Ciprofloxacin selects for RNA polymerase mutations with pleiotropic antibiotic resistance effects

Pietsch, Franziska; Bergman, Jessica; Brandis, Gerrit; Marcusson, Linda L.; Zorzet, Anna; Huseby, Douglas L.; Hughes, Diarmaid

doi:10.1093/jac/dkw364

Cited by 54 publications

(60 citation statements)

References 39 publications

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“…detected mutations in rpoB in an in vitro evolution experiment. 33 These mutations arose after accumulation of other mutations, and were shown to increase the ciprofloxacin MIC of a wild type E. coli by 1.5-3 fold change (Table 2). The mutations in rpoB were shown to increase ciprofloxacin MIC by upregulating the expression of mdtK (also known as ydhE ).…”

Section: Resultsmentioning

confidence: 99%

Quantifying the contribution of four resistance mechanisms to ciprofloxacin minimum inhibitory concentration inEscherichia coli: a systematic review

Remondini

Pasquini

et al. 2018

Preprint

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SynopsisIntroductionCiprofloxacin resistance in Escherichia coli is widespread and adds to the burden of E. coli infections. Reviews assessing the genetic basis of ciprofloxacin resistance have mostly been qualitative. However, to allow for the prediction of a resistance phenotype of clinical relevance based on genotypic characteristics, it is essential to quantify the contribution of prevalent genotypic determinants to resistance. We carried out a systematic review to assess the relative contribution of currently known genomic resistance determinants to the minimum inhibitory concentration (MIC) of ciprofloxacin in E. coli.MethodsPubMed and Web of Science were searched for English language studies that assessed both ciprofloxacin MIC and the presence or introduction of genetic determinants of ciprofloxacin resistance in E. coli. We included experimental and observational studies without time restrictions. Medians and ranges of MIC fold changes were calculated for each resistance determinant and for combinations of determinants.ResultsWe included 66 studies, describing 604 E. coli isolates that carried at least one genetic resistance determinant. Genes coding for targets of ciprofloxacin (gyrA and parC) are strongest contributors to ciprofloxacin resistance, with median MIC fold increases ranging from 24 (range 4-133) for single Ser83Leu (gyrA) mutants to 1533 (range 256-8533) for triple Ser83Leu, Asp87Asn/Gly (gyrA) and Ser80Ile/Arg (parC) mutants. Other resistance mechanisms, including efflux, physical blocking or enzymatic modification, conferred smaller increases in ciprofloxacin MIC (median MIC fold increases typically around 15, range 1-125). However, the (combined) presence of these other resistance mechanisms further increases resistance with median MIC fold increases of up to 4000, and even in the absence of gyrA and parC mutations up to 250.ConclusionThis report provides a comprehensive and quantitative overview of the contribution of different genomic determinants to ciprofloxacin resistance in E. coli. Additionally, the data demonstrate the complexity of resistance phenotype prediction from genomic data and could serve as a reference point for studies aiming to address ciprofloxacin resistance prediction using genomics, in E. coli.

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Section: Resultsmentioning

confidence: 99%

Quantifying the contribution of four resistance mechanisms to ciprofloxacin minimum inhibitory concentration inEscherichia coli: a systematic review

Remondini

Pasquini

et al. 2018

Preprint

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“…The csgD:M4 and ompR:mut2 mutations were introduced into strain MC4100 by Lambda red recombination (Yu et al, 2000) using plasmid pSim5-tet (Koskiniemi et al, 2011). First, a kan-sacB cassette (Pietsch et al, 2017), amplified with primers MHO-100/ MHO-101 for csgD:M4, and MHO-268/MHO-269 for ompR:mut2, was inserted at the site of mutagenesis. A second round of recombination was done with a ssDNA fragment carrying the desired point mutation, followed by counterselection for SacB (Ellis et al, 2001).…”

