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Ramamurthy T, Ghosh A, Chowdhury G, Mukhopadhyay AK, Dutta S, Miyoshi SI. Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens. Front Cell Infect Microbiol 2022; 12:952491. [PMID: 36506027 PMCID: PMC9727169 DOI: 10.3389/fcimb.2022.952491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.
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Affiliation(s)
- Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Thandavarayan Ramamurthy,
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-inchi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National Institute of Cholera and Enteric Diseases, Kolkata, India,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Aeromonas: the multifaceted middleman in the One Health world. Curr Opin Microbiol 2021; 65:24-32. [PMID: 34717260 DOI: 10.1016/j.mib.2021.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 02/06/2023]
Abstract
Aeromonas is at the interface of all the One Health components and represents an amazingly sound test case in the One Health approach, from economic loss in aquaculture tochallenges related to antibiotic-resistant bacteria selected from the environment. In human health, infections following leech therapy is an outstanding example of such One Health challenges. Aeromonads are not only ubiquitous environmental bacteria, able to rapidly colonize and cause opportunistic infections in humans and animals, they are also capable of promoting interactions and gene exchanges between the One Health components. This makes this genus a key amplifier of genetic transfer, especially of antibiotic resistance genes.
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Al-Rafyai HM, Alwash MS, Al-Khafaji NS. Quinolone resistance (qnrA) gene in isolates of Escherichia coli collected from the Al-Hillah River in Babylon Province, Iraq. PHARMACIA 2021. [DOI: 10.3897/pharmacia.68.e57819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aquatic environment contamination remains a foremost global public health hazards, and symbolizes a significant reservoir of releasing antibiotic resistant bacteria. The survival of Escherichia coli in aquatic environments serves as a potential reservoir of antibiotic resistance, encompassing but not restricted to a plasmid-mediated quinolone resistance (PMQR) mechanism. The current study aimed to detect the presence of the PMQR-qnrA gene in quinolone-resistant E. coli isolates. Sixty-one waterborne E. coli with known phylogroups/subgroups isolated from the Al-Hillah River in Babylon Province, Iraq, were screened for the phenotypic resistance to third-generation quinolones (levofloxacin and ofloxacin) and were further analysed for the presence of the qnrA gene using polymerase chain reaction (PCR). Fifty-seven (93.4%) of 61 E. coli isolates were levofloxacin-resistant, and 55 (90.2%) were ofloxacin-resistant. Among the 57 quinolone-resistant E. coli, 40 (65.57%) isolates were found to carry the PMQR-qnrA gene. Among the 40 qnrA-positive E. coli, 22 (36.1%) isolates were in phylogroup B2, followed by 8 (13.1%) isolates in phylogroup D, 6 (9.8%) isolates in phylogroup B1, and 4 (6.6%) isolates in phylogroup A. The presence of the PMQR-qnrA gene in E. coli belonging to phylogroup B2 and D reflects the need for routine monitoring of antibiotic resistance genes (ARGs) in the Al-Hillah River.
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Segura WD, Ramos HP, de Faria Blanc Amorim RE, da Silva Ribeiro ÁC, Pereira EC, Cayô R, Gales AC, Piantino Ferreira AJ, da Rocha Minarini LA. In vitro and in vivo persistence of IncN plasmids carrying qnr genes in uropathogenic Escherichia coli isolates. J Glob Antimicrob Resist 2020; 22:806-810. [PMID: 32688008 DOI: 10.1016/j.jgar.2020.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES This study aimed to evaluate the persistence of the plasmid-mediated quinolone resistance (PMQR) among uropathogenic Escherichia coli strains grown under or without exposure to subinhibitory concentrations of ciprofloxacin. Based on that, we evaluated the possible spontaneous loss or maintenance of PMQR and the possible appearance of compensatory mutations in gyrA and parC genes. METHODS Three uropathogenic E. coli strains harbouring chromosomal mutations in the gyrA and/or parC genes coupled with qnrS1 or qnrB2 determinants carried by distinct plasmid sizes and incompatibility N groups (IncN/ST1, IncN/ST5) were evaluated using in vitro and in vivo assays. RESULTS PMQRs remained stable in all strains throughout the generations evaluated, independently of exposure to ciprofloxacin in both in vivo and in vitro assays. Analysis of gyrA and parC genes after in vivo and in vitro assays revealed that no changes occurred in quinolone-resistance determining regions (QRDR). CONCLUSION We demonstrated that IncN plasmids were persistent over 14 days in E. coli clinical strains independently of exposure to ciprofloxacin, as well as previous mutations in QRDR.
