Fluoroquinolone-resistant Streptococcus pneumoniae

In-vitro antimicrobial activity of new antimicrobial agents against Streptococcus pneumoniae and potential resistance mechanisms: a multicenter study

BACKGROUND

Streptococcus pneumoniae is a major cause of invasive and non-invasive diseases, particularly in children and immunocompromised individuals, with an annual mortality of approximately 800,000 children worldwide. The rise of antibiotic-resistant strains complicates treatment, especially with increasing resistance to penicillin, macrolides, and fluoroquinolones. The study on the resistance of newly developed antimicrobial agents against S. pneumoniae was rarely reported. Furthermore, understanding the relationship between serotypes, resistance mechanisms, and virulence in S. pneumoniae is essential for disease management and vaccine development.

METHODS

A total of 208 S. pneumoniae isolates were collected across nine hospitals in seven Chinese cities/provinces from January 2023 to June 2024. Molecular characteristics were analyzed using whole-genome sequencing to identify serotypes, sequence types, virulence genes, and potential resistance mechanisms. Antibiotic susceptibility test (AST) was performed against 14 agents, involving new antibiotics (eravacycline, omadacycline, nemonoxacin, and contezolid).

RESULTS

Serotypes 19 F (24.6%) and 23 F (11.1%) predominated, with vaccine coverage rates of PCV13 at 66.8%. High resistance rates in S. pneumoniae were observed for erythromycin (208/208, 100%), clindamycin (197/208, 94.7%), and tetracycline (192/208, 92.3%). 13.5% (28/208) and 2.9% (6/208) strains were intermediate and resistant to penicillin, respectively. The new antibiotics showed low resistance, namely, 1.9% (4/208), 0.5% (1/208), 1.9% (4/208), and 7.2% (15/208) resistant to eravacycline, omadacycline, contezolid, and nemonoxacin, respectively. Resistance mechanisms included mutations in 23S rRNA for oxazolidinones, tet genes for tetracyclines, and gyrA/parC for fluoroquinolones.

CONCLUSIONS

S. pneumoniae in China exhibits high genetic diversity and significant antibiotic resistance, underscoring the need for continuous surveillance and updated vaccines. New antibiotics remain effective against multidrug-resistant strains, offering potential treatment options in clinical settings.

Streptococcus pneumoniae favors tolerance via metabolic adaptation over resistance to circumvent fluoroquinolones

Streptococcus pneumoniae is a major human pathogen of global health concern and the rapid emergence of antibiotic resistance poses a serious public health problem worldwide. Fluoroquinolone resistance in S. pneumoniae is an intriguing case because the prevalence of fluoroquinolone resistance does not correlate with increasing usage and has remained rare. Our data indicate that deleterious fitness costs in the mammalian host constrain the emergence of fluoroquinolone resistance both by de novo mutation and recombination. S. pneumoniae was able to circumvent such deleterious fitness costs via the development of antibiotic tolerance through metabolic adaptation that reduced the production of reactive oxygen species, resulting in a fitness benefit during infection of mice treated with fluoroquinolones. These data suggest that the emergence of fluoroquinolone resistance is tightly constrained in S. pneumoniae by fitness tradeoffs and that mutational pathways involving metabolic networks to enable tolerance phenotypes are an important contributor to the evasion of antibiotic-mediated killing.IMPORTANCEThe increasing prevalence of antibiotic resistant bacteria is a major global health concern. While many species have the potential to develop antibiotic resistance, understanding the barriers to resistance emergence in the clinic remains poorly understood. A prime example of this is fluroquinolone resistance in Streptococcus pneumoniae, whereby, despite continued utilization, resistance to this class of antibiotic remains rare. In this study, we found that the predominant pathways for developing resistance to this antibiotic class severely compromised the infectious capacity of the pneumococcus, providing a key impediment for the emergence of resistance. Using in vivo models of experimental evolution, we found that S. pneumoniae responds to repeated fluoroquinolone exposure by modulating key metabolic pathways involved in the generation of redox molecules, which leads to antibiotic treatment failure in the absence of appreciable shifts in resistance levels. These data underscore the complex pathways available to pathogens to evade antibiotic mediating killing via antibiotic tolerance.

