Genetics and molecular biology of beta-lactam-resistant pneumococci

New Aspects of the Interplay between Penicillin Binding Proteins, murM, and the Two-Component System CiaRH of Penicillin-Resistant Streptococcus pneumoniae Serotype 19A Isolates from Hungary

The Streptococcus pneumoniae clone Hungary^19A-6 expresses unusually high levels of β-lactam resistance, which is in part due to mutations in the MurM gene, encoding a transferase involved in the synthesis of branched peptidoglycan. Moreover, it contains the allele ciaH232, encoding the histidine kinase CiaH (M. Müller, P. Marx, R. Hakenbeck, and R. Brückner, Microbiology 157:3104–3112, 2011, https://doi.org/10.1099/mic.0.053157-0). High-level penicillin resistance primarily requires the presence of low-affinity (mosaic) penicillin binding protein (PBP) genes, as, for example, in strain Hu17, a closely related member of the Hungary^19A-6 lineage. Interestingly, strain Hu15 is β-lactam sensitive due to the absence of mosaic PBPs. This unique situation prompted us to investigate the development of cefotaxime resistance in transformation experiments with genes known to play a role in this phenotype, pbp2x, pbp1a, murM, and ciaH, and penicillin-sensitive recipient strains R6 and Hu15. Characterization of phenotypes, peptidoglycan composition, and CiaR-mediated gene expression revealed several novel aspects of penicillin resistance. The murM gene of strain Hu17 (murM_Hu17), which is highly similar to murM of Streptococcus mitis, induced morphological changes which were partly reversed by ciaH232. murM_Hu17 conferred cefotaxime resistance only in the presence of the pbp2x of strain Hu17 (pbp2x_Hu17). The ciaH232 allele contributed to a remarkable increase in cefotaxime resistance in combination with pbp2x_Hu17 and pbp1a of strain Hu17 (pbp1a_Hu17), accompanied by higher levels of expression of CiaR-regulated genes, documenting that ciaH232 responds to PBP1a_Hu17-mediated changes in cell wall synthesis. Most importantly, the proportion of branched peptides relative to the proportion of linear muropeptides increased in cells containing mosaic PBPs, suggesting an altered enzymatic activity of these proteins.

Emergence of Amoxicillin-Resistant Variants of Spain9V-ST156 Pneumococci Expressing Serotype 11A Correlates with Their Ability to Evade the Host Immune Response

Capsular switching allows pre-existing clones of Streptococcus pneumoniae expressing vaccine serotypes to escape the vaccine-induced immunity by acquisition of capsular genes from pneumococci of a non-vaccine serotype. Here, we have analysed the clonal composition of 492 clinical isolates of serotype 11A causing invasive disease in Spain (2000–2012), and their ability to evade the host immune response. Antibiograms, serotyping and molecular typing were performed. The restriction profiles of pbp2x, pbp1a and pbp2b genes were also analysed. Interaction with the complement components C1q, C3b, C4BP, and factor H was explored whereas opsonophagocytosis assays were performed using a human cell line differentiated to neutrophils. Biofilm formation and the polymorphisms of the major autolysin LytA were evaluated. The main genotypes of the 11A pneumococci were: ST62 (447 isolates, 90.6%), followed by ST6521 (35 isolates, 7.3%) and ST838 (10 isolates, 2.1%). Beta lactam resistant serotype 11A variants of genotypes ST838 and ST6521 closely related to the Spain^9V-ST156 clone were first detected in 2005. A different pattern of evasion of complement immunity and phagocytosis was observed between genotypes. The emergence of one vaccine escape variant of Spain^9V-ST156 (ST6521^11A), showing a high potential to avoid the host immune response, was observed. In addition, isolates of ST6521^11A showed higher ability to produce biofilms than ST838^11A or ST62^11A, which may have contributed to the emergence of this PEN-resistant ST6521^11A genotype in the last few years. The emergence of penicillin-resistant 11A invasive variants of the highly successful ST156 clonal complex merits close monitoring.

Advances in pneumococcal antibiotic resistance

Antimicrobial resistance and serotypes in Streptococcus pneumoniae have been evolving with the widespread use of antibiotics and the introduction of pneumococcal conjugate vaccines (PCV). Particularly, among various types of antimicrobial resistance, macrolide resistance has most remarkably increased in many parts of the world, which has been reported to be >70% among clinical isolates from Asian countries. Penicillin resistance has dramatically decreased among nonmeningeal isolates due to the changes in resistance breakpoints, although resistance to other β-lactams such as cefuroxime has increased. Multidrug resistance became a serious concern in the treatment of invasive pneumococcal diseases, especially in Asian countries. After PCV7 vaccination, serotype 19A has emerged as an important cause of invasive pneumococcal diseases which was also associated with increasing prevalence of multidrug resistance in pneumococci. Widespread use of PCV13, which covers additional serotypes 3, 6A and 19A, may contribute to reduce the clonal spread of drug-resistant 19A pneumococci.

Antimicrobial Susceptibilities and Distribution of Resistance Genes for β-Lactams in Streptococcus pneumoniae Isolated in Hamadan

BACKGROUND

β-lactams resistant Streptococcus pneumoniae are an emerging problem throughout the world. Several resistance mechanisms have been reported, including expression of drug-destroying enzymes such as β-lactamases, altered drug targets such as conformational changes in PBPs, decreased bacterial permeability, and increased drug efflux.

OBJECTIVES

The present study aimed to determine the relationship between the results of polymerase chain reaction identification of the Pbp1a, Pbp2b and Pbp2x genes (penicillin-binding proteins) and susceptibilities of β-lactam antibiotics against S. pneumoniae.

MATERIALS AND METHODS

Fifty five isolates of S. pneumoniae were obtained from clinical samples with antimicrobial tests. The susceptibilities of isolates to benzylpenicillin, imipenem, oxacillin, ceftazidime were determined. The resistance genotype was determined by the polymerase chain reaction with primers designed for the PBP genes.