Section: Bacterial Strains and Plasmidsmentioning

confidence: 99%

Hfq‐dependent mRNA unfolding promotes sRNA ‐based inhibition of translation

et al. 2019

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Small RNAs post‐transcriptionally regulate many processes in bacteria. Base‐pairing of sRNAs near ribosome‐binding sites in mRNAs inhibits translation, often requiring the RNA chaperone Hfq. In the canonical model, Hfq simultaneously binds sRNAs and mRNA targets to accelerate pairing. Here, we show that the Escherichia coli sRNAs OmrA and OmrB inhibit translation of the diguanylate cyclase DgcM (previously: YdaM), a player in biofilm regulation. In OmrA/B repression of dgcM, Hfq is not required as an RNA interaction platform, but rather unfolds an inhibitory RNA structure that impedes OmrA/B binding. This restructuring involves distal face binding of Hfq and is supported by RNA structure mapping. A corresponding mutant protein cannot support inhibition in vitro and in vivo; proximal and rim mutations have negligible effects. Strikingly, OmrA/B‐dependent translational inhibition in vitro is restored, in complete absence of Hfq, by a deoxyoligoribonucleotide that base‐pairs to the biochemically mapped Hfq site in dgcM mRNA. We suggest that Hfq‐dependent RNA structure remodeling can promote sRNA access, which represents a mechanism distinct from an interaction platform model.

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“…2013; Pietsch et al. 2017), and there is no reason to believe that we have yet reached a complete understanding of the mechanisms and genetic alterations that could contribute to resistance. Indeed, the recent discovery of mutations in rpoB , which reduce susceptibility to fluoroquinolones by increasing expression of the MdtK efflux pump (Pietsch et al.…”

Section: Genetic Context and Resistance Phenotypementioning

confidence: 99%

“…Indeed, the recent discovery of mutations in rpoB , which reduce susceptibility to fluoroquinolones by increasing expression of the MdtK efflux pump (Pietsch et al. 2017), is a good example of experimental evolution uncovering of some of the previously unsuspected genetic ‘dark matter’ of resistance.…”

Section: Genetic Context and Resistance Phenotypementioning

confidence: 99%

Environmental and genetic modulation of the phenotypic expression of antibiotic resistance

Hughes¹,

Andersson²

2017

FEMS Microbiology Reviews

Self Cite

138

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Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specific resistance genes/mutations. An important implication from these findings is that a given genotype does not always result in the expected phenotype. This dissociation of genotype and phenotype has important consequences for clinical bacteriology and for our ability to predict resistance phenotypes from genetics and DNA sequences. A related problem concerns the degree to which the genes/mutations currently identified in vitro can fully explain the in vivo resistance phenotype, or whether there is a significant additional amount of presently unknown mutations/genes (genetic ‘dark matter’) that could contribute to resistance in clinical isolates. Finally, a very important question is whether/how we can identify the genetic features that contribute to making a successful pathogen, and predict why some resistant clones are very successful and spread globally? In this review, we describe different environmental and genetic factors that influence phenotypic expression of antibiotic resistance genes/mutations and how this information is needed to understand why particular resistant clones spread worldwide and to what extent we can use DNA sequences to predict evolutionary success.

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Ciprofloxacin selects for RNA polymerase mutations with pleiotropic antibiotic resistance effects

Abstract: These data identify mutations in RNA polymerase as novel contributors to the evolution of resistance to ciprofloxacin and show that the phenotype is mediated by increased MdtK-dependent drug efflux.

Cited by 54 publications

References 39 publications

Quantifying the contribution of four resistance mechanisms to ciprofloxacin minimum inhibitory concentration inEscherichia coli: a systematic review

Quantifying the contribution of four resistance mechanisms to ciprofloxacin minimum inhibitory concentration inEscherichia coli: a systematic review

Hfq‐dependent mRNA unfolding promotes sRNA ‐based inhibition of translation

Environmental and genetic modulation of the phenotypic expression of antibiotic resistance

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