Molecular characterization of penicillin-resistant Streptococcus pneumoniae isolates causing respiratory disease in the United States

The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci

Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn916-type and Tn1207.1-type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking homologous arms. Phylodynamic analysis of the most commonly sampled Tn1207.1-type insertion in PMEN9, originating from a commensal and disrupting a competence gene, suggested its expansion across Germany was driven by a high ratio of macrolide-to-β-lactam consumption. Hence, selection from antibiotic consumption was sufficient for these atypically large recombinations to overcome species boundaries across the pneumococcal chromosome.

Bayesian inference of ancestral dates on bacterial phylogenetic trees

The sequencing and comparative analysis of a collection of bacterial genomes from a single species or lineage of interest can lead to key insights into its evolution, ecology or epidemiology. The tool of choice for such a study is often to build a phylogenetic tree, and more specifically when possible a dated phylogeny, in which the dates of all common ancestors are estimated. Here, we propose a new Bayesian methodology to construct dated phylogenies which is specifically designed for bacterial genomics. Unlike previous Bayesian methods aimed at building dated phylogenies, we consider that the phylogenetic relationships between the genomes have been previously evaluated using a standard phylogenetic method, which makes our methodology much faster and scalable. This two-step approach also allows us to directly exploit existing phylogenetic methods that detect bacterial recombination, and therefore to account for the effect of recombination in the construction of a dated phylogeny. We analysed many simulated datasets in order to benchmark the performance of our approach in a wide range of situations. Furthermore, we present applications to three different real datasets from recent bacterial genomic studies. Our methodology is implemented in a R package called BactDating which is freely available for download at https://github.com/xavierdidelot/BactDating.

High-Level Macrolide Resistance Due to the Mega Element [mef(E)/mel] in Streptococcus pneumoniae

Transferable genetic elements conferring macrolide resistance in Streptococcus pneumoniae can encode the efflux pump and ribosomal protection protein, mef(E)/mel, in an operon of the macrolide efflux genetic assembly (Mega) element- or induce ribosomal methylation through a methyltransferase encoded by erm(B). During the past 30 years, strains that contain Mega or erm(B) or both elements on Tn2010 and other Tn916-like composite mobile genetic elements have emerged and expanded globally. In this study, we identify and define pneumococcal isolates with unusually high-level macrolide resistance (MICs > 16 μg/ml) due to the presence of the Mega element [mef(E)/mel] alone. High-level resistance due to mef(E)/mel was associated with at least two specific genomic insertions of the Mega element, designated Mega-2.IVa and Mega-2.IVc. Genome analyses revealed that these strains do not possess erm(B) or known ribosomal mutations. Deletion of mef(E)/mel in these isolates eliminated macrolide resistance. We also found that Mef(E) and Mel of Tn2010-containing pneumococci were functional but the high-level of macrolide resistance was due to Erm(B). Using in vitro competition experiments in the presence of macrolides, high-level macrolide-resistant S. pneumoniae conferred by either Mega-2.IVa or erm(B), had a growth fitness advantage over the lower-level, mef(E)/mel-mediated macrolide-resistant S. pneumoniae phenotypes. These data indicate the ability of S. pneumoniae to generate high-level macrolide resistance by macrolide efflux/ribosomal protection [Mef(E)/Mel] and that high-level resistance regardless of mechanism provides a fitness advantage in the presence of macrolides.

Puzzling Over the Pneumococcal Pangenome

The Gram positive bacterium Streptococcus pneumoniae (pneumococcus) is a major human pathogen. It is a common colonizer of the human host, and in the nasopharynx, sinus, and middle ear it survives as a biofilm. This mode of growth is optimal for multi-strain colonization and genetic exchange. Over the last decades, the far-reaching use of antibiotics and the widespread implementation of pneumococcal multivalent conjugate vaccines have posed considerable selective pressure on pneumococci. This scenario provides an exceptional opportunity to study the evolution of the pangenome of a clinically important bacterium, and has the potential to serve as a case study for other species. The goal of this review is to highlight key findings in the studies of pneumococcal genomic diversity and plasticity.

A Population-Based Assessment of the Impact of 7- and 13-Valent Pneumococcal Conjugate Vaccines on Macrolide-Resistant Invasive Pneumococcal Disease: Emergence and Decline of Streptococcus pneumoniae Serotype 19A (CC320) With Dual Macrolide Resistance Mechanisms

Background

Macrolide efflux encoded by mef(E)/mel and ribosomal methylation encoded by erm(B) confer most macrolide resistance in Streptococcus pneumoniae. Introduction of the heptavalent pneumococcal conjugate vaccine (PCV7) in 2000 reduced macrolide-resistant invasive pneumococcal disease (MR-IPD) due to PCV7 serotypes (6B, 9V, 14, 19F, and 23F).

Methods

In this study, the impact of PCV7 and PCV13 on MR-IPD was prospectively assessed. A 20-year study of IPD performed in metropolitan Atlanta, Georgia, using active, population-based surveillance formed the basis for this study. Genetic determinants of macrolide resistance were evaluated using established techniques.

Results

During the decade of PCV7 use (2000-2009), MR-IPD decreased rapidly until 2002 and subsequently stabilized until the introduction of PCV13 in 2010 when MR-IPD incidence decreased further from 3.71 to 2.45/100000 population. In 2003, serotype 19A CC320 isolates containing both mef(E)/mel and erm(B) were observed and rapidly expanded in 2005-2009, peaking in 2010 (incidence 1.38/100000 population), accounting for 36.1% of MR-IPD and 11.7% of all IPD isolates. Following PCV13 introduction, dual macrolide-resistant IPD decreased 74.1% (incidence 0.32/100000 in 2013). However, other macrolide-resistant serotypes (eg, 15A and 35B) not currently represented in PCV formulations increased modestly.

Conclusions

The selective pressures of widespread macrolide use and PCV7 and PCV13 introductions on S. pneumoniae were associated with changes in macrolide resistance and the molecular basis over time in our population. Durable surveillance and programs that emphasize the judicious use of antibiotics need to continue to be a focus of public health strategies directed at S. pneumoniae.

