Comparison of PCR assay with bacterial culture for detecting Streptococcus pneumoniae in middle ear fluid of children with acute otitis media

Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods

The Mitis group of streptococci includes an important human pathogen, Streptococcus pneumoniae (pneumococcus) and about 20 other related species with much lower pathogenicity. In clinical practice, some representatives of these species, especially Streptococcus pseudopneumoniae and Streptococcus mitis, are sometimes mistaken for S. pneumoniae based on the results of classical microbiological methods, such as optochin susceptibility and bile solubility. Several various molecular approaches that address the issue of correct identification of pneumococci and other Mitis streptococci have been proposed and are discussed in this review, including PCR- and gene sequencing-based tests as well as new developments in the genomic field that represents an important advance in our understanding of relationships within the Mitis group.

Visualization of microbes by 16S in situ hybridization in term and preterm placentas without intraamniotic infection

BACKGROUND

Numerous reports have documented bacteria in the placental membranes and basal plate decidua in the absence of immunopathology using histologic techniques. Similarly, independent metagenomic characterizations have identified an altered taxonomic makeup in association with spontaneous preterm birth. Here we sought to corroborate these findings by localizing presumptive intact bacteria using molecular histology within the placental microanatomy.

OBJECTIVE

Here we examined for microbes in term and preterm gestations using a signal-amplified 16S universal in situ hybridization probe set for bacterial rRNA, alongside traditional histologic methods of Warthin-Starry and Gram stains, as well as clinical culture methodologies. We further sought to differentiate accompanying 16S gene sequencing taxonomic profiles from germ-free (gnotobiotic) mouse and extraction and amplicon contamination controls.

STUDY DESIGN

Placentas were collected from a total of 53 subjects, composed of term labored (n = 4) and unlabored cesarean deliveries (n = 22) and preterm vaginal (n = 18) and cesarean deliveries (n = 8); a placenta from a single subject with clinical and histologic evident choriomanionitis was employed as a positive control (n = 1). The preterm cohort included spontaneous preterm birth with (n = 6) and without (n = 10) preterm premature rupture of membranes, as well as medically indicated preterm births (n = 10). Placental microbes were visualized using an in situ hybridization probe set designed against highly conserved regions of the bacterial 16S ribosome, which produces an amplified stable signal using branched DNA probes. Extracted bacterial nucleic acids from these same samples were subjected to 16S rRNA metagenomic sequencing (Illumina, V4) for course taxonomic analysis, alongside environmental and kit contaminant controls. A subset of unlabored, cesarean-delivered term pregnancies were also assessed with clinical culture for readily cultivatable pathogenic microbes.

RESULTS

Molecular in situ hybridization of bacterial rRNA enabled visualization and localization of low-abundance microbes after systematic high-power scanning. Despite the absence of clinical or histologic chorioamnionitis in 52 of 53 subjects, instances of 16S rRNA signal were confidently observed in 13 of 16 spontaneous preterm birth placentas, which was not significantly different from term unlabored cesarean specimens (18 of 22; P > .05). 16S rRNA signal was largely localized to the villous parenchyma and/or syncytiotrophoblast, and less commonly the chorion and the maternal intervillous space. In all term and unlabored cesarean deliveries, visualization of evident placental microbes by in situ hybridization occurred in the absence of clinical or histologic detection using conventional clinical cultivation, hematoxylin-eosin, and Gram staining. In 1 subject, appreciable villous bacteria localized to an infarction, where 16S microbial detection was confirmed by Warthin-Starry stain. In all instances, parallel sample principle coordinate analysis using Bray-Cutis distances of 16S rRNA gene sequencing data demonstrated consistent taxonomic distinction from all negative or potential contamination controls (P = .024, PERMANOVA). Classification from contaminant filtered data identified a distinct taxonomic makeup among term and preterm cohorts when compared with contaminant controls (false discovery rate <0.05).

CONCLUSION

Presumptively intact placental microbes are visualized as low-abundance, low-biomass and sparse populations within the placenta regardless of gestational age and mode of delivery. Their taxonomic makeup is distinct from contamination controls. These findings further support several previously published findings, including our own, which have used metagenomics to characterize low-abundance and low-biomass microbial communities in the placenta.

Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media

Although S. pneumoniae, H. influenzae, and M. catarrhalis have been long established as the most important pathogens in acute otitis media using culture and specific PCR assays, the knowledge of their mutual quantitative relations and possible roles of other bacteria is incomplete. The advent of unbiased bacteriome 16S rRNA gene profiling has allowed the detection of nearly all bacteria present in the sample, and it helps in depicting their mutual quantitative ratios. Due to the difficulties in performing mass sequencing in low-volume samples, only a few bacteriome-profiling studies of otitis media have been published, all limited to cases of chronic otitis media. Here, we present a study on samples obtained from young children with acute otitis media, successfully using a strategy of nested PCR coupled with mass sequencing, and demonstrate that the method can confer quantitative information hardly obtainable by other methods.

The aim of the study was to analyze the bacteriome of acute otitis media with a novel modification of next-generation sequencing techniques. Outpatient children with acute otitis media were enrolled in the study, and middle ear fluids were collected during 90 episodes from 79 subjects aged 5 to 42 months (median age, 19 months). The bacteriome profiles of middle ear fluid samples were determined by a nested-PCR amplification of the 16S rRNA gene (V4 region), followed by mass sequencing. The profiling results were compared to the results of specific PCR assays targeting selected prevalent pathogens. Bacteriome profiling using nested amplification of low-volume samples was aided by a bioinformatic subtraction of signal contaminants from the recombinant polymerase, achieving a sensitivity slightly lower than that of specific PCR detection. Streptococcus pneumoniae was detected in 28 (31%) samples, Haemophilus influenzae in 24 (27%), Moraxella catarrhalis in 18 (20%), Staphylococcus spp. in 21 (23%), Turicella otitidis in 5 (5.6%), Alloiococcus otitidis in 3 (3.3%), and other bacteria in 14 (16%) using bacteriome profiling. S. pneumoniae was the dominant pathogen in 14 (16%) samples, H. influenzae in 15 (17%), M. catarrhalis in 5 (5.6%), T. otitidis in 2, and Staphylococcus auricularis in 2. Weaker signals of Prevotella melaninogenica, Veillonella dispar, and Veillonella montpellierensis were noted in several samples. Fourteen samples (16%) were not explainable by bacterial pathogens; novel causative agents were not detected. In conclusion, unbiased bacteriome profiling helped in depicting the true mutual quantitative ratios of ear bacteria, but at present, its complicated protocol impedes its routine clinical use.

