Insights into the Evolution of the Mutational Resistome of Pseudomonas Aeruginosa in Cystic Fibrosis
2017; Future Medicine; Volume: 12; Issue: 16 Linguagem: Inglês
10.2217/fmb-2017-0197
ISSN1746-0921
AutoresCarla López-Causapé, Antonio Oliver,
Tópico(s)Plant Pathogenic Bacteria Studies
ResumoFuture MicrobiologyVol. 12, No. 16 EditorialFree AccessInsights into the evolution of the mutational resistome of Pseudomonas aeruginosa in cystic fibrosisCarla López-Causapé & Antonio OliverCarla López-Causapé Servicio de Microbiología & Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Illes Balears (IdISBa), Palma de Mallorca, Spain & Antonio Oliver*Author for correspondence: E-mail Address: antonio.oliver@ssib.es Servicio de Microbiología & Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Illes Balears (IdISBa), Palma de Mallorca, SpainPublished Online:25 Oct 2017https://doi.org/10.2217/fmb-2017-0197AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareShare onFacebookTwitterLinkedInReddit Keywords: antibiotic resistancebacterial evolutionchronic infectionscystic fibrosishypermutationPseudomonas aeruginosaresistomeChronic respiratory infection (CRI) by Pseudomonas aeruginosa is the main driver of morbidity and mortality in cystic fibrosis (CF) patients [1]. CRI results from an intense adaptation process, where bacterial evolution is tested against host immune responses and years of aggressive antimicrobial treatments [2]. Once established, CRI can seldom be eradicated despite intensive antimicrobial treatments, and therefore our therapeutic goals resignedly move from attempting to cure the infection to minimizing its long-term impact through chronic suppressive therapy [3]. The plasticity of P. aeruginosa genome for antimicrobial resistance acquisition, the greatly enhanced mutation supply rate provided by frequent hypermutable variants (mutators) and the highly structured environment determined by the characteristic biofilm growth and the anatomy of the respiratory tract make bacterial evolution and genetic diversification a hallmark of CF CRI [2,4]. While the enhanced evolution of antimicrobial resistance in CF, frequently linked to mutator phenotypes, was noted many years ago [5], it is with the introduction of whole-genome sequencing (WGS) that we are starting to understand its real dimensions [6].The term resistome was first used to account for the set of primary antibiotic resistance genes that could be eventually transferred to human pathogens [7]. Soon after the concept of intrinsic resistome was introduced to include all chromosomal genes that are involved in intrinsic resistance, and whose presence in strains of a bacterial species is independent of previous antibiotic exposure and is not due to horizontal gene transfer (HGT) [8]. Finally, the term mutational resistome was more recently implemented to account for the set of mutations involved in the modulation of antibiotic resistance levels in the absence of HGT [9]. Recent WGS data obtained from in vitro assays on the evolution of antibiotic resistance and clinical isolates, and in particular sequential CF isolates, provide new insights into the evolutionary dynamics and mechanisms of P. aeruginosa antibiotic resistance. However, in too many cases, the documented genomic variations fail to provide causative relations in the absence of phenotypic information. The analysis of WGS mutational resistomes has proven to be useful for understanding the evolutionary dynamics of classical resistance mechanisms and to depict new ones for the majority of antimicrobial classes, including β-lactams, aminoglycosides, fluoroquinolones and polymixins.Regarding β-lactams, the analysis of WGS mutational resistomes has confirmed the major role of classical resistance mutations such as those leading to the overexpression of the chromosomal β-lactamase AmpC (such as DacB [PBP4], AmpD and/or AmpR mutations) or the inactivation of the carbapenem porin OprD. However, the analysis of mutational resistomes of in vitro evolved strains and sequential CF isolates have identified other key mutations, such as those occurring in β-lactam targets (essential PBPs), particularly involving mutations in ftsI which encodes PBP3, an essential high molecular class B penicillin binding protein (PBP) with transpeptidase activity. Indeed, data from CF patients [9,10] as well as from in vitro studies [11] have recently demonstrated that PBP3 is under strong mutational pressure, with specific mutations contributing to β-lactam resistance development. Among them are particularly relevant and frequent mutations affecting amino acids R504 or F533, located within the protein domains responsible for the formation and stabilization of the inactivating complex