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Affiliation(s)
- Wilson Dias Segura
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas - ICAQF, Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas - DCF, Diadema, SP, Brazil
| | - Haissa Pereira Ramos
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas - ICAQF, Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas - DCF, Diadema, SP, Brazil
| | - Renata Ester de Faria Blanc Amorim
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas - ICAQF, Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas - DCF, Diadema, SP, Brazil
| | - Ághata Cardoso da Silva Ribeiro
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas - ICAQF, Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas - DCF, Diadema, SP, Brazil; Universidade Federal de São Paulo - UNIFESP, Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina - Escola Paulista de Medicina, São Paulo, SP, Brazil
| | - Edimar Cristiano Pereira
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas - ICAQF, Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas - DCF, Diadema, SP, Brazil
| | - Rodrigo Cayô
- Universidade Federal de São Paulo - UNIFESP, Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina - Escola Paulista de Medicina, São Paulo, SP, Brazil; LIB, Instituto de Ciências Ambientais, Químicas e Farmacêuticas - ICAQF, Departamento de Ciências Biológicas - DCB, Diadema, SP, Brazil
| | - Ana Cristina Gales
- Universidade Federal de São Paulo - UNIFESP, Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina - Escola Paulista de Medicina, São Paulo, SP, Brazil
| | - Antônio J Piantino Ferreira
- Departamento de Patologia, Faculdade de Medicina Veterinária, Universidade de São Paulo - USP, São Paulo, SP, Brazil
| | - Luciene Andrade da Rocha Minarini
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciências Ambientais, Químicas e Farmacêuticas - ICAQF, Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas - DCF, Diadema, SP, Brazil.
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Abstract
Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been acquired by horizontal gene transfer from other (usually unknown) microorganisms. Similarly, in the case of resistance to antibiotics, besides mutation-driven resistance, the incorporation of novel resistance genes is a widespread evolutionary procedure for the acquisition of this phenotype. Current information in the field supports the idea that most (if not all) genes acquired by horizontal gene transfer by bacterial pathogens and contributing to their virulence potential or to antibiotic resistance originate in environmental, not human-pathogenic, microorganisms. Herein I discuss the potential functions that the genes that are dubbed virulence or antibiotic resistance genes may have in their original hosts in nonclinical, natural ecosystems. In addition, I discuss the potential bottlenecks modulating the transfer of virulence and antibiotic resistance determinants and the consequences in terms of speciation of acquiring one or another of both categories of genes. Finally, I propose that exaptation, a process by which a change of function is achieved by a change of habitat and not by changes in the element with the new functionality, is the basis of the evolution of virulence determinants and of antibiotic resistance genes.