IMPORTANCE Although S. pneumoniae, H. influenzae, and M. catarrhalis have been long established as the most important pathogens in acute otitis media using culture and specific PCR assays, the knowledge of their mutual quantitative relations and possible roles of other bacteria is incomplete. The advent of unbiased bacteriome 16S rRNA gene profiling has allowed the detection of nearly all bacteria present in the sample, and it helps in depicting their mutual quantitative ratios. Due to the difficulties in performing mass sequencing in low-volume samples, only a few bacteriome-profiling studies of otitis media have been published, all limited to cases of chronic otitis media. Here, we present a study on samples obtained from young children with acute otitis media, successfully using a strategy of nested PCR coupled with mass sequencing, and demonstrate that the method can confer quantitative information hardly obtainable by other methods.

Moraxella catarrhalis Might Be More Common than Expected in Acute Otitis Media in Young Finnish Children

According to studies based on bacterial cultures of middle ear fluids, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis have been the most common pathogens in acute otitis media. However, bacterial culture can be affected by reduced viability or suboptimal growth of bacteria. PCR detects bacterial DNA from samples with greater sensitivity than culture. In the present study, we analyzed the middle ear pathogens with both conventional culture and semiquantitative real-time PCR in 90 middle ear fluid samples obtained from children aged 5 to 42 months during acute otitis media episodes. Samples were tested for the presence of S. pneumoniae, H. influenzae, M. catarrhalis, Alloiococcus otitidis, Staphylococcus aureus, and Pseudomonas aeruginosa One or more bacterial pathogens were detected in 42 (47%) samples with culture and in 69 (77%) samples with PCR. According to PCR analysis, M. catarrhalis results were positive in 42 (47%) samples, H. influenzae in 30 (33%), S. pneumoniae in 27 (30%), A. otitidis in 6 (6.7%), S. aureus in 5 (5.6%), and P. aeruginosa in 1 (1.1%). Multibacterial etiology was seen in 34 (38%) samples, and M. catarrhalis was detected in most (85%) of those cases. Fifteen signals for M. catarrhalis were strong, suggesting a highly probable etiological role of the pathogen. In conclusion, even though M. catarrhalis is often a part of mixed flora in acute otitis media, a considerable proportion of cases may be primarily attributable to this pathogen.

Culture-based Methods for Detection of Antibiotic Resistance in Agroecosystems: Advantages, Challenges, and Gaps in Knowledge

Various culture-based methodologies are used in assessment of antibiotic resistance in samples collected in agroecosystems. Culture-based methods commonly involve isolating target bacteria on general or selective media and assessing growth in response to specific concentrations of antibiotics. The advantages of culture-based methods are multifold. In particular, isolation of bacteria is key to understanding phenotypic characteristics of isolates and their resistance patterns, and most national and international antibiotic resistance monitoring projects are isolate based. This review covers current knowledge of bacterial groups and antibiotics commonly targeted in resistance studies using bacterial culture and discusses the range in methods used, data interpretation, and factors supporting and confounding the use of culture-based methods in assessment of antibiotic resistance. Gaps in knowledge related to study design and resistance databases are discussed. Finally, a case is made for the integration of culture-based and molecular methods to better inform our understanding of antibiotic resistance in agroecosystems.

Thermally multiplexed polymerase chain reaction

Amplification of multiple unique genetic targets using the polymerase chain reaction (PCR) is commonly required in molecular biology laboratories. Such reactions are typically performed either serially or by multiplex PCR. Serial reactions are time consuming, and multiplex PCR, while powerful and widely used, can be prone to amplification bias, PCR drift, and primer-primer interactions. We present a new thermocycling method, termed thermal multiplexing, in which a single heat source is uniformly distributed and selectively modulated for independent temperature control of an array of PCR reactions. Thermal multiplexing allows amplification of multiple targets simultaneously-each reaction segregated and performed at optimal conditions. We demonstrate the method using a microfluidic system consisting of an infrared laser thermocycler, a polymer microchip featuring 1 μl, oil-encapsulated reactions, and closed-loop pulse-width modulation control. Heat transfer modeling is used to characterize thermal performance limitations of the system. We validate the model and perform two reactions simultaneously with widely varying annealing temperatures (48 °C and 68 °C), demonstrating excellent amplification. In addition, to demonstrate microfluidic infrared PCR using clinical specimens, we successfully amplified and detected both influenza A and B from human nasopharyngeal swabs. Thermal multiplexing is scalable and applicable to challenges such as pathogen detection where patients presenting non-specific symptoms need to be efficiently screened across a viral or bacterial panel.

Comparison of polymerase chain reaction and immunologic methods for the detection of nanobacterial infection in type-III prostatitis

OBJECTIVE

To compare the results of polymerase chain reaction (PCR) and immunologic methods for the detection of nanobacteria (NB) in the expressed prostatic secretions (EPSs) of patients with type-III prostatitis.

METHODS

In total, 150 patients with type-III prostatitis for whom conventional clinical treatment had failed were selected from September 2009 to April 2010. The EPS of each patient was divided into 3 parts, which were used for PCR analysis, indirect immunofluorescence staining (IIFS), and culture and subsequent indirect immunofluorescence staining (CIIFS).

