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Akshay SD, Deekshit VK, Mohan Raj J, Maiti B. Outer Membrane Proteins and Efflux Pumps Mediated Multi-Drug Resistance in Salmonella: Rising Threat to Antimicrobial Therapy. ACS Infect Dis 2023; 9:2072-2092. [PMID: 37910638 DOI: 10.1021/acsinfecdis.3c00408] [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] [Indexed: 11/03/2023]
Abstract
Despite colossal achievements in antibiotic therapy in recent decades, drug-resistant pathogens have remained a leading cause of death and economic loss globally. One such WHO-critical group pathogen is Salmonella. The extensive and inappropriate treatments for Salmonella infections have led from multi-drug resistance (MDR) to extensive drug resistance (XDR). The synergy between efflux-mediated systems and outer membrane proteins (OMPs) may favor MDR in Salmonella. Differential expression of the efflux system and OMPs (influx) and positional mutations are the factors that can be correlated to the development of drug resistance. Insights into the mechanism of influx and efflux of antibiotics can aid in developing a structurally stable molecule that can be proficient at escaping from the resistance loops in Salmonella. Understanding the strategic responsibilities and developing policies to address the surge of drug resistance at the national, regional, and global levels are the needs of the hour. In this Review, we attempt to aggregate all the available research findings and delineate the resistance mechanisms by dissecting the involvement of OMPs and efflux systems. Integrating major OMPs and the efflux system's differential expression and positional mutation in Salmonella may provide insight into developing strategic therapies for one health application.
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Affiliation(s)
- Sadanand Dangari Akshay
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Department of Bio & Nano Technology, Paneer Campus, Deralakatte, Mangalore-575018, India
| | - Vijaya Kumar Deekshit
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Department of Infectious Diseases & Microbial Genomics, Paneer Campus, Deralakatte, Mangalore-575018, India
| | - Juliet Mohan Raj
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Department of Infectious Diseases & Microbial Genomics, Paneer Campus, Deralakatte, Mangalore-575018, India
| | - Biswajit Maiti
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Department of Bio & Nano Technology, Paneer Campus, Deralakatte, Mangalore-575018, India
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Sabar MA, Van Huy T, Sugie Y, Wada H, Zhao B, Matsuura N, Ihara M, Watanabe T, Tanaka H, Honda R. Antimicrobial resistome and mobilome in the urban river affected by combined sewer overflows and wastewater treatment effluent. JOURNAL OF WATER AND HEALTH 2023; 21:1032-1050. [PMID: 37632379 PMCID: wh_2023_073 DOI: 10.2166/wh.2023.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Abstract
The dissemination of antimicrobial resistance in the environment is an emerging global health problem. Wastewater treatment effluent and combined sewer overflows (CSOs) are major sources of antimicrobial resistance in urban rivers. This study aimed to clarify the effect of municipal wastewater treatment effluent and CSO on antimicrobial resistance genes (ARGs), mobile gene elements, and the microbial community in an urban river. The ARG abundance per 16S-based microbial population in the target river was 0.37-0.54 and 0.030-0.097 during the CSO event and dry weather, respectively. During the CSO event, the antimicrobial resistome in the river shifted toward a higher abundance of ARGs to clinically important drug classes, including macrolide, fluoroquinolone, and β-lactam, whereas ARGs to sulfonamide and multidrug by efflux pump were relatively abundant in dry weather. The abundance of intI1 and tnpA genes were highly associated with the total ARG abundance, suggesting their potential application as an indicator for estimating resistome contamination. Increase of prophage during the CSO event suggested that impact of CSO has a greater potential for horizontal gene transfer (HGT) via transduction. Consequently, CSO not only increases the abundance of ARGs to clinically important antimicrobials but also possibly enhances potential of HGT in urban rivers.
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Affiliation(s)
- Muhammad Adnan Sabar
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192, Japan E-mail:
| | - Than Van Huy
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - Yoshinori Sugie
- Graduate School of Engineering, Kyoto University, Kyoto 615-8530, Japan
| | - Hiroyuki Wada
- Graduate School of Engineering, Kyoto University, Kyoto 615-8530, Japan
| | - Bo Zhao
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Otsu 520-0811, Japan; College of Environment, Hohai University, Nanjing 210098, China
| | - Norihisa Matsuura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Otsu 520-0811, Japan; Faculty of Agriculture and Marine Science, Kochi University, Nankoku 780-8072, Japan
| | - Toru Watanabe
- Department of Food, Life and Environmental Sciences, Yamagata University, Tsuruoka 997-8555, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Otsu 520-0811, Japan
| | - Ryo Honda
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Otsu 520-0811, Japan; Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1192, Japan
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3
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How Do Transposable Elements Activate Expression of Transcriptionally Silent Antibiotic Resistance Genes? Int J Mol Sci 2022; 23:ijms23158063. [PMID: 35897639 PMCID: PMC9330008 DOI: 10.3390/ijms23158063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023] Open
Abstract
The rapidly emerging phenomenon of antibiotic resistance threatens to substantially reduce the efficacy of available antibacterial therapies. Dissemination of resistance, even between phylogenetically distant bacterial species, is mediated mainly by mobile genetic elements, considered to be natural vectors of horizontal gene transfer. Transposable elements (TEs) play a major role in this process—due to their highly recombinogenic nature they can mobilize adjacent genes and can introduce them into the pool of mobile DNA. Studies investigating this phenomenon usually focus on the genetic load of transposons and the molecular basis of their mobility. However, genes introduced into evolutionarily distant hosts are not necessarily expressed. As a result, bacterial genomes contain a reservoir of transcriptionally silent genetic information that can be activated by various transposon-related recombination events. The TEs themselves along with processes associated with their transposition can introduce promoters into random genomic locations. Thus, similarly to integrons, they have the potential to convert dormant genes into fully functional antibiotic resistance determinants. In this review, we describe the genetic basis of such events and by extension the mechanisms promoting the emergence of new drug-resistant bacterial strains.
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Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022; 10:microorganisms10061239. [PMID: 35744757 PMCID: PMC9228545 DOI: 10.3390/microorganisms10061239] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.
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López-Siles M, McConnell MJ, Martín-Galiano AJ. Identification of Promoter Region Markers Associated With Altered Expression of Resistance-Nodulation-Division Antibiotic Efflux Pumps in Acinetobacter baumannii. Front Microbiol 2022; 13:869208. [PMID: 35663863 PMCID: PMC9161033 DOI: 10.3389/fmicb.2022.869208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic alterations leading to the constitutive upregulation of specific efflux pumps contribute to antibacterial resistance in multidrug resistant bacteria. The identification of such resistance markers remains one of the most challenging tasks of genome-level resistance predictors. In this study, 487 non-redundant genetic events were identified in upstream zones of three operons coding for resistance-nodulation-division (RND) efflux pumps of 4,130 Acinetobacter baumannii isolates. These events included insertion sequences, small indels, and single nucleotide polymorphisms. In some cases, alterations explicitly modified the expression motifs described for these operons, such as the promoter boxes, operators, and Shine-Dalgarno sequences. In addition, changes in DNA curvature and mRNA secondary structures, which are structural elements that regulate expression, were also calculated. According to their influence on RND upregulation, the catalog of upstream modifications were associated with “experimentally verified,” “presumed,” and “probably irrelevant” degrees of certainty. For experimental verification, DNA of upstream sequences independently carrying selected markers, three for each RND operon, were fused to a luciferase reporter plasmid system. Five out of the nine selected markers tested showed significant increases in expression with respect to the wild-type sequence control. In particular, a 25-fold expression increase was observed with the ISAba1 insertion sequence upstream the adeABC pump. Next, overexpression of each of the three multi-specific RND pumps was linked to their respective antibacterial substrates by a deep A. baumannii literature screen. Consequently, a data flow framework was then developed to link genomic upregulatory RND determinants to potential antibiotic resistance. Assignment of potential increases in minimal inhibitory concentrations at the “experimentally verified” level was permitted for 42 isolates to 7–8 unrelated antibacterial agents including tigecycline, which is overlooked by conventional resistome predictors. Thus, our protocol may represent a time-saving filter step prior to laborious confirmation experiments for efflux-driven resistance. Altogether, a computational-experimental pipeline containing all components required for identifying the upstream regulatory resistome is proposed. This schema may provide the foundational stone for the elaboration of tools approaching antibiotic efflux that complement routine resistome predictors for preventing antimicrobial therapy failure against difficult-to-threat bacteria.
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Dey N, Kamatchi C, Vickram AS, Anbarasu K, Thanigaivel S, Palanivelu J, Pugazhendhi A, Ponnusamy VK. Role of nanomaterials in deactivating multiple drug resistance efflux pumps - A review. ENVIRONMENTAL RESEARCH 2022; 204:111968. [PMID: 34453898 DOI: 10.1016/j.envres.2021.111968] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
The changes in lifestyle and living conditions have affected not only humans but also microorganisms. As man invents new drugs and therapies, pathogens alter themselves to survive and thrive. Multiple drug resistance (MDR) is the talk of the town for decades now. Many generations of medications have been termed useless as MDR rises among the infectious population. The surge in nanotechnology has brought a new hope in reducing this aspect of resistance in pathogens. It has been observed in several laboratory-based studies that the use of nanoparticles had a synergistic effect on the antibiotic being administered to the pathogen; several resistant strains scummed to the stress created by the nanoparticles and became susceptible to the drug. The major cause of resistance to date is the efflux system, which makes the latest generation of antibiotics ineffective without reaching the target site. If species-specific nanomaterials are used to control the activity of efflux pumps, it could revolutionize the field of medicine and make the previous generation resistant medications active once again. Therefore, the current study was devised to assess and review nanoparticles' role on efflux systems and discuss how specialized particles can be designed towards an infectious host's particular drug ejection systems.
