Molecular epidemiology of penicillin-resistant and ciprofloxacin-resistant Streptococcus pneumoniae in Canada

Molecular analysis of pbp2b in Streptococcus pneumonia isolated from clinical and normal flora samples

Streptococcus pneumoniae is an important bacterial pathogen responsible for respiratory infections, bacteraemia, and meningitis remains an important cause of disease and mortality in infants and younger children around the world, with penicillin being considered the drug of choice for the treatment of infections. However, penicillin-resistant S. pneumonia is now becoming endemic worldwide. In this study, a total of 80 pneumococcal isolates were collected from different clinical sources as well as normal flora. These isolates were subjected to antimicrobial susceptibility testing and MIC determination. The penicillin-binding proteins, pbp2b, were amplified by PCR, and they were sequenced. The genetic relationship of the penicillin-resistant isolates was performed by BOX PCR. Overall, 36 pneumococcal (45 %) isolates were found to be resistant to penicillin with different MICs. The majority of them (80 %) were intermediately resistant with MIC of 0.12-1 µg/ml, whereas 20 % of isolates were penicillin resistant with MICs of >2 µg/ml. The results identified seven groups which were based on the amino acid substitutions of pbp2b. Sequencing analysis revealed that the most prevalent mutation was the substitution of Adenine for Thymine at the position 445 which is next to the second PBP2b-conserved motif (SSN). This study indicates that resistance to penicillin appears to be dependent on specific mutations in pbp2b, and the substitution in S620 → T near to the third PBP2b-conserved motif appears to be important in developing highly antibiotic-resistant isolates. Moreover, there was a positive correlation between the mutations in pbp2b gene and MIC.

Reprint of: Serotyping and antibiotic susceptibility of Streptococcus pneumoniae strains isolated in Algeria from 2001 to 2010

INTRODUCTION

Pneumococcal infections are a major public health problem because of the virulence of this bacterium and its ability to develop resistance.

MATERIAL AND METHOD

Two hundred and ninety-four strains of Streptococcus pneumoniae were isolated from sterile (56.8%) and non-sterile samples (43.2%), from January 2001 to July 2010.

RESULTS

The interpretation of antibiotic susceptibility testing, according to CLSI criteria (M100-S21 2011), yielded a 25.2% overall resistance to penicillin, with 23.5% of strains isolated from CSF (meningitis), and only 1.7% in other samples. Resistance to cefotaxime was 8.1% (including 4.4% at a high level). The most common serotypes were: 14 (19.5%), 23F (9.7%), 6B (9.3%), 19F (5.4%), and serotype 1 (5%). The percentage of these serotypes isolated from normally sterile sites in children under 5 years of age was 31.25% for 14, 10.4% for 23F, 8.3% for 19F, 6.25% for 6B, and 4.2% for serotype 1. The theoretical vaccinal coverage against invasive infections in children under 2 years of age was 61.5%, 69.2%, and 76.9% for the 7-valent, 10-valent, and 13-valent conjugate vaccines, respectively. Penicillin non-susceptible Streptococcus pneumoniae (PNSP) strains accounted for 67.1, 68.6, and 72.8% for each of these three vaccines.

CONCLUSION

There was a variation of serotype rates compared to previous studies. The increase in pneumococcal antibiotic resistance is concerning, particularly for the treatment of pneumococcal infections in children and infants. Pneumococcal vaccination is not compulsory yet in Algeria.

Crystal structure of prephenate dehydrogenase from Streptococcus mutans

Prephenate dehydrogenase (PDH) is a bacterial enzyme that catalyzes conversion of prephenate to 4-hydroxyphenylpyruvate through the oxidative decarboxylation pathway for tyrosine biosynthesis. This enzymatic pathway exists in prokaryotes but is absent in mammals, indicating that it is a potential target for the development of new antibiotics. The crystal structure of PDH from Streptococcus mutans in a complex with NAD(+) shows that the enzyme exists as a homo-dimer, each monomer consisting of two domains, a modified nucleotide binding N-terminal domain and a helical prephenate C-terminal binding domain. The latter is the dimerization domain. A structural comparison of PDHs from mesophilic S. mutans and thermophilic Aquifex aeolicus showed differences in the long loop between β6 and β7, which may be a reason for the high K(m) values of PDH from Streptococcus mutans.