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Metabolic Compensation of Fitness Costs Is a General Outcome for Antibiotic-Resistant Pseudomonas aeruginosa Mutants Overexpressing Efflux Pumps. mBio 2017; 8:mBio.00500-17. [PMID: 28743808 PMCID: PMC5527304 DOI: 10.1128/mbio.00500-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is generally assumed that the acquisition of antibiotic resistance is associated with a fitness cost. We have shown that overexpression of the MexEF-OprN efflux pump does not decrease the fitness of a resistant Pseudomonas aeruginosa strain compared to its wild-type counterpart. This lack of fitness cost was associated with a metabolic rewiring that includes increased expression of the anaerobic nitrate respiratory chain when cells are growing under fully aerobic conditions. It was not clear whether this metabolic compensation was exclusive to strains overexpressing MexEF-OprN or if it extended to other resistant strains that overexpress similar systems. To answer this question, we studied a set of P. aeruginosa mutants that independently overexpress the MexAB-OprM, MexCD-OprJ, or MexXY efflux pumps. We observed increased expression of the anaerobic nitrate respiratory chain in all cases, with a concomitant increase in NO3 consumption and NO production. These efflux pumps are proton/substrate antiporters, and their overexpression may lead to intracellular H+ accumulation, which may in turn offset the pH homeostasis. Indeed, all studied mutants showed a decrease in intracellular pH under anaerobic conditions. The fastest way to eliminate the excess of protons is by increasing oxygen consumption, a feature also displayed by all analyzed mutants. Taken together, our results support metabolic rewiring as a general mechanism to avoid the fitness costs derived from overexpression of P. aeruginosa multidrug efflux pumps. The development of drugs that block this metabolic “reaccommodation” might help in reducing the persistence and spread of antibiotic resistance elements among bacterial populations. It is widely accepted that the acquisition of resistance confers a fitness cost in such a way that in the absence of antibiotics, resistant populations will be outcompeted by susceptible ones. Based on this assumption, antibiotic cycling regimes have been proposed in the belief that they will reduce the persistence and spread of resistance among bacterial pathogens. Unfortunately, trials testing this possibility have frequently failed, indicating that resistant microorganisms are not always outcompeted by susceptible ones. Indeed, some mutations do not result in a fitness cost, and in case they do, the cost may be compensated for by a secondary mutation. Here we describe an alternative nonmutational mechanism for compensating for fitness costs, which consists of the metabolic rewiring of resistant mutants. Deciphering the mechanisms involved in the compensation of fitness costs of antibiotic-resistant mutants may help in the development of drugs that will reduce the persistence of resistance by increasing said costs.
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Chantziaras I, Smet A, Haesebrouck F, Boyen F, Dewulf J. Studying the effect of administration route and treatment dose on the selection of enrofloxacin resistance in commensal Escherichia coli in broilers. J Antimicrob Chemother 2017; 72:1991-2001. [DOI: 10.1093/jac/dkx104] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/10/2017] [Indexed: 11/13/2022] Open
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Fitness costs associated with the acquisition of antibiotic resistance. Essays Biochem 2017; 61:37-48. [PMID: 28258228 DOI: 10.1042/ebc20160057] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/20/2016] [Accepted: 01/03/2017] [Indexed: 01/09/2023]
Abstract
Acquisition of antibiotic resistance is a relevant problem for human health. The selection and spread of antibiotic-resistant organisms not only compromise the treatment of infectious diseases, but also the implementation of different therapeutic procedures as organ transplantation, advanced surgery or chemotherapy, all of which require proficient methods for avoiding infections. It has been generally accepted that the acquisition of antibiotic resistance will produce a general metabolic burden: in the absence of selection, the resistant organisms would be outcompeted by the susceptible ones. If that was always true, discontinuation of antibiotic use would render the disappearance of resistant microorganisms. However, several studies have shown that, once resistance emerges, the recovery of a fully susceptible population even in the absence of antibiotics is not easy. In the present study, we review updated information on the effect of the acquisition of antibiotic resistance in bacterial physiology as well as on the mechanisms that allow the compensation of the fitness costs associated with the acquisition of resistance.
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Plasmid-mediated quinolone resistance: Two decades on. Drug Resist Updat 2016; 29:13-29. [PMID: 27912841 DOI: 10.1016/j.drup.2016.09.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/03/2016] [Accepted: 08/29/2016] [Indexed: 11/21/2022]
Abstract
After two decades of the discovery of plasmid-mediated quinolone resistance (PMQR), three different mechanisms have been associated to this phenomenon: target protection (Qnr proteins, including several families with multiple alleles), active efflux pumps (mainly QepA and OqxAB pumps) and drug modification [AAC(6')-Ib-cr acetyltransferase]. PMQR genes are usually associated with mobile or transposable elements on plasmids, and, in the case of qnr genes, are often incorporated into sul1-type integrons. PMQR has been found in clinical and environmental isolates around the world and appears to be spreading. Although the three PMQR mechanisms alone cause only low-level resistance to quinolones, they can complement other mechanisms of chromosomal resistance to reach clinical resistance level and facilitate the selection of higher-level resistance, raising a threat to the treatment of infections by microorganisms that host these mechanisms.
