Prevalence of first-step mutants among levofloxacin-susceptible invasive isolates of Streptococcus pneumoniae in the United States

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.

Fluoroquinolone resistance in Streptococcus pneumoniae isolates in Germany from 2004-2005 to 2014-2015

Streptococcus pneumoniae is a major cause of bacterial pneumonia, sepsis and meningitis worldwide. Prevalence of levofloxacin-resistant S. pneumoniae isolates in Germany and associated mutations in the quinolone resistance determining regions (QRDRs), as well as serotype distribution and multi locus sequence types (MLST) are shown. 21,764 invasive S. pneumoniae isolates from Germany, isolated in the epidemiological seasons from 2004/05 to 2014/15 were analyzed at the German National Reference Centre for Streptococci (GNRCS) for their levofloxacin resistance by micro broth dilution method. All resistant (minimal inhibitory concentration (MIC) ≥8μg/ml) and intermediate (MIC >2μg/ml and <8μg/ml) isolates were selected for the present study. Additionally, 29 susceptible isolates were randomly selected. A total of ninety isolates were tested for their levofloxacin-MIC by Etest, their serotype and sequence type, as well as for point-mutations at the QRDRs in the genes parC, parE, gyrA and gyrB. Twenty-five isolates exhibited levofloxacin MICs <2μg/ml (Etest) and no mutations in the QRDRs. Four isolates with MICs=2μg/ml had one mutation in parC; isolates with MICs >2μg/ml all had one or more mutations in the QRDRs. Four of nine intermediate isolates had a mutation in either parC or gyrA, and four isolates had mutations in both parC and gyrB. One isolate had mutations in both parC and gyrA. All isolates with MICs ≥8μg/ml (52) had mutations in both topoisomerase IV and gyrase. Serotypes associated with levofloxacin resistance shifted from a majority of PCV13 serotypes before the introduction of the PCV13 vaccine towards non-PCV serotypes. Resistant isolates were almost exclusively found among adults (98.1%).

Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data

Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics. With the premise that accumulation of putative resistance-conferring SNPs, potentially in combination with specific resistance genes, precedes full resistance, we retrogressively surveyed the hotspot loci and quantified the number of SNPs and/or genes, which if accumulated would confer full resistance to an otherwise susceptible strain. We name this approach the ‘distance to resistance’. It can be used to identify the creep towards complete antibiotics resistance in bacteria using genome sequencing. This approach serves as a basis for the development of future sequencing-based methods for predicting resistance profiles of bacterial strains in hospital microbiology and public health settings.

Whole Genome Sequencing of 39 Invasive Streptococcus pneumoniae Sequence Type 199 Isolates Revealed Switches from Serotype 19A to 15B

Streptococcus pneumoniae is a major pathogen that causes different invasive pneumococcal diseases (IPD). The pneumococcal polysaccharide capsule is a main virulence factor. More than 94 capsule types have been described, but only a limited number of capsule types accounted for the majority of IPD cases before the introduction of pneumococcal vaccines. After the introduction of the conjugated pneumococcal vaccine PCV7, which covered the seven most frequent serotypes in IPD in the USA, an increase in IPD caused by non-vaccine serotypes was observed, and serotype 19A, which belongs to sequence type (ST) 199, was among the most prevalent STs. After the introduction of the extended vaccine PCV13, which includes serotype 19A, serogroup 15B/C increased in IPD. Therefore, whole genome sequences of 39 isolates of ST199 from Germany (collected between 1998 and 2011) with serotype 19A (n = 24) and serogroup 15B/C (n = 15) were obtained using an Illumina platform and were analysed to identify capsular switches within ST199. Two 19A to 15B/C serotype switch events were identified. Both events occurred before the introduction of PCV7, which indicates that a capsular switch from 19A to 15B among ST199 isolates is not unusual and is not directly linked to the vaccination. The observed serotype replacement appears to be the result of a vacant niche due to the displacement of vaccine serotypes that is now successfully occupied by ST199 clones.

Hospital-based strategies to reduce antibiotic resistance: are they valid in the community setting?