Selection of agyrAMutation and Treatment Failure with Gatifloxacin in a Patient withStreptococcus pneumoniaewith a PreexistingparCMutation

An 81-year-old woman had pneumonia caused by Streptococcus pneumoniae (levofloxacin Etest minimum inhibitory concentration [MIC] 1.5 microg/ml) and was treated with intravenous gatifloxacin 200 mg/day. After 3 days of therapy, repeat sputum cultures were positive for S. pneumoniae, which was resistant to levofloxacin (Etest MIC > 32 microg/ml). The isolate obtained before therapy showed a preexisting parC mutation of aspartic acid-83 to asparagine (Asp83-->Asn), and the isolate obtained during therapy showed an acquired gyrA mutation from serine-81 to phenylalanine (Ser81-->Phe) and a second parC mutation from lysine-137 to Asn (Lys137-->Asn). Both isolates were the same strain, as determined with pulsed-field gel electrophoresis. This case demonstrates the potential for resistance to emerge during 8-methoxy fluoroquinolone therapy for fluoroquinolone-susceptible S. pneumoniae with a preexisting parC mutation. Additional clinical failures with a fluoroquinolone may occur unless these first-step parC mutants can be identified to assist clinicians in selecting appropriate antimicrobial therapy.

Phenotypic and molecular analysis of penicillin-nonsusceptible Streptococcus pneumoniae isolates in Poland

beta-Lactams are the drugs of choice for the treatment of infections caused by the important bacterial pathogen Streptococcus pneumoniae. The recent growth of resistance of this organism to penicillin observed worldwide is of the highest concern. In this study, using 887 surveillance pneumococcal isolates recovered in Poland from 1998 to 2002, we observed the increase in penicillin nonsusceptibility from 8.7% to 20.3%. All of the 109 penicillin-nonsusceptible S. pneumoniae (PNSP) isolates identified, together with 22 archival PNSP isolates from 1995 to 1997, were subsequently analyzed by susceptibility testing, serotyping, profiling of pbp genes, pulsed-field gel electrophoresis, and multilocus sequence typing (MLST). Four predominant serotypes, serotypes 6B, 9V, 14, and 23F, characterized 85.5% of the isolates. MLST revealed the presence of 34 sequence types, 15 of which were novel types. Representatives of seven multiresistant international clones (Spain(23F)-1, Spain(6B)-2, Spain(9V)-3, Taiwan(23F)-15, Poland(23F)-16, Poland(6B)-20, and Sweden(15A)-25) or their closely related variants comprised the majority of the study isolates. The spread of Spain(9V)-3 and its related clone of serotype 14/ST143 has remarkably contributed to the recent increase in penicillin resistance in pneumococci in the country.

Molecular characterization of increasing fluoroquinolone resistance in Streptococcus pneumoniae isolates in Canada, 1997 to 2005

Molecular characterization of fluoroquinolone-resistant Streptococcus pneumoniae in Canada was conducted from 1997 to 2005. Over the course of the study, 205 ciprofloxacin-resistant isolates were evaluated for ParC and GyrA quinolone resistance-determining region (QRDR) substitutions, substitutions in the full genes of ParC, ParE, and GyrA, reserpine sensitivity, and serotype and by pulsed-field gel electrophoresis. Rates of ciprofloxacin resistance of S. pneumoniae increased significantly, from less than 1% in 1997 to 4.2% in 2005. Ciprofloxacin resistance was greatest in people >64 years of age and least in those <16 years of age. Significant increases were also noted in rates of resistance to gatifloxacin, gemifloxacin, levofloxacin, and moxifloxacin, to the current rates of 1.6%, 1.0%, 1.1%, and 1.0%, respectively. The most common genotype observed consisted of QRDR substitutions in GyrA (Ser81Phe) and ParC (Ser79Phe). Substitutions outside the QRDR of GyrA, ParC, and ParE were not associated with fluoroquinolone resistance in this study. Overall, 21% of isolates were reserpine-sensitive and were thus assumed to be efflux positive. The ciprofloxacin-resistant isolates belonged to 35 different serotypes, but 10 (19F, 11A, 23F, 6B, 22F, 12F, 6A, 14, 9V, and 19A) accounted for 72% of all isolates. The majority of the isolates were found to be genetically unrelated by pulsed-field gel electrophoresis. Within the observed clusters, there was considerable genetic heterogeneity with regard to fluoroquinolone resistance mechanisms and serotypes. Continued surveillance and molecular analysis of fluoroquinolone-resistant S. pneumoniae in Canada are essential for appropriate empirical treatment of infections and early detection of novel resistance mechanisms.