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Affiliation(s)
- Nibedita Dey
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - C Kamatchi
- Department of Biotechnology, The Oxford College of Science, Bengaluru, India
| | - A S Vickram
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - K Anbarasu
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - S Thanigaivel
- Department of Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Jeyanthi Palanivelu
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai, India
| | | | - Vinoth Kumar Ponnusamy
- Department of Medicinal and Applied Chemistry & Research Center for Environmental Medicine, Kaohsiung Medical University (KMU), Kaohsiung City, 807, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital (KMUH), Kaohsiung City, 807, Taiwan; Program of Aquatic Science and Technology, College of Hydrosphere Science, National Kaohsiung University of Science and Technology (NKUST), Kaohsiung City, Taiwan.
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Abstract
Many antibiotic resistant uropathogenic Escherichia coli (UPEC) strains belong to clones defined by their multilocus sequence type (ST), with ST131 being the most dominant. Although we have a good understanding of resistance development to fluoroquinolones and third-generation cephalosporins by ST131, our understanding of the virulence repertoire that has contributed to its global dissemination is limited. Here we show that the genes encoding Afa/Dr fimbriae, a group of adhesins strongly associated with UPEC that cause gestational pyelonephritis and recurrent cystitis, are found in approximately one third of all ST131 strains. Sequence comparison of the AfaE adhesin protein revealed a unique allelic variant carried by 82.9% of afa-positive ST131 strains. We identify the afa regulatory region as a hotspot for the integration of insertion sequence (IS) elements, all but one of which alter afa transcription. Close investigation demonstrated that the integration of an IS1 element in the afa regulatory region leads to increased expression of Afa/Dr fimbriae, promoting enhanced adhesion to kidney epithelial cells and suggesting a mechanism for altered virulence. Finally, we provide evidence for a more widespread impact of IS1 on ST131 genome evolution, suggesting that IS dynamics contribute to strain level microevolution that impacts ST131 fitness. IMPORTANCE E. coli ST131 is the most common antibiotic resistant UPEC clone associated with human urinary tract and bloodstream infections. Understanding the features of ST131 that have driven its global dissemination remains a critical priority if we are to counter its increasing antibiotic resistance. Here, we utilized a large collection of ST131 isolates to investigate the prevalence, regulation, and function of Afa/Dr fimbriae, a well-characterized UPEC colonization and virulence factor. We show that the afa genes are found frequently in ST131 and demonstrate how the integration of IS elements in the afa regulatory region modulates Afa expression, presenting an example of altered virulence capacity. We also exploit a curated set of ST131 genomes to map the integration of the antibiotic resistance-associated IS1 element in the ST131 pangenome, providing evidence for its widespread impact on ST131 genome evolution.
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Garcia ÍR, de Oliveira Garcia FA, Pereira PS, Coutinho HDM, Siyadatpanah A, Norouzi R, Wilairatana P, de Lourdes Pereira M, Nissapatorn V, Tintino SR, Rodrigues FFG. Microbial resistance: The role of efflux pump superfamilies and their respective substrates. Life Sci 2022; 295:120391. [PMID: 35149116 DOI: 10.1016/j.lfs.2022.120391] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/02/2022] [Accepted: 02/06/2022] [Indexed: 12/24/2022]
Abstract
The microorganism resistance to antibiotics has become one of the most worrying issues for science due to the difficulties related to clinical treatment and the rapid spread of diseases. Efflux pumps are classified into six groups of carrier proteins that are part of the different types of mechanisms that contribute to resistance in microorganisms, allowing their survival. The present study aimed to carry out a bibliographic review on the superfamilies of carriers in order to understand their compositions, expressions, substrates, and role in intrinsic resistance. At first, a search for manuscripts was carried out in the databases Medline, Pubmed, ScienceDirect, and Scielo, using as descriptors: efflux pump, expression, pump inhibitors and efflux superfamily. For article selection, two criteria were taken into account: for inclusion, those published between 2000 and 2020, including textbooks, and for exclusion, duplicates and academic collections. In this research, 139,615 published articles were obtained, with 312 selected articles and 7 book chapters that best met the aim. From the comprehensive analysis, it was possible to consider that the chromosomes and genetic elements can contain genes encoding efflux pumps and are responsible for multidrug resistance. Even though this is a well-explored topic in the scientific community, understanding the behavior of antibiotics as substrates that increase the expression of pump-encoding genes has challenged medicine. This review study succinctly summarizes the most relevant features of these systems, as well as their contribution to multidrug resistance.
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Affiliation(s)
| | | | | | | | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand, Iran
| | - Roghayeh Norouzi
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Maria de Lourdes Pereira
- CICECO-Aveiro Institute of Materials & Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences and Research Excellence Center for Innovation and Health, Walailak University, Thailand
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Limited Multidrug Resistance Efflux Pump Overexpression among Multidrug-Resistant Escherichia coli Strains of ST131. Antimicrob Agents Chemother 2021; 65:AAC.01735-20. [PMID: 33468485 DOI: 10.1128/aac.01735-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/28/2020] [Indexed: 12/30/2022] Open
Abstract
Gram-negative bacteria partly rely on efflux pumps to facilitate growth under stressful conditions and to increase resistance to a wide variety of commonly used drugs. In recent years, Escherichia coli sequence type 131 (ST131) has emerged as a major cause of extraintestinal infection frequently exhibiting a multidrug resistance (MDR) phenotype. The contribution of efflux to MDR in emerging E. coli MDR clones, however, is not well studied. We characterized strains from an international collection of clinical MDR E. coli isolates by MIC testing with and without the addition of the AcrAB-TolC efflux inhibitor 1-(1-naphthylmethyl)-piperazine (NMP). MIC data for 6 antimicrobial agents and their reversion by NMP were analyzed by principal-component analysis (PCA). PCA revealed a group of 17 MDR E. coli isolates (n = 34) exhibiting increased susceptibility to treatment with NMP, suggesting an enhanced contribution of efflux pumps to antimicrobial resistance in these strains (termed enhanced efflux phenotype [EEP] strains). Only 1/17 EEP strains versus 12/17 non-EEP MDR strains belonged to the ST131 clonal group. Whole-genome sequencing revealed marked differences in efflux-related genes between EEP and control strains, with the majority of notable amino acid substitutions occurring in AcrR, MarR, and SoxR. Quantitative reverse transcription-PCR (qRT-PCR) of multiple efflux-related genes showed significant overexpression of the AcrAB-TolC system in EEP strains, whereas in the remaining strains, we found enhanced expression of alternative efflux proteins. We conclude that a proportion of MDR E. coli strains exhibit an EEP, which is linked to an overexpression of the AcrAB-TolC efflux pump and a distinct array of genomic variations. Members of ST131, although highly successful, are less likely to exhibit the EEP.
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Couchoud C, Bertrand X, Valot B, Hocquet D. Deciphering the role of insertion sequences in the evolution of bacterial epidemic pathogens with panISa software. Microb Genom 2020; 6:e000356. [PMID: 32213253 PMCID: PMC7371109 DOI: 10.1099/mgen.0.000356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/02/2020] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing (NGS) is now widely used in microbiology to explore genome evolution and the structure of pathogen outbreaks. Bioinformatics pipelines readily detect single-nucleotide polymorphisms or short indels. However, bacterial genomes also evolve through the action of small transposable elements called insertion sequences (ISs), which are difficult to detect due to their short length and multiple repetitions throughout the genome. We designed panISa software for the ab initio detection of IS insertions in the genomes of prokaryotes. PanISa has been released as open source software (GPL3) available from https://github.com/bvalot/panISa. In this study, we assessed the utility of this software for evolutionary studies, by reanalysing five published datasets for outbreaks of human major pathogens in which ISs had not been specifically investigated. We reanalysed the raw data from each study, by aligning the reads against reference genomes and running panISa on the alignments. Each hit was automatically curated and IS-related events were validated on the basis of nucleotide sequence similarity, by comparison with the ISFinder database. In Acinetobacter baumannii, the panISa pipeline identified ISAba1 or ISAba125 upstream from the ampC gene, which encodes a cephalosporinase in all third-generation cephalosporin-resistant isolates. In the genomes of Vibrio cholerae isolates, we found that early Haitian isolates had the same ISs as Nepalese isolates, confirming the inferred history of the contamination of this island. In Enterococcus faecalis, panISa identified regions of high plasticity, including a pathogenicity island enriched in IS-related events. The overall distribution of ISs deduced with panISa was consistent with SNP-based phylogenic trees, for all species considered. The role of ISs in pathogen evolution has probably been underestimated due to difficulties detecting these transposable elements. We show here that panISa is a useful addition to the bioinformatics toolbox for analyses of the evolution of bacterial genomes. PanISa will facilitate explorations of the functional impact of ISs and improve our understanding of prokaryote evolution.
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Affiliation(s)
- Charlotte Couchoud
- Laboratoire d’Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Xavier Bertrand
- Laboratoire d’Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Benoit Valot
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
- Bioinformatique et big data au service de la santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
| | - Didier Hocquet
- Laboratoire d’Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
- Bioinformatique et big data au service de la santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
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Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance. Front Microbiol 2020; 11:761. [PMID: 32435238 PMCID: PMC7219019 DOI: 10.3389/fmicb.2020.00761] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Coralia Bleotu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
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Alosaimy S, Abdul-Mutakabbir JC, Kebriaei R, Jorgensen SCJ, Rybak MJ. Evaluation of Eravacycline: A Novel Fluorocycline. Pharmacotherapy 2020; 40:221-238. [PMID: 31944332 DOI: 10.1002/phar.2366] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Eravacycline (ERV), formerly known as TP-434, is a novel tetracycline (TET) antibiotic that exhibits in vitro activity against various gram-positive, gram-negative aerobic and anaerobic pathogens, including those exhibiting TET-specific acquired resistance mechanisms. Similar to other TETs, it inhibits protein synthesis through binding to the 30S ribosomal subunit. Eravacycline was approved by the United States Food and Drug Administration (FDA) in August 2018 for the treatment of complicated intraabdominal infections (cIAIs) in adults following the Investigating Gram-Negative Infections Treated with Eravacycline (IGNITE)1 and IGNITE4 phase III trials. In these two, double-blind, multicenter clinical trials, ERV was proven noninferior in terms of clinical response in comparison to ertapenem and meropenem, respectively. Eravacycline was well tolerated with nausea, vomiting, and infusion site reactions being the most commonly reported adverse reactions. Clinicians now have ERV as a novel therapeutic option for the treatment of adults with intraabdominal infections, allergies to β-lactam agents, Clostridioides difficile-associated diarrhea, or if tolerability to other agents is a concern.