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Reales-Calderon JA, Blanco P, Alcalde-Rico M, Corona F, Lira F, Hernando-Amado S, Bernardini A, Sánchez MB, Martínez JL. Use of phenotype microarrays to study the effect of acquisition of resistance to antimicrobials in bacterial physiology. Res Microbiol 2016; 167:723-730. [PMID: 27106258 DOI: 10.1016/j.resmic.2016.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/03/2016] [Accepted: 04/07/2016] [Indexed: 01/17/2023]
Abstract
It is widely accepted that the acquisition of resistance to antimicrobials confers a fitness cost. Different works have shown that the effect of acquiring resistance in bacterial physiology may be more specific than previously thought. Study of these specific changes may help to predict the outcome of resistant organisms in different ecosystems. In addition to changing bacterial physiology, acquisition of resistance either increases or reduces susceptibility to other antimicrobials. In the current article, we review recent information on the effect of acquiring resistance upon bacterial physiology, with a specific focus on studies using phenotype microarray technology.
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Affiliation(s)
- Jose A Reales-Calderon
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Paula Blanco
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Manuel Alcalde-Rico
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Fernando Corona
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Felipe Lira
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Sara Hernando-Amado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Alejandra Bernardini
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - María B Sánchez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - José L Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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Machuca J, Briales A, Díaz-de-Alba P, Martínez-Martínez L, Pascual Á, Rodríguez-Martínez JM. Effect of the efflux pump QepA2 combined with chromosomally mediated mechanisms on quinolone resistance and bacterial fitness in Escherichia coli. J Antimicrob Chemother 2015; 70:2524-7. [PMID: 26041043 DOI: 10.1093/jac/dkv144] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/04/2015] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The aim of the study was to determine the interplay between the plasmid-mediated qepA2 gene and multiple chromosomally mediated fluoroquinolone resistance determinants in the development of fluoroquinolone resistance in Escherichia coli and its influence on bacterial fitness. METHODS E. coli ATCC 25922 and derived isogenic strains harbouring different chromosomally mediated fluoroquinolone resistance determinants were electroporated with pBK-CMV vector encoding QepA2. The MICs of fluoroquinolones were determined by standardized microdilution. The mutant prevention concentration (MPC) was evaluated. Bacterial fitness was analysed using ΔlacZ system competition assays. RESULTS The ciprofloxacin MIC for strains harbouring the qepA2 gene was 4- to 8-fold higher compared with strains without the qepA2 gene. The qepA2 gene also increased the MPC of ciprofloxacin 4- to 16-fold. Combination of the qepA2 gene plus two to three additional mechanisms conferred a clinically relevant resistance level. The presence of the qepA2 gene was associated with fitness costs in strains with mutations in the gyrA and/or parC genes, although the presence of an additional deletion of the marR gene compensated for this fitness cost by increasing bacterial fitness by 5%-23%. CONCLUSIONS The additive effect of chromosomally mediated fluoroquinolone resistance mechanisms and the qepA2 gene led to clinical levels of fluoroquinolone resistance. Under competitive conditions, the qepA2 gene had a biological cost in E. coli that was compensated for by the presence of an additional deletion in the marR gene.