RESULTS

The number of S. pneumoniae isolates resistant to benzylpenicillin, imipenem, oxacillin and ceftazidime were 94.5%, 100%, 100%, and 21.8%, respectively. Analysis of mutation in the genes for pbp showed that 85% of isolates had mutations in pbp2x, pbp2b and pbp1a. Susceptibility to benzylpenicillin was decreased once the number of mutated pbp genes in S. pneumonia increased. According to the results of this study, S. pneumoniae isolates showed reduced susceptibility due to accumulation of resistance genes.

CONCLUSIONS

We suggest that studies should be performed to evaluate changes in Minimum Inhibitory Concentration (MIC) values as well as genetic mutations in order to determine prevalence of S. pneumoniae resistance against antimicrobial agents.

Dihydrostreptomycin or streptomycin in combination with penicillin G in dairy cattle therapeutics: A review and re-analysis of published data Part 2: Resistance and residues

Combination formulations of penicillin G salts and dihydrostreptomycin were developed during the 1960s and are currently marketed in New Zealand for parenteral and intramammary use in dairy cattle. In this paper, the second part of a two paper series, the mechanisms by which bacteria develop resistance to each of these drugs independently is reviewed and the impact of this resistance on potential for synergy is discussed. Further, the considerable potential for tissue drug residues with dihydrostreptomycin or streptomycin from these formulations is examined by re-analysis of literature data, demonstrating an urgent need to reassess the place for aminoglycoside-containing formulations in dairy cattle therapeutics.

The nonserotypeable pneumococcus: phenotypic dynamics in the era of anticapsular vaccines

Nonserotypeable pneumococci (NSP) are commonly carried by Australian Indigenous children in remote communities. The purpose of this study was to characterize carriage isolates of NSP from Indigenous children vaccinated with the seven-valent pneumococcal conjugate vaccine (PCV7) and to use these data to guide decisions on reporting of NSP. A total of 182 NSP were characterized by BOX typing, antibiogram analysis, and multilocus sequence typing (MLST) of common BOX types. NSP positive for the wzg capsule gene were analyzed by a multiplex PCR-based reverse line blot hybridization assay (mPCR/RLB-H) targeting capsule genes to determine the serotype. Among 182 NSP, 49 BOX types were identified. MLST of 10 representative isolates found 7 STs, including ST448 (which accounted for 11% of NSP). Non-penicillin susceptibility was evident in 51% of the isolates. Pneumococcal wzg sequences were detected in only 23 (13%) NSP, including 10 that contained an approximately 1.2-kb insert in the region. mPCR/RLB-H identified serotype 14 wzy sequences in all 10 NSP, and 1 also contained a serotype 3-specific wze sequence. Among the remaining 13 wzg-positive NSP, few belonged to the serotypes represented in PCV7. It appears that most NSP identified in Australian Indigenous children are from a true nonencapsulated lineage. Few NSP represented serotypes in PCV7 that suppress capsular expression. High rates of carriage and penicillin resistance and the occasional presence of capsule genes suggest a role for NSP in the maintenance and survival of capsulated pneumococci. To avoid the inflation of pneumococcal carriage and antibiotic resistance rates, in clinical trials, we recommend separate reporting of rates of capsular strains and NSP and the exclusion of data for NSP from primary analyses.

Comparative genome analysis of high-level penicillin resistance in Streptococcus pneumoniae

Streptococcus pneumoniae strains with very high levels of penicillin resistance (minimum inhibitory concentration [MIC] >or=8 microg/ml) emerged in the 1990 s. Previous studies have traced the changes in penicillin binding proteins (PBP) that result in decreased penicillin susceptibility, and the role of several PBP genes in high-level resistance. In the present study, we investigated the changes that occurred at the two highest levels of penicillin resistance using NimbleGen's Comparative Genome Sequencing (CGS) technology. DNA from a highly resistant (Pen MIC 16 microg/ml) pneumococcus was used to serially transform the R6 strain to high-level resistance. Four distinct levels of penicillin resistance above the susceptible R6 strain (MIC 0.016 microg/ml) were identified. Using CGS technology, the entire genome sequences of the two highest levels of resistant transformants were examined for changes associated with the resistance phenotypes. At the third level of resistance, changes in PBPs 1a, 2b, and 2x were found, very similar to previous reports. At the fourth resistance level, two additional changes were observed in the R6 transformants. More changes were observed in PBP2x, as well as in peptidoglycan GlcNAc deacetylase (pdgA), which had a missense mutation in the coding region. Genetic transformation with polymerase chain reaction (PCR) products generated from the high-level resistant parent containing either the additional PBP2x or mutant pdgA gene did not increase the MIC of the third-level transformant. Only when both PCR products were simultaneously transformed into the third-level transformant did colonies emerge that were at the highest level of resistance (16-32 microg/ml), equivalent to the highly resistant parent strain. This is the first instance of the involvement of a variant pdgA gene in penicillin resistance. It is also clear from these experiments and the literature that there are multiple paths to the pneumococcus achieving high-level penicillin resistance.

Removal of antibiotic resistance gene-carrying plasmids from Lactobacillus reuteri ATCC 55730 and characterization of the resulting daughter strain, L. reuteri DSM 17938

The spread of antibiotic resistance in pathogens is primarily a consequence of the indiscriminate use of antibiotics, but there is concern that food-borne lactic acid bacteria may act as reservoirs of antibiotic resistance genes when distributed in large doses to the gastrointestinal tract. Lactobacillus reuteri ATCC 55730 is a commercially available probiotic strain which has been found to harbor potentially transferable resistance genes. The aims of this study were to define the location and nature of beta-lactam, tetracycline, and lincosamide resistance determinants and, if they were found to be acquired, attempt to remove them from the strain by methods that do not genetically modify the organism before subsequently testing whether the probiotic characteristics were retained. No known beta-lactam resistance genes was found, but penicillin-binding proteins from ATCC 55730, two additional resistant strains, and three sensitive strains of L. reuteri were sequenced and comparatively analyzed. The beta-lactam resistance in ATCC 55730 is probably caused by a number of alterations in the corresponding genes and can be regarded as not transferable. The strain was found to harbor two plasmids carrying tet(W) tetracycline and lnu(A) lincosamide resistance genes, respectively. A new daughter strain, L. reuteri DSM 17938, was derived from ATCC 55730 by removal of the two plasmids, and it was shown to have lost the resistances associated with them. Direct comparison of the parent and daughter strains for a series of in vitro properties and in a human clinical trial confirmed the retained probiotic properties of the daughter strain.