Promiscuous signaling by a regulatory system unique to the pandemic PMEN1 pneumococcal lineage

Streptococcus pneumoniae (pneumococcus) is a leading cause of death and disease in children and elderly. Genetic variability among isolates from this species is high. These differences, often the product of gene loss or gene acquisition via horizontal gene transfer, can endow strains with new molecular pathways, diverse phenotypes, and ecological advantages. PMEN1 is a widespread and multidrug-resistant pneumococcal lineage. Using comparative genomics we have determined that a regulator-peptide signal transduction system, TprA2/PhrA2, was acquired by a PMEN1 ancestor and is encoded by the vast majority of strains in this lineage. We show that TprA2 is a negative regulator of a PMEN1-specific gene encoding a lanthionine-containing peptide (lcpA). The activity of TprA2 is modulated by its cognate peptide, PhrA2. Expression of phrA2 is density-dependent and its C-terminus relieves TprA2-mediated inhibition leading to expression of lcpA. In the pneumococcal mouse model with intranasal inoculation, TprA2 had no effect on nasopharyngeal colonization but was associated with decreased lung disease via its control of lcpA levels. Furthermore, the TprA2/PhrA2 system has integrated into the pneumococcal regulatory circuitry, as PhrA2 activates TprA/PhrA, a second regulator-peptide signal transduction system widespread among pneumococci. Extracellular PhrA2 can release TprA-mediated inhibition, activating expression of TprA-repressed genes in both PMEN1 cells as well as another pneumococcal lineage. Acquisition of TprA2/PhrA2 has provided PMEN1 isolates with a mechanism to promote commensalism over dissemination and control inter-strain gene regulation.

Streptococcus pneumoniae (pneumococcus), an important human pathogen, exhibits a dual lifestyle featuring asymptomatic colonization of the host on the one hand as well as infliction of severe local and systemic disease on the other. In pneumococcal strains, differences in gene possession often lead to varied phenotypic outcomes. Epidemiologically, pandemic strains of the PMEN1 lineage show high prevalence in disease as well as carriage, posing an interesting question on the composition and function of the genomic toolkit that leads to their widespread success. Here, we characterize TprA2/PhrA2 sensory system, a genomic region acquired exclusively by the PMEN1 strains. The system consists of a regulator-peptide pair that was horizontally acquired into PMEN1 along with its regulatory circuitry. The regulatory peptide PhrA2 is receptive to cell density of PMEN1 cells and is an example of elegant communication signaling between bacterial cells. The regulatory influence of PhrA2 extends beyond PMEN1 cells such that it controls genes of a widespread signaling system and virulence regulon in non-PMEN1 strains. This work contributes to the knowledge of peptide-communication signals in pneumococcus and further adds a novel mechanism by which an ecologically successful linage may modify the transcriptomic and functional landscape of a multi-strain pneumococcal community.

Macrolide Resistance in Streptococcus pneumoniae

Streptococcus pneumoniae is a common commensal and an opportunistic pathogen. Suspected pneumococcal upper respiratory infections and pneumonia are often treated with macrolide antibiotics. Macrolides are bacteriostatic antibiotics and inhibit protein synthesis by binding to the 50S ribosomal subunit. The widespread use of macrolides is associated with increased macrolide resistance in S. pneumoniae, and the treatment of pneumococcal infections with macrolides may be associated with clinical failures. In S. pneumoniae, macrolide resistance is due to ribosomal dimethylation by an enzyme encoded by erm(B), efflux by a two-component efflux pump encoded by mef (E)/mel(msr(D)) and, less commonly, mutations of the ribosomal target site of macrolides. A wide array of genetic elements have emerged that facilitate macrolide resistance in S. pneumoniae; for example erm(B) is found on Tn917, while the mef (E)/mel operon is carried on the 5.4- or 5.5-kb Mega element. The macrolide resistance determinants, erm(B) and mef (E)/mel, are also found on large composite Tn916-like elements most notably Tn6002, Tn2009, and Tn2010. Introductions of 7-valent and 13-valent pneumococcal conjugate vaccines (PCV-7 and PCV-13) have decreased the incidence of macrolide-resistant invasive pneumococcal disease, but serotype replacement and emergence of macrolide resistance remain an important concern.

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.

Characterization of a Multipeptide Lantibiotic Locus in Streptococcus pneumoniae

Bacterial communities are established through a combination of cooperative and antagonistic interactions between the inhabitants. Competitive interactions often involve the production of antimicrobial substances, including bacteriocins, which are small antimicrobial peptides that target other community members. Despite the nearly ubiquitous presence of bacteriocin-encoding loci, inhibitory activity has been attributed to only a small fraction of gene clusters. In this study, we characterized a novel locus (the pld locus) in the pathogen Streptococcus pneumoniae that drives the production of a bacteriocin called pneumolancidin, which has broad antimicrobial activity. The locus encodes an unusual tandem array of four inhibitory peptides, three of which are absolutely required for antibacterial activity. The three peptide sequences are similar but appear to play distinct roles in regulation and inhibition. A modification enzyme typically found in loci encoding a class of highly modified bacteriocins called lantibiotics was required for inhibitory activity. The production of pneumolancidin is controlled by a two-component regulatory system that is activated by the accumulation of modified peptides. The locus is located on a mobile element that has been found in many pneumococcal lineages, although not all elements carry the pld genes. Intriguingly, a minimal region containing only the genes required for pneumolancidin immunity was found in several Streptococcus mitis strains. The pneumolancidin-producing strain can inhibit nearly all pneumococci tested to date and provided a competitive advantage in vivo. These peptides not only represent a unique strategy for bacterial competition but also are an important resource to guide the development of new antimicrobials.

IMPORTANCE

Successful colonization of a polymicrobial host surface is a prerequisite for the subsequent development of disease for many bacterial pathogens. Bacterial factors that directly inhibit the growth of neighbors may provide an advantage during colonization if the inhibition of competitors outweighs the energy for production. In this work, we found that production of a potent antimicrobial called pneumolancidin conferred a competitive advantage to the pathogen Streptococcus pneumoniae. S. pneumoniae secreting pneumolancidin inhibits a wide array of Gram-positive organisms, including all but one tested pneumococcal strain. The pneumolancidin genetic locus is of particular interest because it encodes three similar modified peptides (lantibiotics), each of which has a distinct role in the function of the locus. Lantibiotics represent a relatively untapped resource for the development of clinically useful antibiotics which are desperately needed. The broad inhibitory activity of pneumolancidin makes it an ideal candidate for further characterization and development.

Community-acquired pneumonia: An overview

Community-acquired pneumonia is still a significant cause of morbidity and mortality and is often misdiagnosed and inappropriately treated. Although it can be caused by a wide variety of micro-organisms, the pneumococcus, atypicals, such as Mycoplasma pneumoniae and Chlamydophila pneumoniae,Staphylococcus aureus and certain Gram-negative rods are the usual pathogens encountered. The site-of-care decision is critical in determining the site and type of care as well as the extent of diagnostic workup. Antimicrobial therapy should be started as soon as possible particularly in those requiring admission to hospital, but typically the physician does not know with any degree of certainty the identity of the etiologic pathogen. A number of national guidelines have been published to help the physician with this choice. The initial drug(s) can be modified if necessary if the pathogen and its antimicrobial susceptibility pattern becomes known. Adjunctive therapy such as pressors and fluid replacement are of value and macrolides appear to help as well, likely secondary to their immunomodulatory effects. Recent data also suggest a role for steroids.