RESULTS

PCR analysis has a higher sensitivity than IIFS for the detection of NB in EPSs. Of 83 CIIFS-positive EPS samples, 79 (95.2%) were positive by PCR. Of 67 EPS samples that were negative by CIIFS, 60 (89.6%) were negative by PCR. The sensitivity of PCR for the detection of NB compared with the CIIFS method was 95.2%, with a specificity of 89.6%. The positive predictive value was 91.9%, and the negative predictive value was 93.8%. A comparative evaluation showed no statistically significant difference between PCR and CIIFS in the detection of NB in EPSs. A strong agreement in the positive and the negative results obtained by PCR and CIIFS for NB detection was found for all EPS samples.

CONCLUSION

PCR analysis has a higher sensitivity than IIFS for NB detection in type-III prostatitis. PCR can detect nanobacterial infection in type-III prostatitis equally well as CIIFS and offers significant advantages for the rapid, simple, and economical detection of nanobacterial infection in type-III prostatitis.

Screening of pneumococcal pneumonia by amplification of pneumolysin gene in children visiting hospitals in lahore, pakistan

OBJECTIVE

Streptococcus pneumoniae is a common worldwide potential pathogen causing pneumonia among children and the detection of pneumococcal infections by conventional culturing techniques is cumbersome. The present study describes a comparative analysis of sensitive nested-PCR and bacterial culture in pediatric patients with clinical and radiological indication of S. pneumoniae infection.

METHODS

PCR was performed using outer primers to amplify a 348-bp region and inner primers a 208-bp region of the pneumolysin gene. For pneumolysin PCR assay, DNA from peripheral blood and middle ear fluid (MEF) samples was extracted by salting out method. The sensitivity of the assay was evaluated with about 0.06 pg of purified S. pneumoniae genomic DNA.

FINDINGS

Among 90 MEF culture negative samples from acute otitis media pediatric patients, 8.8% pneumolysin-PCR positivity was detected, demonstrating the sensitivity and reliability of PCR for rapid pneumonia evaluation. Binomial test of proportionality performed on (SPSS 17) gives P< 0.05 indicating that PCR technique is statistically significant and sensitive in the diagnosis of S. pneumoniae infection.

CONCLUSION

The research work evaluated the effectiveness and efficacy of nested-PCR for detecting S. pneumoniae in pediatric patients with clinical and radiological confirmation of bacterial infection. This simplified method permitted quick selection of the patients and played a significant role in preliminary management of pneumococcal infections.

Enhanced detection and serotyping of Streptococcus pneumoniae using multiplex polymerase chain reaction

Purpose

Methods for quick and reliable detection of Streptococcus pneumoniae are needed for the diagnosis of pneumococcal disease and vaccine studies. This study aimed to show that sequential multiplex polymerase chain reaction (PCR) is more efficient than conventional culture in achieving S. pneumoniae-positive results.

Methods

Nasopharyngeal (NP) secretions were obtained from 842 pediatric patients admitted with lower respiratory infections at Severance Children's Hospital in Korea between March 2009 and June 2010. For identification and serotype determination of pneumococci from the NP secretions, the secretions were evaluated via multiplex PCR technique with 35 serotype-specific primers arranged in 8 multiplex PCR sets and conventional bacteriological culture technique.

Results

Among the results for 793 samples that underwent both bacterial culture and PCR analysis for pneumococcal detection, 153 (19.3%) results obtained by PCR and 81 (10.2%) results obtained by conventional culture technique were positive for S. pneumoniae. The predominant serotypes observed, in order of decreasing frequency, were 19A (23%), 6A/B (16%), 19F (11%), 15B/C (5%), 15A (5%), and 11A (4%); further, 26% of the isolates were non-typeable.

Conclusion

As opposed to conventional bacteriological tests, PCR analysis can accurately and rapidly identify pneumococcal serotypes.

Nasopharyngeal carriage of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Alloiococcus otitidis in young children in the era of pneumococcal immunization, Taiwan

We applied a multiplex polymerase chain reaction (PCR) and culture to detect Streptococcus pneumoniae and detected 3 other respiratory pathogens--Haemophilus influenzae, Moraxella catarrhalis, and Alloiococcus otitidis--simultaneously by PCR, in the nasopharynx of 386 children aged under 5 y. S. pneumoniae was the most common pathogen carried by children in all age groups, with the rate ranging from 15.8% in children aged 3-4 y to 28.6% in children aged 2-3 y. H. influenzae and M. catarrhalis showed similar carriage rates across all the age groups. Only 2 young children (0.5%) carried A. otitidis. Higher carriage of S. pneumoniae was found in children who had not received the heptavalent pneumococcal conjugate vaccine (PCV7). Cefotaxime non-susceptibility was high (51.4%) in S. pneumoniae nasopharyngeal isolates. Serotype 6B was the most common in fully immunized carriers and also in those who received catch-up immunization. Due to low PCV7 coverage in Taiwan, the carriage of vaccine and non-vaccine serotypes of S. pneumoniae in children remains common.

Predominance of nontypeable Haemophilus influenzae in children with otitis media following introduction of a 3+0 pneumococcal conjugate vaccine schedule

In Australia the 7-valent pneumococcal conjugate vaccine (PCV7) is administered at 2, 4 and 6 months of age, with no booster dose. Information on bacterial carriage and the aetiology of recurrent acute otitis media (rAOM) after introduction of PCV7 using the 3+0 schedule is required to evaluate the potential impact of second generation pneumococcal vaccines. We found that 2-4 years after introduction of PCV7 in the National Immunisation Program, nontypeable Haemophilus influenzae (NTHi) was the predominant pathogen isolated from the nasopharynx and middle ear of children with a history of rAOM. Compared with healthy controls (n=81), NTHi and Streptococcus pneumoniae carriage rates were significantly higher in children with a history of rAOM (n=186) (19% vs. 56% p<0.0001 and 26% vs. 41%, p=0.02, respectively). Carriage of PCV7 pneumococcal serotypes was rare, whereas PCV7-related and non-PCV7 serotypes were isolated of 38% of cases and 24% of controls. Serotype 19A was the most common serotype isolated from the nasopharynx and middle ear and accounted for 36% (14/39) of total pneumococcal isolates with reduced susceptibility to cotrimoxazole. Of the 119 children carrying NTHi, 17% of isolates were β-lactamase positive. The scarcity of PCV7 serotypes in children with and without a history of rAOM indicates that the 3+0 PCV7 schedule is preventing carriage and rAOM from PCV7 serotypes. Introduction of new vaccines in Australia with increased pneumococcal serotype and pathogen coverage, including 19A and NTHi, should decrease the circulation of antibiotic-resistant bacteria and reduce the burden of rAOM.