Epidemiological relationships among penicillin non-susceptible Streptococcus pneumoniae strains recovered in the Czech Republic

Since 1986, penicillin non-susceptible pneumococci (PNSP) have been found in the Czech Republic. As documented by a nationwide study, the proportion of invasive strains with reduced susceptibility to penicillin has fluctuated around 5 % in the past decade. Although the level of resistance to penicillin remains stable, the contribution of different capsular serotypes among the PNSP population varies. Whereas serotype 19A was predominantly associated with penicillin resistance until 1997, serotype 9V became most common among PNSP strains in 1998. In a collection of PNSP strains (n=225) isolated from 2000 to 2002, the most frequent serotype was 9V (n=91, 40.4 %), followed by 19F (n=30, 13.3 %) and 14 (n=25, 11.5 %). PFGE and multilocus sequence typing were used to characterize a set of PNSP of the currently predominant serotypes 9V (n=42), 14 (n=15) and 19F (n=14). The Spain(9V)-3 clone [sequence type (ST) 156] was responsible for a large proportion (100 % of serotype 9V strains, n=42; 93.3 % of serotype 14 strains, n=14) of the analysed strains. A representative of the Taiwan(19F)-14 clone (ST 236) was also recovered in the Czech Republic (a single isolate of serotype 19F). These findings confirm the spread of the major penicillin-resistant clones in the Czech Republic.

Detection of Very High–Level Penicillin-Resistant Variants of the Tennessee23F-4 Clone Via Single and Serial Transformations with Four Serotype 19A International Pneumococcal Clones

In the United States, penicillin-resistant variants of the Tennessee (Tenn) (23 F)-4 clone account for a substantial proportion of the very-high-level penicillin-resistant (MIC 8 microg/ml) infections in the 7-valent pneumococcal protein conjugate vaccine (PCV 7) era. Serotype 19 A strains account for an increasing proportion of penicillin-nonsusceptible Streptococcus pneumoniae infections. Sequential transformations of the Tenn (23 F)-4 clone (penicillin MIC 0.1 microg/ml) were performed with four penicillin-nonsusceptible serotype 19 A international clones (penicillin MIC): S. Africa (19 A)-7 (0.5 microg/ml), Hungary (19 A)-6 (2 microg/ml), Slovakia (19 A)-11 (8 microg/ml), and South Africa (19 A)-13 (8 microg/ml). Fifty-two transformants were characterized by MICs, serogroup-specific PCR, pbp PCR restriction profile and sequence, psp A PCR restriction profile, and erm/mef PCR. A subset was analyzed with multilocus sequence typing (MLST) and pulsed-field gel electrophoresis. Serotype 23 F transformants with penicillin MIC >or= 8 microg/ml were detected through a single transformation with the Hungary (19 A)-6 clone or serial transformations using two to three different clones. Forty-four percent (14/32) of the transformants incorporated >or=1 new MLST allele. Using encapsulated donors, very-high-level penicillin resistant variants of the Tenn (23 F)-4 clone were detected. In addition to detecting stepwise increases in penicillin MIC, a 12-fold increase in penicillin MIC was achieved through a single transformation. This large increase in MIC may explain why this clone is commonly associated with very-high-level resistance in natural populations. Recombination within the MLST housekeeping genes was commonly detected in the transformants that had acquired penicillin resistance.

Identical penicillin-binding domains in penicillin-binding proteins of Streptococcus pneumoniae clinical isolates with different levels of beta-lactam resistance

We have sequenced the penicillin-binding domains of the complete repertoire of penicillin-binding proteins and MurM from 22 clinical isolates of Streptococcus pneumoniae that span a wide range of beta-lactam resistance levels. Evidence of mosaicism was found in the genes encoding PBP 1a, PBP 2b, PBP 2x, MurM, and, possibly, PBP 2a. Five isolates were found to have identical PBP and MurM sequences, even though the MICs for penicillin G ranged from 0.25 to 2.0 mg/liter. When the sequences encoding PBP 1a, PBP 2b, and PBP 2x from one of these isolates were used to transform laboratory strain R6, the resulting strain had a resistance level higher than that of the less resistant isolates carrying that PBP set but lower than that of the most resistant isolates carrying that PBP set. This result demonstrates that if the R6 strain is arbitrarily defined as the standard genotype, some wild genetic backgrounds can either increase or decrease the PBP-based resistance phenotype.

Antimicrobial resistance and treatment of community-acquired pneumonia

This article discusses the problem of antimicrobial resistance and how it affects the management of community-acquired pneumonia (CAP). The discussion is limited to infection with Streptococcus pneumoniae and to the treatment of patients hospitalized in a medical ward or an intensive care unit because of pneumococcal CAP.

Rapidly increasing prevalence of penicillin-resistant Streptococcus pneumoniae in middle Tennessee: a 10-year clinical and molecular analysis

The clinical and molecular epidemiology of penicillin-resistant Streptococcus pneumoniae and the diagnostic accuracy of a six-primer PCR assay in identifying penicillin resistance were analyzed by using clinical isolates recovered over a 10-year period in middle Tennessee. The prevalence of non-penicillin-susceptible S. pneumoniae isolates (MIC, > or =0.1 microg/ml) increased from 10% in 1990 to 70% in 1999 (P < 0.001). Among S. pneumoniae isolates for which the penicillin MIC was > or =2 microg/ml (highly penicillin-resistant S. pneumoniae [PRSP]), 23 and 5% were resistant to at least three and at least five other antimicrobial classes, respectively. Pulsed-field gel electrophoresis identified 13 unique strain types, with type B accounting for 33% of PRSP isolates. The sensitivity, specificity, and negative and positive predictive values of the PCR assay in detecting PRSP were 99, 100, 99, and 100%, respectively. Penicillin resistance is rapidly increasing among S. pneumoniae isolates in Tennessee. The simultaneous detection of S. pneumoniae and high-level penicillin resistance can be accurately performed with the six-primer PCR assay.