Natural transformation and genome evolution in Streptococcus pneumoniae

Streptococcus pneumoniae is a frequent colonizer of the human nasopharynx that has the potential to cause severe infections such as pneumonia, bacteremia and meningitis. Despite considerable efforts to reduce the burden of pneumococcal disease, it continues to be a major public health problem. After the Second World War, antimicrobial therapy was introduced to fight pneumococcal infections, followed by the first effective vaccines more than half a century later. These clinical interventions generated a selection pressure that drove the evolution of vaccine-escape mutants and strains that were highly resistant against antibiotics. The remarkable ability of S. pneumoniae to acquire drug resistance and evade vaccine pressure is due to its recombination-mediated genetic plasticity. S. pneumoniae is competent for natural genetic transformation, a property that enables the pneumococcus to acquire new traits by taking up naked DNA from the environment and incorporating it into its genome through homologous recombination. In the present paper, we review current knowledge on pneumococcal transformation, and discuss how the pneumococcus uses this mechanism to adapt and survive under adverse and fluctuating conditions.

Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape

The multidrug-resistant Streptococcus pneumoniae Taiwan(19F)-14, or PMEN14, clone was first observed with a 19F serotype, which is targeted by the heptavalent polysaccharide conjugate vaccine (PCV7). However, "vaccine escape" PMEN14 isolates with a 19A serotype became an increasingly important cause of disease post-PCV7. Whole genome sequencing was used to characterize the recent evolution of 173 pneumococci of, or related to, PMEN14. This suggested that PMEN14 is a single lineage that originated in the late 1980s in parallel with the acquisition of multiple resistances by close relatives. One of the four detected serotype switches to 19A generated representatives of the sequence type (ST) 320 isolates that have been highly successful post-PCV7. A second produced an ST236 19A genotype with reduced resistance to β-lactams owing to alteration of pbp1a and pbp2x sequences through the same recombination that caused the change in serotype. A third, which generated a mosaic capsule biosynthesis locus, resulted in serotype 19A ST271 isolates. The rapid diversification through homologous recombination seen in the global collection was similarly observed in the absence of vaccination in a set of isolates from the Maela refugee camp in Thailand, a collection that also allowed variation to be observed within carriage through longitudinal sampling. This suggests that some pneumococcal genotypes generate a pool of standing variation that is sufficiently extensive to result in "soft" selective sweeps: The emergence of multiple mutants in parallel upon a change in selection pressure, such as vaccine introduction. The subsequent competition between these mutants makes this phenomenon difficult to detect without deep sampling of individual lineages.

The majority of a collection of U.S. endocarditis Enterococcus faecalis isolates obtained from 1974 to 2004 lack capsular genes and belong to diverse, non-hospital-associated lineages

Eighty-one endocarditis-derived Enterococcus faecalis isolates that were collected from individual patients in the United States between 1974 and 2004 were sequence typed and analyzed for the presence of various genes, including some previously associated with virulence. Overall, using our previously described trilocus sequence typing (TLST), 44 different sequence types (STs) were found within this collection; 26 isolates were singletons (a unique TLST sequence type [ST(T)]), some ST(T)s contained multiple isolates (up to 6 isolates), and 16% of the isolates (13 isolates) could be grouped by additional sequence typing into clonal cluster 21 (CC21). Of note, only four isolates (7%) of the 56 whose multilocus sequence types were determined were found to belong to one of the previously described hospital-associated clonal clusters CC2 and CC9, and only 15% and 37% of all isolates had high-level resistance to gentamicin and streptomycin, respectively, including 10% that were resistant to both. We also found that 64% of the isolates lacked the genes for production of capsule polysaccharide, which has been proposed to enhance the pathogenic potential of the hospital-associated clonal clusters. In summary, while our collection is not a random sample of cases of E. faecalis endocarditis, these results indicate that nonencapsulated strains belonging to non-hospital-associated lineages were predominant among endocarditis E. faecalis isolates recovered during this time period.

Future Trends in Antimicrobial Chemotherapy: Expert Opinion on the 43rdICAAC

The current document bestows an expert synopsis of key new information presented at the 43rd Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) meeting in 2003. Data is presented on the socio-political aspects of and policies on antimicrobial prescribing, novel mechanisms of resistance in Streptococcus pneumoniae, and current epidemiological trends in global resistance. Novel information on new (and existing) antimicrobial agents--new penicillins, cephalosporins, monobactams and oxipenem inhibitors, ketolides, glycopeptides, fluoroquinolones (and hybrids), peptides, daptomycin, aminomethylcyclines, glycylcyclines, and newer formulations of agents such as amoxycillin-clavulanate--provides renewed hope that resistant pathogens can be controlled through use of more potent agents. Improved strategies for the use of existing antimicrobial agents, such as the use of high-dose regimens, short-course therapy, also may delay or reduce the development of resistance and preserve the value of our antibiotic armamentarium.

The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success

BACKGROUND

Streptococcus pneumoniae, also called the pneumococcus, is a major bacterial pathogen. Since its introduction in the 1940s, penicillin has been the primary treatment for pneumococcal diseases. Penicillin resistance rapidly increased among pneumococci over the past 30 years, and one particular multidrug-resistant clone, PMEN1, became highly prevalent globally. We studied a collection of 426 pneumococci isolated between 1937 and 2007 to better understand the evolution of penicillin resistance within this species.

RESULTS

We discovered that one of the earliest known penicillin-nonsusceptible pneumococci, recovered in 1967 from Australia, was the likely ancestor of PMEN1, since approximately 95% of coding sequences identified within its genome were highly similar to those of PMEN1. The regions of the PMEN1 genome that differed from the ancestor contained genes associated with antibiotic resistance, transmission and virulence. We also revealed that PMEN1 was uniquely promiscuous with its DNA, donating penicillin-resistance genes and sometimes many other genes associated with antibiotic resistance, virulence and cell adherence to many genotypically diverse pneumococci. In particular, we describe two strains in which up to 10% of the PMEN1 genome was acquired in multiple fragments, some as long as 32 kb, distributed around the recipient genomes. This type of directional genetic promiscuity from a single clone to numerous unrelated clones has, to our knowledge, never before been described.

CONCLUSIONS

These findings suggest that PMEN1 is a paradigm of genetic success both through its epidemiology and promiscuity. These findings also challenge the existing views about horizontal gene transfer among pneumococci.