Prevalence of pilus-encoding islets and clonality of pneumococcal isolates from children with acute otitis media

We characterized the prevalence of pilus islets 1 (PI-1) and 2 (PI-2) and the clonality of Streptococcus pneumoniae isolates taken from children with acute otitis media (AOM) to study the association between pilus existence and AOM disease potential prior to pneumococcal conjugate vaccine and increased antimicrobial resistance. The study material consisted of 75 pneumococcal isolates cultured from the middle ear fluid and/or nasopharyngeal aspirate of 56 children with AOM in Finland during the period 1990-1992. Isolates were studied for antimicrobial susceptibility and were serotyped, genotyped by multilocus sequence typing (MLST), and tested for the presence of pneumococcal PI-1 and PI-2 genes. All isolates were susceptible to penicillin, 14 different serotypes were found, and 20% of the isolates were positive for PI-1 genes. PI-2 genes were not found. MLST showed high heterogeneity: 52 AOM isolates belonged to 18 known clonal complexes (CC). PI-1 was associated with serotypes 6A, 6B, and 9V, and genotype CC490. In the time prior to 7-valent pneumococcal conjugate vaccine (PCV7) and increased antimicrobial resistance, pneumococcal AOM isolates carried PI-1 genes at a rather low prevalence. PI-2 genes were not detected. PI-1 was related to serotype rather than genotype. The importance of PI-1 in AOM infections and its association with the spread of antimicrobial resistance requires further research.

Identification of Streptococcus pneumoniae and Haemophilus influenzae in culture-negative middle ear fluids from children with acute otitis media by combination of multiplex PCR and multi-locus sequencing typing

OBJECTIVE

Streptococcus pneumoniae (Spn) and Haemophilus influenzae (Hflu) are major etiologic pathogens for acute otitis media (AOM). However, when Spn and Hflu strains are not identified by traditional culture methods, use of alternative PCR-based diagnosis becomes critical. This study aimed to develop a combined molecular method to accurately detect these otopathogens.

METHODS

Middle ear fluid (MEF) samples were collected by tympanocentesis from children with AOM to isolate Spn and Hflu by standard culture procedures. Multiplex PCR (mPCR) and multi-locus sequence typing (MLST) techniques were used to detect Spn and Hflu in culture-negative MEF samples.

RESULTS

We found 20 Spn or Hflu culture-positive MEF samples that were mPCR-positive and typeable by MLST. The sequences of the housekeeping genes and the MLST allelic profiles obtained from Spn or Hflu culture isolates matched exactly MEF samples that were tested directly without culture isolation. Of 63 MEF samples that were culture-negative for Spn, 38% (24/63) were mPCR-positive for Spn. Of 50 MEF samples that were culture-negative for Hflu, 24% (12/50) were mPCR-positive for Hflu. Among these culture-negative but mPCR-positive MEF samples, 25% (6/24) and 25% (3/12) were typeable by MLST for Spn and Hflu, respectively.

CONCLUSIONS

MEF samples may be analyzed with mPCR and MLST directly without culture isolation and the addition of mPCR and MLST may accurately identify Spn and Hflu in MEF of children with AOM when bacterial culture is negative.

Efficacy of pneumococcal conjugate vaccine against PCR-positive acute otitis media

We aimed to assess the efficacy of a pneumococcal conjugate vaccine against acute otitis media (AOM) positive by pneumolysin-PCR (Ply-PCR). 1662 infants vaccinated with PncCRM or control vaccine using random allocation were followed for AOM up to 24 months of age. When AOM was diagnosed a middle ear fluid sample was obtained for etiological assays. During the per protocol follow-up period the PncCRM vaccine efficacy was 19% against Ply-PCR-positive AOM but only 3% when culture-positive cases were excluded. The data do not support effect of PncCRM on AOM in which only Ply-PCR suggests pneumococcal etiology.

Large scale multiplex PCR improves pathogen detection by DNA microarrays

Background

Medium density DNA microchips that carry a collection of probes for a broad spectrum of pathogens, have the potential to be powerful tools for simultaneous species identification, detection of virulence factors and antimicrobial resistance determinants. However, their widespread use in microbiological diagnostics is limited by the problem of low pathogen numbers in clinical specimens revealing relatively low amounts of pathogen DNA.

Results

To increase the detection power of a fluorescence-based prototype-microarray designed to identify pathogenic microorganisms involved in sepsis, we propose a large scale multiplex PCR (LSplex PCR) for amplification of several dozens of gene-segments of 9 pathogenic species. This protocol employs a large set of primer pairs, potentially able to amplify 800 different gene segments that correspond to the capture probes spotted on the microarray. The LSplex protocol is shown to selectively amplify only the gene segments corresponding to the specific pathogen present in the analyte. Application of LSplex increases the microarray detection of target templates by a factor of 100 to 1000.

Conclusion

Our data provide a proof of principle for the improvement of detection of pathogen DNA by microarray hybridization by using LSplex PCR.