Coevolutionary networks: a novel approach to understanding the relationships of humans with the infectious agents

Human organism is interpenetrated by the world of microorganisms, from the conception until the death. This interpenetration involves different levels of interactions between the partners including trophic exchanges, bi-directional cell signaling and gene activation, besides genetic and epigenetic phenomena, and tends towards mutual adaptation and coevolution. Since these processes are critical for the survival of individuals and species, they rely on the existence of a complex organization of adaptive systems aiming at two apparently conflicting purposes: the maintenance of the internal coherence of each partner, and a mutually advantageous coexistence and progressive adaptation between them. Humans possess three adaptive systems: the nervous, the endocrine and the immune system, each internally organized into subsystems functionally connected by intraconnections, to maintain the internal coherence of the system. The three adaptive systems aim at the maintenance of the internal coherence of the organism and are functionally linked by interconnections, in such way that what happens to one is immediately sensed by the others. The different communities of infectious agents that live within the organism are also organized into functional networks. The members of each community are linked by intraconnections, represented by the mutual trophic, metabolic and other influences, while the different infectious communities affect each other through interconnections. Furthermore, by means of its adaptive systems, the organism influences and is influenced by the microbial communities through the existence of transconnections. It is proposed that these highly complex and dynamic networks, involving gene exchange and epigenetic phenomena, represent major coevolutionary forces for humans and microorganisms.

Novel penicillin-, cephalosporin-, and macrolide-resistant clones of Streptococcus pneumoniae serotypes 23F and 19F in Taiwan which differ from international epidemic clones

A cluster (14 of 18) of Streptococcus pneumoniae serotype 23F isolates that were resistant to penicillin (PEN), cephalosporin, and macrolide was found in one day care center in Kaohsiung, Taiwan. We analyzed the 18 isolates by pulsed field gel electrophoresis (PFGE). All but one serotype 23F isolate demonstrated identical PFGE patterns, which were different from the established pattern of the internationally spread Spanish 23F clone. The three strains of serotype 19F also showed a uniform pattern. These data strongly suggest that two novel clones of PEN-, cephalosporin-, and macrolide-resistant S. pneumoniae serotypes 23F and 19F are present in Taiwan.

Antibiotic resistance in the absence of selective pressure

Antibiotic resistance poses a serious threat to modern medical practice making treatment more difficult and is associated with increased mortality among patients infected with resistant organisms. There is clear evidence that acquisition of resistance is associated with a decrease in the fitness of the organisms at least in the short term. Evidence from in vitro experiments indicates that bacteria have the ability to adapt to this deficit and recover fitness on serial passage. More recent results show that identical organisms isolated from patients in outbreaks have an initial deficit but that adaptation occurs in vivo. Strategies directed towards controlling resistance must move beyond wishful thinking that supposes that these organisms will disappear merely with control of prescribing. In some cases, resistance will not disappear because there is no evolutionary disadvantage in being resistant once adaptation has taken place. It is important, therefore, that we direct our efforts towards preventing primary resistance emerging and in limiting the spread of resistant strains. Ultimately, we must look again to new drug discovery to improve our therapeutic armoury.

Genetic diversity and clonal patterns among antibiotic-susceptible and -resistant Streptococcus pneumoniae colonizing children: day care centers as autonomous epidemiological units

Characterization by antibiotype of the 1,096 Streptococcus pneumoniae recovered from 2,111 nasopharyngeal samples of children attending 16 day care centers (DCCs) in Lisbon, Portugal, and molecular typing of 413 drug-resistant pneumococci (DRPn) and 89 fully drug-susceptible pneumococci (DSPn) has allowed several conclusions. (i) There was an increase in the frequency of DRPn colonizing children in DCCs from 40% in 1996 to 45% in 1997 to 50% in 1998. (ii) Drug resistance spread by cross-transmission of DRPn clones. A few (8 out of 57) DRPn clones were repeatedly isolated from a large number of children in several DCCs and during each period of surveillance, suggesting the epidemic nature of these clones, which included lineages representing internationally spread S. pneumoniae clones. (iii) Dissemination of resistance determinants among pneumococci colonizing the nasopharynx occurred. Association of identical pulsed-field gel electrophoresis patterns with diverse antibiotypes among pneumococci colonizing children suggests that the high prevalence of DRPn involves not only cross-transmission of resistant strains but also dispersal of resistance genes through recombinational mechanisms. (iv) DCCs are autonomous epidemiological units. Among the 413 DRPn, 57 different lineages were detected; these lineages were dispersed among the 16 DCCs to produce unique microbiological profiles for each of the DCCs. Higher genetic diversity and less sharing of clonal types were observed among the DSPn.

Effects of amoxicillin/clavulanate or azithromycin on nasopharyngeal carriage of Streptococcus pneumoniae and Haemophilus influenzae in children with acute otitis media

The effect of antibiotic therapy on nasopharyngeal colonization by Streptococcus pneumoniae and Haemophilus influenzae was evaluated in children diagnosed with acute otitis media. Children were randomly assigned to receive either amoxicillin/clavulanate or azithromycin therapy, and nasopharyngeal swabs were obtained for culture before and after starting therapy. Amoxicillin/clavulanate therapy eradicated or suppressed all strains of S. pneumoniae susceptible to penicillin, 75% of strains with intermediate resistance, and 40% of strains resistant to penicillin. Azithromycin therapy cleared two-thirds of azithromycin-susceptible strains of S. pneumoniae but none of azithromycin-nonsusceptible strains. Selection for antibiotic-resistant strains in individual children was not observed in children who received amoxicillin/clavulanate therapy but was observed in 2 children who received azithromycin therapy. Carriage of H. influenzae was also reduced by antimicrobial therapy but more so by amoxicillin/clavulanate. Antibiotic therapy does not directly increase the number of resistant strains in the population but, by eradicating susceptible strains, allows greater opportunity for carriage and spread of resistant strains.

Emerging infectious diseases in the 21st century

The emergence of novel infectious diseases, and the re-emergence of others, is not new. The global ecosystem is constantly changing, influencing the micro- and macroenvironments in which humans and their microbial companions reside and interact. Sometimes the environmental circumstances favour the pathogen and there is an unexpected increase in disease activity or emergence of a new infection. Alternatively, pathogenicity factors are acquired by the microbe, allowing new diseases to emerge or old diseases to increase in importance. The forces that drive the emergence, submergence and re-emergence of infectious diseases are varied, but the influence that humans have on the global ecosystem is often of central importance. This review considers infections that are of particular emerging importance.