Genotype replacement within serotype 23FStreptococcus pneumoniaein Beijing, China: characterization of serotype 23F

We investigated the genetic structure of 99 isolates of serotype 23FStreptococcus pneumoniaefrom children with acute respiratory infections collected over two periods from 1997 to 2006, and 2010. All isolates were susceptible to vancomycin and amoxicillin–clavulanic acid; 97 were resistant to erythromycin, 95 of which carried theermBgene and two carried bothmefA/EandermBgenes. Multidrug resistance to three or more classes of antibiotics was exhibited by 90 isolates. Sequence types ST342 and ST81 were the most frequent in 1997–2006 and 2010, respectively. All CC81 isolates were non-susceptible to β-lactam antibiotics and had higher minimum inhibitory concentration values for penicillin than other clone complexes and sequence types. The increased β-lactam antibiotic resistance may have resulted from the replacement of multidrug-resistant clones related to ST81. Long-term studies onS. pneumoniaeserotype 23F, especially the ST81 clone, should be conducted to better understand the epidemiological picture of this pathogen in China.

Comparison of Clarithromycin and Amoxicillin/Clavulanic Acid for Community-Acquired Pneumonia in an Era of Drug-Resistant Streptococcus pneumoniae

OBJECTIVE

To compare the safety and efficacy of clarithromycin and amoxicillin/clavulanic acid in patients with community-acquired pneumonia due to penicillin-resistant and/or macrolide-resistant Streptococcus pneumoniae, by selecting clinical investigators who practice in study populations from geographic areas in which a high incidence of resistant strains is reported by surveillance.

DESIGN AND SETTING

Prospective, randomised, investigator-blinded, multicentre study conducted in 45 sites in primary-care and referral centre settings.

PATIENTS AND INTERVENTIONS

327 ambulatory patients diagnosed with radio-graphically confirmed community-acquired pneumonia administered clarithromycin 500mg immediate-release or amoxicillin/clavulanic acid 875mg/125mg twice daily for 7 days.

MAIN OUTCOME MEASURES AND RESULTS

Similarly high clinical cure rates were observed among evaluable patients in both treatment groups at the test-of-cure visit (28-35 days post-treatment): 92% (114/124) for clarithromycin and 91% (117/129) for amoxicillin/clavulanic acid. Of 85 S. pneumoniae strains isolated pretreatment, four (5%) were classified as resistant to macrolides (one mefA, two ermB, and one ermB + mefA) and eight (9%) had reduced susceptibility to penicillin. The overall eradication rate for pathogens isolated from bacteriologically and clinically evaluable patients was 91% for clarithromycin and 93% for amoxicillin/clavulanic acid, and 89% and 92%, respectively, for S. pneumoniae strains. The rates of resolution and/or improvement in clinical signs and symptoms and radiological improvement were similar with clarithromycin to those with amoxicillin/clavulanic acid, as was overall incidence of adverse events.

CONCLUSION

A 7-day course of clarithromycin immediate-release was similar to amoxicillin/clavulanic acid based on high rates (>90%) of clinical cure, radiological improvement and pathogen eradication among ambulatory-care patients with community-acquired pneumonia. As the resistance rate at baseline was low, no conclusion could be made about clarithromycin's efficacy for infections caused by macrolide-resistant S. pneumoniae. Both treatments were well tolerated.

An extended multi-locus molecular typing schema for Streptococcus pneumoniae demonstrates that a limited number of capsular switch events is responsible for serotype heterogeneity of closely related strains from different countries

Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide. Pneumococcal strains are classified according to their capsular serotype and through a Multi-Locus Sequence Typing schema (MLST) based on the sequencing of seven housekeeping genes. However, strains with a defined allelic profile (Sequence Type, ST) can have different serotypes, suggesting that the micro-evolution of the MLST lineages leads to a considerable degree of phenotypic variability. To better investigate the genetic diversity within these lineages, we set-up and then validated an extended molecular typing schema (96-MLST) based on the sequencing of ninety-six genomic loci. 96-MLST loci were designed within core-genes in a collection of 39 complete genomes of S. pneumoniae. None of the capsular genes was included in the schema. When tested on a collection of 69 isolates, 96-MLST was able to partition strains with the same ST and diverse serotypes into groups that were homogenous for capsular serotype, improving our understanding of the evolution of epidemiologically relevant lineages. Phylogenetic sequence analysis showed that the capsular heterogeneity of three STs that were sampled more extensively could be traced back to a limited number of capsular switch events, indicating that changes of serotype occur occasionally during the short term expansion of clones. Moreover, a geographical structure of ST156 was identified, suggesting that the resolution guaranteed by this method is sufficient for phylogeographic studies. In conclusion, we showed that an extended typing schema was able to characterize the expansion of individual lineages in a complex species such as S. pneumoniae.

International pneumococcal clones match or exceed the fitness of other strains despite the accumulation of antibiotic resistance

A few international pneumococcal clones dominate the population of antibiotic-resistant pneumococci. Despite the scientific paradigm that a loss in fitness is the price for acquisition of resistance, these clones spread successfully. One hundred fifty-four isolates from adult patients with community-acquired pneumonia (CAP) were analyzed. Thirty percent showed a close relationship to international clones and had fitness equal to or exceeding that of other strains (P = 0.015); these factors may result in the endurance of these strains despite a reduction of antibiotic usage.

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.

Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81

Streptococcus pneumoniae is a human commensal and pathogen able to cause a variety of diseases that annually result in over a million deaths worldwide. The S. pneumoniae(Spain23F) sequence type 81 lineage was among the first recognized pandemic clones and was responsible for almost 40% of penicillin-resistant pneumococcal infections in the United States in the late 1990s. Analysis of the chromosome sequence of a representative strain, and comparison with other available genomes, indicates roles for integrative and conjugative elements in the evolution of pneumococci and, more particularly, the emergence of the multidrug-resistant Spain 23F ST81 lineage. A number of recently acquired loci within the chromosome appear to encode proteins involved in the production of, or immunity to, antimicrobial compounds, which may contribute to the proficiency of this strain at nasopharyngeal colonization. However, further sequencing of other pandemic clones will be required to establish whether there are any general attributes shared by these strains that are responsible for their international success.