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Affiliation(s)
- Sara Alosaimy
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan
| | - Jacinda C Abdul-Mutakabbir
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan
| | - Razie Kebriaei
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan
| | - Sarah C J Jorgensen
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan
| | - Michael J Rybak
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan.,Department of Pharmacy, Detroit Medical Center, Detroit, Michigan.,Division of Infectious Diseases, Department of Medicine, School of Medicine, Wayne State University, Detroit, Michigan
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Colclough AL, Scadden J, Blair JMA. TetR-family transcription factors in Gram-negative bacteria: conservation, variation and implications for efflux-mediated antimicrobial resistance. BMC Genomics 2019; 20:731. [PMID: 31606035 PMCID: PMC6790063 DOI: 10.1186/s12864-019-6075-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Background TetR-family transcriptional regulators (TFTRs) are DNA binding factors that regulate gene expression in bacteria. Well-studied TFTRs, such as AcrR, which regulates efflux pump expression, are usually encoded alongside target operons. Recently, it has emerged that there are many TFTRs which act as global multi-target regulators. Our classical view of TFTRs as simple, single-target regulators therefore needs to be reconsidered. As some TFTRs regulate essential processes (e.g. metabolism) or processes which are important determinants of resistance and virulence (e.g. biofilm formation and efflux gene expression) and as TFTRs are present throughout pathogenic bacteria, they may be good drug discovery targets for tackling antimicrobial resistant infections. However, the prevalence and conservation of individual TFTR genes in Gram-negative species, has to our knowledge, not yet been studied. Results Here, a wide-scale search for TFTRs in available proteomes of clinically relevant pathogens Salmonella and Escherichia species was performed and these regulators further characterised. The majority of identified TFTRs are involved in efflux regulation in both Escherichia and Salmonella. The percentage variance in TFTR genes of these genera was found to be higher in those regulating genes involved in efflux, bleach survival or biofilm formation than those regulating more constrained processes. Some TFTRs were found to be present in all strains and species of these two genera, whereas others (i.e. TetR) are only present in some strains and some (i.e. RamR) are genera-specific. Two further pathogens on the WHO priority pathogen list (K. pneumoniae and P. aeruginosa) were then searched for the presence of the TFTRs conserved in Escherichia and Salmonella. Conclusions Through bioinformatics and literature analyses, we present that TFTRs are a varied and heterogeneous family of proteins required for the regulation of numerous important processes, with consequences to antimicrobial resistance and virulence, and that the roles and responses of these proteins are frequently underestimated. Electronic supplementary material The online version of this article (10.1186/s12864-019-6075-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A L Colclough
- Institute of Microbiology and Infection, Biosciences Building, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - J Scadden
- Institute of Microbiology and Infection, Biosciences Building, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - J M A Blair
- Institute of Microbiology and Infection, Biosciences Building, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Deletion of the major Escherichia coli multidrug transporter AcrB reveals transporter plasticity and redundancy in bacterial cells. PLoS One 2019; 14:e0218828. [PMID: 31251753 PMCID: PMC6599122 DOI: 10.1371/journal.pone.0218828] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 06/11/2019] [Indexed: 12/28/2022] Open
Abstract
Multidrug Transporters (MDTs) are major contributors to the acquisition and maintenance of Antimicrobial Resistance (AMR), a growing public health threat of broad concern. Despite the large number of MDTs, the overwhelming majority of the studies performed thus far in Gram-negative bacteria emphasize the supremacy of the AcrAB-TolC complex. To unveil the potential role of other MDTs we studied the behavior of a null AcrB Escherichia coli strain when challenged with chloramphenicol, a bacteriostatic antibiotic. We found that such a strain developed an extremely high-level of resistance to chloramphenicol, cross resistance to quinolones and erythromycin and displayed high levels of expression of the single component MFS transporter MdfA and multiple TolC-dependent transporters. The results suggest that the high versatility of the whole ensemble of transporters, the bacterial Effluxome, is an essential part of a strategy of survival in everchanging, at times noxious, environments. The concept of a functional Effluxome presents an alternative to the existing paradigms in the field and provides novel targets for the search for inhibitors of transporters as adjuvants of existing antibiotics.
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Türkel İ, Yıldırım T, Yazgan B, Bilgin M, Başbulut E. Relationship between antibiotic resistance, efflux pumps, and biofilm formation in extended-spectrum β-lactamase producing Klebsiella pneumoniae. J Chemother 2019; 30:354-363. [DOI: 10.1080/1120009x.2018.1521773] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- İbrahim Türkel
- Department of Biology, Faculty of Arts and Sciences, Amasya University, Amasya, Turkey,
| | - Tuba Yıldırım
- Department of Biology, Faculty of Arts and Sciences, Amasya University, Amasya, Turkey,
- Central Research Laboratory, Amasya University, Amasya, Turkey,
| | - Burak Yazgan
- Central Research Laboratory, Amasya University, Amasya, Turkey,
- Department of Medical Sevices and Techniques, Amasya University Sabuncuoğlu Serefeddin Vocational Higher School of Health Services, Amasya, Turkey,
| | - Melek Bilgin
- Microbiology Laboratory, Education and Research Hospital, Samsun, Turkey
| | - Eşe Başbulut
- Microbiology Laboratory, Education and Research Hospital, Samsun, Turkey
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16
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Hoeksema M, Jonker MJ, Bel K, Brul S, Ter Kuile BH. Genome rearrangements in Escherichia coli during de novo acquisition of resistance to a single antibiotic or two antibiotics successively. BMC Genomics 2018; 19:973. [PMID: 30591014 PMCID: PMC6307192 DOI: 10.1186/s12864-018-5353-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/07/2018] [Indexed: 11/25/2022] Open
Abstract
Background The ability of bacteria to acquire resistance to antibiotics relies to a large extent on their capacity for genome modification. Prokaryotic genomes are highly plastic and can utilize horizontal gene transfer, point mutations, and gene deletions or amplifications to realize genome expansion and rearrangements. The contribution of point mutations to de novo acquisition of antibiotic resistance is well-established. In this study, the internal genome rearrangement of Escherichia coli during to de novo acquisition of antibiotic resistance was investigated using whole-genome sequencing. Results Cells were made resistant to one of the four antibiotics and subsequently to one of the three remaining. This way the initial genetic rearrangements could be documented together with the effects of an altered genetic background on subsequent development of resistance. A DNA fragment including ampC was amplified by a factor sometimes exceeding 100 as a result of exposure to amoxicillin. Excision of prophage e14 was observed in many samples with a double exposure history, but not in cells exposed to a single antibiotic, indicating that the activation of the SOS stress response alone, normally the trigger for excision, was not sufficient to cause excision of prophage e14. Partial deletion of clpS and clpA occurred in strains exposed to enrofloxacin and tetracycline. Other deletions were observed in some strains, but not in replicates with the exact same exposure history. Various insertion sequence transpositions correlated with exposure to specific antibiotics. Conclusions Many of the genome rearrangements have not been reported before to occur during resistance development. The observed correlation between genome rearrangements and specific antibiotic pressure, as well as their presence in independent replicates indicates that these events do not occur randomly. Taken together, the observed genome rearrangements illustrate the plasticity of the E. coli genome when exposed to antibiotic stress. Electronic supplementary material The online version of this article (10.1186/s12864-018-5353-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marloes Hoeksema
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijs J Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Keshia Bel
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Benno H Ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands. .,Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, The Netherlands.
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17
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Chetri S, Dolley A, Bhowmik D, Chanda DD, Chakravarty A, Bhattacharjee A. Transcriptional Response of AcrEF-TolC against Fluoroquinolone and Carbapenem in Escherichia coli of Clinical Origin. Indian J Med Microbiol 2018; 36:537-540. [DOI: 10.4103/ijmm.ijmm_18_308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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18
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Zheng JX, Lin ZW, Sun X, Lin WH, Chen Z, Wu Y, Qi GB, Deng QW, Qu D, Yu ZJ. Overexpression of OqxAB and MacAB efflux pumps contributes to eravacycline resistance and heteroresistance in clinical isolates of Klebsiella pneumoniae. Emerg Microbes Infect 2018; 7:139. [PMID: 30068997 PMCID: PMC6070572 DOI: 10.1038/s41426-018-0141-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 06/21/2018] [Accepted: 07/03/2018] [Indexed: 01/04/2023]
Abstract
This study investigated the characteristics and mechanisms of eravacycline resistance and heteroresistance in clinical Klebsiella pneumoniae isolates. A total of 393 clinical K. pneumoniae isolates were collected and subjected to eravacycline and tigecycline MIC determinations using the agar dilution method. Eravacycline heteroresistance was assessed by a population analysis profile (PAP). The expression levels of efflux pumps and their regulators were determined by quantitative reverse-transcription PCR (qRT-PCR). This study identified 67 eravacycline-nonsusceptible isolates; among the extended-spectrum β-lactamase (ESBL)-positive isolates, eravacycline-nonsusceptible isolates were detected more frequently than tigecycline-nonsusceptible isolates (21.7% vs. 9.4%, p = 0.001). The study sample was observed to include 20 K. pneumoniae isolates with eravacycline heteroresistance. Compared to the reference strain, oqxA or oqxB overexpression was observed in nine eravacycline-nonsusceptible isolates (range, 35.64–309.02-fold) and 13 eravacycline-heteroresistant isolates (8.42–296.34-fold). The overexpression of macA or macB was detected in 12 eravacycline-heteroresistant isolates (3.23–28.35-fold). Overexpression of the efflux pump regulator gene ramA was observed in 11 eravacycline-nonsusceptible isolates (3.33–94.05-fold) and 18 eravacycline-heteroresistant isolates (3.89–571.70-fold). The eravacycline MICs were increased by one–fourfold by overexpression of oqxAB or macAB in three eravacycline-sensitive isolates. In conclusion, the overexpression of OqxAB and MacAB efflux pumps and the transcriptional regulator RamA were suggested to be involved in K. pneumoniae eravacycline resistance and heteroresistance.