Effect of swab composition and use of swabs versus swab-containing skim milk-tryptone-glucose-glycerol (STGG) on culture- or PCR-based detection of Streptococcus pneumoniae in simulated and clinical respiratory specimens in STGG transport medium

To detect Streptococcus pneumoniae colonization, the nasopharynx is sampled using a swab placed in skim milk-tryptone-glucose-glycerol (STGG) transport medium, and then the swab specimen or STGG medium is cultured or subjected to PCR. We evaluated the effect of swab composition and compared the sensitivities of detection of culture and PCR using swabs and swab-containing medium. Calcium alginate, Dacron polyester, or rayon-tipped swabs were inoculated with pneumococci or were immersed in nasal wash specimens from children and then placed in STGG medium. Swabs and medium inoculated with pneumococci were cultured. Swabs grew significantly more colonies than medium. The number of colonies cultured from rayon swabs or medium was significantly higher than the number cultured from the calcium alginate swab or medium. The number of colonies from both the Dacron polyester swabs and medium were significantly lower than with either calcium alginate or rayon swabs. When DNA was separately extracted from the calcium alginate swab and medium and subjected to PCR for pneumococcal detection from either S. pneumoniae-inoculated swabs or clinical specimens that grew S. pneumoniae, the sensitivity was at least 10 times higher using the swab. With Dacron polyester or rayon-tipped swabs, there was no consistent difference between the sensitivity of PCR using swabs and that of PCR using medium. Thus, calcium alginate swabs may be superior to STGG medium for the culture and PCR-based detection of S. pneumoniae. For culture, rayon swabs are superior and Dacron polyester swabs are inferior. The sensitivity of the swab and swab-containing medium for culture or PCR detection of S. pneumoniae varies with swab composition.

Diagnosis of Streptococcus pneumoniae meningitis by polymerase chain reaction amplification of the gene for pneumolysin

Diagnosis of bacterial meningitis has long been based on classical methods of Gram stain, serological tests, and culture of cerebrospinal fluid (CSF). The performance of these methods, especially culture and direct smear is thwarted by failure to detect bacteria following administration of antimicrobial agents and reluctance to performance lumbar punctures at admission. Indeed, patients with meningitis frequently receive antibiotics orally or by injection before the diagnosis is suspected or established Thus an alternative method has become necessary to help clinicians and epidemiologists to management and control of bacterial meningitis. We evaluate the application of a polymerase chain reaction-based (PCR) assay for amplification of pneumolysin gene (ply) to diagnosis of Streptococcus pneumoniae meningitis. The PCR assay sensitivity for CSF was 96% (95% confidence interval, CI, 90-99%) compared to a sensitivity of 59% for culture (95% CI 49-69%), 66% for Gram stain (95% CI 56-74%), and 78% for latex agglutination test (95% CI 69-86%); PCR specificity was 100% (95% CI 83-100%). PCR results were available within 4 h of the start of the assay. This molecular approach proved to be reliable and useful to identify this bacterium compared with other classical laboratory methods for identification of bacterial meningitis pathogens.

Viral upper respiratory tract infections in young children with emphasis on acute otitis media

Viral upper respiratory infection is the most common reason for seeking medical care for children. Recurrent viral respiratory infections and subsequent complications (e.g. acute otitis media (AOM)) are a burden for children, their families and society. Over the past decade, our knowledge on the significance of respiratory viruses has broadened remarkably. Viruses cause large variety of respiratory diseases and cause alone diseases, which previously have been assumed to be bacterial only (e.g. AOM and pneumonia). Methods for detection analysis of respiratory viruses are developing making both the diagnosis and epidemiological investigations of respiratory infections easier. Accurate diagnosis of respiratory infections and awareness of possible viral etiology could reduce the use of antibiotics. Etiologic studies of viral infections are becoming increasingly important, with the emergence of new antiviral drugs and vaccines.

Real-time pneumolysin polymerase chain reaction with melting curve analysis differentiates pneumococcus from other alpha-hemolytic streptococci

The majority of pneumococcal isolates can be identified by the conventional methods based on phenotypic characteristics. Occasionally, however, the differentiation of alpha-hemolytic streptococci from pneumococci, especially those isolated from nasopharynx, is problematic due to the discrepant results obtained by the conventional identification methods. Several gene technological methods based on the amplification of genes encoding pneumococcal virulence factors, such as pneumolysin (ply) and autolysin, have been used as additional identification methods. Recent studies have shown that especially the ply gene is frequently also present in nonpneumococcal alpha-hemolytic streptococci. In this study, we compared the commonly used phenotypic identification methods with nucleic acid-based methods, commercial AccuProbetrade mark, conventional pneumolysin polymerase chain reaction (Ply-PCR), and real-time Ply-PCR in the identification of alpha-hemolytic streptococcal strains isolated from 100 consecutive nasopharyngeal specimens. We also studied if melting curve analysis and sequencing of the amplification products of a ply gene fragment could be helpful in the identification. Our results suggest that the ply gene present in alpha-hemolytic streptococci differs from that present in pneumococcus, and that melting curve analysis would prove useful in the differentiation of these bacteria.

Serum antibodies to putative proteinase maturation protein A in children with acute otitis media

The pneumococcal genes encoding for the surface associated proteins have been proposed to be important for pneumococcal protein vaccine development. We cloned the full-length putative proteinase maturation protein A gene SP098l/ppmA (as published by Tettelin et al. in 2001) and produced the encoded protein in high levels in E. coli. The purified recombinant PpmA was used as an antigen in Western blotting to study systemic antibody responses to PpmA in animals and in children with acute otitis media (AOM). In children, the geometric mean titers of serum IgG antibodies against PpmA increased with age and differed significantly in relation to pneumococcal findings in middle ear fluid and/or nasopharyngeal aspirate. The serum IgG antibody titers against PpmA were low in children with Streptococcus pneumoniae cultured in the middle ear, and the highest in children with pneumococci in the nasopharynx, without them being found in the middle ear fluid. We conclude that PpmA is immunogenic in humans, and therefore an interesting antigen to study further in developing pneumococcal multicomponent protein vaccines.

Isolation of pneumococcal DNA from nasopharyngeal samples for real-time, quantitative PCR: comparison of three methods

BACKGROUND

Real-time PCR is a useful method for detecting and quantifying bacterial DNA in clinical samples. DNA extraction is a crucial step when performing quantitative PCR.