A new serotype 14 variant of the pneumococcal Spain9V-3 international clone detected in the central region of Argentina

The penicillin-resistant Spain(9V)-3 clone of Streptococcus pneumoniae is widespread and presents different serotype variants originating from recombination of the capsular genes. In this work, the genetic relatedness of 29 invasive pneumococci isolated from the central region of Argentina (Cordoba, Buenos Aires, Santa Fe and La Pampa provinces) was assessed by multilocus sequence typing (MLST). All of the penicillin-non-susceptible isolates studied (21/29) belonged to a serotype 14 variant of the Spain(9V)-3 clone. This clone was predominant, suggesting that it was responsible for the penicillin resistance spread in this region. Interestingly, this serotype 14 variant (named Cordoba S14V) could be differentiated from the European one by its pbp1a gene, suggesting a different recombinational replacement of the capsular genes. The putative recombination sites were analysed, resulting in the proximal crossover point being clearly localized in the spr0309 gene, with the distal site restricted to the recU gene, confirming a different recombination event. Analysis of the dexB, cpsB, aliA and pbp1a genes from these strains showed a high similarity with the corresponding genes of the Spain(14)-5 clone, suggesting that the capsular genes were provided by this international clone. Analysis of the genetic polymorphisms of the pbp1a (nt 1473-1922) and spr0309 (nt 1-790) genes is proposed as an epidemiological tool to help recognize the Cordoba S14V of the Spain(9V)-3 clone. On the other hand, BOX-repeat-based PCR and MLST analyses of serotype 14 strains revealed a divergent epidemiology of the Cordoba S14V, suggesting a non-recent dissemination in the paediatric population. It is suggested that this molecular epidemiology work will be a reference for monitoring the evolution of S14Vs of Spain(9V)-3, the emergence of new clones and the impact of pneumococcal vaccination programmes in Argentina.

Mechanisms of macrolide resistance among Streptococcus pneumoniae isolates from Russia

Among 76 macrolide-nonsusceptible Streptococcus pneumoniae isolates collected between 2003 and 2005 from Central Russia, the resistance mechanisms detected in the isolates included erm(B) alone (50%), mef alone [mef(E), mef(I), or a different mef subclass; 19.7%], or both erm(B) and mef(E) (30.3%). Isolates with dual resistance genes [erm(B) and mef(E)] belonged to clonal complex CC81 or CC271.

Tetracycline consumption and occurrence of tetracycline resistance in Salmonella typhimurium phage types from Danish pigs

The aims of the present study were to investigate at the farm-owner level the effect of prescribed tetracycline consumption in pigs and different Salmonella Typhimurium phage types on the probability that the S. Typhimurium was resistant to tetracycline. In this study, 1,307 isolates were included, originating from 877 farm owners, and data were analyzed using logistic regression. The analysis showed that both the S. Typhimurium phage type (p < 0.0001) and an increase in tetracycline consumption (p = 0.0007) were significantly associated with tetracycline resistance. In particular, the phage type was strongly associated with tetracycline resistance. A further analysis of data from the Danish Integrated Antimicrobial Resistance Monitoring and Research Programme (DANMAP) indicates that the tetracycline-susceptible phage types only slowly become tetracycline resistant, although tetracycline consumption more than doubled at the national level from 12,000-13,000 kg of active compound in 1996-1998 to 29,000 kg of active compound in 2004. Instead, tetracycline-resistant S. Typhimurium phage types became more prevalent. This suggests that the spread of already established or new resistant clones, rather than conversion of "old" well-established susceptible clones to resistant clones by uptake of resistance genes, explains most of the increased levels of tetracycline resistance in S. Typhimurium in Danish swine production in response to increased tetracycline consumption.

Trends in antibacterial resistance among Streptococcus pneumoniae isolated in the USA: update from PROTEKT US Years 1-4

Background

The increasing prevalence of resistance to established antibiotics among key bacterial respiratory tract pathogens, such as Streptococcus pneumoniae, is a major healthcare problem in the USA. The PROTEKT US study is a longitudinal surveillance study designed to monitor the susceptibility of key respiratory tract pathogens in the USA to a range of commonly used antimicrobials. Here, we assess the geographic and temporal trends in antibacterial resistance of S. pneumoniae isolates from patients with community-acquired respiratory tract infections collected between Year 1 (2000–2001) and Year 4 (2003–2004) of PROTEKT US.

Methods

Antibacterial minimum inhibitory concentrations were determined centrally using the Clinical and Laboratory Standards Institute (CLSI) broth microdilution method; susceptibility was defined according to CLSI interpretive criteria. Macrolide resistance genotypes were determined by polymerase chain reaction.

Results

A total of 39,495 S. pneumoniae isolates were collected during 2000–2004. The percentage of isolates resistant to erythromycin, penicillin, levofloxacin, and telithromycin were 29.3%, 21.2%, 0.9%, and 0.02%, respectively, over the 4 years, with marked regional variability. The proportion of isolates exhibiting multidrug resistance (includes isolates known as penicillin-resistant S. pneumoniae and isolates resistant to ≥ 2 of the following antibiotics: penicillin; second-generation cephalosporins, e.g. cefuroxime; macrolides; tetracyclines; and trimethoprim-sulfamethoxazole) remained stable at ~30% over the study period. Overall mef(A) was the most common macrolide resistance mechanism. The proportion of mef(A) isolates decreased from 68.8% to 62.3% between Year 1 and Year 4, while the percentage of isolates carrying both erm(B) and mef(A) increased from 9.7% to 18.4%. Over 99% of the erm(B)+mef(A)-positive isolates collected over Years 1–4 exhibited multidrug resistance. Higher than previously reported levels of macrolide resistance were found for mef(A)-positive isolates.

Conclusion

Over the first 4 years of PROTEKT US, penicillin and erythromycin resistance among pneumococcal isolates has remained high. Although macrolide resistance rates have stabilized, the prevalence of clonal isolates, with a combined erm(B) and mef(A) genotype together with high-level macrolide and multidrug resistance, is increasing, and their spread may have serious health implications. Telithromycin and levofloxacin both showed potent in vitro activity against S. pneumoniae isolates irrespective of macrolide resistance genotype.

Regional trends in β-lactam, macrolide, fluoroquinolone and telithromycin resistance among Streptococcus pneumoniae isolates 2001–2004

OBJECTIVES

To determine global antibacterial resistance rates among community-acquired isolates of Streptococcus pneumoniae.

METHODS

Between 2001 and 2004, 20,142 S. pneumoniae isolates from 151 centres in 40 countries were collected and tested for susceptibility to common antibacterials in the PROTEKT surveillance study.

RESULTS

The prevalence of beta-lactam and macrolide resistance did not change, but there was marked geographic variability. The most common macrolide resistance mechanism was ribosomal methylation mediated by erm(B), except in Canada, Greece and the USA where drug efflux mediated by mef(A) was predominant. The erythromycin minimum inhibitory concentration for mef(A) isolates increased significantly (P<0.001; chi2 test). The global prevalence of macrolide-resistant isolates positive for both erm(B) and mef(A) was 12.0% in 2003-2004; erm(B)+mef(A) strains were particularly common in South Korea (40.8%), South Africa (46.4%) and the USA (29.6%). Telithromycin was the most active antibacterial tested. Over the studied period, > or = 99.7% of all isolates and > 99% of erythromycin-resistant isolates, irrespective of genotype, were susceptible to telithromycin.

CONCLUSIONS

These results confirm the high worldwide prevalence of resistance to commonly used antibacterial agents and multiple resistance phenotypes among clinical isolates of S. pneumoniae and suggest that high-level macrolide resistance is continuing to increase in most countries.