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Affiliation(s)
- Jin-Xin Zheng
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital, Shenzhen University School of Medicine, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China.,Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, 200032, Shanghai, China
| | - Zhi-Wei Lin
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital, Shenzhen University School of Medicine, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China
| | - Xiang Sun
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital, Shenzhen University School of Medicine, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China
| | - Wei-Hong Lin
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, 200032, Shanghai, China
| | - Zhong Chen
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital, Shenzhen University School of Medicine, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China.,Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, 200032, Shanghai, China
| | - Yang Wu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, 200032, Shanghai, China
| | - Guo-Bin Qi
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, 200032, Shanghai, China
| | - Qi-Wen Deng
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital, Shenzhen University School of Medicine, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China
| | - Di Qu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, 200032, Shanghai, China.
| | - Zhi-Jian Yu
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital, Shenzhen University School of Medicine, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China.
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Alonso CA, Cortés-Cortés G, Maamar E, Massó M, Rocha-Gracia RDC, Torres C, Centrón D, Quiroga MP. Molecular diversity and conjugal transferability of class 2 integrons among Escherichia coli isolates from food, animal and human sources. Int J Antimicrob Agents 2018; 51:905-911. [DOI: 10.1016/j.ijantimicag.2018.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/21/2017] [Accepted: 02/03/2018] [Indexed: 01/03/2023]
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20
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Analysis of resistance genes of clinical Pannonibacter phragmitetus strain 31801 by complete genome sequencing. Arch Microbiol 2018; 200:1101-1109. [PMID: 29761214 DOI: 10.1007/s00203-018-1522-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 04/13/2018] [Accepted: 05/03/2018] [Indexed: 12/19/2022]
Abstract
To clarify the resistance mechanisms of Pannonibacter phragmitetus 31801, isolated from the blood of a liver abscess patient, at the genomic level, we performed whole genomic sequencing using a PacBio RS II single-molecule real-time long-read sequencer. Bioinformatic analysis of the resulting sequence was then carried out to identify any possible resistance genes. Analyses included Basic Local Alignment Search Tool searches against the Antibiotic Resistance Genes Database, ResFinder analysis of the genome sequence, and Resistance Gene Identifier analysis within the Comprehensive Antibiotic Resistance Database. Prophages, clustered regularly interspaced short palindromic repeats (CRISPR), and other putative virulence factors were also identified using PHAST, CRISPRfinder, and the Virulence Factors Database, respectively. The circular chromosome and single plasmid of P. phragmitetus 31801 contained multiple antibiotic resistance genes, including those coding for three different types of β-lactamase [NPS β-lactamase (EC 3.5.2.6), β-lactamase class C, and a metal-dependent hydrolase of β-lactamase superfamily I]. In addition, genes coding for subunits of several multidrug-resistance efflux pumps were identified, including those targeting macrolides (adeJ, cmeB), tetracycline (acrB, adeAB), fluoroquinolones (acrF, ceoB), and aminoglycosides (acrD, amrB, ceoB, mexY, smeB). However, apart from the tripartite macrolide efflux pump macAB-tolC, the genome did not appear to contain the complete complement of subunit genes required for production of most of the major multidrug-resistance efflux pumps.
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21
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Schuldiner S. The Escherichia coli effluxome. Res Microbiol 2018; 169:357-362. [PMID: 29574104 DOI: 10.1016/j.resmic.2018.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 02/20/2018] [Accepted: 02/20/2018] [Indexed: 11/30/2022]
Abstract
Multidrug transporters function in a coordinated mode to provide an essential first-line defense mechanism that prevents antibiotics from reaching lethal concentrations, until a number of stable efficient adaptations occur that allow survival. Single-component efflux transporters remove the toxic compounds from the cytoplasm to the periplasmic space where TolC-dependent transporters expel them from the cell. The close interaction between the two types of transporters ensures handling of a wide range of xenobiotics and prevents rapid leak of the hydrophobic substrates back into the cell. In this review, we discuss the concept of the bacterial effluxome of the Gram-negative Escherichia coli that is the entire set of transporters expressed at a given time, under defined conditions. The process of identification of its members and the elucidation of the nature of the interactions throw a novel light on the roles of transporters in bacterial physiology and drug resistance development. We anticipate that the concept of an effluxome where each member contributes to the removal of noxious chemicals from the cell should contribute to improving the present strategy of searching for transport inhibitors as adjuvants of existing antibiotics and provide novel targets for this urgent undertaking.
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Affiliation(s)
- Shimon Schuldiner
- Department of Biological Chemistry, Institute of Life Sciences, Silberman Bldg. 1-339, Edmond J. Safra Campus, Hebrew University of Jerusalem, Givat Ram, Jerusalem, 91904, Israel.
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22
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XCC2366, A Gene Encoding A Putative TetR Family Transcriptional Regulator, is Required for Acriflavin Resistance and Virulence of Xanthomonas campestris pv. campestris. Curr Microbiol 2017; 74:1373-1381. [DOI: 10.1007/s00284-017-1328-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/04/2017] [Indexed: 10/19/2022]
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23
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Vandecraen J, Chandler M, Aertsen A, Van Houdt R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol 2017; 43:709-730. [PMID: 28407717 DOI: 10.1080/1040841x.2017.1303661] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new niches. This review focuses on the impact of insertion sequences (IS), arguably the smallest TE, on bacterial genome plasticity and concomitant adaptability of phenotypic traits, including resistance to antibacterial agents, virulence, pathogenicity and catabolism. The direct consequence of IS transposition is the insertion of one DNA sequence into another. This event can result in gene inactivation as well as in modulation of neighbouring gene expression. The latter is usually mediated by de-repression or by the introduction of a complete or partial promoter located within the element. Furthermore, transcription and transposition of IS are affected by host factors and in some cases by environmental signals offering the host an adaptive strategy and promoting genetic variability to withstand the environmental challenges.
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Affiliation(s)
- Joachim Vandecraen
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium.,b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Michael Chandler
- c Laboratoire de Microbiologie et Génétique Moléculaires, Centre national de la recherche scientifique , Toulouse , France
| | - Abram Aertsen
- b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Rob Van Houdt
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium
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24
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Fàbrega A, Ballesté-Delpierre C, Vila J. Differential impact of ramRA mutations on both ramA transcription and decreased antimicrobial susceptibility in Salmonella Typhimurium. J Antimicrob Chemother 2015; 71:617-24. [PMID: 26679248 DOI: 10.1093/jac/dkv410] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/03/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES This study was focused on analysing the heterogeneity of mutations occurring in the regulators of efflux-mediated MDR in Salmonella Typhimurium. Moreover, the impact of such mutations on impairing the transcription of ramA, acrB, tolC and acrF was also assessed as was the impact on the resistance or decreased susceptibility phenotype. METHODS Strains were selected in vitro under increasing ciprofloxacin concentrations. Etest and broth microdilution tests were used to determine the MICs of several unrelated compounds. Screening of mutations in the quinolone target genes and MDR regulators was performed. RT-PCR analysis was used to detect the levels of expression of acrB, tolC, ompF, acrF, emrB, acrR, ramA, soxS and marA. RESULTS All mutant strains showed increased MICs of most of the antimicrobials tested, with the exception of kanamycin. Mutations in the quinolone target genes did not occur in all the mutants, which all harboured mutations in the ramRA regulatory region. All the mutants overexpressed ramA, tolC and acrB (only tested in 60-wt derivatives), whereas differential results were seen for the remaining genes. CONCLUSIONS Mutations in the ramRA region related to resistance and/or decreased susceptibility to antimicrobials predominate in Salmonella. There is heterogeneity in the types of mutations, with deletions affecting RamR-binding sites having a greater impact on ramA expression and the MDR phenotype.
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Affiliation(s)
- Anna Fàbrega
- 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
| | - Jordi Vila
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
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25
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González-Prieto C, Agúndez L, Llosa M. Chloramphenicol Selection of IS10 Transposition in the cat Promoter Region of Widely Used Cloning Vectors. PLoS One 2015; 10:e0138615. [PMID: 26375469 PMCID: PMC4574204 DOI: 10.1371/journal.pone.0138615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/01/2015] [Indexed: 11/19/2022] Open
Abstract
The widely used pSU8 family of cloning vectors is based on a p15A replicon and a chloramphenicol acetyltransferase (cat) gene conferring chloramphenicol resistance. We frequently observed an increase in the size of plasmids derived from these vectors. Analysis of the bigger molecular species shows that they have an IS10 copy inserted at a specific site between the promoter and the cat open reading frame. Promoter activity from both ends of IS10 has been reported, suggesting that the insertion events could lead to higher CAT production. Insertions were observed in certain constructions containing inserts that could lead to plasmid instability. To test the possibility that IS10 insertions were selected as a response to chloramphenicol selection, we have grown these constructs in the presence of different amounts of antibiotic and we observed that insertions arise promptly under higher chloramphenicol selective pressure. IS10 is present in many E. coli laboratory strains, so the possibility of insertion in constructions involving cat-containing vectors should be taken into account. Using lower chloramphenicol concentrations could solve this problem.