Capsular type distribution and susceptibility to antibiotics of Streptococcus pneumoniae clinical strains isolated from Uruguayan children with systemic infections. Pneumococcus Study Group

Children under 24 months of age are at high risk for serious infection with Streptococcus pneumoniae but they do not elicit effective immune responses to the currently available capsular polysaccharide vaccines. A polysaccharide protein conjugated vaccine involving the most frequent types has become an urgent need. To produce such a vaccine for Latin America, information on type distribution is required. Recently, Uruguay was 1 of the 6 countries in Latin America where surveillance for invasive pneumococcal infections in children under the age of 5 years was carried out. Seventy percent of the 182 invasive S. pneumoniae isolates were recovered from patients under 24 months of age, and 19% were recovered from infants under 6 months. The 7 most frequent types were 14, 5, 1, 6B, 3, 7F, and 19A; representing 80% of invasive isolates. Twenty-one types were identified, 16 in pneumonia and 14 in meningitis. Resistance to penicillin increased during the study period, from 29% in 1994, to 40% in 1995-1996, mainly because of the spread of type 14 strains resistant to penicillin and trimethoprim/sulphamethoxazol (89% of resistant isolates). The high proportion of systemic pneumococcal infections recorded in patients under 24 months of age and the increasing resistance of these agents to first-choice antibiotics point to an urgent need for a capsular polysaccharide protein conjugated vaccine.

Antimicrobial susceptibility profiles of oropharyngeal viridans group streptococci isolates from cystic fibrosis and non-cystic fibrosis patients

The antimicrobial susceptibility profile of 77 oropharyngeal viridans streptococci isolates from 34 cystic fibrosis (CF) patients and 58 isolates from 43 healthy non-CF patients were studied by the E-test and the standard disk diffusion methods. Overall penicillin and cefotaxime resistances (intermediate plus resistant isolates) were significantly higher (p < 0.05) among CF isolates (72.7% and 45.5%, respectively) than among non-CF isolates (51.7% and 15.5%, respectively). No significant difference was observed in overall (intermediate plus resistant) erythromycin resistance rates, although high-level erythromycin resistance (> or =32 microg/mL) was more frequently found in CF isolates (24.6%) than in non-CF isolates (12.1%). An unexpected high percentage of isolates showed low level erythromycin resistance (MIC range, 0.5-15 microg/mL): 41.5% in cystic fibrosis and 46.5% in non-CF isolates. No significant differences were observed regarding the percentage of colonized patients with at least one penicillin-resistant isolate. On the contrary, colonization with cefotaxime (p < 0.001) or erythromycin (p = 0.014) resistant isolates were significantly more prevalent in CF patients. Similar tetracycline and chloramphenicol resistance rates were observed for both groups. Viridans isolates resistant to a single antibiotic were more prevalent among non-CF patients and multiple resistance was higher among CF patients. Prior antibiotic exposure could result in differences in beta-lactam resistance and colonization rates with resistant isolates between both groups. None of the non-CF patients was previously treated with antimicrobials for a period of three months before sampling. In contrast, 94.1% of CF patients were treated with antimicrobials within the same period; 65.6% with beta-lactam antibiotics. Patients with CF disease, frequently exposed to antimicrobials, may be a reservoir of viridans streptococci isolates with resistance determinants, particularly to beta-lactam antibiotics.

Serotype 19A variants of the Spanish serotype 23F multiresistant clone of Streptococcus pneumoniae

Multiply-antibiotic-resistant isolates of serogroup 19 Streptococcus pneumoniae, possessing altered penicillin-binding protein (PBP) 1A, 2B, and 2X genes that are indistinguishable from those of the Spanish multiresistant serogroup 23F clone, are now commonly encountered in Spain. Those isolates that have been serotyped express type 19F capsular polysaccharide. Serotyping of further isolates, and hybridization using a serotype 19F-specific probe, has shown that some of them are serotype 19A, rather than 19F. The Spanish multiresistant serotype 19A, 19F, and 23F multiresistant strains were all shown to be very closely related in overall genotype, as they were indistinguishable by REP-PCR and by the sequencing of internal fragments of three house-keeping genes. The serotype 19A multiresistant strains, like the serotype 19F multiresistant strains, therefore appear to be a serotype variant of the Spanish multiresistant serotype 23F clone, which presumably has arisen by recombination at the capsular locus.

Genotypic survey of recent beta-lactam-resistant pneumococcal nasopharyngeal isolates from asymptomatic children in Chile

To assess pneumococcal strain variability among young asymptomatic carriers in Chile, we used serotyping, antibiotic susceptibility testing, and genotyping to analyze 68 multidrug-resistant pneumococcal isolates recovered from 54 asymptomatic children 6 to 48 months of age. The isolates represented capsular serotypes 19F (43 isolates), 14 (14 isolates), 23F (7 isolates), 6B (3 isolates), and 6A (1 isolate). Genotypic analysis, which included pulsed-field gel electrophoresis (PFGE) of chromosomal digests, penicillin binding protein (PBP) gene fingerprinting, and dhf gene fingerprinting, revealed that the isolates represented six different genetic lineages. Clear circumstantial evidence of capsular switching was seen within each of four of the genetically related sets. The majority of the isolates, consisting of the 43 19F isolates and 2 type 6B isolates, appeared to represent a genetically highly related set distinct from previously characterized pneumococcal strains. Each of three other genetically defined lineages was closely related to one of the previously characterized clones Spain(6B)-2, France(9V)-3, or Spain(23F)-1. A fifth lineage was comprised of four type 23F isolates that, by the techniques used for this study, were genetically indistinguishable from three recent type 19F sterile-site isolates from the United States. Finally, a sixth lineage was represented by a single type 23F isolate which had a unique PFGE type and unique PBP and dhf gene fingerprints.