Antimicrobial resistance is an increasing problem worldwide in both the hospital and community settings. Various approaches have been proposed and tested mainly in the hospital environment to reduce this problem; however, few of these have been examined from the perspective of applicability to reversing community-based resistance. It is clear that, in addition to specific antibiotic usage campaigns, a major educational initiative for both prescribers and patients alike is required for the full societal impact of growing antibiotic resistance to be appreciated. This inexorable increase is occurring in the face of a dearth of new antibiotics for community use and even fewer for treating resistant nosocomial gram-negative species. The possible strategies and consequences are discussed.

Prevalence of first-step mutants among levofloxacin-susceptible isolates of Streptococcus pneumoniae in north Lebanon

Resistance of Streptococcus pneumoniae to fluoroquinolones arises by stepwise accumulation of spontaneous point mutations in the quinolone-resistance determining regions (QRDRs). Fluoroquinolones treatment of infections caused by first-step mutants (pre-resistant) can lead to the selection of resistant isolates, resulting in treatment failure. First-step mutants cannot however be reliably detected by routine resistance testing. Levofloxacin has been used as a surrogate marker to predict fluoroquinolone susceptibility in clinical laboratories. By use of a PCR followed by pyrosequencing, we examined 45 levofloxacin-susceptible pneumococcal strains [minimal inhibitory concentration (MIC) < 0.5 μg/ml] for first-step parC and parE mutations in the QRDR: 51.2% of isolates were recovered from pulmonary and nasal secretions, 22.2% from blood, 24.4% from ear and eye discharge, and 2.2% from cerebrospinal fluid. The results showed that three strains (6.6%) had first-step parC (Asp83-Asn) or parE (Asp435-Asn) mutations. This test could be useful for some high-risk patients or in national surveys.

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.

Global fluoroquinolone resistance epidemiology and implictions for clinical use

This paper on the fluoroquinolone resistance epidemiology stratifies the data according to the different prescription patterns by either primary or tertiary caregivers and by indication. Global surveillance studies demonstrate that fluoroquinolone resistance rates increased in the past years in almost all bacterial species except S. pneumoniae and H. influenzae, causing community-acquired respiratory tract infections. However, 10 to 30% of these isolates harbored first-step mutations conferring low level fluoroquinolone resistance. Fluoroquinolone resistance increased in Enterobacteriaceae causing community acquired or healthcare associated urinary tract infections and intraabdominal infections, exceeding 50% in some parts of the world, particularly in Asia. One to two-thirds of Enterobacteriaceae producing extended spectrum β-lactamases were fluoroquinolone resistant too. Furthermore, fluoroquinolones select for methicillin resistance in Staphylococci. Neisseria gonorrhoeae acquired fluoroquinolone resistance rapidly; actual resistance rates are highly variable and can be as high as almost 100%, particularly in Asia, whereas resistance rates in Europe and North America range from <10% in rural areas to >30% in established sexual networks. In general, the continued increase in fluoroquinolone resistance affects patient management and necessitates changes in some guidelines, for example, treatment of urinary tract, intra-abdominal, skin and skin structure infections, and traveller's diarrhea, or even precludes the use in indications like sexually transmitted diseases and enteric fever.

Resistance surveillance studies: a multifaceted problem--the fluoroquinolone example

INTRODUCTION

This review summarizes data on the fluoroquinolone resistance epidemiology published in the previous 5 years.

