1249. Genetic Evidence That Gepotidacin Shows Well-balanced Dual Targeting against DNA Gyrase And Topoisomerase IV in Neisseria gonorrhoeae

Background

Gepotidacin (GEP) is a novel triazaacenaphthylene bacterial type II topoisomerase inhibitor targeting both bacterial DNA gyrase and topoisomerase IV by a different mechanism from fluoroquinolone antibiotics. Although in vitro frequency of resistance to GEP in Neisseria gonorrhoeae (NG) is low, during a phase 2 trial, clinical resistance to gepotidacin in NG emerged in a subset of fluoroquinolone-resistant NG isolates that contained a pre-existing ParC D86N mutation by introduction of a new GyrA A92T mutation. The objective of this study was to evaluate the role of GyrA A92T & Parc D86N mutations in resistance to GEP.

Methods

We utilized the high frequency of natural transformation to introduce GyrA A92T and ParC D86N mutations, individually and in combination, into NG isolates either with GyrA S91F D95G mutations or with wild type (WT) GyrA by selection on ciprofloxacin (CIP) or GEP to generate isogenic strains for susceptibility evaluation.

Results

Results are summarized in enclosed table. Overall, GyrA A92T and ParC D86N mutations alone did not confer a significant (>4-fold) increase in GEP MIC; whereas together they gave >16-fold increases in GEP MIC. Importantly, quinolone target mutations (GyrA S91F D95G and ParC D86N) together showed no significant effect on the GEP MIC; while they gave >1000-fold increase in CIP MIC. As expected, GyrA A92T and ParC D86N mutations alone or together in WT GyrA background had no significant effect on CIP susceptibility.

Susceptibility of isogenic NG strains to gepotidacin and ciprofloxacin

Conclusion

Our results indicated that unlike fluoroquinolones that primarily target DNA gyrase in NG, there is no obvious primary target for GEP, supporting well-balanced dual targeting of DNA gyrase and topoisomerase IV by GEP in NG. Though, the pre-existing ParC D86N mutation is a potential risk marker for clinical resistance development, as this mutation compromises dual targeting of GEP, our studies provide mechanistic insight for appropriate clinical dose selection to potentially suppress further resistance development in this subset of clinical isolates.

Disclosures

Pan Chan, PhD, GlaxoSmithKline (Employee, Shareholder) Karen Ingraham, MS, GlaxoSmithKline (Employee, Shareholder) Sharon Min, MS, GlaxoSmithKline (Employee, Shareholder) Nicole Scangarella-Oman, MS, GlaxoSmithKline plc. (Employee, Shareholder) Steve Rittenhouse, PhD, GlaxoSmithKline (Employee, Shareholder) Jianzhong Huang, PhD, GlaxoSmithKline (Employee, Shareholder)

1440. The Genetic Basis for a Neisseria gonorrhoeae Clinical Isolate That Contains mtrR-79 Mutation But Is Highly Susceptible to Antibiotics Effluxed by the Mtr Pump System

Background

Neisseria gonorrhoeae (NG) possesses multiple drug efflux systems that play an important role in evading antibiotics in the treatment for gonorrhea and in helping this pathogen to evade innate antimicrobial defenses during infection. The mtrR_-79 and mtr₁₂₀ mutations in the promoter region between mtrR and mtrCDE are common mutations contributing to overexpression of the MtrCDE efflux pump resulting in increased efflux to multiple antibiotics including macrolides, β-lactams and tetracycline. However, we found a NG clinical isolate that contains the mtrR_-79 mutation but is highly susceptible to antibiotics effluxed by the MtrCDE pump system.

Methods

PCR amplification, DNA sequencing and natural transformation were used to investigate the genetic basis responsible for the increased susceptibility by this isolate.

Results

We amplified by PCR the individual genes of mtrCDE, respectively, from this susceptible isolate as well as a NG isolate that contains the mtrR_-79 mutation with increased efflux; there was no difference in the size of PCR products between the susceptible isolate and the isolate with increased efflux, indicating there was no large deletion/insertion in these genes. DNA sequence analysis of mtrCDE revealed the susceptible isolate also contained a loss-of-function mutation ΔGC from a 6 GC repeat GCGCGCGCGCGC in mtrC resulting in MtrC A117 frameshift predicted to produce a truncated MtrC protein that results in a low efflux phenotype. Natural transformation of the susceptible isolate with a wild type mtrC and selection with ciprofloxacin generated transformants that corrected the ΔGC mutation and restored the increased efflux phenotype.

Conclusion

Our results indicate that genotyping of mtrR and the promoter region between mtrR and mtrCDE is insufficient to predict increased efflux phenotype and provide direct evidence that NG isolates with elevated efflux is able to genetically revert to low efflux via loss-of-function mutations in the coding region of the efflux pump genes.