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Affiliation(s)
- Coral González-Prieto
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC-SODERCAN), Santander, Spain
| | - Leticia Agúndez
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC-SODERCAN), Santander, Spain
- Department of Genetics, University College London, Institute of Ophthalmology, London, United Kingdom
| | - Matxalen Llosa
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC-SODERCAN), Santander, Spain
- * E-mail:
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26
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Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H, Hall RM, Holt KE. ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. BMC Genomics 2015; 16:667. [PMID: 26336060 PMCID: PMC4558774 DOI: 10.1186/s12864-015-1860-2] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/18/2015] [Indexed: 11/23/2022] Open
Abstract
Background Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copies in a single genome, which complicates genome assembly and the identification of IS insertion sites. Here we present ISMapper, a mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes, directly from paired-end short read data. Results ISMapper was validated using three types of short read data: (i) simulated reads from a variety of species, (ii) Illumina reads from 5 isolates for which finished genome sequences were available for comparison, and (iii) Illumina reads from 7 Acinetobacter baumannii isolates for which predicted IS locations were tested using PCR. A total of 20 genomes, including 13 species and 32 distinct IS, were used for validation. ISMapper correctly identified 97 % of known IS insertions in the analysis of simulated reads, and 98 % in real Illumina reads. Subsampling of real Illumina reads to lower depths indicated ISMapper was able to correctly detect insertions for average genome-wide read depths >20x, although read depths >50x were required to obtain confident calls that were highly-supported by evidence from reads. All ISAba1 insertions identified by ISMapper in the A. baumannii genomes were confirmed by PCR. In each A. baumannii genome, ISMapper successfully identified an IS insertion upstream of the ampC beta-lactamase that could explain phenotypic resistance to third-generation cephalosporins. The utility of ISMapper was further demonstrated by profiling genome-wide IS6110 insertions in 138 publicly available Mycobacterium tuberculosis genomes, revealing lineage-specific insertions and multiple insertion hotspots. Conclusions ISMapper provides a rapid and robust method for identifying IS insertion sites directly from short read data, with a high degree of accuracy demonstrated across a wide range of bacteria.
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Affiliation(s)
- Jane Hawkey
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Mohammad Hamidian
- School of Molecular Bioscience, The University of Sydney, Sydney, 2006, Australia.
| | - Ryan R Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Helen Billman-Jacobe
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Ruth M Hall
- School of Molecular Bioscience, The University of Sydney, Sydney, 2006, Australia.
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Cosby DE, Cox NA, Harrison MA, Wilson JL, Buhr RJ, Fedorka-Cray PJ. Salmonella and antimicrobial resistance in broilers: A review. J APPL POULTRY RES 2015. [DOI: 10.3382/japr/pfv038] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Insertion Sequence IS26 Reorganizes Plasmids in Clinically Isolated Multidrug-Resistant Bacteria by Replicative Transposition. mBio 2015; 6:e00762. [PMID: 26060276 PMCID: PMC4471558 DOI: 10.1128/mbio.00762-15] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Carbapenemase-producing Enterobacteriaceae (CPE), which are resistant to most or all known antibiotics, constitute a global threat to public health. Transposable elements are often associated with antibiotic resistance determinants, suggesting a role in the emergence of resistance. One insertion sequence, IS26, is frequently associated with resistance determinants, but its role remains unclear. We have analyzed the genomic contexts of 70 IS26 copies in several clinical and surveillance CPE isolates from the National Institutes of Health Clinical Center. We used target site duplications and their patterns as guides and found that a large fraction of plasmid reorganizations result from IS26 replicative transpositions, including replicon fusions, DNA inversions, and deletions. Replicative transposition could also be inferred for transposon Tn4401, which harbors the carbapenemase blaKPC gene. Thus, replicative transposition is important in the ongoing reorganization of plasmids carrying multidrug-resistant determinants, an observation that carries substantial clinical and epidemiological implications for understanding how such extreme drug resistance phenotypes evolve. Although IS26 is frequently reported to reside in resistance plasmids of clinical isolates, the characteristic hallmark of transposition, target site duplication (TSD), is generally not observed, raising questions about the mode of transposition for IS26. The previous observation of cointegrate formation during transposition implies that IS26 transposes via a replicative mechanism. The other possible outcome of replicative transposition is DNA inversion or deletion, when transposition occurs intramolecularly, and this would also generate a specific TSD pattern that might also serve as supporting evidence for the transposition mechanism. The numerous examples we present here demonstrate that replicative transposition, used by many mobile elements (including IS26 and Tn4401), is prevalent in the plasmids of clinical isolates and results in significant plasmid reorganization. This study also provides a method to trace the evolution of resistance plasmids based on TSD patterns.
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Importance of Real-Time Assays To Distinguish Multidrug Efflux Pump-Inhibiting and Outer Membrane-Destabilizing Activities in Escherichia coli. J Bacteriol 2015; 197:2479-88. [PMID: 25962916 DOI: 10.1128/jb.02456-14] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 05/05/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The constitutively expressed AcrAB multidrug efflux system of Escherichia coli shows a high degree of homology with the normally silent AcrEF system. Exposure of a strain with acrAB deleted to antibiotic selection pressure frequently leads to the insertion sequence-mediated activation of the homologous AcrEF system. In this study, we used strains constitutively expressing either AcrAB or AcrEF from their normal chromosomal locations to resolve a controversy about whether phenylalanylarginine β-naphthylamide (PAβN) inhibits the activities of AcrAB and AcrEF and/or acts synergistically with antibiotics by destabilizing the outer membrane permeability barrier. Real-time efflux assays allowed a clear distinction between the efflux pump-inhibiting activity of PAβN and the outer membrane-destabilizing action of polymyxin B nonapeptide (PMXBN). When added in equal amounts, PAβN, but not PMXBN, strongly inhibited the efflux activities of both AcrAB and AcrEF pumps. In contrast, when outer membrane destabilization was assessed by the nitrocefin hydrolysis assay, PMXBN exerted a much greater damaging effect than PAβN. Strong action of PAβN in inhibiting efflux activity compared to its weak action in destabilizing the outer membrane permeability barrier suggests that PAβN acts mainly by inhibiting efflux pumps. We concluded that at low concentrations, PAβN acts specifically as an inhibitor of both AcrAB and AcrEF efflux pumps; however, at high concentrations, PAβN in the efflux-proficient background not only inhibits efflux pump activity but also destabilizes the membrane. The effects of PAβN on membrane integrity are compounded in cells unable to extrude PAβN. IMPORTANCE The increase in multidrug-resistant bacterial pathogens at an alarming rate has accelerated the need for implementation of better antimicrobial stewardship, discovery of new antibiotics, and deeper understanding of the mechanism of drug resistance. The work carried out in this study highlights the importance of employing real-time fluorescence-based assays in differentiating multidrug efflux-inhibitory and outer membrane-destabilizing activities of antibacterial compounds.
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Wyres KL, Gorrie C, Edwards DJ, Wertheim HFL, Hsu LY, Van Kinh N, Zadoks R, Baker S, Holt KE. Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258. Genome Biol Evol 2015; 7:1267-79. [PMID: 25861820 PMCID: PMC4453057 DOI: 10.1093/gbe/evv062] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Klebsiella pneumoniae clonal group (CG) 258, comprising sequence types (STs) 258, 11, and closely related variants, is associated with dissemination of the K. pneumoniae carbapenemase (KPC). Hospital outbreaks of KPC CG258 infections have been observed globally and are very difficult to treat. As a consequence, there is renewed interest in alternative infection control measures such as vaccines and phage or depolymerase treatments targeting the K. pneumoniae polysaccharide capsule. To date, 78 immunologically distinct capsule variants have been described in K. pneumoniae. Previous investigations of ST258 and a small number of closely related strains suggested that capsular variation was limited within this clone; only two distinct ST258 capsule polysaccharide synthesis (cps) loci have been identified, both acquired through large-scale recombination events (>50 kb). In contrast to previous studies, we report a comparative genomic analysis of the broader K. pneumoniae CG258 (n = 39). We identified 11 different cps loci within CG258, indicating that capsular switching is actually common within the complex. We observed several insertion sequences (IS) within the cps loci, and show further intraclone diversification of two cps loci through IS activity. Our data also indicate that several large-scale recombination events have shaped the genomes of CG258, and that definition of the complex should be broadened to include ST395 (also reported to harbor KPC). As only the second report of extensive intraclonal cps variation among Gram-negative bacterial species, our findings alter our understanding of the evolution of these organisms and have key implications for the design of control measures targeting K. pneumoniae capsules.
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Affiliation(s)
- Kelly L Wyres
- IBM Research-Australia, Carlton, Victoria, Australia Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Claire Gorrie
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Heiman F L Wertheim
- Wellcome Trust Major Overseas Programme, Clinical Research Unit, Oxford University Hanoi, Vietnam Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Li Yang Hsu
- National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Nguyen Van Kinh
- Wellcome Trust Major Overseas Programme, Clinical Research Unit, Oxford University Hanoi, Vietnam Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Ruth Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom Moredun Research Institute, Pentlands Science Park, Penicuik, Midlothian, United Kingdom
| | - Stephen Baker
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, United Kingdom The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
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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: 899] [Impact Index Per Article: 99.9] [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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Andersen JL, He GX, Kakarla P, K C R, Kumar S, Lakra WS, Mukherjee MM, Ranaweera I, Shrestha U, Tran T, Varela MF. Multidrug efflux pumps from Enterobacteriaceae, Vibrio cholerae and Staphylococcus aureus bacterial food pathogens. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:1487-547. [PMID: 25635914 PMCID: PMC4344678 DOI: 10.3390/ijerph120201487] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/15/2015] [Indexed: 02/07/2023]
Abstract
Foodborne illnesses caused by bacterial microorganisms are common worldwide and constitute a serious public health concern. In particular, microorganisms belonging to the Enterobacteriaceae and Vibrionaceae families of Gram-negative bacteria, and to the Staphylococcus genus of Gram-positive bacteria are important causative agents of food poisoning and infection in the gastrointestinal tract of humans. Recently, variants of these bacteria have developed resistance to medically important chemotherapeutic agents. Multidrug resistant Escherichia coli, Salmonella enterica, Vibrio cholerae, Enterobacter spp., and Staphylococcus aureus are becoming increasingly recalcitrant to clinical treatment in human patients. Of the various bacterial resistance mechanisms against antimicrobial agents, multidrug efflux pumps comprise a major cause of multiple drug resistance. These multidrug efflux pump systems reside in the biological membrane of the bacteria and actively extrude antimicrobial agents from bacterial cells. This review article summarizes the evolution of these bacterial drug efflux pump systems from a molecular biological standpoint and provides a framework for future work aimed at reducing the conditions that foster dissemination of these multidrug resistant causative agents through human populations.