β-lactam–PBP3. Moreover, PBP3 mutations seem to play a role in the emergence of resistance to novel β-lactam–β-lactamase inhibitor combinations, such as ceftolozane/tazobactam [9]. Another relevant mutational β-lactam resistance mechanism is the selection of large (>200 kb) deletions affecting specific parts of the chromosome. Although the basis of the conferred resistance phenotype still needs to be further clarified, these mutants can be recognized by the characteristic brown pigment (pyomelanine) caused by the deletion of one of the affected genes, hmgA, coding for a homogentisate-1,2-dioxygenase. This type of deletion has been documented in both, in vitro evolved β-lactam-resistant mutants and CF isolates [11,12]. However, the deletion of hmgA is not responsible for the resistance phenotype, which may be linked to the deletion of another of the affected genes, galU, coding for a UDP-glucose pyrophosphorylase required for lipopolysaccharide core synthesis. Indeed, analysis of transposon mutant libraries has shown that inactivation of galU increases ceftazidime and meropenem minimum inhibitory concentrations [13,14]. Finally, another emerging mutational β-lactam resistance mechanism is the structural modification of AmpC [10,11].With respect to aminoglycosides, results from analysis of mutational resistomes of CF isolates point to the underlying strong evolutionary pressure of mexZ and the relevance of MexXY overexpression for resistance development [15–17]. Moreover, recent in vitro studies and findings from CF isolates have revealed that high-level aminoglycoside resistance requires the acquisition of additional mutations; among them, those in FusA1 seem to be particularly frequent and relevant [9,16,18–19]. Likewise, the fluoroquinolone resistome frequently includes mutations in efflux pump regulators, among which nfxB, leading to the overexpression of MexCD-OprJ, is particularly noteworthy in the CF setting. However, high-level ciprofloxacin resistance generally involves one or several mutations in the quinolone resistance determining regions of GyrA/B and/or ParC/E [9]. Regarding polymixin resistance, findings from WGS studies of in vitro evolved strains and CF isolates have shown that development of high-level colistin resistance requires the acquisition of multiple mutations, including those in the two-component regulators (PmrAB, PhoPQ or ParRS) involved in the addition of 4-amino-4-deoxy-L-arabinose to lipid A from the lipopolysaccharide [9,20]. Finally, in addition to the resistance mechanisms to classical antipseudomonal agents, the CF mutational resistome may also include resistance to other used antibiotics such as the frequent mutations of domain V of 23S rRNA – conferring macrolide resistance [21].The complexity of the CF isolates resistomes is further enhanced when the intrapatient genetic diversity of CF P. aeruginosa populations is introduced. Certainly, to understand the resistance dynamics and evolution, future steps should endeavor to analyze the mutational resistomes in CF at the whole population level, as opposed to the analysis of single isolated colonies. Indeed, full understanding of the evolution of the mutational resistome requires a longitudinal and transversal analysis of P. aeruginosa populations in the CF patient. Moreover, recent evidence suggests that interpatient transmission should also be considered when analyzing the evolution of the mutational resistome, especially when introducing mutator lineages of epidemic clones [9].Beyond addressing a relevant scientific question, the analysis of mutational resistomes would be useful for therapeutic strategy design and monitoring the efficacy of administered antibiotic treatments. Obviously, the evolution of the mutational resistome is a direct consequence of antimicrobial exposure. As such, it is not surprising that exposure to one antibiotic drives evolution of the mutational resistome for that antibiotic. However, the complexity of the actual resistance profile is further increased by the specificity and interactions among different resistance mechanisms. A classic example is cross resistance (or collateral resistance), which implies that exposure to one antibiotic drives also the development of resistance to a different one. Typically this is caused by the developed resistance mechanism (such as efflux pump overexpression) affecting simultaneous different antibiotics. Indeed, potential development of cross resistance is a major issue to consider when using antibiotic combinations [22].Perhaps less obvious is collateral susceptibility, which implies that exposure to one antibiotic increases the susceptibility to a different one. This might be achieved through two mechanisms. One possible