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Affiliation(s)
- Jesús Machuca
- Unidad de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - Alejandra Briales
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Luis Martínez-Martínez
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain Hospital Universitario Marques de Valdecilla and Valdecilla Biomedical Research Institute (IDIVAL), Santander, Spain Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Álvaro Pascual
- Unidad de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Sevilla, Spain Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
| | - José-Manuel Rodríguez-Martínez
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
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Martinez JL. General principles of antibiotic resistance in bacteria. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 11:33-9. [PMID: 24847651 DOI: 10.1016/j.ddtec.2014.02.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Given the impact of antibiotic resistance on human health, its study is of great interest from a clinical view- point. In addition, antibiotic resistance is one of the few examples of evolution that can be studied in real time. Knowing the general principles involved in the acquisition of antibiotic resistance is therefore of interest to clinicians, evolutionary biologists and ecologists. The origin of antibiotic resistance genes now possessed by human pathogens can be traced back to environmental microorganisms. Consequently, a full understanding of the evolution of antibiotic resistance requires the study of natural environments as well as clinical ecosystems. Updated information on the evolutionary mechanisms behind resistance, indicates that ecological connectivity, founder effect and fitness costs are important bottle- necks that modulate the transfer of resistance from environmental microorganisms to pathogens.
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Abstract
Metagenomic studies have shown that antibiotic resistance genes are ubiquitous in the environment, which has led to the suggestion that there is a high risk that these genes will spread to bacteria that cause human infections. If this is true, estimating the real risk of dissemination of resistance genes from environmental reservoirs to human pathogens is therefore very difficult. In this Opinion article, we analyse the current definitions of antibiotic resistance and antibiotic resistance genes, and we describe the bottlenecks that affect the transfer of antibiotic resistance genes to human pathogens. We propose rules for estimating the risks associated with genes that are present in environmental resistomes by evaluating the likelihood of their introduction into human pathogens, and the consequences of such events for the treatment of infections.
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14
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Machuca J, Briales A, Labrador G, Díaz-de-Alba P, López-Rojas R, Docobo-Pérez F, Martínez-Martínez L, Rodríguez-Baño J, Pachón ME, Pascual A, Rodríguez-Martínez JM. Interplay between plasmid-mediated and chromosomal-mediated fluoroquinolone resistance and bacterial fitness in Escherichia coli. J Antimicrob Chemother 2014; 69:3203-15. [PMID: 25139837 DOI: 10.1093/jac/dku308] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVES The aim of this study was to analyse the interplay among plasmid-mediated qnr genes, alone or in combination with multiple chromosomal-mediated fluoroquinolone (FQ) resistance determinants, susceptibility to FQs and bacterial fitness in an isogenic Escherichia coli collection. METHODS E. coli ATCC 25922 was used to modify or delete chromosomal genes. qnr genes were cloned into the pBK-CMV vector. The MICs of FQs were determined by microdilution. Mutant prevention concentration and frequency of mutants were evaluated. Bacterial fitness was analysed using ΔlacZ system competition assays using in vitro and in vivo models. RESULTS The relationships between the number of resistance mutations and bacterial fitness were complex. With specific combinations of resistance mechanisms the addition of a new resistance mutation was shown to improve bacterial fitness. qnrA1 caused a decrease in fitness (7%-21%) while qnrS1 caused an increase in fitness (9%-21%) when combined with chromosomal mutations. We identified susceptible triple mutants in which the acquisition of a fourth resistance mutation significantly increased fitness and at the same time reached the clinical resistance level (the acquisition of qnrS1 in a S83L + D87N + ΔmarR genetic background). A strong correlation with the production of reactive oxygen species, as well as changes in susceptibility, was observed following treatment with ciprofloxacin. CONCLUSIONS Our data indicate that there may be critical stages (depending on the genotype) in resistance development, including chromosomal- and plasmid-mediated mechanisms, at which some low-fitness mutants below the resistance breakpoint are able to evolve clinical resistance with just one or two mutations, and show increased fitness.