MATERIALS AND METHODS

The data reviewed are stratified according to the different prescription patterns by either primary- or tertiary-care givers and by indication. Global surveillance studies demonstrate that fluoroquinolone- resistance rates increased in the past several years in almost all bacterial species except Staphylococcus pneumoniae and Haemophilus influenzae causing community-acquired respiratory tract infections (CARTIs), as well as Enterobacteriaceae causing community-acquired urinary tract infections. Geographically and quantitatively varying fluoroquinolone resistance rates were recorded among Gram-positive and Gram-negative pathogens causing healthcare-associated respiratory tract infections. One- to two-thirds of Enterobacteriaceae producing extended-spectrum β-lactamases (ESBLs) were fluoroquinolone resistant too, thus, limiting the fluoroquinolone use in the treatment of community- as well as healthcare-acquired urinary tract and intra-abdominal infections. The remaining ESBL-producing or plasmid-mediated quinolone resistance mechanisms harboring Enterobacteriaceae were low-level quinolone resistant. Furthermore, 10-30 % of H. influenzae and S. pneumoniae causing CARTIs harbored first-step quinolone resistance determining region (QRDR) mutations. These mutants pass susceptibility testing unnoticed and are primed to acquire high-level fluoroquinolone resistance rapidly, thus, putting the patient at risk. The continued increase in fluoroquinolone resistance affects patient management and necessitates changes in some current guidelines for the treatment of intra-abdominal infections or even precludes the use of fluoroquinolones in certain indications like gonorrhea and pelvic inflammatory diseases in those geographic areas in which fluoroquinolone resistance rates and/or ESBL production is high. Fluoroquinolone resistance has been selected among the commensal flora colonizing the gut, nose, oropharynx, and skin, so that horizontal gene transfer between the commensal flora and the offending pathogen as well as inter- and intraspecies recombinations contribute to the emergence and spread of fluoroquinolone resistance among pathogenic streptococci. Although interspecies recombinations are not yet the major cause for the emergence of fluoroquinolone resistance, its existence indicates that a large reservoir of fluoroquinolone resistance exists. Thus, a scenario resembling that of a worldwide spread of β-lactam resistance in pneumococci is conceivable. However, many resistance surveillance studies suffer from inaccuracies like the sampling of a selected patient population, restricted geographical sampling, and undefined requirements of the user, so that the results are biased. The number of national centers is most often limited with one to two participating laboratories, so that such studies are point prevalence but not surveillance studies. Selected samples are analyzed predominantly as either hospitalized patients or patients at risk or those in whom therapy failed are sampled; however, fluoroquinolones are most frequently prescribed by the general practitioner. Selected sampling results in a significant over-estimation of fluoroquinolone resistance in outpatients. Furthermore, the requirements of the users are often not met; the prescribing physician, the microbiologist, the infection control specialist, public health and regulatory authorities, and the pharmaceutical industry have diverse interests, which, however, are not addressed by different designs of a surveillance study. Tools should be developed to provide customer-specific datasets.

CONCLUSION

Consequently, most surveillance studies suffer from well recognized but uncorrected biases or inaccuracies. Nevertheless, they provide important information that allows the identification of trends in pathogen incidence and antimicrobial resistance.

The use of systemic and topical fluoroquinolones

Appropriate prescribing practices for fluoroquinolones are essential as evolving resistance patterns are considered, additional treatment indications are identified, and the toxicity profile of fluoroquinolones in children becomes better defined. Earlier recommendations for systemic therapy remain; expanded uses of fluoroquinolones for the treatment of certain infections are outlined in this report. Although fluoroquinolones are reasonably safe in children, clinicians should be aware of the specific adverse reactions. Use of fluoroquinolones in children should continue to be limited to treatment of infections for which no safe and effective alternative exists.

The newer fluoroquinolones

Clinicians have enthusiastically used fluoroquinolones owing to their good safety profile and wide range of indications. This article reviews fluoroquinolone pharmacology, pharmacodynamic principles, and fluoroquinolone resistance mechanisms, highlighting recent trends in the epidemiology of fluoroquinolone resistance among gram-negative organisms and Streptococcus pneumonia. Important fluoroquinolone safety concerns are discussed, along with indications for the most commonly used fluoroquinolones--ciprofloxacin, levofloxacin, and moxifloxacin.

The newer fluoroquinolones

Clinicians have enthusiastically used fluoroquinolones owing to their good safety profile and wide range of indications. This article reviews fluoroquinolone pharmacology, pharmacodynamic principles, and fluoroquinolone resistance mechanisms, highlighting recent trends in the epidemiology of fluoroquinolone resistance among gram-negative organisms and Streptococcus pneumonia. Important fluoroquinolone safety concerns are discussed, along with indications for the most commonly used fluoroquinolones-ciprofloxacin, levofloxacin, and moxifloxacin.