METHODS

We compared three methods, QIAamp. The use of tradenames is for product identification purposes only and does not imply endorsement. DNA Mini kit, MagNAPure trade mark LC DNA Isolation Kit II together with PickPen trade mark magnetic particle transfer device, and KingFisher genomic DNA purification Kit with KingFisher mL instrument, for purification of Streptococcus pneumoniae DNA from 50 nasopharyngeal swab samples, collected into skim milk-tryptone-glucose-glycerin medium. Pneumococcal DNA was detected and quantified by real-time PCR and results were compared to culture findings.

RESULTS

The 22 (44%) pneumococcal culture-positive specimens were all positive by PCR regardless of DNA extraction method used, except that one KingFisher-extracted sample was positive only when repeatedly tested. Additionally, 71%, 57%, and 82% of the culture-negative samples were positive by real-time PCR when DNA was extracted by QIAamp, MagNAPure-PickPen, and KingFisher methods, respectively. The number of genome equivalents detected by real-time PCR varied, but was mainly low in culture-negative samples. The sensitivities of culture and real-time PCR were hence compared by analyzing different dilutions of a pneumococcal suspension. Real-time PCR detected significantly higher numbers of genome equivalents than the numbers of bacteria detected by culture.

CONCLUSIONS

The results indicate that the DNA extraction method used for quantitative PCR should be evaluated and that real-time PCR is more sensitive than bacterial culture for detecting pneumococcus in nasopharyngeal swab samples.

Advances in Pneumococcal Vaccines

The introduction of Haemophilus influenzae type b (Hib) vaccine into the universal immunisation schedules of many industrialised countries and the subsequent remarkable decline in the incidence of invasive Hib disease has further highlighted the impact of invasive pneumococcal diseases. Streptococcus pneumoniae is now the leading cause of bacterial meningitis in children in many settings and a leading cause of vaccine-preventable bacterial disease in children worldwide. The currently marketed 23-valent pneumococcal polysaccharide vaccine provides large serotype coverage at a relatively low cost. However, it is not efficacious in young children. Pneumococcal conjugate vaccines (PCVs) are highly effective in preventing invasive disease in infants and young children, with favourable safety and immunogenicity profiles. These vaccines have also shown efficacy in reducing cases of non-invasive disease (i.e. otitis media), nasopharyngeal acquisition of vaccine-specific serotypes of S. pneumoniae, and protection against pneumococcal disease caused by resistant strains. However, PCV contains a limited number of pneumococcal serotypes and, given adequate ecological pressure, replacement disease by non-vaccine serotypes remains a threat, particularly in areas with very high disease burden. Furthermore, although capsular-specific antibodies have been shown to be highly protective, it remains unclear what concentration of these serotype-specific antibodies protect against disease and, more recently, it has become clear that opsonic activity and avidity of these antibodies are more critical determinants of protection than concentration. Therefore, monitoring disease burden and defining immune correlates of protection after widespread use of conjugate vaccines are crucial for the evaluation of these new generation vaccines. Furthermore, a need exists to develop pneumococcal vaccines with lower cost and larger serotype coverage. Development of one or more protein vaccines that might be easier and, thus, less expensive to manufacture, and which might provide protection against multiple serotypes, is in progress. This article reviews the current state of pneumococcal disease and pneumococcal vaccines in clinical use.

Accuracy of phenotypic and genotypic testing for identification of Streptococcus pneumoniae and description of Streptococcus pseudopneumoniae sp. nov

We have identified an unusual group of viridans group streptococci that resemble Streptococcus pneumoniae. DNA-DNA homology studies suggested that a subset of these isolates represent a novel species that may be included in the S. oralis-S. mitis group of viridans group streptococci. We suggest that this novel species be termed Streptococcus pseudopneumoniae. A combination of phenotypic and genetic reactions allows its identification. S. pseudopneumoniae strains do not have pneumococcal capsules, are resistant to optochin (inhibition zones, less than 14 mm) when they are incubated under an atmosphere of increased CO2 but are susceptible to optochin (inhibition zones, >14 mm) when they are incubated in ambient atmospheres, are not soluble in bile, and are positive by the GenProbe AccuProbe Pneumococcus test. The bile solubility test is more specific than the optochin test for identification of S. pneumoniae. Genetic tests for pneumolysin (ply) and manganese-dependent superoxide dismutase (sodA) and identification tests with a commercial probe, AccuProbe Pneumococcus, do not discriminate between the new species and S. pneumoniae.

Pneumolysin is a key factor in misidentification of macrolide-resistant Streptococcus pneumoniae and is a putative virulence factor of S. mitis and other streptococci

We evaluated the applicability of ply PCR for confirmation of the identification of Streptococcus pneumoniae. lytA PCR, 16S rRNA sequencing, and amplified-fragment length polymorphism were used as reference methods. In contrast to the lytA gene, the ply gene proved to be not specific for S. pneumoniae. The presence of the ply gene in other streptococci, in particular Streptococcus mitis, suggests that pneumolysin plays a pathogenic role.

Streptococcus pneumoniae in nasopharyngeal secretions of healthy children: comparison of real-time PCR and culture from STGG-transport medium

Precise methods for the detection of Streptococcus pneumoniae are needed for predicting the consequences of pneumococcal conjugate vaccines on nasopharyngeal carriage. In this study, 400 nasopharyngeal swab samples from children were analyzed using a real-time pneumolysin (ply)-PCR method. The specimens were originally collected into STGG-transport medium and cultured in 1999, after which they were stored at -80 degrees C until analyzed by real-time PCR in 2001. The sensitivities of real-time PCR and culture methods were also studied by analyzing 10-fold dilutions of a pneumococcal broth culture using both methods. Of the 400 nasopharyngeal swab samples, 158 (40%) were positive in culture and 276 (69%) by real-time PCR. A minor part (4%) of the culture-positive samples remained negative by PCR. There was a trend between the quantity of genome equivalents detected by PCR and the number of colonies found in culture. When analyzing 10-fold dilutions of a pneumococcal broth culture, a higher number of genome equivalents were detected using real-time PCR than the number of colonies detected by culture. Quantitative real-time PCR provides feasible means for quantifying pneumococcal carriage. Further studies are needed to confirm that positive PCR findings really indicate the presence of viable pneumococcus in nasopharyngeal specimens.