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Affiliation(s)
- Jesús Machuca
- Infectious Diseases and Clinical Microbiology Unit, University Hospital Virgen Macarena, Seville, Spain
| | - Alejandra Briales
- Department of Microbiology, University of Seville, Seville, Spain Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Labrador
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | | | - Rafael López-Rojas
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Fernando Docobo-Pérez
- Infectious Diseases and Clinical Microbiology Unit, University Hospital Virgen Macarena, Seville, Spain Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Martínez-Martínez
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain University Hospital Marques de Valdecilla and Valdecilla Biomedical Research Institute (IDIVAL), Santander, Spain Department of Molecular Biology, University of Cantabria, Santander, Spain
| | - Jesús Rodríguez-Baño
- Infectious Diseases and Clinical Microbiology Unit, University Hospital Virgen Macarena, Seville, Spain Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain Medicine Department, University of Seville, Seville, Spain
| | - Maria Eugenia Pachón
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Alvaro Pascual
- Infectious Diseases and Clinical Microbiology Unit, University Hospital Virgen Macarena, Seville, Spain Department of Microbiology, University of Seville, Seville, Spain Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
| | - José-Manuel Rodríguez-Martínez
- Department of Microbiology, University of Seville, Seville, Spain Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
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15
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Baek JH, Kim CO, Jeong SJ, Ku NS, Han SH, Choi JY, Yong D, Song YG, Lee K, Kim JM. Clinical factors associated with acquisition of resistance to levofloxacin in Stenotrophomonas maltophilia. Yonsei Med J 2014; 55:987-93. [PMID: 24954328 PMCID: PMC4075404 DOI: 10.3349/ymj.2014.55.4.987] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Fluoroquinolones, rapidly gaining prominence in treatment of Stenotrophomonas maltophilia (SMP), are noted for their potency and tolerability. However, SMP may rapidly acquire resistance to fluoroquinolones. We evaluated associations of clinical factors with acquisition of levofloxacin resistance (LFr) in SMP. MATERIALS AND METHODS Our retrospective cohort study was based on patient data collected between January 2008 and June 2010. Through screening of 1275 patients, we identified 122 patients with data for SMP antibiotic susceptibility testing in ≥3 serial SMP isolates. RESULTS We assigned the 122 patients to either the SS group (n=54) in which levofloxacin susceptibility was maintained or the SR group (n=31) in which susceptible SMP acquired resistance. In multivariate regression analysis, exposure to levofloxacin for more than 3 weeks [odds ratio (OR) 15.39, 95% confidential interval (CI) 3.08-76.93, p=0.001] and co-infection or co-colonization with Klebsiella pneumoniae resistant to levofloxacin (OR 4.85, 95% CI 1.16-20.24, p=0.030) were independently associated with LFr acquisition in SMP. CONCLUSION Acquisition of LFr during serial sampling of SMP was related to the levofloxacin exposure.
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Affiliation(s)
- Ji Hyeon Baek
- Department of Infectious Disease, Inha University Hospital, Incheon, Korea
| | - Chang Oh Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Su Jin Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Nam Soo Ku
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Hoon Han
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.
| | - Jun Yong Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Young Goo Song
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - June Myung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
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16
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Gibello A, Díaz de Alba P, Blanco MM, Machuca J, Cutuli MT, Rodríguez-Martínez JM. Lactococcus garvieae carries a chromosomally encoded pentapeptide repeat protein that confers reduced susceptibility to quinolones in Escherichia coli producing a cytotoxic effect. Res Microbiol 2014; 165:590-9. [PMID: 24965125 DOI: 10.1016/j.resmic.2014.05.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/09/2014] [Accepted: 05/13/2014] [Indexed: 01/09/2023]
Abstract
This study characterises a chromosomal gene of Lactococcus garvieae encoding a pentapeptide repeat protein designated as LgaQnr. This gene has been implicated in reduced susceptibility to quinolones in this bacterium, which is of relevance to both veterinary and human medicine. All of the L. garvieae isolates analysed were positive for the lgaqnr gene. The expression of lgaqnr in Escherichia coli reduced the susceptibility to quinolones, producing an adverse effect. The reduced susceptibility to ciprofloxacin was 16-fold in E. coli ATCC 25922 and 32-fold in E. coli DH10B, compared to the control strains. The minimum inhibitory concentration of nalidixic acid was also increased 4 or 5-fold. The effect of the expression of lgaqnr in E. coli was investigated by electron microscopy and was observed to affect the structure of the cell and the inner membrane of the recombinant cells.
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Affiliation(s)
- Alicia Gibello
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | - Paula Díaz de Alba
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain.
| | - M Mar Blanco
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | - Jesus Machuca
- Unidad de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Macarena, 41007 Sevilla, Spain.
| | - M Teresa Cutuli
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain.