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Affiliation(s)
- Jody L Andersen
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Gui-Xin He
- Department of Clinical Laboratory and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA.
| | - Prathusha Kakarla
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Ranjana K C
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Sanath Kumar
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India.
| | - Wazir Singh Lakra
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India.
| | - Mun Mun Mukherjee
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Indrika Ranaweera
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Ugina Shrestha
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Thuy Tran
- Department of Clinical Laboratory and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA.
| | - Manuel F Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
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Blair JMA, Richmond GE, Piddock LJV. Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance. Future Microbiol 2014; 9:1165-77. [DOI: 10.2217/fmb.14.66] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT Gram-negative bacteria express a plethora of efflux pumps that are capable of transporting structurally varied molecules, including antibiotics, out of the bacterial cell. This efflux lowers the intracellular antibiotic concentration, allowing bacteria to survive at higher antibiotic concentrations. Overexpression of some efflux pumps can cause clinically relevant levels of antibiotic resistance in Gram-negative pathogens. This review discusses the role of efflux in resistance of clinical isolates of Gram-negative bacteria, the regulatory mechanisms that control efflux pump expression, the recent advances in our understanding of efflux pump structure and how inhibition of efflux is a promising future strategy for tackling multidrug resistance in Gram-negative pathogens.
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Affiliation(s)
- Jessica MA Blair
- Antimicrobials Research Group, Institute of Microbiology & Infection, School of Immunity & Infection, College of Medical & Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Grace E Richmond
- Antimicrobials Research Group, Institute of Microbiology & Infection, School of Immunity & Infection, College of Medical & Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Laura JV Piddock
- Antimicrobials Research Group, Institute of Microbiology & Infection, School of Immunity & Infection, College of Medical & Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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Sun J, Deng Z, Yan A. Bacterial multidrug efflux pumps: mechanisms, physiology and pharmacological exploitations. Biochem Biophys Res Commun 2014; 453:254-67. [PMID: 24878531 DOI: 10.1016/j.bbrc.2014.05.090] [Citation(s) in RCA: 432] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/20/2014] [Indexed: 01/11/2023]
Abstract
Multidrug resistance (MDR) refers to the capability of bacterial pathogens to withstand lethal doses of structurally diverse drugs which are capable of eradicating non-resistant strains. MDR has been identified as a major threat to the public health of human being by the World Health Organization (WHO). Among the four general mechanisms that cause antibiotic resistance including target alteration, drug inactivation, decreased permeability and increased efflux, drug extrusion by the multidrug efflux pumps serves as an important mechanism of MDR. Efflux pumps not only can expel a broad range of antibiotics owing to their poly-substrate specificity, but also drive the acquisition of additional resistance mechanisms by lowering intracellular antibiotic concentration and promoting mutation accumulation. Over-expression of multidrug efflux pumps have been increasingly found to be associated with clinically relevant drug resistance. On the other hand, accumulating evidence has suggested that efflux pumps also have physiological functions in bacteria and their expression is subject tight regulation in response to various of environmental and physiological signals. A comprehensive understanding of the mechanisms of drug extrusion, and regulation and physiological functions of efflux pumps is essential for the development of anti-resistance interventions. In this review, we summarize the development of these research areas in the recent decades and present the pharmacological exploitation of efflux pump inhibitors as a promising anti-drug resistance intervention.
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Affiliation(s)
- Jingjing Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Ziqing Deng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
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Fàbrega A, Soto SM, Ballesté-Delpierre C, Fernández-Orth D, Jiménez de Anta MT, Vila J. Impact of quinolone-resistance acquisition on biofilm production and fitness in Salmonella enterica. J Antimicrob Chemother 2014; 69:1815-24. [PMID: 24706735 DOI: 10.1093/jac/dku078] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To investigate the potential relationship between quinolone resistance and biofilm production in a collection of Salmonella enterica clinical isolates and in S. enterica serovar Typhimurium serial mutants with increasing resistance to ciprofloxacin. METHODS Nalidixic acid susceptibility and biofilm formation were assessed in a collection of 122 S. enterica clinical isolates. An in vitro quinolone-resistant mutant, 59-64, was obtained from a biofilm-producing and quinolone-susceptible clinical isolate, 59-wt, in a multistep selection process after increasing ciprofloxacin concentrations. The quinolone resistance mechanisms [target gene and multidrug resistance (MDR) regulatory mutations, MICs of several antibiotics, cell envelope protein analysis, real-time PCR and ciprofloxacin accumulation] were characterized for mutant strains. In addition, analysis of fitness, biofilm formation, rdar morphotype and expression of biofilm-related genes by real-time PCR were also determined. RESULTS Nalidixic acid-susceptible S. enterica strains were more prevalent in producing biofilm than the resistant counterparts. Strain 59-64 acquired five target gene mutations and showed an MDR phenotype. AcrAB and acrF overexpression were ruled out, whereas TolC did show increased expression in 59-64, which, in addition, accumulated less ciprofloxacin. Consistently, increased ramA expression was seen in 59-64 and attributed to a mutation within its promoter. Reduced biofilm production related to diminished csgB expression as well as reduced fitness was seen for 59-64, which was unable to form the rdar morphotype. CONCLUSIONS Quinolone resistance acquisition may be associated with decreased production of biofilm due to lower csgB expression. Efflux, biofilm production and fitness seem to be interrelated.
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Affiliation(s)
- Anna Fàbrega
- Barcelona Centre for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain
| | - Sara M Soto
- Barcelona Centre for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain
| | - Clara Ballesté-Delpierre
- Barcelona Centre for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain
| | - Dietmar Fernández-Orth
- Barcelona Centre for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain
| | - M Teresa Jiménez de Anta
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Jordi Vila
- Barcelona Centre for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
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Siguier P, Gourbeyre E, Chandler M. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev 2014; 38:865-91. [PMID: 24499397 PMCID: PMC7190074 DOI: 10.1111/1574-6976.12067] [Citation(s) in RCA: 373] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/19/2014] [Accepted: 01/22/2014] [Indexed: 01/06/2023] Open
Abstract
Insertion sequences (ISs), arguably the smallest and most numerous autonomous transposable elements (TEs), are important players in shaping their host genomes. This review focuses on prokaryotic ISs. We discuss IS distribution and impact on genome evolution. We also examine their effects on gene expression, especially their role in activating neighbouring genes, a phenomenon of particular importance in the recent upsurge of bacterial antibiotic resistance. We explain how ISs are identified and classified into families by a combination of characteristics including their transposases (Tpases), their overall genetic organisation and the accessory genes which some ISs carry. We then describe the organisation of autonomous and nonautonomous IS‐related elements. This is used to illustrate the growing recognition that the boundaries between different types of mobile element are becoming increasingly difficult to define as more are being identified. We review the known Tpase types, their different catalytic activities used in cleaving and rejoining DNA strands during transposition, their organisation into functional domains and the role of this in regulation. Finally, we consider examples of prokaryotic IS domestication. In a more speculative section, we discuss the necessity of constructing more quantitative dynamic models to fully appreciate the continuing impact of TEs on prokaryotic populations.
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Affiliation(s)
- Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, Unité Mixte de Recherche 5100, Centre National de Recherche Scientifique, Toulouse Cedex, France
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Baucheron S, Monchaux I, Le Hello S, Weill FX, Cloeckaert A. Lack of efflux mediated quinolone resistance in Salmonella enterica serovars Typhi and Paratyphi A. Front Microbiol 2014; 5:12. [PMID: 24478769 PMCID: PMC3902205 DOI: 10.3389/fmicb.2014.00012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 01/09/2014] [Indexed: 11/23/2022] Open
Abstract
Salmonella enterica serovars Typhi and Paratyphi A isolates from human patients in France displaying different levels of resistance to quinolones or fluoroquinolones were studied for resistance mechanisms to these antimicrobial agents. All resistant isolates carried either single or multiple target gene mutations (i.e., in gyrA, gyrB, or parC) correlating with the resistance levels observed. Active efflux, through upregulation of multipartite efflux systems, has also been previously reported as contributing mechanism for other serovars. Therefore, we investigated also the occurrence of non-target gene mutations in regulatory regions affecting efflux pump expression. However, no mutation was detected in these regions in both Typhi and Paratyphi isolates of this study. Besides, no overexpression of the major efflux systems was observed for these isolates. Nevertheless, a large deletion of 2334 bp was identified in the acrS-acrE region of all S. Typhi strains but which did not affect the resistance phenotype. As being specific to S. Typhi, this deletion could be used for specific molecular detection purposes. In conclusion, the different levels of quinolone or FQ resistance in both S. Typhi and S. Paratyphi A seem to rely only on target modifications.