mechanism is that exposure to one antibiotic directly causes increased susceptibility to a different one, for example, mutations in the β-lactamase AmpC increases cephalosporin hydrolysis while reducing that of penicillins or carbapenems [23]. The second possibility is that the development of a resistance mechanism impairs the activity of another existing resistance mechanism, for example, competition between the different efflux pumps, the overexpression of one may impair the expression of another [24]. Indeed, in the CF setting it is very frequent that the overexpression of efflux pump MexXY, involved in aminoglycoside resistance, is linked to the impaired expression of efflux pump MexAB, involved in the resistance to a broad range of antibiotics including most β-lactams [25]. Thus, the evolution of the mutational resistome for a given antibiotic is not only dependent on the exposure to this antibiotic, but it is also conditioned by the simultaneous or even previous exposures to other antibiotics. An illustrative example is provided in a recent in vitro study that demonstrated, for a broad range of antibiotic classes, that the history of exposure and resistance development to a given antibiotic, conditions the dynamics and mechanisms of resistance development when exposed to a second one [18].Moreover, knowledge of the interactions between resistance mechanisms could be useful in the design of sequential treatments that minimize the risk of resistance development. Such is the case for a recent in vitro study showing the effectiveness of aztreonam–tobramycin sequential treatment, based on the antagonism between the resistance mechanisms for each of the antibiotics; overexpression of the efflux pump MexAB (aztreonam) or MexXY (tobramycin) which compete for the same outer membrane channel (OprM) [26].Finally, it should be noted that a hallmark of P. aeruginosa CRI in CF is the biofilm mode of growth. Indeed, biofilm growth, in addition to providing a compact structured environment likely facilitating the evolution of mutational resistance [27], they also add further complexity due to the major differences in the mechanisms involved when compared with conventional planktonic growth that needs to be considered [28]. Likewise, persistence of P. aeruginosa in the CF lung despite intensive antimicrobial treatments relays in the acquisition of a vast number of adaptive mutations that extend far beyond classical antibiotic resistance mutations [29].In summary, the comprehensive analysis of the mutational resistomes of P. aeruginosa in CF CRI is expected to become a useful tool for optimizing therapeutic strategies and monitoring the efficacy of administered antibiotic treatments in the near future.Financial & competing interests disclosureThe authors are supported by the Ministerio de Economía y Competitividad of Spain, Instituto de Salud Carlos III – co-financed by European Regional Development Fund 'A way to achieve Europe' ERDF, through the Spanish Network for the Research in Infectious Diseases (RD12/0015 and RD16/0016). 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USA 103(22), 8487–8492 (2006).Crossref, Medline, CAS, Google ScholarFiguresReferencesRelatedDetailsCited ByThe methylation-independent mismatch repair machinery in Pseudomonas aeruginosaMicrobiology, Vol. 167, No. 12Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease4 July 2020 | Microorganisms, Vol. 8, No. 7In vitro activity of ceftolozane/tazobactam alone and in combination with amikacin against MDR/XDR Pseudomonas aeruginosa isolates from Greece25 May 2020 | Journal of Antimicrobial Chemotherapy, Vol. 15Hypermutator Pseudomonas aeruginosa Exploits Multiple Genetic Pathways To Develop Multidrug Resistance during Long-Term Infections in the Airways of Cystic Fibrosis PatientsAntimicrobial Agents and Chemotherapy, Vol. 64, No. 5 Vol. 12, No. 16 Follow us on social media for the latest updates Metrics History Received 6 September 2017 Accepted 12 September 2017 Published online 25 October 2017 Published in print December 2017 Information© 2017 Future Medicine LtdKeywordsantibiotic resistancebacterial evolutionchronic infectionscystic fibrosishypermutation Pseudomonas aeruginosa resistomeFinancial & competing interests disclosureThe authors are supported by the Ministerio de Economía y Competitividad of Spain, Instituto de Salud Carlos III – co-financed by European Regional Development Fund 'A way to achieve Europe' ERDF, through the Spanish Network for the Research in Infectious Diseases (RD12/0015 and RD16/0016). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.No writing assistance was utilized in the production of this manuscript.PDF download
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