Clinical impact of antibiotic resistance in respiratory tract infections

Streptococcus pneumoniae is the most common causative pathogen of community-acquired respiratory tract infections. In vitro evidence indicates that S. pneumoniae is increasingly resistant to commonly prescribed antimicrobial agents including the macrolides. The clinical relevance of resistance, however, has not been clearly established. This article reviews the risk factors influencing selection of resistant pneumococci, discusses endpoints used to assess the impact of resistance on clinical outcome, and proposes strategies to minimise the impact of resistance. Evidence demonstrating treatment failures due to macrolide-resistant S. pneumoniae is also reviewed. Increasing rates of resistance among S. pneumoniae present numerous clinical challenges, and require carefully selected treatment strategies to preserve antibacterial efficacy. Antibiotics with a low propensity for stimulating resistance should be chosen wherever possible.

Optimizing the management of community-acquired respiratory tract infections in the age of antimicrobial resistance

Community-acquired respiratory tract infections (CARTIs) are the most common reason for prescribing antibiotics in the primary care setting. However, over the last decade, the management of CARTIs has become increasingly complicated by the steady increase in prevalence of drug-resistant pathogens responsible for these infections. As a result, significant attention has been directed at understanding the mechanisms of pathogen acquisition of resistance, drivers of resistance and methods for preventing the development of resistance. Data from recent surveillance studies suggest a slowing or decline in resistance rates to agents, such as beta-lactams, macrolides, tetracyclines and folic acid metabolism inhibitors. However, resistance to one antimicrobial family--the fluoroquinolones--while still low, appears to be on the increase. This is of significant concern given the rapid increase in resistance noted with older antibiotics in recent history. While the clinical implications of antibacterial resistance are poorly understood, the overall rates of antimicrobial resistance, as reported in recent surveillance studies, do not correspond to current rates of failure in patients with CARTIs. This disconnection between laboratory-determined resistance and clinical outcome has been termed the in vitro-in vivo paradox and several explanations have been offered to explain this phenomenon. Solving the problem of antimicrobial resistance will be multifactorial. Important factors in this effort include the education of healthcare providers, patients and the general healthcare community regarding the hazards of inappropriate antibiotic use, prevention of infections through vaccination, development of accurate, inexpensive and timely point-of-care diagnostic tests to aid in patient assessment, institution of objective treatment guidelines and use of more potent agents, especially those with a focused spectrum of activity, earlier in the treatment of CARTIs as opposed to reserving them as second-line treatment options. Ultimately, the single-most important factor will be the judicious use of antibiotics, as fewer antibiotic prescriptions lead to fewer antimicrobial-resistant bacteria.

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.

Otitis media today: a challenge for physicians and the community

Acute otitis media is one of the most common causes of medical consultation worldwide, and has a high economic impact. In this review, a clear definition between acute otitis media and otitis media with effusion is presented. The microbiology and characterization of the main bacterial isolates in acute otitis media and the susceptibility patterns are reviewed, and the latest concepts in antimicrobial treatment are discussed. The need for courses that improve the capability of primary care physicians to diagnose acute otitis media using pneumatic otoscopy, and for parental education is also discussed.

Attenuation of penicillin resistance in a peptidoglycan O-acetyl transferase mutant of Streptococcus pneumoniae

The level of penicillin resistance in clinical isolates of Streptococcus pneumoniae depends not only on the reduced affinity of penicillin binding proteins (PBPs) but also on the functioning of enzymes that modify the stem peptide structure of cell wall precursors. We used mariner mutagenesis in search of additional genetic determinants that may further attenuate the level of penicillin resistance in the bacteria. A mariner mutant of the highly penicillin-resistant S. pneumoniae strain Pen6 showed reduction of the penicillin minimum inhibitory concentration (MIC) from 6 to 0.75 microg ml(-1). Decrease in penicillin MIC was also observed upon introduction of the mutation (named provisionally adr, for attenuator of drug resistance) into representatives of major epidemic clones of penicillin-resistant pneumococci. Attenuation of resistance levels was specific for beta-lactams. The adr mutant has retained unchanged (low affinity) PBPs, unaltered murM gene and unchanged cell wall stem peptide composition, but the mutant became hypersensitive to exogenous lysozyme and complementation experiments showed that both phenotypes--reduced resistance and lysozyme sensitivity--were linked to the defective adr gene. DNA sequence comparison and chemical analysis of the cell wall identified adr as the structural gene of the pneumococcal peptidoglycan O-acetylase.

Rise of Streptococcus pneumoniae isolates containing both erm(B) and mef(E) genes from an adult tertiary care community hospital system

The emergence of macrolide- and lincosamide-resistant Streptococcus pneumoniae is a worldwide concern. Of particular interest is the increasing prevalence of erythromycin and clindamycin-resistant isolates containing both erm(B) and mef genes. This study determined the prevalence of erythromycin and clindamycin resistance in 596 clinical S. pneumoniae isolates from 2 adult tertiary care hospitals over a 4-year period (2001-2004). Erythromycin resistance increased from 24% to 34%, but S. pneumoniae isolates resistant to clindamycin as well as to erythromycin increased from 3% in 2001 to 15.5% in 2004 (5-fold increase). Among erythromycin-resistant isolates, those also resistant to clindamycin (MLS(B) phenotype) increased 3-fold (12.8-45%). Of forty-one erythromycin/clindamycin-resistant S. pneumoniae isolates tested, 29 (71%) contained both erm(B) and mef(E) genes. Pulsed-field gel electrophoresis performed on 28 erm(B) + mef(E) positive isolates identified 2 predominant and possibly related clones, which made up 64% of the isolates.

Genomic Backgrounds of Drug-Resistant Streptococcus pneumoniae in Ankara, Turkey: Identification of Emerging New Clones

Streptococcus pneumoniae exhibiting decreased susceptibility to penicillin are isolated with an increasing prevalence in Turkey during the last decade. This study was undertaken to investigate the molecular epidemiology of non-penicillin-susceptible pneumococci isolated in Ankara, Turkey. Among a population of 246 pneumococci, 90 pneumococci with penicillin MIC > or = 0.1 microg/ml were serotyped, genotyped by pulsed-field gel electrophoresis (PFGE), and sequence typed by multilocus sequence typing (MLST). The overall resistance to penicillin, cefotaxime, erythromycin, clindamycin, chloramphenicol, tetracycline, rifampicin, ciprofloxacin, and vancomycin were 36.6%, 4%, 27.6%, 10.9%, 5.3%, 22.4%, 4.5%, 2%, and 0, respectively. The most frequent serotypes were 14, 23B, 9V, 19F, 19A, and 23F. PFGE types represented 17 genetic clusters. PFGE and MLST data revealed that there were isolates identical or closely related to the Spain(9V)-3 ST 156 clone, Portugal(19F)- 21 ST 177 clone, and Spain(23F)-1 ST81 clone. Eleven serotype 14 isolates with emerging resistance to penicillin belonged to the ST 230 complex, a predominantly susceptible clone. Serotype 19A, 19F, and 7F variants of the ST 230 clone were also identified in the study population. Eight serotype 23B isolates with a new ST 1349 (18-13-8-6-3-6-8) created another clone with no relation to the currently defined international clones. Although the pandemic clones Spain(9V)-3, Portugal1(9F)-21, and Spain(23F)-1 are present in our region, the emergence of a new 23B clone with a unique ST and the emergence of resistance in the ST230 clone, has presumably contributed to the increase in the prevalence of drug-resistant pneumococci in Turkey.

