detected were OprD loss (65%), mexB overexpression (53%), ampC derepression (29%), quinolone target gene mutations (24%) and increased mexY expression (24%). Five (29%) B isolates developed multidrug resistance. Meropenem was the most frequently (71%) received treatment, explaining the high prevalence of oprD mutations and likely mexB overexpression. Previous exposure to ceftazidime showed a higher impact on selection of increased MICs than previous exposure to piperacillin/tazobactam. CONCLUSIONS Stepwise acquisition of resistance has a critical impact on the resistance phenotypes of P. aeruginosa, leading to a complex scenario for finding effective antimicrobial regimens. In the clinical setting, meropenem seems to be the most frequent driver of multidrug resistance development, while piperacillin/tazobactam, in contrast to ceftazidime, seems to be the β-lactam least associated with the selection of resistance mechanisms.
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Affiliation(s)
- Mar Solé
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Anna Fàbrega
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | | | - Laura Zamorano
- University Hospital Son Espases, Palma de Mallorca, Spain
| | - Mario Ferrer-Navarro
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Clara Ballesté-Delpierre
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Anna Reustle
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Pedro Castro
- Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | | | - Antonio Oliver
- University Hospital Son Espases, Palma de Mallorca, Spain
| | | | - Jordi Vila
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
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Li XZ, Plésiat P, Nikaido H. The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria. Clin Microbiol Rev 2015; 28:337-418. [PMID: 25788514 PMCID: PMC4402952 DOI: 10.1128/cmr.00117-14] [Citation(s) in RCA: 924] [Impact Index Per Article: 102.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The global emergence of multidrug-resistant Gram-negative bacteria is a growing threat to antibiotic therapy. The chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. Multidrug pumps, particularly those represented by the clinically relevant AcrAB-TolC and Mex pumps of the resistance-nodulation-division (RND) superfamily, not only mediate intrinsic and acquired multidrug resistance (MDR) but also are involved in other functions, including the bacterial stress response and pathogenicity. Additionally, efflux pumps interact synergistically with other resistance mechanisms (e.g., with the outer membrane permeability barrier) to increase resistance levels. Since the discovery of RND pumps in the early 1990s, remarkable scientific and technological advances have allowed for an in-depth understanding of the structural and biochemical basis, substrate profiles, molecular regulation, and inhibition of MDR pumps. However, the development of clinically useful efflux pump inhibitors and/or new antibiotics that can bypass pump effects continues to be a challenge. Plasmid-borne efflux pump genes (including those for RND pumps) have increasingly been identified. This article highlights the recent progress obtained for organisms of clinical significance, together with methodological considerations for the characterization of MDR pumps.
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Affiliation(s)
- Xian-Zhi Li
- Human Safety Division, Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Patrick Plésiat
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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Target-based resistance in Pseudomonas aeruginosa and Escherichia coli to NBTI 5463, a novel bacterial type II topoisomerase inhibitor. Antimicrob Agents Chemother 2014; 59:331-7. [PMID: 25348539 DOI: 10.1128/aac.04077-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In a previous report (T. J. Dougherty, A. Nayar, J. V. Newman, S. Hopkins, G. G. Stone, M. Johnstone, A. B. Shapiro, M. Cronin, F. Reck, and D. E. Ehmann, Antimicrob Agents Chemother 58:2657-2664, 2014), a novel bacterial type II topoisomerase inhibitor, NBTI 5463, with activity against Gram-negative pathogens was described. First-step resistance mutations in Pseudomonas aeruginosa arose exclusively in the nfxB gene, a regulator of the MexCD-OprJ efflux pump system. The present report describes further resistance studies with NBTI 5463 in both Pseudomonas aeruginosa and Escherichia coli. Second-step mutations in P. aeruginosa arose at aspartate 82 of the gyrase A subunit and led to 4- to 8-fold increases in the MIC over those seen in the parental strain with a first-step nfxB efflux mutation. A third-step mutant showed additional GyrA changes, with no changes in topoisomerase IV. Despite repeated efforts, resistance mutations could not be selected in E. coli. Genetic introduction of the Asp82 mutations observed in P. aeruginosa did not significantly increase the NBTI MIC in E. coli. However, with the aspartate 82 mutation present, it was possible to select second-step mutations in topoisomerase IV that did lead to MIC increases of 16- and 128-fold. As with the gyrase aspartate 82 mutation, the mutations in topoisomerase IV did not by themselves raise the NBTI MIC in E. coli. Only the presence of mutations in both targets of E. coli led to an increase in NBTI MIC values. This represents a demonstration of the value of balanced dual-target activity in mitigating resistance development.
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