Evidence of clonal dissemination of multidrug-resistant Streptococcus pneumoniae in Hong Kong

The relationship between the phenotypic and genotypic characteristics of 105 penicillin-intermediate or -resistant Streptococcus pneumoniae isolates saved during 1994 to 1997 at the Prince of Wales Hospital and Pamela Youde Nethersole Eastern Hospital, Hong Kong, was studied. The pbp genes for penicillin-binding proteins 1a, 2b, and 2x for each isolate were amplified by PCR, and the products were digested with restriction enzymes HinfI and AluI. A combination of the pulsed-field gel electrophoresis (PFGE) profiles, pbp fingerprints, and phenotypic characteristics of capsular types and antibiograms enabled these isolates to be divided into four major groups. Seventy-four percent (78 of 105) of the strains, belonging to serotypes 23F, 19F, and 14, showed indistinguishable pbp fingerprint patterns (group A1, 1-1-1, 1-1-1), with PFGE patterns belonging to group A and its subtypes, suggesting that these strains were closely related. Eighty-three percent (65 of 78) of these isolates were also resistant to tetracycline, erythromycin, chloramphenicol, and trimethoprim. The type 23F isolates were indistinguishable from representative strains of the Spanish 23F clone by these molecular methods, indicating that these strains may be variants of the Spanish 23F clone. Serotype 6B accounted for 19% (20 of 105) of the isolates with reduced penicillin susceptibility and was made up of variants belonging to four different pbp fingerprint groups with the PFGE pattern group B, the predominant group being indistinguishable from that of the Spanish 6B clone. Other PFGE and fingerprint groups were mainly obtained from penicillin-susceptible strains of various serotypes. The results suggest that the rapid emergence of drug-resistant S. pneumoniae in Hong Kong has been due to the rapid dissemination of several successful clones.

A cross-Canada surveillance of antimicrobial resistance in respiratory tract pathogens

OBJECTIVE

To determine the prevalence of antimicrobial resistance in clinical isolates of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis from medical centres across Canada.

METHODS

Fifty laboratories from across Canada were asked to collect up to 25 consecutive clinical isolates of S pneumoniae, H influenzae and M catarrhalis at some time between September 1994 and May 1995, and then again between September and December of 1996. A total of 2364 S pneumoniae, 575 H influenzae and 200 M catarrhalis samples were collected. H influenzae and M catarrhalis isolates were tested for the production of beta-lactamase. S pneumoniae isolates were characterized as penicillin susceptible, intermediately resistant or high level penicillin-resistant. Minimal inhibitory concentrations (MICs) were determined using a microbroth dilution technique described by the National Committee of Clinical Laboratory Standards.

RESULTS

Between the two collection periods, there was a significant increase in highly penicillin-resistant S pneumoniae from 2.1% to 4.4% (P<0.05) and an increase in intermediately penicillin-resistant strains from 6.4% to 8.9% (P<0.05). A significant increase in high level penicillin-resistant S pneumoniae was noted among paediatric isolates. No significant difference in the susceptibilities of comparator agents was detected. A significant increase in the number of beta-lactamase producing H influenzae, 34% to 43% (P<0.05) was observed. Ninety-five per cent of M catarrhalis isolates were beta-lactamase producers in both time periods.

CONCLUSIONS

During the course of this study, the incidence of penicillin resistance in S pneumoniae doubled. As a result of this increase, infections due to this organism in sites where poor penetration of beta-lactam antibiotics occur may become increasingly difficult to manage.

Application of pbp1A PCR in identification of penicillin-resistant Streptococcus pneumoniae

A seminested PCR assay, based on the amplification of the pneumococcal pbp1A gene, was developed for the detection of penicillin resistance in clinical isolates of Streptococcus pneumoniae. The assay was able to differentiate between intermediate (MICs = 0.25 to 0.5 microgram/ml) and higher-level (MICs = >/=1 microgram/ml) resistance. Two species-specific primers, 1A-1 and 1A-2, which amplified a 1,043-bp region of the pbp1A penicillin-binding region, were used for pneumococcal detection. Two resistance primers, 1A-R1 and 1A-R2, were designed to bind to altered areas of the pbp1A gene which, together with the downstream primer 1A-2, amplify DNA from isolates with penicillin MICs of >/=0.25 and >/=1 microgram/ml, respectively. A total of 183 clinical isolates were tested with the pbp1A assay. For 98.3% (180 of 183) of these isolates, the PCR results obtained were in agreement with the MIC data. The positive and negative predictive values of the assay were 100 and 91%, respectively, for detecting strains for which the MICs were >/=0.25 microgram/ml and were both 100% for strains for which the MICs were >/=1 microgram/ml.

Identification of three major clones of multiply antibiotic-resistant Streptococcus pneumoniae in Taiwanese hospitals by multilocus sequence typing

In this paper we demonstrate the advantages of a new molecular typing procedure, multilocus sequence typing, for the unambiguous characterization of penicillin-resistant pneumococci. The sequences of approximately 450-bp fragments of seven housekeeping genes were determined for 74 penicillin-resistant Taiwanese isolates of Streptococcus pneumoniae (MIC of penicillin > 0.5 microgram/ml). The combination of alleles at the seven loci defined an allelic profile for each strain, and a dendrogram, based on the pairwise mismatches in allelic profiles, grouped 86% of the isolates into one of three penicillin-resistant clones for which the MICs of penicillin were 1 to 2 microgram/ml. Isolates within each clone had identical alleles at all seven loci or differed at only a single locus, and the fingerprints of their pbp1A, pbp2B, and pbp2X genes were uniform. Isolates of the Taiwan-19F clone and the Taiwan-23F clone were resistant to penicillin, tetracycline, and erythromycin but were susceptible to chloramphenicol. A second serotype 23F clone and serotype 19F variants of this clone were resistant to penicillin, tetracycline, chloramphenicol, and, in some cases, erythromycin. Comparisons of the allelic profiles of the three major clones with those of reference isolates of the known penicillin-resistant clones showed that the Taiwan-19F and Taiwan-23F clones were previously undescribed, whereas the second serotype 23F clone was indistinguishable from the Spanish multidrug-resistant serotype 23F clone. Single isolates of the Spanish penicillin-resistant serotype 9V clone and the Spanish multidrug-resistant serotype 6B clone were also identified in the collection.

PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori

Genes that are characteristic of only certain strains of a bacterial species can be of great biologic interest. Here we describe a PCR-based subtractive hybridization method for efficiently detecting such DNAs and apply it to the gastric pathogen Helicobacter pylori. Eighteen DNAs specific to a monkey-colonizing strain (J166) were obtained by subtractive hybridization against an unrelated strain whose genome has been fully sequenced (26695). Seven J166-specific clones had no DNA sequence match to the 26695 genome, and 11 other clones were mixed, with adjacent patches that did and did not match any sequences in 26695. At the protein level, seven clones had homology to putative DNA restriction-modification enzymes, and two had homology to putative metabolic enzymes. Nine others had no database match with proteins of assigned function. PCR tests of 13 unrelated H. pylori strains by using primers specific for 12 subtracted clones and complementary Southern blot hybridizations indicated that these DNAs are highly polymorphic in the H. pylori population, with each strain yielding a different pattern of gene-specific PCR amplification. The search for polymorphic DNAs, as described here, should help identify previously unknown virulence genes in pathogens and provide new insights into microbial genetic diversity and evolution.

Description of two new isolates of Streptococcus pneumoniae in spain that are highly resistant to cefotaxime

Two strains of Streptococcus pneumoniae isolated from sputum and bronchoalveolar samples with high-level resistance to cefotaxime (MIC = 8 to 16 microg/ml) are described. One of them, belonging to serogroup 19, was also highly resistant to penicillin (MIC = 16 microg/ml), while the other, of serogroup 14, was intermediate in its resistance to penicillin (MIC = 0.25 microg/ml). To our knowledge, these are the first two strains to be isolated in Spain with such high levels of resistance to cefotaxime.

Antibiotic resistance in community-acquired respiratory tract infections: current issues

OBJECTIVE

In recent years, antibiotic resistance has emerged as an important global problem. The major goal of this review is to update important issues pertaining to antibiotic resistance, with an emphasis on antibiotic resistance involving community-acquired respiratory pathogens. In addition, this review examines potential reasons why antibiotic resistance has increased in recent years, how clinicians can better understand commonly used laboratory antibiotic resistance tests, and possible solutions to the increasing problem of antibiotic resistance. The article emphasizes the diagnosis, therapy, and prevention of antibiotic-resistant infections.

DATA SOURCES

We identified relevant English-language articles through MEDLINE search (1966 to March 1998). All articles related to antibiotic resistance and the scope of the articles included original investigative articles, reviews, letters, and editorials. In addition, we selected additional references from the bibliographies of the identified articles.

STUDY SELECTION

We selected articles for detailed review if they provided direct insight into the cause of antibiotic resistance, testing for antibiotic resistance, or the treatment of antibiotic resistance. Most, but not all, of the articles selected pertained to antibiotic resistance and respiratory tract infections. We performed a detailed review on approximately 40% of the originally selected articles.

RESULTS

Multiple factors that play a significant role in the development of antibiotic resistance include the overuse of antibiotics in both humans and animals, situations such as day care that enhance transmission via frequent close personal contact, and widespread dissemination of resistant strains via global travel. Most respiratory pathogens have developed resistance to commonly used antibiotics either by producing beta-lactamase or by altering binding site proteins.

CONCLUSIONS

In many regions of the United States, the level of antibiotic resistance has impacted the clinical management of common respiratory pathogens. Future efforts to curtail antibiotic resistance will require a concerted effort in multiple areas, particularly enhanced epidemiologic surveillance to better detect resistance trends, judicious use of antibiotics, and new drug development.

Antibiotic resistance among clinically important gram-positive bacteria in the UK

The resistance of bacteria to antibiotics, particularly those used for first-line therapy, is an increasing cause for concern. In the UK, the prevalence of resistance to methicillin and mupirocin in Staphylococcus aureus, and to penicillin and macrolides in Streptococcus pneumoniae, appear to be increasing. There has also been an increase in the number of hospitals where glycopeptide-resistant enterococci are known to have been isolated. The increases in methicillin-resistant S. aureus and glycopeptide-resistant enterococci are due, in part, to the inter-hospital spread of epidemic strains. Although new quinolones and streptogramins with activity against Gram-positive bacteria (including strains resistant to currently available agents) are under development, there is no reason to believe that resistance to these agents will not emerge. The control of resistance in Gram-positive bacteria will require a multi-faceted approach, including continued and improved surveillance, a reduction in the unnecessary use of antibiotics, and the application of other strategies such as vaccination.

Trends in the resistance to antimicrobial agents of Streptococcus suis isolates from Denmark and Sweden

This study was conducted to determine the MIC values of historical and contemporary Streptoccocus suis (serotypes 2 and 7) from Denmark and S. suis (serotype 2) from Sweden. A total of 52 isolates originating from 1967 through 1981 and 156 isolates from 1992 through 1997 in Denmark and 13 isolates from Sweden were examined for their MICs against 20 different antimicrobial agents. Most antimicrobials were active against most isolates. A frequent occurrence of resistance to sulphamethoxazole was observed, with most resistance among historic isolates of serotype 7 and least resistance among isolates from Sweden. A large number of the isolates was resistant to macrolides. However, all historic serotype 2 isolates from Denmark were susceptible, whereas 20.4% of the contemporary isolates were resistant. Among serotype 7 isolates 23.3% of the historic isolates were resistant to macrolides, whereas resistance was found in 44.8% of the contemporary isolates. All isolates from Sweden were susceptible to macrolides. Time-associated frequency of resistance to tetracycline was also found. Only a single historic isolate of serotype 2 was resistant to tetracycline, whereas 43.9% of the contemporary serotype 2 isolates and 15.5% of the contemporary serotype 7 isolates were resistant. Only one (7.7%) of the isolates from Sweden was resistant. The differences in resistance between historic and contemporary isolates from Denmark were statistically significant. This study demonstrated a significant serotype-associated difference in the susceptibility to macrolides and tetracycline and demonstrated that an increase in resistance among S. suis isolates has taken place during the last 15 years to the two most commonly used antimicrobial agents (tylosin and tetracycline) in pig production in Denmark.