Molecular characterisation of Canadian paediatric multidrug-resistant Streptococcus pneumoniae from 1998-2004

Multidrug-resistant (MDR) Streptococcus pneumoniae (i.e. resistant to three different antimicrobial classes) is a global concern. The molecular epidemiology of MDR S. pneumoniae has not been characterised in Canadian paediatric isolates. Paediatric MDR S. pneumoniae were obtained from a national surveillance study. Susceptibility testing was performed by the methods of the Clinical and Laboratory Standards Institute. Phenotypic and genotypic relatedness were assessed by serotyping and pulsed-field gel electrophoresis (PFGE). Penicillin resistance was assessed with polymerase chain reaction (PCR) followed by DNA sequencing of penicillin-binding proteins (PBPs) 1A, 2B and 2X. Macrolide resistance was assessed by PCR-based detection of mef(E) and erm(B). PCR and sequencing of the dihydrofolate reductase (DHFR) gene was performed to assess resistance to trimethoprim/sulphamethoxazole (T/S). Seventy (98.6%) of 71 MDR paediatric isolates were concomitantly resistant to penicillin, erythromycin and T/S. Resistance genes mef(E) (66.2%) or erm(B) (22.5%) or both mef(E) and erm(B) (8.5%) were associated with macrolide resistance, and the prevalence of erm(B) increased significantly (P=0.0001) over time. Penicillin resistance was associated with amino acid substitutions in PBPs 1A, 2B and 2X. Resistance to T/S was associated with amino acid substitutions in the DHFR gene; in particular, Ile100-->Leu was detected in all isolates analysed. PFGE revealed three clusters of isolates that were genetically related and associated with specific serotypes (Taiwan(19F), Spain(23F), Spain(14) and France(9V)), suggesting clonal expansion as the primary means of paediatric MDR S. pneumoniae dissemination in Canada. The heptavalent pneumococcal vaccine Prevnar, currently approved in Canada for use in children < or =2 years of age, provided excellent coverage (90.2%) of paediatric MDR S. pneumoniae. In conclusion, paediatric MDR S. pneumoniae simultaneously resistant to penicillin, erythromycin and T/S are genetically similar and disseminating across Canada. Prevnar provides excellent coverage of paediatric MDR S. pneumoniae.

In vitro antibacterial activity of beta-lactams and non-beta-lactams against Streptococcus pneumoniae isolates from Sydney, Australia

AIMS

This study was undertaken to determine the antimicrobial resistance patterns of strains of Streptococcus pneumoniae from Sydney, Australia, comparing penicillin-susceptible, -intermediate and -resistant isolates.

METHODS

Non-duplicate cultures of S. pneumoniae were collected from 1 January to 31 December 2002 in the three penicillin-susceptibility categories. Minimum inhibitory concentrations (MICs) of 19 antibacterial agents were determined by agar dilution based on the National Committee for Clinical Laboratory Standards (NCCLS) methodology. Overall for 2002, 687 non-duplicate isolates were obtained, of which 190 (28%) were intermediate or resistant to penicillin. From this set, 183 isolates were selected for study: 88 (48%) in the penicillin-susceptible group (MIC <or= 0.06 mg/L), 25 (14%) in the penicillin-intermediate group (MIC 0.125-1.0 mg/L) and 70 (38%) in the penicillin-resistant group (MIC >or= 2.0 mg/L).