Antimicrobial-resistant bacteria in the community setting

Over the past decade, antimicrobial resistance has emerged as a major public-health crisis. Common bacterial pathogens in the community such as Streptococcus pneumoniae have become progressively more resistant to traditional antibiotics. Salmonella strains are beginning to show resistance to crucial fluoroquinolone drugs. Community outbreaks caused by a resistant form of Staphylococcus aureus, known as community-associated meticillin (formerly methicillin)-resistant Staphylococcus aureus, have caused serious morbidity and even deaths in previously healthy children and adults. To decrease the spread of such antimicrobial-resistant pathogens in the community, a greater understanding of their means of emergence and survival is needed.

Evidence for tetracycline resistance determinant tet(M) allele replacement in a Streptococcus pneumoniae population of limited geographical origin

A collection of 185 Streptococcus pneumoniae isolates was tested for their susceptibility to antipneumococcal drugs, with a focus on the distribution of tetracycline resistance determinants tet(M) and tet(O). Resistance patterns were compared with established correlates of multidrug resistance, and tetracycline-resistant isolates were tested for clonality and allelic variation within tet(M). Resistance to tetracyclines, penicillins and macrolides were all strongly related to multidrug resistance. Over one-quarter of the strains were tetracycline resistant, all via the tet(M)-mediated mechanism. Restriction fragment length polymorphism analysis revealed a high degree of allelic variation within tet(M) and gave evidence of a clonal and horizontal spread of selected alleles. A tet(M) variant that emerged with the onset of epidemic multidrug-resistant strains was replacing old alleles in the population.

Mechanisms by which antibiotics promote dissemination of resistant pneumococci in human populations

Mechanisms by which antimicrobials contribute to dissemination of pneumococcal resistance are incompletely characterized. A serial cross-sectional study of nasopharyngeal pneumococcal carriage in healthy, home-living children <or=6 years of age was conducted in four rural communities-two in Utah (1998-2003) and two in Idaho (2002-2003). Prevalence odds ratios for carriage of resistant pneumococci (OR(res)) and of susceptible pneumococci (OR(sus)) were estimated. Dynamic transmission models were developed to facilitate a mechanistic interpretation of OR(res) and OR(sus) and to compare the population impact of distinct antimicrobial classes. A total of 5,667 cultures were obtained; 25% of the cultures were positive, and 29% of isolates exhibited reduced susceptibility to penicillin. The adjusted OR(res) for recent individual and sibling cephalosporin use was 2.2 (95% confidence interval: 1.4, 3.4) and 1.8 (95% confidence interval: 1.0, 3.3), respectively. Neither individual nor sibling penicillin use was associated with increased OR(res). Rather, recent use of penicillins was associated with decreased carriage of susceptible pneumococci (OR(sus) = 0.2, 95% confidence interval: 0.1, 0.3). In simulations, both types of effects promoted dissemination of resistant pneumococci at the population level. Findings show that oral cephalosporins enhance the risk of acquiring resistant pneumococci. Penicillins accelerate clearance of susceptible strains. The effect of penicillins in increasing resistance is shared equally by treated and untreated members of the population.

Serogroup 19 pneumococci containing both mef and erm macrolide resistance determinants in an American city

BACKGROUND

Asia has experienced a striking incidence of infection by highly resistant pneumococi containing both principal macrolide resistance determinants, namely, the mef efflux pump and the erm ribosomal methylase. mef/erm-containing pneumococci have not been identified in significant numbers in North America.

METHODS

Pneumococci were isolated as part of a larger study in Cleveland, OH examining colonization patterns among children randomized to 1 of 4 outpatient antibiotics for acute otitis media. Azithromycin-resistant organisms were tested for the presence of mef and erm sequences by polymerase chain reaction. The clonal relationship of pneumococci containing both genes was determined by pulsed field gel electrophoresis and multilocus sequence testing. Selected characteristics of children harboring mef/erm-containing organisms were compared with other participants of the larger study.

RESULTS

Of 221 children colonized by pneumococci, 17 (7.7%) were colonized with an organism containing both determinants. All mef/erm-positive organisms demonstrated azithromycin minimum inhibitory concentrations > or =256 microg/mL and were coresistant to all other agents tested. The mef/erm-containing organisms were serotype 19A and 19F, all but 1 of which manifested similar pulsed field gel electrophoresis patterns. Multilocus sequence testing analysis indicated a relationship to the Taiwan-14 macrolide-resistant strain that has spread throughout Eastern Asia. More than one-third of children colonized by a mef/erm-containing organism had received > or =1 dose of conjugate pneumococcal vaccine, a significantly higher proportion than children carrying less resistant organisms (P< 0.01). No other characteristics distinguished children harboring a mef/erm-containing pneumococcus from other children enrolled in the larger study.

CONCLUSION

Clonally related mef/erm-containing serogroup 19 pneumococci were prominent among otherwise healthy children in a North American metropolitan area. Our findings suggest that spread of these organisms may be poorly contained by immunization.

Emergence of a Streptococcus pneumoniae clinical isolate highly resistant to telithromycin and fluoroquinolones

Streptococcus pneumoniae is a major pathogen causing community-acquired pneumonia and acute bronchitis. Macrolides, fluoroquinolones (FQs), and, recently, telithromycin (TEL) constitute primary therapeutic options, and rare cases of resistance have been reported. In this report, we describe the emergence of an S. pneumoniae clinical isolate with high-level TEL resistance (MIC, 256 microg/ml) and simultaneous resistance to FQs. Ongoing studies are oriented to elucidate the precise mechanism of resistance to TEL.

Trends in anti-bacterial resistance among Streptococcus pneumoniae isolated in the USA, 2000–2003: PROTEKT US years 1–3

OBJECTIVES

To determine geographic and temporal trends in anti-bacterial resistance among Streptococcus pneumoniae isolated from patients with respiratory tract infections as part of the PROTEKT US surveillance study (2000-2003).