Comparison of four polymerase chain reaction assays for specificity in the identification of Streptococcus pneumoniae

We determined the usefulness of 4 conventional polymerase chain reaction (PCR) assays, lytA, psaA, and two primer sets from the ply gene, for accuracy in the discrimination of nontypeable (NT) Streptococcus pneumoniae from closely related atypical streptococci. The study used 100 strains. We compared the PCR results with laboratory tests that included optochin (ethylhydrocupreine hydrochloride) sensitivity, bile solubility, the Quellung reaction, and AccuProbe (Gen-Probe Inc., San Diego, CA). These latter tests did not discriminate the atypical streptococci from the NT pneumococci. All PCR primer sets amplified the NT pneumococcal isolates in agreement with the other laboratory tests. However, the IA and IB ply primers were positive for 8 of the 16 atypical streptococcal isolates, and the IIA and IIB ply primers amplified all atypical isolates. The psaA primers had only one discrepant result, a positive among the atypical streptococci. The lytA primers were the most specific with 100% specificity for all strains tested.

Detection rates of bacteria in chronic otitis media with effusion in children

This study was performed to investigate polymerase chain reaction-based detection of bacterial DNA in middle ear fluid and assess the correlation between the PCR-positive rate with several factors associated with middle ear effusion. The purpose was to gain a further understanding of bacterial infection as a major cause of otitis media with effusion. Of the 278 specimens of middle ear fluid, 39 (14%) tested positive by ordinary culture. The overall detection rate of bacterial DNA using the PCR method was 36.7% for middle ear effusion, and bacterial DNA detection rates of Hemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis in the middle ear effusion were 29.1%, 4.7% and 10.8%, respectively. The bacterial DNA detection rate was higher in ears with a history of acute otitis media than those without the history. High detection rates were observed in patients younger than 48 months who have had a higher tendency to present with acute otitis media. We concluded that PCR is a more sensitive method for the detection of bacteria in middle ear effusion than ordinary culture, and acute otitis media is a major contributor to the pathogenesis of otitis media with effusion.

Persistent Colonization byHaemophilus influenzaein Chronic Obstructive Pulmonary Disease

Nontypeable Haemophilus influenzae colonizes the respiratory tract of adults with chronic obstructive pulmonary disease (COPD) and causes intermittent exacerbations. Isolates of H. influenzae collected monthly in a prospective study were subjected to molecular typing. During a 7-year study spanning 345 patient-months of observation, 122 episodes of negative cultures lasting 1 month or more, and that were preceded and followed by isolation of an apparently identical strain of H. influenzae, were found. Seventeen such episodes of negative cultures, lasting 6 months or more and spanning 203 patient-months, were studied in detail to test the hypothesis that these periods of negative cultures represented continuous colonization by the same strain of H. influenzae. Molecular typing by three independent methods established that the strains preceding and following the episodes of negative cultures were indeed identical. Strain-specific H. influenzae DNA was detected in some of the sputum samples that had yielded negative cultures. These results indicate that some patients with COPD are persistently colonized with H. influenzae and that sputum cultures underestimate the frequency of colonization of the respiratory tract by H. influenzae in COPD. This observation has a significant impact on understanding bacterial colonization in COPD.

Type-specific enzyme immunoassay for detection of pneumococcal capsular polysaccharide antigens in nasopharyngeal specimens

We developed a new competitive EIA method for the demonstration of pneumococcal capsular polysaccharides from respiratory samples. The pediatric types 4, 6B, 9V, 14, 18C, 19F and 23F were selected for this study, because these capsular polysaccharides were included in the first heptavalent pneumococcal conjugate vaccines, which were used in the Finnish Otitis Media Vaccine Trial. Sensitivity of the EIA tests for purified polysaccharide antigens varied between 5 and 100 ng/ml, depending on the type. The assays performed well in 100 nasopharyngeal samples (NPS) samples processed through an enrichment culture, with an almost 100% sensitivity compared with routine culture. The method appeared type-specific, except that EIA for 6B capsule also detected 6A. The method is applicable for type-specific identification of pneumococcus in carriage studies.

Alloiococcus otitidis in acute otitis media

OBJECTIVE

The bacterium Alloiococcus otitidis has been found to be associated with otitis media with effusion (OME). When the culture method is used, its detection rate is low, whereas applying the polymerase chain reaction (PCR) yields significantly higher frequencies. This study was carried out to investigate the incidence of A. otitidis in children with acute otitis media (AOM).

METHODS

Multiplex PCR was used to detect A. otitidis together with Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae in the middle ear effusions (MEEs) of 118 children with AOM. The clinical outcome of AOM and the bacterial findings of MEEs were compared.

RESULTS

A. otitidis was detected in 25% (30 of 118) of the tested MEE samples. Children over 2 years of age had significantly more often A. otitidis-positive MEEs (37%; 22 of 59) than younger children (14%; 8 of 59) (chi-square test, P<0.01). There were no significant differences in the duration, clinical failures (after antibiotic treatment), or number of recurrences of AOM between the A. otitidis-positive and A. otitidis-negative children.

CONCLUSIONS

A. otitidis is found from the MEEs of AOM. The present data suggest that it has no clinical significance in AOM, and it does not increase the risk of developing OME after AOM.