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Affiliation(s)
- Sylvie Baucheron
- UMR1282 Infectiologie et Santé Publique, Institut National de la Recherche Agronomique Nouzilly, France ; UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours Tours, France
| | - Isabelle Monchaux
- UMR1282 Infectiologie et Santé Publique, Institut National de la Recherche Agronomique Nouzilly, France ; UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours Tours, France
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Institut Pasteur, Shigella et Salmonella Paris, France
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Institut Pasteur, Shigella et Salmonella Paris, France
| | - Axel Cloeckaert
- UMR1282 Infectiologie et Santé Publique, Institut National de la Recherche Agronomique Nouzilly, France ; UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours Tours, France
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Analysis of triclosan-selected Salmonella enterica mutants of eight serovars revealed increased aminoglycoside susceptibility and reduced growth rates. PLoS One 2013; 8:e78310. [PMID: 24205194 PMCID: PMC3799642 DOI: 10.1371/journal.pone.0078310] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/19/2013] [Indexed: 11/19/2022] Open
Abstract
The biocide triclosan (TRC) is used in a wide range of household, personal care, veterinary, industrial and medical products to control microbial growth. This extended use raises concerns about a possible association between the application of triclosan and the development of antibiotic resistance. In the present study we determined triclosan mutant prevention concentrations (MPC) for Salmonella enterica isolates of eight serovars and investigated selected mutants for their mechanisms mediating decreased susceptibility to triclosan. MPCTRC values were 8 - 64-fold higher than MIC values and ranged between 1 - 16 µg/ml. The frequencies at which mutants were selected varied between 1.3 x 10-10 - 9.9 x 10-11. Even if MIC values of mutants decreased by 3-7 dilution steps in the presence of the efflux pump inhibitor Phe-Arg-β-naphtylamide, only minor changes were observed in the expression of genes encoding efflux components or regulators, indicating that neither the major multidrug efflux pump AcrAB-TolC nor AcrEF are up-regulated in triclosan-selected mutants. Nucleotide sequence comparisons confirmed the absence of alterations in the regulatory regions acrRA, soxRS, marORAB, acrSE and ramRA of selected mutants. Single bp and deduced Gly93→Val amino acid exchanges were present in fabI, the target gene of triclosan, starting from a concentration of 1 µg/ml TRC used for MPC determinations. The fabI genes were up to 12.4-fold up-regulated. Complementation experiments confirmed the contribution of Gly93→Val exchanges and fabI overexpression to decreased triclosan susceptibility. MIC values of mutants compared to parent strains were even equal or resulted in a more susceptible phenotype (1-2 dilution steps) for the aminoglycoside antibiotics kanamycin and gentamicin as well as for the biocide chlorhexidine. Growth rates of selected mutants were significantly lower and hence, might partly explain the rare occurrence of Salmonella field isolates exhibiting decreased susceptibility to triclosan.
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Guo W, Cui S, Xu X, Wang H. Resistant mechanism study of benzalkonium chloride selected Salmonella Typhimurium mutants. Microb Drug Resist 2013; 20:11-6. [PMID: 23987991 DOI: 10.1089/mdr.2012.0225] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Benzalkonium chloride is one of the invaluable biocides that is extensively used in healthcare settings as well as in the food processing industry. After exposing wild-type Salmonella Typhimurium 14028s or its AcrAB inactivation mutant to gradually increasing levels of benzalkonium chloride, resistance mutants S-41, S-150, S-AB-23, S-AB-38, and S-AB-73 were selected and these mutants also showed a 2-64-fold stable minimum inhibitory concentration (MIC) increase to chloramphenicol, ciprofloxacin, nalidixic acid, and tetracycline. In S-41 and S-150, the expression of acrB was increased 2.7- and 7.6-fold, and ΔtolC or ΔacrAB mutants of S-41 and S-150 showed the same MICs to all tested antimicrobials as the equivalent Salmonella Typhimurium 14028s mutants. However, in S-AB-23, S-AB-38, and S-AB-73, the expression of acrF was increased 96-, 230-, and 267-fold, respectively, and ΔtolC or ΔacrEF mutants of S-AB-23, S-AB-38, and S-AB-73 showed the similar MICs to all tested antimicrobials as the ΔtolC mutant of Salmonella Typhimurium 14028s. Our data showed that constitutively over-expressed AcrAB working through TolC was the main resistance mechanism in ST14028s benzalkonium chloride resistance mutants. However, after AcrAB had been inactivated, benzalkonium chloride-resistant mutants could still be selected and constitutively over-expressed, AcrEF became the dominant efflux pump working through TolC and being responsible for the increasing antimicrobial resistance. These data indicated that different mechanisms existed for acrB and acrF constitutive over-expression. Since exposure to benzalkonium chloride may lead to Salmonella mutants with a decreased susceptibility to quinolones, which is currently one of the drugs of choice for the treatment of life-threatening salmonelosis, research into the pathogenesis and epidemiology of the benzalkonium chloride resistance mutants will be of increasing importance.
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Affiliation(s)
- Wei Guo
- 1 Department of Respiratory Medicine, Beijing Friendship Hospital, Capital Medical University , Beijing, China
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Baucheron S, Le Hello S, Doublet B, Giraud E, Weill FX, Cloeckaert A. ramR mutations affecting fluoroquinolone susceptibility in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198. Front Microbiol 2013; 4:213. [PMID: 23914184 PMCID: PMC3728480 DOI: 10.3389/fmicb.2013.00213] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 07/09/2013] [Indexed: 11/13/2022] Open
Abstract
A screening for non-target mutations affecting fluoroquinolone susceptibility was conducted in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198. Among a panel of representative isolates (n = 27), covering the epidemic, only three showed distinct mutations in ramR resulting in enhanced expression of genes encoding the AcrAB-TolC efflux system and low increase in ciprofloxacin MIC. No mutations were detected in other regulatory regions of this efflux system. Ciprofloxacin resistance in serovar Kentucky ST198 is thus currently mainly due to multiple target gene mutations.
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Affiliation(s)
- Sylvie Baucheron
- INRA, UMR1282 Infectiologie et Santé Publique Nouzilly, France ; Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique Tours, France
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41
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Cantas L, Shah SQA, Cavaco LM, Manaia CM, Walsh F, Popowska M, Garelick H, Bürgmann H, Sørum H. A brief multi-disciplinary review on antimicrobial resistance in medicine and its linkage to the global environmental microbiota. Front Microbiol 2013; 4:96. [PMID: 23675371 PMCID: PMC3653125 DOI: 10.3389/fmicb.2013.00096] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 04/04/2013] [Indexed: 01/14/2023] Open
Abstract
The discovery and introduction of antimicrobial agents to clinical medicine was one of the greatest medical triumphs of the 20th century that revolutionized the treatment of bacterial infections. However, the gradual emergence of populations of antimicrobial-resistant pathogenic bacteria resulting from use, misuse, and abuse of antimicrobials has today become a major global health concern. Antimicrobial resistance (AMR) genes have been suggested to originate from environmental bacteria, as clinically relevant resistance genes have been detected on the chromosome of environmental bacteria. As only a few new antimicrobials have been developed in the last decade, the further evolution of resistance poses a serious threat to public health. Urgent measures are required not only to minimize the use of antimicrobials for prophylactic and therapeutic purposes but also to look for alternative strategies for the control of bacterial infections. This review examines the global picture of antimicrobial resistance, factors that favor its spread, strategies, and limitations for its control and the need for continuous training of all stake-holders i.e., medical, veterinary, public health, and other relevant professionals as well as human consumers, in the appropriate use of antimicrobial drugs.
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Affiliation(s)
- L Cantas
- Department of Food Safety and Infection Biology, Norwegian School of Veterinary Science Oslo, Norway
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42
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Ferrari RG, Galiana A, Cremades R, Rodríguez JC, Magnani M, Tognim MCB, Oliveira TCRM, Royo G. Expression of the marA, soxS, acrB and ramA genes related to the AcrAB/TolC efflux pump in Salmonella enterica strains with and without quinolone resistance-determining regions gyrA gene mutations. Braz J Infect Dis 2013; 17:125-30. [PMID: 23453941 PMCID: PMC9427363 DOI: 10.1016/j.bjid.2012.09.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 09/10/2012] [Accepted: 09/13/2012] [Indexed: 12/02/2022] Open
Abstract
Several studies have been conducted in recent years to elucidate the structure, function and significance of AcrB, MarA, SoxS and RamA in Salmonella enterica. In this study, the relative quantification of acrB, soxS, marA and ramA genes expression was evaluated in 14 strains of S. enterica, with or without accompanying mutations in the quinolone resistance-determining regions of the gyrA gene, that were exposed to ciprofloxacin during the exponential growth phase. The presence of ciprofloxacin during the log phase of bacterial growth activated the genes marA, soxS, ramA and acrB in all S. enterica strains analyzed in this study. The highest expression levels for acrB were observed in strains with gyrA mutation, and marA showed the highest expression in the strains without mutation. Considering only the strains with ciprofloxacin minimum inhibitory concentration values < 0.125 μg/mL (sensitive to ciprofloxacin), the most expressed gene in the strains both with and without mutations was acrB. In the strains with ciprofloxacin minimum inhibitory concentration values ≥ 0.125 μg/mL (low susceptibility), with and without mutations in gyrA, the most expressed gene was marA. In this study, we observed that strains resistant to nalidixic acid may express genes associated with the efflux pump and the expression of the AcrAB-TolC pump genes seems to occur independently of mutations in gyrA.
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Affiliation(s)
- Rafaela Gomes Ferrari
- Agricultural Sciences Center, Department of Food Science and Technology, Universidade Estadual de Londrina, Londrina, PR, Brazil.
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Mebrhatu MT, Cenens W, Aertsen A. An overview of the domestication and impact of the Salmonella mobilome. Crit Rev Microbiol 2013; 40:63-75. [PMID: 23356413 DOI: 10.3109/1040841x.2012.755949] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Salmonella spp. are accountable for a large fraction of the global infectious disease burden, with most of their infections being food- or water-borne. The phenotypic features and adaptive potential of Salmonella spp. appear to be driven to a large extent by mobile or laterally acquired genetic elements. A better understanding of the conduct and diversification of these important pathogens consequently requires a more profound insight into the different mechanisms by which these pivotal elements establish themselves in the cell and affect its behavior. This review, therefore, provides an overview of the physiological impact and domestication of the Salmonella mobilome.