Characteristics of Clonal Complex Changes and Quinolone Resistance-Determining Region Mutations of Levofloxacin-Resistant Streptococcus pneumoniae in South Korea

Streptococcus pneumoniae is the most common causative agent of community-acquired pneumonia and invasive pneumococcal diseases with high mortality rates. The aims of this study were to evaluate clonal complex (CC) changes of levofloxacin-resistant S. pneumoniae (LRSP) strains and to investigate the relationship between levofloxacin resistance and pneumococcal serotypes. We analyzed the antimicrobial susceptibility of 145 LRSP strains to 18 antimicrobial agents and the quinolone resistance-determining region mutation. Multilocus sequence typing was performed to investigate the genetic relatedness among LRSP strains. Most LRSP strains (96.6%) were multidrug resistant and had simultaneous mutations in gyrA, parC, and parE (91.7%). The serotypes 11A (44.1%) and 13 (14.5%) accounted for 58.6% of LRSP strains, and 32.0% were nonvaccine serotypes. Most LRSP strains were grouped as CC8279 (N = 83; 57.2%), CC189 (N = 10; 6.9%), or CC320 (N = 5; 3.4%). CC8279 was commonly combined with serotypes 11A and 13. There were numerous changes of serotype and CC accompanying the emergence and spread of LRSP. Continuous monitoring of changes in the serotype and sequence type of LRSP is required to follow the spread of LRSP for public health monitoring.

Genomic Insight into the Spread of Meropenem-Resistant Streptococcus pneumoniae Spain23F-ST81, Taiwan

Incidence of invasive pneumococcal disease caused by antimicrobial-resistant Streptococcus pneumoniae types not included in pneumococcal conjugate vaccines has increased, including a penicillin- and meropenem-resistant serotype 15A-ST63 clone in Japan. During 2013-2017, we collected 206 invasive pneumococcal isolates in Taiwan for penicillin and meropenem susceptibility testing. We found serotypes 15B/C-ST83 and 15A-ST63 were the most prevalent penicillin- and meropenem-resistant clones. A transformation study confirmed that penicillin-binding protein (PBP) 2b was the primary meropenem resistance determinant, and PBP1a was essential for high-level resistance. The rate of serotype 15B/C-ST83 increased during the study. All 15B/C-ST83 isolates showed an ermB macrolide resistance genotype. Prediction analysis of recombination sites revealed 12 recombination regions in 15B/C-ST83 compared with the S. pneumoniae Spain^23F-ST81 genome. Pneumococcal clones rapidly recombine to acquire survival advantages and undergo local expansion under the selective pressure exerted by vaccines and antimicrobial drugs. The spread of 15B/C-ST83 is alarming for countries with high antimicrobial pressure.

Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective

Streptococcus pneumoniae inflicts a huge disease burden as the leading cause of community-acquired pneumonia and meningitis. Soon after mainstream antibiotic usage, multiresistant pneumococcal clones emerged and disseminated worldwide. Resistant clones are generated through adaptation to antibiotic pressures imposed while naturally residing within the human upper respiratory tract. Here, a huge array of related commensal streptococcal strains transfers core genomic and accessory resistance determinants to the highly transformable pneumococcus. β-Lactam resistance is the hallmark of pneumococcal adaptability, requiring multiple independent recombination events that are traceable to nonpneumococcal origins and stably perpetuated in multiresistant clonal complexes. Pneumococcal strains with elevated MICs of β-lactams are most often resistant to additional antibiotics. Basic underlying mechanisms of most pneumococcal resistances have been identified, although new insights that increase our understanding are continually provided. Although all pneumococcal infections can be successfully treated with antibiotics, the available choices are limited for some strains. Invasive pneumococcal disease data compiled during 1998 to 2013 through the population-based Active Bacterial Core surveillance program (U.S. population base of 30,600,000) demonstrate that targeting prevalent capsular serotypes with conjugate vaccines (7-valent and 13-valent vaccines implemented in 2000 and 2010, respectively) is extremely effective in reducing resistant infections. Nonetheless, resistant non-vaccine-serotype clones continue to emerge and expand.

Antihypertensives suppress the emergence of fluoroquinolone-resistant mutants in pneumococci: an in vitro study

BACKGROUND

The antihypertensives reserpine and verapamil are also inhibitors of pneumococcal efflux pumps. We addressed the following questions: (i) Do verapamil and reserpine influence the mutation ratio of pneumococci in the presence of ciprofloxacin? (ii) At which concentrations does this occur? (iii) Is this limited to isolates with efflux phenotype?

METHODS

14 clinical isolates, nested in 6 genetically similar clusters, were used, 7 strains with efflux and 7 without. The mutation ratio in the presence of ciprofloxacin (3 × MIC) and increasing concentrations of reserpine and verapamil was determined and the quinolone-resistance determining regions (QRDR) of selected mutants were sequenced. Analysis of the efficacy was performed using a mixed linear model, supported by descriptive statistics.

RESULTS

Reserpine and verapamil reduced the mutation ratio of QRDR in the presence of ciprofloxacin with the required concentration for a reduction ≥ 50% of 1mg/l for reserpine and 50mg/l for verapamil. The mutation prevention effect is not limited to, but is more pronounced in efflux positive phenotypes.