RESULTS

Resistance to non-beta-lactams was more common in penicillin-intermediate or -resistant strains. Multidrug resistance (resistance to >or= 2 non-beta-lactams) was found in 3% of penicillin-susceptible, 52% of penicillin-intermediate and 87% of penicillin-resistant isolates. Erythromycin resistance was seen in 22% of the penicillin-susceptible strains but increased significantly to 60% and 89% in the penicillin-intermediate and resistant strains, respectively. Clindamycin, tetracycline and trimethoprim/sulfamethoxazole showed similar diminished activity in penicillin-intermediate and -resistant strains; 64, 84 and 91% of the penicillin-resistant isolates were resistant to clindamycin, tetracycline and to trimethoprim/sulfamethoxazole, respectively. Chloramphenicol resistance was comparatively low level except 19% of the penicillin-resistant strains were resistant. Ciprofloxacin MICs for 14 strains were raised (MICs 4-16 mg/L); three of these were penicillin-susceptible, one penicillin-intermediate and 10 penicillin-resistant. Only one isolate was resistant to moxifloxacin and to gatifloxacin. Resistance to rifampicin, vancomycin, oritavancin, or linezolid was not detected. Twenty-three isolates were intermediate and one resistant to quinupristin/dalfopristin - 22 of these were penicillin resistant.

CONCLUSIONS

Streptococcus pneumoniae isolates from Sydney are commonly resistant to beta-lactams and available non-beta-lactam agents, especially if they are penicillin non-susceptible. Resistance to moxifloxacin and gatifloxacin is still rare, but some isolates were non-susceptible to quinupristin/dalfopristin. It is important to continue to survey resistance patterns to recognise emerging resistances which affect the selection of empirical antimicrobials to treat infections with S. pneumoniae.

Nonmolecular test for detection of low-level resistance to fluoroquinolones in Streptococcus pneumoniae

With respect to pneumococci, there is a need to detect first-step mutants with reduced fluoroquinolone (FQ) susceptibility from which second-step, resistant mutants are likely to be selected in the presence of antipneumococcal FQs. Here, we describe an interpretative disk diffusion test, of which three options are presented, that allows the distinction between first- and second-step mutants. Using five FQ disks (pefloxacin, norfloxacin, levofloxacin, ciprofloxacin, and sparfloxacin, option 1), all known mechanisms of altered FQ susceptibility found in first-step mutants (ParC, ParE, GyrA, or efflux) and in second-step mutants (ParC and GyrA or ParE and GyrA) can be accurately detected, making this option a useful epidemiological tool. Using three FQ disks (pefloxacin, norfloxacin, and levofloxacin, option 2), the most prevalent FQ-resistant mutants, but not the first-step GyrA mutants, can be detected. With only two FQ disks (norfloxacin and levofloxacin) in the third and simplest option, first-step mutants can be distinguished from second-step mutants, however, without differentiation of ParC, ParE, or efflux alterations.

Relative fitness of fluoroquinolone-resistant Streptococcus pneumoniae

Fluoroquinolone resistance in Streptococcus pneumoniae is primarily mediated by point mutations in the quinolone resistance–determining regions of gyrA and parC. Antimicrobial resistance mutations in housekeeping genes often decrease fitness of microorganisms. To investigate the fitness of quinolone-resistant S. pneumoniae (QRSP), the relative growth efficiencies of 2 isogenic QRSP double mutants were compared with that of their fluoroquinolone-susceptible parent, EF3030, by using murine nasopharyngeal colonization and pneumonia models. Strains containing the GyrA: Ser81Phe, ParC: Ser79Phe double mutations, which are frequently seen in clinical QRSP, competed poorly with EF3030 in competitive colonization or competitive lung infections. However, they efficiently produced lung infection even in the absence of EF3030. The strain containing the GyrA: Ser81Phe, ParC: Ser79Tyr double mutations, which is seen more frequently in laboratory-derived QRSP than in clinical QRSP, demonstrated reduced nasal colonization in competitive or noncompetitive lung infections. However, the strain was equally able to cause competitive or noncompetitive lung infections as well as EF3030.