Rapid screening for penicillin susceptibility of systemic pneumococcal isolates by restriction enzyme profiling of the pbp2B gene

Restriction digest profiling of pneumococcal pbp2b-specific amplicons was effective for screening penicillin resistance. The pbp2b amplicon of all pneumococcal isolates for which the MICs of penicillin were < or = 0.03 microgram/ml had one of two different susceptible restriction profiles, and all 33 isolates for which MICs were 0.5 microgram/ml or greater had one of seven distinct resistant profiles. Low-concentration penicillin resistance (MICs = 0.06 microgram/ml to 0.25 microgram/ml) was associated with sensitive HaeIII profiles in some isolates; however, RsaI profiling and pbp2b sequence analysis of such isolates revealed that some isolates contained low-level resistant pbp2b alleles, while others had susceptible pbp2b alleles. This data indicates that low-level penicillin resistance is sometimes conferred by determinants other than pbp2b.

Application of molecular typing to the epidemiology of Streptococcus pneumoniae

The spread of antibiotic resistance and the development of new vaccines have focused attention on the epidemiology of Streptococcus pneumoniae over recent years. While serotyping and the determination of antibiotic resistance remain primary methods for characterising pneumococci, molecular typing can add greater discrimination and complementary information. Methods based on restriction fragment length polymorphism within total DNA or non-specific polymerase chain reaction provide information representative of the whole genome and can be used to recognise closely related isolates from different sources, whether in the investigation of possible cross infection at the local level or in the investigation of national or international spread of antibiotic resistant strains. Fingerprinting of penicillin binding protein genes adds further information in the analysis of penicillin resistant isolates. The use of a combination of typing methods to analyse both the genome as a whole and specific loci has led to the realisation that pneumococci undergo horizontal gene transfer much more often than most other bacterial species. In particular the spread of penicillin resistance has been characterised by a combination of the spread of epidemic strains, transfer of chromosomal resistance genes from such strains into other genetic backgrounds, and transfer of capsule genes resulting in the switch of serotypes within strains. In the future molecular typing will have an important role in discovering whether widespread vaccination leads to genetic modification of the pneumococcal population causing invasive disease.

Rapid detection of penicillin-resistant Streptococcus pneumoniae in cerebrospinal fluid by a seminested-PCR strategy

A seminested-PCR assay, based on the amplification of the pneumococcal penicillin-binding protein 2B gene (pbp2B), was developed for the detection of penicillin-resistant and -susceptible pneumococci in cerebrospinal fluid (CSF) specimens. Species-specific primers (P5 and P6) which amplified a 682-bp conserved region of the transpeptidase-encoding region of the pbp2B gene were used. Four "resistance" primers were designed to bind to altered areas of the pbp2B gene identified in penicillin-resistant South African wild-type strains. Together with the downstream primer P6, the upstream resistance primers amplified fragments which were used to detect the presence of penicillin resistance. This system identified all 35 of the S. pneumoniae isolates evaluated, including strains of 11 different serotypes and a range of penicillin-resistant and -susceptible strains. The specificity of the assay was demonstrated by its inability to amplify DNA from other bacterial species which commonly cause meningitis. It was possible to detect pneumococcal DNA from culture-negative CSF inoculated with 2.5 pg of purified DNA or 18 CFU. Analysis of 285 CSF specimens showed that PCR detected the pneumococcus in 18 samples positive by culture, including the identification of four penicillin-resistant isolates. The positive predictive value and the negative predictive value of the assay were each 100%.

In vitro susceptibility of 90 penicillin-susceptible and -resistant pneumococci to penicillin G, amoxicillin, amoxicillin/clavulanate, cefaclor, cefuroxime, cefpodoxime, cefixime and imipenem

In vitro susceptibility of eight antibiotics was compared using three groups of pneumococci and agar dilution method comprising 30 penicillin-susceptible, 30 intermediately penicillin-resistant, and 30 highly penicillin-resistant pneumococci. Decreased sensitivity to all beta-lactam agents of intermediately penicillin-resistant and highly penicillin-resistant pneumococci is shown. MIC50 and MIC90 was lower with amoxicillin with and without clavulanate by one dilution than with penicillin. Cephalosporin MIC90s were all significantly higher for intermediately resistant and fully resistant strains. Only imipenem was more active than penicillin with MIC90 of susceptible pneumococci 0.015 mg/L, intermediately resistant pneumococci 0.25 mg/L, resistant pneumococci 1 mg/L.

The clinical impact of resistance in the management of pneumococcal disease

The prevalence of drug-resistant Streptococcus pneumoniae (DRSP) has increased worldwide. Although unfavorable outcomes in meningitis due to DRSP have been well-described, the clinical impact of DRSP on other manifestations of pneumococcal infection warrants further study. Empiric combination vancomycin and extended-spectrum cephalosporin (cefotaxime or ceftriaxone) therapy is indicated for the following clinical indications: purulent meningitis, life-threatening pneumonia, and suspected sepsis in patients predisposed to invasive pneumococcal disease, for example, sickle cell disease, HIV infection, and nephrotic syndrome. In addition to clinical management issues, other implications of the emergence of DRSP include identification of resistant strains, local and national surveillance, and prevention. Preventive measures include judicious antibiotic use, appropriate use of the currently available 23-valent pneumococcal vaccine, and development and implementation of a protein-conjugate vaccine.

Antibiotic management of pneumococcal infections in an era of increased resistance

Pneumococci are a leading cause of bacterial meningitis and bacteraemia, as well as pneumonia, otitis media and sinusitis in childhood. These organisms recently have shown a dramatic increase in antibiotic resistance. Penicillin-resistant pneumococci are of special concern as they are often resistant to other unrelated antibiotics. This is of particular significance to Aboriginal children who have among the highest rates of pneumococcal infection in the world. Laboratories should now test all invasive pneumococcal isolates for penicillin and third generation cephalosporin resistance. Local treatment guidelines are required for pneumococcal infections, especially for meningitis, taking into account the prevalence of resistant strains within the community. At present, penicillin and amoxycillin remain the drugs of choice for pneumococcal infections, with the exception of meningitis where initial empirical therapy must be with a third generation cephalosporin. Judicious antibiotic use, which avoids over-prescribing and unnecessary use of broad-spectrum agents, improved living standards in underprivileged communities and introduction of an effective conjugate vaccine, able to reduce the rates of pneumococcal infection and hopefully colonization, may limit the spread of resistant strains.