CONCLUSION

Reserpine and verapamil can prevent the selection of ciprofloxacin resistant isolates by reduction of the mutation ratio, particularly in strain with an efflux phenotype. However, the required concentrations are too toxic for clinical use.

Rapid pneumococcal evolution in response to clinical interventions

Epidemiological studies of the naturally transformable bacterial pathogen Streptococcus pneumoniae have previously been confounded by high rates of recombination. Sequencing 240 isolates of the PMEN1 (Spain(23F)-1) multidrug-resistant lineage enabled base substitutions to be distinguished from polymorphisms arising through horizontal sequence transfer. More than 700 recombinations were detected, with genes encoding major antigens frequently affected. Among these were 10 capsule-switching events, one of which accompanied a population shift as vaccine-escape serotype 19A isolates emerged in the USA after the introduction of the conjugate polysaccharide vaccine. The evolution of resistance to fluoroquinolones, rifampicin, and macrolides was observed to occur on multiple occasions. This study details how genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales.

Emergence of ciprofloxacin-nonsusceptible Streptococcus pyogenes isolates from healthy children and pediatric patients in Portugal

We describe 66 ciprofloxacin-nonsusceptible Streptococcus pyogenes isolates recovered from colonized and infected children. The ParC S79A substitution was frequent and associated with the emm6/sequence type 382 (emm6/ST382) lineage. The ParC D83G substitution was detected in two isolates (emm5/ST99 and emm28/ST52 lineages). One isolate (emm89/ST101) had no quinolone resistance-determining region codon substitutions or other resistance mechanisms. Five of 66 isolates were levofloxacin resistant. Although fluoroquinolones are not used in children, they may be putative disseminators of fluoroquinolone-nonsusceptible strains in the community.

Real-time PCR detection of gyrA and parC mutations in Streptococcus pneumoniae

Fluoroquinolone resistance in Streptococcus pneumoniae mainly involves stepwise mutations predominantly in the parC and gyrA genes. We have developed a single-run real-time PCR assay for detection of the four most common mutations in the quinolone resistance-determining regions of these genes. This assay provides a useful tool for both clinical and epidemiological use.

Activity of garenoxacin, an investigational des-F(6)-quinolone, tested against pathogens from community-acquired respiratory tract infections, including those with elevated or resistant-level fluoroquinolone MIC values

Garenoxacin, a novel des-F(6)-quinolone, was tested against 40423 pathogenic isolates associated with community-acquired respiratory tract infections (CA-RTIs). The strains included Streptococcus pneumoniae (18887), Haemophilus influenzae (15555), and Moraxella catarrhalis (5981), each isolated from a significant infection monitored by the SENTRY Antimicrobial Surveillance Program (1999-2005; North America, Latin America, and Europe). All tests were performed by reference broth microdilution methods for garenoxacin and 19 comparison agents. The garenoxacin MIC(90) and percentage (%) of strains inhibited at < or =1 microg/mL (proposed susceptible breakpoint) were S. pneumoniae (0.06 microg/mL, >99.9% susceptible), H. influenzae (< or =0.03 microg/mL, >99.9%), and M. catarrhalis (< or =0.03 microg/mL, 100.0%). The garenoxacin potency versus the pneumococci was 16- to 32-fold greater than levofloxacin or ciprofloxacin and 2-fold superior to moxifloxacin (MIC(90), 0.12 microg/mL). Resistances to other classes of antimicrobials did not adversely influence garenoxacin MIC results. Ciprofloxacin- or levofloxacin-resistant (MIC, > or =4 microg/mL) S. pneumoniae had higher garenoxacin MIC(90) values (1 microg/mL), but 90.6% to 97.5% of strains remained susceptible. Strains of all 3 monitored pathogens with mutations in the quinolone resistance determining region (QRDR) had higher garenoxacin MIC results, with > or =3 to 4 QRDR mutations required to elevate garenoxacin MIC values to > or =2 microg/mL. In conclusion, garenoxacin possesses a potent activity against pneumococci, H. influenzae, and M. catarrhalis strains worldwide, at a level significantly greater than the available tested agents in the fluoroquinolone class (ciprofloxacin, levofloxacin, and moxifloxacin). Only 13 and 4 isolates (0.07% and 0.03%) of S. pneumoniae and H. influenzae, respectively, had a garenoxacin MIC at > or =2 microg/mL, thus, making this new "respiratory antipneumococcal" quinolone an attractive candidate for the therapy of contemporary CA-RTI (bronchitis, pneumonia, and sinusitis).