Inhibition of mutation and combating the evolution of antibiotic resistance

The emergence of drug-resistant bacteria poses a serious threat to human health. In the case of several antibiotics, including those of the quinolone and rifamycin classes, bacteria rapidly acquire resistance through mutation of chromosomal genes during therapy. In this work, we show that preventing induction of the SOS response by interfering with the activity of the protease LexA renders pathogenic Escherichia coli unable to evolve resistance in vivo to ciprofloxacin or rifampicin, important quinolone and rifamycin antibiotics. We show in vitro that LexA cleavage is induced during RecBC-mediated repair of ciprofloxacin-mediated DNA damage and that this results in the derepression of the SOS-regulated polymerases Pol II, Pol IV and Pol V, which collaborate to induce resistance-conferring mutations. Our findings indicate that the inhibition of mutation could serve as a novel therapeutic strategy to combat the evolution of antibiotic resistance.

Molecular epidemiology and prevalence of macrolide efflux genes mef(A) and mef(E) in Streptococcus pneumoniae obtained in Canada from 1997 to 2002

One hundred forty M phenotype Streptococcus pneumoniae isolates were evaluated by PCR-restriction fragment length polymorphism, serotyping, and pulsed-field gel electrophoresis. Molecular genotyping revealed that the predominant macrolide resistance mechanism in S. pneumoniae in Canada is mef(E) and resistance dissemination is due to both spread of the genetic element MEGA as well as clonal dissemination of penicillin- and/or macrolide-resistant strains.

Stability of fluoroquinolone resistance in Streptococcus pneumoniae clinical isolates and laboratory-derived mutants

The stability of fluoroquinolone resistance in Streptococcus pneumoniae was evaluated in laboratory-derived mutants and clinical isolates. Isolates with various genotypes and phenotypes were subcultured for 20 days on antibiotic-free media and were monitored by E-tests to identify any alterations in resistance. Fluoroquinolone resistance mechanisms, whether efflux or chromosomally mediated, remained stable in both clinical and laboratory-derived mutants.

Guide to selection of fluoroquinolones in patients with lower respiratory tract infections

Newer fluoroquinolones such as levofloxacin, moxifloxacin, gatifloxacin and gemifloxacin have several attributes that make them excellent choices for the therapy of lower respiratory tract infections. In particular, they have excellent intrinsic activity against Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and the atypical respiratory pathogens. Fluoroquinolones may be used as monotherapy to treat high-risk patients with acute exacerbation of chronic bronchitis, and for patients with community-acquired pneumonia requiring hospitalisation, but not admission to intensive care. Overall, the newer fluoroquinolones often achieve clinical cure rates in > or =90% of these patients. However, rates may be lower in hospital-acquired pneumonia, and this infection should be treated on the basis of anticipated organisms and evaluation of risk factors for specific pathogens such as Pseudomonas aeruginosa. In this setting, an antipseudomonal fluoroquinolone may be used in combination with an antipseudomonalbeta-lactam. Concerns are now being raised about the widespread use, and possibly misuse, of fluoroquinolones and the emergence of resistance among S. pneumoniae, Enterobacteriaceae and P. aeruginosa. A number of pharmacokinetic parameters such as the peak concentration of the antibacterial after a dose (C(max)), and the 24-hour area under the concentration-time curve (AUC24) and their relationship to pharmacodynamic parameters such as the minimum inhibitory and the mutant prevention concentrations (MIC and MPC, respectively) have been proposed to predict the effect of fluoroquinolones on bacterial killing and the emergence of resistance. Higher C(max)/MIC or AUC24/MIC and C(max)/MPC or AUC24/MPC ratios, either as a result of dose administration or the susceptibility of the organism, may lead to a better clinical outcome and decrease the emergence of resistance, respectively. Pharmacokinetic profiles that are optimised to target low-level resistant minor subpopulations of bacteria that often exist in infections may help preserve fluoroquinolones as a class. To this end, optimising the AUC24/MPC or C(max)/MPC ratios is important, particularly against S. pneumoniae, in the setting of lower respiratory tract infections. Agents such as moxifloxacin and gemifloxacin with high ratios against this organism are preferred, and agents such as ciprofloxacin with low ratios should be avoided. For agents such as levofloxacin and gatifloxacin, with intermediate ratios against S. pneumoniae, it may be worthwhile considering alternative dose administration strategies, such as using higher dosages, to eradicate low-level resistant variants. This must, of course, be balanced against the potential of toxicity. Innovative approaches to the use of fluoroquinolones are worth testing in further in vitro experiments as well as in clinical trials.