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Affiliation(s)
- Mehari Tesfazgi Mebrhatu
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, KU Leuven , Leuven , Belgium
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Adaptive and mutational resistance: role of porins and efflux pumps in drug resistance. Clin Microbiol Rev 2013; 25:661-81. [PMID: 23034325 DOI: 10.1128/cmr.00043-12] [Citation(s) in RCA: 528] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The substantial use of antibiotics in the clinic, combined with a dearth of new antibiotic classes, has led to a gradual increase in the resistance of bacterial pathogens to these compounds. Among the various mechanisms by which bacteria endure the action of antibiotics, those affecting influx and efflux are of particular importance, as they limit the interaction of the drug with its intracellular targets and, consequently, its deleterious effects on the cell. This review evaluates the impact of porins and efflux pumps on two major types of resistance, namely, mutational and adaptive types of resistance, both of which are regarded as key phenomena in the global rise of antibiotic resistance among pathogenic microorganisms. In particular, we explain how adaptive and mutational events can dramatically influence the outcome of antibiotic therapy by altering the mechanisms of influx and efflux of antibiotics. The identification of porins and pumps as major resistance markers has opened new possibilities for the development of novel therapeutic strategies directed specifically against these mechanisms.
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Vallé M, Schneider M, Galland D, Giboin H, Woehrlé F. Pharmacokinetic and pharmacodynamic testing of marbofloxacin administered as a single injection for the treatment of bovine respiratory disease. J Vet Pharmacol Ther 2011; 35:519-28. [PMID: 22126438 DOI: 10.1111/j.1365-2885.2011.01350.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
New approaches in Pharmacokinetic/Pharmacodynamic (PK/PD) integration suggested that marbofloxacin, a fluoroquinolone already licensed for the treatment of bovine respiratory disease at a daily dosage of 2 mg/kg for 3-5 days, would be equally clinically effective at 10 mg/kg once (Forcyl(®)), whilst also reducing the risk of resistance. This marbofloxacin dosage regimen was studied using mutant prevention concentration (MPC), PK simulation, PK/PD integration and an in vitro dynamic system. This system simulated the concentration-time profile of marbofloxacin in bovine plasma established in vivo after a single 10 mg/kg intramuscular dose and killing curves of field isolated Pasteurellaceae strains of high (minimum inhibitory concentration (MIC) MIC ≤ 0.03 μg/mL), average (MIC of 0.12-0.25 μg/mL) and low (MIC of 1 μg/mL) susceptibility to marbofloxacin. The marbofloxacin MPC values were 2- to 4-fold the MIC values for all Mannheimia haemolytica, Pasteurella multocida tested. Marbofloxacin demonstrated a concentration-dependent killing profile with bactericidal activity observed within 1 h for most strains. No resistance development (MIC ≥ 4 μg/mL) was detected in the dynamic tests. Target values for risk of resistance PK/PD surrogates (area under the curve (AUC) AUC(24 h) /MPC and T(>MPC) /T(MSW) ratio) were achieved for all clinically susceptible pathogens. The new proposed dosing regimen was validated in vitro and by PK/PD integration confirming the single-injection short-acting antibiotic concept.
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Affiliation(s)
- M Vallé
- Le Petit Curtil, Sainte Bénigne, France
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46
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Kim KY, Woo GJ. Expression of acrB and ramA in fluoroquinolone resistant mutants from multi-drug resistant Salmonella enterica serovar Haardt. Lett Appl Microbiol 2011; 52:484-90. [DOI: 10.1111/j.1472-765x.2011.03027.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Al Safadi R, Amor S, Hery-Arnaud G, Spellerberg B, Lanotte P, Mereghetti L, Gannier F, Quentin R, Rosenau A. Enhanced expression of lmb gene encoding laminin-binding protein in Streptococcus agalactiae strains harboring IS1548 in scpB-lmb intergenic region. PLoS One 2010; 5:e10794. [PMID: 20520730 PMCID: PMC2875397 DOI: 10.1371/journal.pone.0010794] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 05/01/2010] [Indexed: 11/19/2022] Open
Abstract
Group B streptococcus (GBS) is the main cause of neonatal sepsis and meningitis. Bacterial surface proteins play a major role in GBS binding to and invasion of different host surfaces. The scpB and lmb genes, coding for fibronectin-binding and laminin-binding surface proteins, are present in almost all human GBS isolates. The scpB-lmb intergenic region is a hot spot for integration of two mobile genetic elements (MGEs): the insertion element IS1548 or the group II intron GBSi1. We studied the structure of scpB-lmb intergenic region in 111 GBS isolates belonging to the intraspecies major clonal complexes (CCs). IS1548 was mostly found (72.2%) in CC19 serotype III strains recovered more specifically (92.3%) from neonatal meningitis. GBSi1 was principally found (70.6%) in CC17 strains, mostly (94.4%) of serotype III, but also (15.7%) in CC19 strains, mostly (87.5%) of serotype II. No MGE was found in most strains of the other CCs (76.0%), notably CC23, CC10 and CC1. Twenty-six strains representing these three genetic configurations were selected to investigate the transcription and expression levels of scpB and lmb genes. Quantitative RT-PCR showed that lmb transcripts were 5.0- to 9.6-fold higher in the group of strains with IS1548 than in the other two groups of strains (P<0.001). Accordingly, the binding ability to laminin was 3.8- to 6.6-fold higher in these strains (P≤0.001). Moreover, Lmb amount expressed on the cell surface was 2.4- to 2.7-fold greater in these strains (P<0.001). By contrast, scpB transcript levels and fibronectin binding ability were similar in the three groups of strains. Deletion of the IS1548 sequence between scpB and lmb genes in a CC19 serotype III GBS strain substantially reduced the transcription of lmb gene (13.5-fold), the binding ability to laminin (6.2-fold), and the expression of Lmb protein (5.0-fold). These data highlight the importance of MGEs in bacterial virulence and demonstrate the up-regulation of lmb gene by IS1548; the increased lmb gene expression observed in CC19 serotype III strains with IS1548 may play a role in their ability to cause neonatal meningitis and endocarditis.
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Affiliation(s)
- Rim Al Safadi
- Equipe d'Accueil 3854 Bactéries et Risque Materno-Fœtal, Institut Fédératif de Recherche 136 Agents Transmissibles et Infectiologie, UFR Médecine, Université François Rabelais de Tours, Tours, France
| | - Souheila Amor
- Equipe d'Accueil 3854 Bactéries et Risque Materno-Fœtal, Institut Fédératif de Recherche 136 Agents Transmissibles et Infectiologie, UFR Médecine, Université François Rabelais de Tours, Tours, France
| | - Geneviève Hery-Arnaud
- Equipe d'Accueil 3854 Bactéries et Risque Materno-Fœtal, Institut Fédératif de Recherche 136 Agents Transmissibles et Infectiologie, UFR Médecine, Université François Rabelais de Tours, Tours, France
| | - Barbara Spellerberg
- Institut für Medizinische Mikrobiologie und Hygiene, Universitäsklinikum Ulm, Ulm, Germany
| | - Philippe Lanotte
- Equipe d'Accueil 3854 Bactéries et Risque Materno-Fœtal, Institut Fédératif de Recherche 136 Agents Transmissibles et Infectiologie, UFR Médecine, Université François Rabelais de Tours, Tours, France
| | - Laurent Mereghetti
- Equipe d'Accueil 3854 Bactéries et Risque Materno-Fœtal, Institut Fédératif de Recherche 136 Agents Transmissibles et Infectiologie, UFR Médecine, Université François Rabelais de Tours, Tours, France
| | - François Gannier
- Unité Mixte de Recherche CNRS FRE 3092 Physiologie des Cellules Cardiaques et Vasculaires, UFR Sciences, Université François Rabelais de Tours, Tours, France
| | - Roland Quentin
- Equipe d'Accueil 3854 Bactéries et Risque Materno-Fœtal, Institut Fédératif de Recherche 136 Agents Transmissibles et Infectiologie, UFR Médecine, Université François Rabelais de Tours, Tours, France
- Service de Bactériologie et Hygiène Hospitalière, Hôpital Trousseau, CHRU de Tours, Tours, France
| | - Agnès Rosenau
- Equipe d'Accueil 3854 Bactéries et Risque Materno-Fœtal, Institut Fédératif de Recherche 136 Agents Transmissibles et Infectiologie, UFR Médecine, Université François Rabelais de Tours, Tours, France
- * E-mail:
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Kehrenberg C, Cloeckaert A, Klein G, Schwarz S. Decreased fluoroquinolone susceptibility in mutants of Salmonella serovars other than Typhimurium: detection of novel mutations involved in modulated expression of ramA and soxS. J Antimicrob Chemother 2009; 64:1175-80. [DOI: 10.1093/jac/dkp347] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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49
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Abstract
Drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. There has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. These pumps are mostly encoded on the chromosome, although they can also be plasmid-encoded. A previous article in this journal provided a comprehensive review regarding efflux-mediated drug resistance in bacteria. In the past 5 years, significant progress has been achieved in further understanding of drug resistance-related efflux transporters and this review focuses on the latest studies in this field since 2003. This has been demonstrated in multiple aspects that include but are not limited to: further molecular and biochemical characterization of the known drug efflux pumps and identification of novel drug efflux pumps; structural elucidation of the transport mechanisms of drug transporters; regulatory mechanisms of drug efflux pumps; determining the role of the drug efflux pumps in other functions such as stress responses, virulence and cell communication; and development of efflux pump inhibitors. Overall, the multifaceted implications of drug efflux transporters warrant novel strategies to combat multidrug resistance in bacteria.
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Affiliation(s)
- Xian-Zhi Li
- Human Safety Division, Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario K1A OK9, Canada
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202, USA
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H-NS modulates multidrug resistance of Salmonella enterica serovar Typhimurium by repressing multidrug efflux genes acrEF. Antimicrob Agents Chemother 2009; 53:3541-3. [PMID: 19506059 DOI: 10.1128/aac.00371-09] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Screening of Salmonella mutants for the ability to increase beta-lactam resistance has led to the identification of a mutation in hns, which codes for the histone-like nucleoid structuring protein (H-NS). In this study, we report that H-NS modulates multidrug resistance through repression of the genes that encode the AcrEF multidrug efflux pump in Salmonella enterica serovar Typhimurium.
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