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17
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Abstract
The emergence and spread of antibiotic resistance among human pathogens is a relevant problem for human health and one of the few evolution processes amenable to experimental studies. In the present review, we discuss some basic aspects of antibiotic resistance, including mechanisms of resistance, origin of resistance genes, and bottlenecks that modulate the acquisition and spread of antibiotic resistance among human pathogens. In addition, we analyse several parameters that modulate the evolution landscape of antibiotic resistance. Learning why some resistance mechanisms emerge but do not evolve after a first burst, whereas others can spread over the entire world very rapidly, mimicking a chain reaction, is important for predicting the evolution, and relevance for human health, of a given mechanism of resistance. Because of this, we propose that the emergence and spread of antibiotic resistance can only be understood in a multi-parameter space. Measuring the effect on antibiotic resistance of parameters such as contact rates, transfer rates, integration rates, replication rates, diversification rates, and selection rates, for different genes and organisms, growing under different conditions in distinct ecosystems, will allow for a better prediction of antibiotic resistance and possibilities of focused interventions.
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Affiliation(s)
- José Luis Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049, Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) and CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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18
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Baquero F, Tedim AP, Coque TM. Antibiotic resistance shaping multi-level population biology of bacteria. Front Microbiol 2013; 4:15. [PMID: 23508522 PMCID: PMC3589745 DOI: 10.3389/fmicb.2013.00015] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 01/22/2013] [Indexed: 12/21/2022] Open
Abstract
Antibiotics have natural functions, mostly involving cell-to-cell signaling networks. The anthropogenic production of antibiotics, and its release in the microbiosphere results in a disturbance of these networks, antibiotic resistance tending to preserve its integrity. The cost of such adaptation is the emergence and dissemination of antibiotic resistance genes, and of all genetic and cellular vehicles in which these genes are located. Selection of the combinations of the different evolutionary units (genes, integrons, transposons, plasmids, cells, communities and microbiomes, hosts) is highly asymmetrical. Each unit of selection is a self-interested entity, exploiting the higher hierarchical unit for its own benefit, but in doing so the higher hierarchical unit might acquire critical traits for its spread because of the exploitation of the lower hierarchical unit. This interactive trade-off shapes the population biology of antibiotic resistance, a composed-complex array of the independent "population biologies." Antibiotics modify the abundance and the interactive field of each of these units. Antibiotics increase the number and evolvability of "clinical" antibiotic resistance genes, but probably also many other genes with different primary functions but with a resistance phenotype present in the environmental resistome. Antibiotics influence the abundance, modularity, and spread of integrons, transposons, and plasmids, mostly acting on structures present before the antibiotic era. Antibiotics enrich particular bacterial lineages and clones and contribute to local clonalization processes. Antibiotics amplify particular genetic exchange communities sharing antibiotic resistance genes and platforms within microbiomes. In particular human or animal hosts, the microbiomic composition might facilitate the interactions between evolutionary units involved in antibiotic resistance. The understanding of antibiotic resistance implies expanding our knowledge on multi-level population biology of bacteria.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Ana P. Tedim
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
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19
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Abstract
The analysis of the genomes of bacterial pathogens indicates that they have acquired their pathogenic capability by incorporating different genetic elements through horizontal gene transfer. The ancestors of virulent bacteria, as well as the origin of virulence determinants, lay most likely in the environmental microbiota. Studying the role that these determinants may have in non-clinical ecosystems is thus of value for understanding in detail the evolution and the ecology of bacterial pathogens. In this article, I propose that classical virulence determinants might be relevant for basic metabolic processes (for instance iron-uptake systems) or in modulating prey/predator relationships (toxins) in natural, non-infective ecosystems. The different role that horizontal gene transfer and mutation may have in the evolution of bacterial pathogens either for their speciation or in short-sighted evolution processes is also discussed.
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Affiliation(s)
- José L Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Darwin 3, Cantoblanco, 28049-Madrid, Spain.
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