Disclosures

Jianzhong Huang, PhD, GlaxoSmithKline (Employee, Shareholder) Karen Ingraham, MS, GlaxoSmithKline (Employee, Shareholder)

1438. Dissecting the Multifaceted Nature of Antibiotic Resistance in Clinical Isolates of Neisseria gonorrhoeae by Natural Transformation

Background

Neisseria gonorrhoeae (NG) causes the sexually transmitted disease gonorrhea. It has developed resistance to every antibiotic introduced for gonorrhea treatment such that NG clinical isolates with multidrug resistance (MDR) are increasingly common. We hypothesize that natural transformation could be used to transfer genetic determinants of antibiotic resistance from drug-resistant NG clinical isolates without pre-knowledge of the genetic determinants to a new background under antibiotic selection to generate isogenic transformants for further characterization.

Methods

Natural transformation, PCR amplification and DNA sequencing, and antibiotic susceptibility testing were used in the studies.

Results

We have validated the hypothesis using genomic DNA from an MDR including ciprofloxacin-resistant NG clinical isolate as a donor and a ciprofloxacin-susceptible NG isolate as a recipient under the selective pressure of ciprofloxacin. This led to a series of transformants that contain single or multiple genetic resistance determinants being generated depending on the resistance levels and transformation frequencies. Antibiotic susceptibility testing and genetic characterization of the transformants allowed us to (i) identify ciprofloxacin resistance determinants including efflux mutation mtrR_-79 and target mutations GyrA S91F D95G and ParC D86N, (ii) quantify the contribution of each genetic determinant responsible for the ciprofloxacin resistance and (iii) regenerate the ciprofloxacin resistance phenotype of the donor isolate to detect multiple paths of possible resistance development for ciprofloxacin. Furthermore, we also validated the hypothesis with a novel antibiotic gepotidacin to identify pre-existing genetic determinants contributing to varying susceptibility to this antibiotic. Finally, we envision that, along with whole genome sequencing, natural transformation could be used to identify and quantify novel genetic resistance determinants to current or novel antibiotics in drug-resistant NG clinical isolates.

Conclusion

We demonstrated the utility of natural transformation in dissecting the multifaceted nature of antibiotic resistance in NG clinical isolates.

Disclosures

Jianzhong Huang, PhD, GlaxoSmithKline (Employee, Shareholder) Karen Ingraham, MS, GlaxoSmithKline (Employee, Shareholder) Pan Chan, PhD, GlaxoSmithKline (Employee, Shareholder) Steve Rittenhouse, PhD, GlaxoSmithKline (Employee, Shareholder)

Author Correction: Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening

This corrects the article DOI: 10.1038/ncomms16081.

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase

A paucity of novel acting antibacterials is in development to treat the rising threat of antimicrobial resistance, particularly in Gram-negative hospital pathogens, which has led to renewed efforts in antibiotic drug discovery. Fluoroquinolones are broad-spectrum antibacterials that target DNA gyrase by stabilizing DNA-cleavage complexes, but their clinical utility has been compromised by resistance. We have identified a class of antibacterial thiophenes that target DNA gyrase with a unique mechanism of action and have activity against a range of bacterial pathogens, including strains resistant to fluoroquinolones. Although fluoroquinolones stabilize double-stranded DNA breaks, the antibacterial thiophenes stabilize gyrase-mediated DNA-cleavage complexes in either one DNA strand or both DNA strands. X-ray crystallography of DNA gyrase-DNA complexes shows the compounds binding to a protein pocket between the winged helix domain and topoisomerase-primase domain, remote from the DNA. Mutations of conserved residues around this pocket affect activity of the thiophene inhibitors, consistent with allosteric inhibition of DNA gyrase. This druggable pocket provides potentially complementary opportunities for targeting bacterial topoisomerases for antibiotic development.

Selective Spectrum Antibiotic Modulation of the Gut Microbiome in Obesity and Diabetes Rodent Models

The gastrointestinal tract microbiome has been suggested as a potential therapeutic target for metabolic diseases such as obesity and Type 2 diabetes mellitus (T2DM). However, the relationship between changes in microbial communities and metabolic disease-phenotypes are still poorly understood. In this study, we used antibiotics with markedly different antibacterial spectra to modulate the gut microbiome in a diet-induced obesity mouse model and then measured relevant biochemical, hormonal and phenotypic biomarkers of obesity and T2DM. Mice fed a high-fat diet were treated with either ceftazidime (a primarily anti-Gram negative bacteria antibiotic) or vancomycin (mainly anti-Gram positive bacteria activity) in an escalating three-dose regimen. We also dosed animals with a well-known prebiotic weight-loss supplement, 10% oligofructose saccharide (10% OFS). Vancomycin treated mice showed little weight change and no improvement in glycemic control while ceftazidime and 10% OFS treatments induced significant weight loss. However, only ceftazidime showed significant, dose dependent improvement in key metabolic variables including glucose, insulin, protein tyrosine tyrosine (PYY) and glucagon-like peptide-1 (GLP-1). Subsequently, we confirmed the positive hyperglycemic control effects of ceftazidime in the Zucker diabetic fatty (ZDF) rat model. Metagenomic DNA sequencing of bacterial 16S rRNA gene regions V1-V3 showed that the microbiomes of ceftazidime dosed mice and rats were enriched for the phylum Firmicutes while 10% OFS treated mice had a greater abundance of Bacteroidetes. We show that specific changes in microbial community composition are associated with obesity and glycemic control phenotypes. More broadly, our study suggests that in vivo modulation of the microbiome warrants further investigation as a potential therapeutic strategy for metabolic diseases.

Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin

New antibacterials are needed to tackle antibiotic-resistant bacteria. Type IIA topoisomerases (topo2As), the targets of fluoroquinolones, regulate DNA topology by creating transient double-strand DNA breaks. Here we report the first co-crystal structures of the antibacterial QPT-1 and the anticancer drug etoposide with Staphylococcus aureus DNA gyrase, showing binding at the same sites in the cleaved DNA as the fluoroquinolone moxifloxacin. Unlike moxifloxacin, QPT-1 and etoposide interact with conserved GyrB TOPRIM residues rationalizing why QPT-1 can overcome fluoroquinolone resistance. Our data show etoposide's antibacterial activity is due to DNA gyrase inhibition and suggests other anticancer agents act similarly. Analysis of multiple DNA gyrase co-crystal structures, including asymmetric cleavage complexes, led to a ‘pair of swing-doors' hypothesis in which the movement of one DNA segment regulates cleavage and religation of the second DNA duplex. This mechanism can explain QPT-1's bacterial specificity. Structure-based strategies for developing topo2A antibacterials are suggested.

Type IIA topoisomerases (topo2As) create transient double-strand DNA breaks. Here, the authors report structures showing how QPT-1 binds in the DNA/topo2A complex at the same site as the fluoroquinolone moxifloxacin, and discuss the potential for developing new classes of antibiotics.

Horizontal transfer of drug-resistant aminoacyl-transfer-RNA synthetases of anthrax and Gram-positive pathogens

The screening of new antibiotics against several bacterial strains often reveals unexpected occurrences of natural drug resistance. Two examples of this involve specific inhibitors of Staphylococcus aureus isoleucyl-transfer-RNA synthetase 1 (IleRS1) and, more recently, Streptococcus pneumoniae methionyl-tRNA synthetase 1 (MetRS1). In both cases, resistance is due to the presence of a second gene that encodes another synthetase (IleRS2 or MetRS2). Here, we show that both S. pneumoniae MetRS2 and S. aureus IleRS2 have closely related homologues in the Gram-positive bacterium Bacillus anthracis, the causative agent of anthrax. Furthermore, similar to drug-resistant pathogens, strains of B. anthracis and its closest relative, B. cereus, also have wild-type ileS1 and metS1 genes. Clostridium perfringens, the causative agent of gangrene, also has two metS genes, whereas Oceanobacillus iheyensis isolated from deep-sea sediments has a single ileS2-type gene. This study shows the importance of understanding complex evolutionary networks of ancient horizontal gene transfer for the development of novel antibiotics.

Lipid modification of prelipoproteins is dispensable for growth in vitro but essential for virulence in Streptococcus pneumoniae

A Deltalgt (Lgt, lipoprotein diacylglyceryl transferase) isogenic mutant was obtained which indicates that lgt is not essential for cell growth in vitro, like in the Gram-positive bacterium Bacillus subtilis, but unlike in the proteobacteria Escherichia coli and Salmonella typhimurium. The mutation was transduced to a virulent strain. A 5 log attenuation was observed in a respiratory tract model of infection. Metabolic labeling by [U-14C]palmitate revealed the presence of eight to ten lipoproteins in the wild-type strain only, with molecular masses between 15 and 80 kDa. Our findings suggest a major difference in the role of lipoproteins in Gram-positive bacteria versus the proteobacteria.

Genetic characterization of gram-positive homologs of the XerCD site-specific recombinases

Homologs of the XerCD enzymes, which in Escherichia coli have been shown to be responsible for resolving chromosomal multimers prior to chromosome segregation, were identified in the genomes of Staphylococcus aureus and Streptococcus pneumoniae. Phylogenetic and conservation pattern analysis suggests that the S. aureus gene products are orthologs of XerC and D. A S. aureus xerC null mutant displayed in vitro characteristics consistent with the segregation defect reported for E. coli xer mutants, and was found to be attenuated in a murine infection model. Strikingly, the S. aureus xerD gene appears to be absolutely required for viability, and may therefore be the first example of an essential gene of the lambda integrase family. In contrast, phylogenetic and conservation pattern analysis show that the S. pneumoniae gene products are more closely related to phage integrases than to XerCD. S. pneumoniae xer1, 2 and 3 null mutants were each found to be attenuated in a murine infection model, suggesting that they may control processes which affect virulence.