Multidrug-resistant Streptococcus pneumoniae infections: current and future therapeutic options

Antibacterial resistance in Streptococcus pneumoniae is increasing worldwide, affecting principally beta-lactams and macrolides (prevalence ranging between approximately 1% and 90% depending on the geographical area). Fluoroquinolone resistance has also started to emerge in countries with high level of antibacterial resistance and consumption. Of more concern, 40% of pneumococci display multi-drug resistant phenotypes, again with highly variable prevalence among countries. Infections caused by resistant pneumococci can still be treated using first-line antibacterials (beta-lactams), provided the dosage is optimised to cover less susceptible strains. Macrolides can no longer be used as monotherapy, but are combined with beta-lactams to cover intracellular bacteria. Ketolides could be an alternative, but toxicity issues have recently restricted the use of telithromycin in the US. The so-called respiratory fluoroquinolones offer the advantages of easy administration and a spectrum covering extracellular and intracellular pathogens. However, their broad spectrum raises questions regarding the global risk of resistance selection and their safety profile is far from optimal for wide use in the community. For multi-drug resistant pneumococci, ketolides and fluoroquinolones could be considered. A large number of drugs with activity against these multi-drug resistant strains (cephalosporins, carbapenems, glycopeptides, lipopeptides, ketolides, lincosamides, oxazolidinones, glycylcyclines, quinolones, deformylase inhibitors) are currently in development. Most of them are only new derivatives in existing classes, with improved intrinsic activity or lower susceptibility to resistance mechanisms. Except for the new fluoroquinolones, these agents are also primarily targeted towards methicillin-resistant Staphylococcus aureus infections; therefore, demonstration of their clinical efficacy in the management of pneumococcal infections is still awaited.

[Will we still have antibiotics tomorrow?]

Since the discovery of antibiotics, it has been generally believed that these antimicrobials are capable of curing almost all bacterial infections. More recently, the appearance of increasing resistance to antibiotics and the emergence of multiresistant microorganisms have given rise to growing concern among physicians, and that concern has now started to filter through to society in general. The problem is further aggravated by a situation that not many people are currently aware of, that is, the limited prospects for future development of new antibiotics in the short to medium term. Appropriate use of available antibiotics based on a thorough understanding of their in vivo activity and the emergence of new forms of administration, such as inhalers, may help to alleviate the problem.

Longitudinally tracking fluoroquinolone resistance and its determinants in penicillin-susceptible and -nonsusceptible Streptococcus pneumoniae isolates in Hong Kong, 2000 to 2005

Of 1,388 Streptococcus pneumoniae isolates collected from 2000 to 2005, 10.5% had a ciprofloxacin MIC of >/=4.0 mug/ml and 1.6% (range, 0.8% to 4.3% per year) had a levofloxacin MIC of >/=4.0 mug/ml. Molecular characterization indicated that fluoroquinolone resistance occurred independently in our prevalent Spain(23F)-1 clone, expressing serotypes 23F, 19F, and 14. Rates of resistance to levofloxacin in S. pneumoniae have remained stable at a Hong Kong hospital.

Fitness costs of fluoroquinolone resistance in Streptococcus pneumoniae

The fitness cost of the genes responsible for resistance to fluoroquinolones in clinical isolates of Streptococcus pneumoniae were estimated in vitro in a common genetic background. Naturally occurring parC, parE, and gyrA loci containing mutations in the quinolone-resistance-determining regions were introduced by transformation into S. pneumoniae strain R6 individually and in combinations. The fitness of these transformants was estimated by pairwise competition experiments with a common R6 strain. On average, single par and gyr mutants responsible for low-level MIC resistance (first-step resistance) impose a fitness burden of approximately 8%. Some of these mutants engender no measurable cost, while one, a parE mutant, reduces the fitness of these bacteria by more than 40%. Most interestingly, the addition of the second par or gyr mutations required for clinically significant, high-MIC fluoroquinolone resistance does not increase the fitness burden imposed by these single genes and can even reduce it. We discuss the implications of these results for the epidemiology of fluoroquinolone resistance and the evolution of acquired resistance in treated patients.