METHODS

From 2000 to 2003, 31 001 isolates of S. pneumoniae were collected. Anti-bacterial minimum inhibitory concentrations were determined at a central laboratory using the CLSI broth microdilution method. Macrolide resistance genotypes were determined by PCR.

RESULTS

Overall, 29.4, 22.5, 0.9, and 0.02% of S. pneumoniae isolates were resistant to erythromycin, penicillin, levofloxacin, and telithromycin, respectively, with considerable regional variability. Multidrug resistance was stable at approx. 31%. Among macrolide-resistant isolates, mef(A) was the most prevalent resistance gene identified; however, the percentage of isolates with this gene decreased from 68.8% (2000) to 63.9% (2003), while the prevalence of isolates containing both the erm(B) and mef(A) genes increased (2000, 9.7%; 2003, 16.4%). Over 90% of these erm(B)+mef(A)-positive isolates were also resistant to penicillin, tetracycline, or trimethoprim-sulfamethoxazole, while 98.6% were susceptible to levofloxacin and 99.1% were susceptible to telithromycin.

CONCLUSIONS

Penicillin and erythromycin resistance among isolates of S. pneumoniae from the U.S.A. remained high over the 3 years of the study. Telithromycin demonstrated potent in vitro activity against pneumococcal strains.

Characterization of Erythromycin-ResistantStreptococcus pneumoniaein Korea, andIn VitroActivity of Telithromycin against Erythromycin-ResistantStreptococcus pneumoniae

To characterize the phenotypes and genotypes of erythromycin-resistant clinical isolates of Streptococcus pneumoniae in Korea and to evaluate the in vitro activity of telithromycin against these erythromycin-resistant isolates, we tested a total of 676 isolates of S. pneumoniae collected from 1997 to 2002 in a tertiary hospital in Seoul, Republic of Korea. MICs for erythromycin and telithromycin were determined by the agar dilution method. The macrolide resistance phenotypes of erythromycin-resistant isolates were determined by the erythromycin- clindamycin-rokitamycin triple disk (ECRTD) and MIC induction tests, whereas their macrolide resistance genotypes were determined by PCR for the erm(B), erm(A), subclass erm(TR), and mef genes. To discriminate between mef(A) and mef(E), PCR-restriction fragment length polymorphism (RFLP) analyses were performed. Of the 676 S. pneumoniae isolates, 459 (67.9%) were resistant to erythromycin. Of the 459 erythromycin-resistant isolates, 343 (74.7%) were assigned to the cMLS phenotype, 48 (10.4%) to the iMcLS phenotype, 4 (0.9%) to the iMLS phenotype, and 64 (14.0%) to the M phenotype. The erm(B) gene was detected in 251 (54.6%) isolates, the mef gene was detected in 64 (14.0%), and both the erm(B) and mef genes were detected in 144 (31.4%) isolates. All of the mef genes detected were identified as mef(E). Of the 459 erythromycin- resistant isolates, all but one were susceptible to telithromycin. The MIC(50)/MIC(90) to telithromycin of isolates carrying erm(B), mef(E), and both genes was 0.06/0.5 microg/ml, 0.03/0.125 microg/ml, and 0.5/1.0 microg/ml, respectively. Although the MICs of telithromycin for the erythromycin-resistant isolates varied according to genotype, telithromycin was very active against these erythromycin-resistant S. pneumoniae.

Estudo fenotípico e genotípico da resistência aos macrolídeos de "Streptococcus pneumoniae" isolados em hospitais de Porto Alegre - RS

OBJETIVO: O objetivo deste estudo foi determinar a prevalência do S. pneumoniae resistente aos macrolídeos e identificar suas características fenotípicas e genotípicas. MÉTODOS: Amostras de S. pneumoniae isoladas entre maio de 2002 e agosto de 2004, em Porto Alegre (RS), a partir de materiais clínicos coletados de diferentes sítios anatômicos foram analisadas. Para o teste de difusão em ágar foram utilizados discos de eritromicina, claritromicina, azitromicina e clindamicina. As concentrações inibitórias mínimas de eritromicina foram determinadas nos isolados resistentes aos macrolídeos pelo método de diluição em ágar. Os fenótipos dos isolados resistentes aos macrolídeos foram investigados pelo teste de difusão em ágar e a genotipagem pela reação em cadeia da polimerase. RESULTADOS: Foram avaliados 229 isolados de pneumococos, e 12 mostraram-se resistentes aos macrolídeos (5,2%). Entre estes, 9 apresentaram o fenótipo MLSB (75%) e 3 o fenótipo M (25%). A reação em cadeia da polimerase indicou que 8 isolados com o fenótipo MLSB portavam apenas o gene ermB, enquanto que o gene mefE estava presente em todos os 3 isolados com o fenótipo M. Um isolado com o fenótipo MLSB apresentou ambos os genes. CONCLUSÃO: A resistência aos macrolídeos do S. pneumoniae em Porto Alegre permanece baixa, sendo devida principalmente à presença do gene ermB, com expressão do fenótipo MLSB.

Emergence and spread of Streptococcus pneumoniae with erm(B) and mef(A) resistance

Streptococcus pneumoniae isolates (N = 31,001) were collected from patients with community-acquired respiratory tract infections during the PROTEKT US surveillance study (2000–2003). While the macrolide (erythromycin) resistance rate remained stable at ≈29%, the prevalence of resistant isolates containing both erm(B) and mef(A) increased from 9.7% in year 1 to 16.4% in year 3, with substantial regional variability. Almost all (99.2%) dual erm(B)+mef(A) macrolide-resistant isolates exhibited multidrug resistance, whereas 98.6% and 99.0% were levofloxacin- and telithromycin-susceptible, respectively. These strains were most commonly isolated from the ear or middle-ear fluid of children. Of 152 representative erm(B)+mef(A) isolates, >90% were clonally related to the multidrug-resistant international Taiwan^19F-14 clonal complex 271 (CC271). Of 366 erm(B)+mef(A) isolates from the PROTEKT global study (1999–2003), 83.3% were CC271, with the highest prevalence seen in South Africa, South Korea, and the United States. This study confirms the increasing global emergence and rapidly increasing US prevalence of this multidrug-resistant pneumococcal clone.

Rapid and reliable real-time PCR assay for detection of the macrolide efflux gene and subsequent discrimination between its distinct subclasses mef(A) and mef(E)

A real-time PCR assay is described for detection of the macrolide efflux gene, mef. Following amplification, unambiguous discrimination between the two mef subclasses, mef(A) and mef(E), is easily established using a melting curve analysis. The results of this novel assay were 100% concordant with a conventional PCR-RFLP approach but requires far less hands-on time. Furthermore, the real-time format offers semiquantitative results allowing identification of contaminated cultures and/or DNA preparations.