Genomic Analysis Reveals Distinct Concentration-Dependent Evolutionary Trajectories for Antibiotic Resistance in Escherichia coli

Mogre, Aalap; Sengupta, Titas; Veetil, Reshma T; Ravi, Preethi; Seshasayee, Aswin Sai Narain

doi:10.1093/dnares/dsu032

Cited by 33 publications

(27 citation statements)

References 52 publications

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“…We tested this hypothesis by searching published datasets and genomes for fusA1, ptsP, cyoA , and cyoB mutations (Methods). Mutations in fusA1 were found in several different species including E. coli , S. typhimurium , and S. aureus (Ibacache-Quiroga et al, 2018; Jahn et al, 2017; Johanson and Hughes, 1994; Kim et al, 2014; Mogre et al, 2014; Norström et al, 2007), and all laboratory studies reported these mutations either in response to aminoglycoside selection or as a direct cause of aminoglycoside resistance (Figure 4). Mutations in cyoA and cyoB were also found in E. coli and S. typhimurium in these experiments (Ibacache-Quiroga et al, 2018; Jahn et al, 2017; Johanson and Hughes, 1994).…”

Section: Resultsmentioning

confidence: 99%

Parallel evolution of tobramycin resistance across species and environments

Scribner

Santos-López

Marshall

et al. 2019

Preprint

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words)13 An important problem in evolution is identifying the genetic basis of how different species adapt 14 to similar environments. Understanding how various bacterial pathogens evolve in response to 15 antimicrobial treatment is a pressing example of this problem, where discovery of molecular 16 parallelism could lead to clinically useful predictions. Evolution experiments with pathogens in 17 environments containing antibiotics combined with periodic whole population genome 18 sequencing can be used to characterize the evolutionary dynamics of the pathways to 19 antimicrobial resistance. We separately propagated two clinically relevant Gram-negative 20 pathogens, Pseudomonas aeruginosa and Acinetobacter baumannii, in increasing 21 concentrations of tobramycin in two different environments each: planktonic and biofilm. 22Independent of the pathogen, populations adapted to tobramycin selection by parallel evolution 23 of mutations in fusA1, encoding elongation factor G, and ptsP, encoding phosphoenolpyruvate 24 phosphotransferase. As neither gene is a direct target of this aminoglycoside, both are relatively 25 novel and underreported causes of resistance. Additionally, both species acquired antibiotic-26 associated mutations that were more prevalent in the biofilm lifestyle than planktonic, in electron 27 transport chain components in A. baumannii and LPS biosynthesis enzymes in P. aeruginosa 28 populations. Using existing databases, we discovered both fusA1 and ptsP mutations to be 29 prevalent in antibiotic resistant clinical isolates. Additionally, we report site-specific parallelism of 30 fusA1 mutations that extend across several bacterial phyla. This study suggests that strong 31 selective pressures such as antibiotic treatment may result in high levels of predictability in 32 molecular targets of evolution despite differences between organisms' genetic background and 33 environment.The notion that evolution can be forecasted at the level of phenotype, gene, or even 36 amino acid is no longer a fantasy in the post-genomic era (Lässig et al., 2017). If we 37 acknowledge that most forecasting efforts rely on history to anticipate the future, the explosive 38 growth of whole-genome sequencing (WGS) sets the stage to resolve evolutionary phenomena 39 in action and suggest the next selected path. Among the best examples, bacterial populations 40 exposed to strong selection like antibiotics and analyzed by WGS are likely to identify gene 41 regions that produce resistance (Ahmed et al., 2018a; Cooper, 2018; Feng et al., 2016; Palmer 42 and Kishony, 2013). Repeated instances of the same antibiotic selection may enrich the same 43 types of mutations and ultimately enable some measure of predictability (Ibacache-Quiroga et 44 al., 2018; Wong et al., 2012). For instance, we can be confident that exposure of many bacteria 45 to high doses of fluoroquinolones like ciprofloxacin may select for substitutions in residues 83 or 46 87 of the drug target, DNA gyrase A (Fàbrega et al., 2009; Wong and Kassen, 2011).47 Furt...

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Section: Resultsmentioning

confidence: 99%

Parallel evolution of tobramycin resistance across species and environments

Scribner

Santos-López

Marshall

et al. 2019

Preprint

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“…By modifying the conformation of EF-G, these amino acid substitutions could modify the interactions of the elongation factor with the ribosome recycling factor (RRF), 16S rRNA (helix 69), 23S rRNA (helix 44), P-site tRNA, mRNA, and/or associated ribosomal proteins L6, L11, L12, and S12 (45,46). In Escherichia coli, kanamycin resistance was found to be associated with mutations strictly located in domain IV (47,48). The E. coli mutants harboring such mutations were temperature sensitive and had a slower elongation rate than the parental strain (48).…”