Molecular Characterization of Clinical Streptococcus pneumoniae Isolates with Reduced Susceptibility to Fluoroquinolones Emerging in Italy

Fifteen Streptococcus pneumoniae clinical isolates with reduced fluoroquinolone susceptibility (defined as a ciprofloxacin MIC of > or = 4 microg/ml), all collected in Italy in 2000-2003, were typed and subjected to extensive molecular characterization to define the contribution of drug target alterations and efflux mechanisms to their resistance. Serotyping and pulsed-field gel electrophoresis analysis indicated substantial genetic unrelatedness among the 15 isolates, suggesting that the new resistance traits arise in multiple indigenous strains rather than through clonal dissemination. Sequencing of the quinolone resistance-determining regions of gyrA, gyrB, parC, and parE demonstrated that point mutations producing single amino acid changes were more frequent in topoisomerase IV (parC mutations in 14 isolates and parE mutations in 13) than in DNA gyrase subunits (gyrA mutations in 7 isolates and no gyrB mutations observed). No isolate displayed a quinolone efflux system susceptible to carbonyl cyanide m-chlorophenylhydrazone; conversely, four-fold or greater MIC reductions in the presence of reserpine were observed in all 15 isolates with ethidium bromide, in 13 with ulifloxacin, in 9 with ciprofloxacin, in 5 with norfloxacin, and in none with five other fluoroquinolones. The effect of efflux pump activity on the level and profile of fluoroquinolone resistance in our strains was minor compared with that of target site modifications. DNA mutations and/or efflux systems other than those established so far might contribute to the fluoroquinolone resistance expressed by our strains. Susceptibility profiles to nonquinolone class antibiotics and resistance-associated phenotypic and genotypic characteristics were also determined and correlated with fluoroquinolone resistance. A unique penicillin-binding protein profile was observed in all five penicillin-resistant isolates, whereas the same PBP profile as S. pneumoniae R6 was exhibited by all six penicillin-susceptible isolates. This is the first attempt to molecularly characterize clinical isolates of S. pneumoniae with reduced susceptibility to fluoroquinolones emerging in Italy.

Genetic relatedness of levofloxacin-nonsusceptible Streptococcus pneumoniae isolates from North America

We characterized 32 levofloxacin-nonsusceptible Streptococcus pneumoniae (LNSP) isolates obtained from a broad geographic region of North America over a 5-year period by using capsular serotypes, antimicrobial susceptibility profiles, BOX-PCR, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). Sixteen international clones identified by the Pneumococcal Molecular Epidemiology Network also were included for comparison. Fifteen serotypes were represented, with serogroups 6, 9, 14, 19, and 23 accounting for 63% of isolates. Among isolates whose quinolone resistance-determining regions were sequenced, all contained gyrA and parC point mutations. Sixty-three percent were penicillin susceptible, and 84% were erythromycin susceptible. BOX-PCR analysis identified 39 different band patterns among 32 LNSP and 16 international clones and grouped 16 isolates, including 2 international clones, into seven unrelated groups of 2 to 4 isolates each. PFGE analysis identified 35 different band patterns among 32 LNSP and 16 international clones and grouped 21 isolates, including 3 international clones, into eight unrelated groups of 2 to 6 isolates each. MLST performed on 10 isolates identified five allelic profiles and separated 9 isolates into four groups of 2 to 3 isolates each. Overall, each typing method indicated that the LNSP were heterogeneous and that resistance to fluoroquinolones was not closely associated with a particular serotype or with coresistance to other antimicrobial classes and suggests that LNSP have likely arisen through independent mutational events as a result of selective pressure. However, seven LNSP were found to be related to three international clones by PFGE.