Section: Correlation Between Genomic Data and Resistance Phenotypesmentioning

confidence: 99%

Mutations in Gene fusA1 as a Novel Mechanism of Aminoglycoside Resistance in Clinical Strains of Pseudomonas aeruginosa

Bolard

Plésiat

Jeannot

2018

Antimicrob Agents Chemother

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Resistance of clinical strains of to aminoglycosides can result from production of transferable aminoglycoside-modifying enzymes, of 16S rRNA methylases, and/or mutational derepression of intrinsic multidrug efflux pump MexXY(OprM). We report here the characterization of a new type of mutant that is 4- to 8-fold more resistant to 2-deoxystreptamine derivatives (e.g., gentamicin, amikacin, and tobramycin) than the wild-type strain PAO1. The genetic alterations of three mutants were mapped on and found to result in single amino acid substitutions in domains II, III, and V of elongation factor G (EF-G1A), a key component of translational machinery. Transfer of the mutated alleles into PAO1 reproduced the resistance phenotype. Interestingly, mutants with other amino acid changes in domains G, IV, and V of EF-G1A were identified among clinical strains with decreased susceptibility to aminoglycosides. Allelic-exchange experiments confirmed the relevance of these latter mutations and of three other previously reported alterations located in domains G and IV. Pump MexXY(OprM) partly contributed to the resistance conferred by the mutated EF-G1A variants and had additive effects on aminoglycoside MICs when mutationally upregulated. Altogether, our data demonstrate that cystic fibrosis (CF) and non-CF strains of can acquire a therapeutically significant resistance to important aminoglycosides via a new mechanism involving mutations in elongation factor EF-G1A.

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“…In this work, we serendipitously identified a SNP in the fusA1 gene of P. aeruginosa which gave rise to increased gentamicin resistance and global changes in expression of the T3 and T6 (HSI-I) secretion systems and exopolysaccharide biosynthetic pathways. FusA1 mutations are a common feature in certain clinical P. aeruginosa isolates (such as those derived from CF sputum), and appear to be a lowcost response to exposure to sub-lethal concentrations of aminoglycosides in vitro (Chung et al, 2012;Mogre et al, 2014;Bolard et al, 2018). However, to our knowledge, the wider phenotypic consequences of such mutations have not been explored further.…”

Section: Discussionmentioning

confidence: 99%

Global reprogramming of virulence and antibiotic resistance inPseudomonas aeruginosaby a single nucleotide polymorphism in the elongation factor-encoding gene,fusA1

Maunders¹,

Triniman²,

Rahman³

et al. 2019

Preprint

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Pseudomonas aeruginosa is a common opportunistic pathogen. The organism displays elevated intrinsic antibiotic resistance and can cause life-threatening infections. The gene encoding an elongation factor, FusA1, is frequently mutated in clinical isolates of P. aeruginosa from patients with cystic fibrosis (CF). Recent work has shown that fusA1 mutants often display elevated aminoglycoside resistance due to increased expression of the aminoglycoside efflux pump, MexXY. In the current work, we isolated a spontaneous gentamicin-resistant fusA1 mutant (FusA1 P443L ) in which mexXY expression was increased. Through a combination of proteomic and transcriptomic analyses, we found that the fusA1 mutant also exhibited large-scale but discrete changes in the expression of key pathogenicity-associated genes. Most notably, the fusA1 mutant displayed greatly increased expression of the Type III Secretion system (T3SS), widely considered to be the most potent virulence factor in the P. aeruginosa arsenal, and also elevated expression of the Type VI Secretion (T6S) machinery. This was unexpected because expression of the T3SS is usually reciprocally coordinated with T6S system expression. The fusA1 mutant also displayed elevated exopolysaccharide production, dysregulated siderophore production, elevated ribosomal protein synthesis, and transcriptomic signatures indicative of translational stress. Each of these phenotypes (and almost all of the transcriptomic and proteomic changes associated with the fusA1 mutation) were restored to levels comparable to that in the PAO1-derived progenitor strain by expression of the wild-type fusA1 gene in trans, indicating that the mutant gene is recessive. Our data show that in addition to elevating antibiotic resistance through mexXY expression (although we also identify additional contributory resistance mechanisms), mutations in fusA1 can lead to highly-selective dysregulation of virulence gene expression.

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Genomic Analysis Reveals Distinct Concentration-Dependent Evolutionary Trajectories for Antibiotic Resistance in Escherichia coli

Cited by 33 publications

References 52 publications

Parallel evolution of tobramycin resistance across species and environments

Parallel evolution of tobramycin resistance across species and environments

Mutations in Gene fusA1 as a Novel Mechanism of Aminoglycoside Resistance in Clinical Strains of Pseudomonas aeruginosa

Global reprogramming of virulence and antibiotic resistance inPseudomonas aeruginosaby a single nucleotide polymorphism in the elongation factor-encoding gene,fusA1

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