Comparison of five genotypic techniques for identification of optochin-resistant pneumococcus-like isolates

Three PCR techniques (amplification of the psaA, ply, and lytA genes) and a commercial kit (AccuProbe [GenProbe, San Diego, Calif.], based on hybridization with the 16S rRNA gene), all four of which claimed to be specific for Streptococcus pneumoniae, were used to identify 49 alpha-hemolytic streptococcal isolates suspected of being pneumococci. The definite phenotypic identification of these organisms as S. pneumoniae was difficult when optochin susceptibility and the presence of a capsule were taken as markers. Furthermore, RsaI digestion of the amplified 16S rRNA gene was applied. All 49 strains were optochin resistant. Eleven of these were encapsulated and were identified as pneumococci by all tests. Twenty of the 38 unencapsulated strains were unambiguously identified as nonpneumococci by all tests. The identities of another 18 unencapsulated strains remained inconclusive due to highly variable reactions for all phenotypic and genotypic techniques applied. The AccuProbe test was positive for seven strains for which the results of the other tests were inconclusive. RsaI restriction of the amplified 16S rRNA gene confirmed the AccuProbe result for all strains, while the result of the psaA-specific PCR was in concordance with encapsulation for all strains. The results presented here indicate that identification problems continue to exist for some strains, despite the application of genotypic and phenotypic tests in combination. We found the psaA-specific PCR to be the genotypic technique best suited for the identification of genuine pneumococci and optochin-resistant pneumococci.

Viridans group streptococci are donors in horizontal transfer of topoisomerase IV genes to Streptococcus pneumoniae

A total of 46 ciprofloxacin-resistant (Cip(r)) Streptococcus pneumoniae strains were isolated from 1991 to 2001 at the Hospital of Bellvitge. Five of these strains showed unexpectedly high rates of nucleotide variations in the quinolone resistance-determining regions (QRDRs) of their parC, parE, and gyrA genes. The nucleotide sequence of the full-length parC, parE, and gyrA genes of one of these isolates revealed a mosaic structure compatible with an interspecific recombination origin. Southern blot analysis and nucleotide sequence determinations showed the presence of an ant-like gene in the intergenic parE-parC regions of the S. pneumoniae Cip(r) isolates with high rates of variations in their parE and parC QRDRs. The ant-like gene was absent from typical S. pneumoniae strains, whereas it was present in the intergenic parE-parC regions of the viridans group streptococci (Streptococcus mitis and Streptococcus oralis). These results suggest that the viridans group streptococci are acting as donors in the horizontal transfer of fluoroquinolone resistance genes to S. pneumoniae.

Importance of respiratory viruses in acute otitis media

Acute otitis media is usually considered a simple bacterial infection that is treated with antibiotics. However, ample evidence derived from studies ranging from animal experiments to extensive clinical trials supports a crucial role for respiratory viruses in the etiology and pathogenesis of acute otitis media. Viral infection of the upper respiratory mucosa initiates the whole cascade of events that finally leads to the development of acute otitis media as a complication. The pathogenesis of acute otitis media involves a complex interplay between viruses, bacteria, and the host's inflammatory response. In a substantial number of children, viruses can be found in the middle-ear fluid either alone or together with bacteria, and recent studies indicate that at least some viruses actively invade the middle ear. Viruses appear to enhance the inflammatory process in the middle ear, and they may significantly impair the resolution of otitis media. Prevention of the predisposing viral infection by vaccination against the major viruses would probably be the most effective way to prevent acute otitis media. Alternatively, early treatment of the viral infection with specific antiviral agents would also be effective in reducing the occurrence of acute otitis media.

Acute mastoiditis caused by Moraxella catarrhalis

Acute mastoiditis is the most frequent intratemporal complication of otitis media. The bacteriology of acute otitis media is changing continuously and it differs markedly from the bacteriology of acute mastoiditis. Moraxella catarrhalis (M. catarrhalis) is the third most common bacteria found in acute otitis media, and in recent years its importance as an etiological factor of acute otitis media has markedly increased in certain geographic areas. However, there are no reports of acute mastoiditis caused solely by M. catarrhalis. This report describes a case of a 2-year-old girl with acute mastoiditis and M. catarrhalis in the bacterial culture of middle ear effusion.

Real-time quantitative PCR for the detection of Streptococcus pneumoniae in the middle ear fluid of children with acute otitis media

PCR based on the amplification of pneumolysin gene fragments has previously been applied to demonstrate Streptococcus pneumoniae in clinical specimens. Here, a real-time PCR method for the detection and quantification of pneumococci by amplifying a 206-bp fragment of the pneumolysin-encoding gene is described. The amplified fragments were detected simultaneously using fluorescent-labeled sequence-specific hybridization probes. The applicability of the assay to clinical samples was evaluated by studying 50 middle ear fluid (MEF) specimens from children with acute otitis media. Twenty-six of the MEF samples were positive by real-time PCR and the numbers of genome equivalents detected varied from 90 to 88,000/microl in 17 culture-positive samples and from 1 to 1,200/microl in 9 culture-negative samples. The results were compared to culture findings and to results obtained by using agarose gel electrophoresis or Europium-labeled hybridization probes for the detection of amplification products of conventional PCR. The sensitivity and specificity of the real-time PCR assay developed in the present study compared to culture were 100 and 73%, and to conventional PCR with agarose gel and/or TRF detection 93 and 96%, respectively. The real-time PCR assay was found to be rapid, easy to use, and sensitive in detecting and quantifying pneumococci.

Evaluation of gene-technological and conventional methods in the identification of Streptococcus pneumoniae

To find reliable methods able to identify the "difficult" Streptococcus pneumoniae isolates, an in-house polymerase chain reaction (PCR) for pneumolysin gene (Ply-PCR) and a commercial RNA hybridisation test (AccuProbe) were evaluated. Selected isolates of suspected pneumococci, sent for confirmation of identification and for serotyping, were classified into four groups based on their optochin sensitivity and capsule reaction. All isolates in Group 1, which consisted of 24 typical, optochin-sensitive, encapsulated pneumococcal strains, were positive in the Ply-PCR and AccuProbe tests. In Group 2, which consisted of 25 optochin-sensitive, but unencapsulated pneumococcal strains, all the isolates were positive in the Ply-PCR test, and 23 were positive in the AccuProbe test. In Group 3, which consisted of 15 atypical, optochin-resistant but encapsulated pneumococci, 12 of the isolates were positive in the Ply-PCR and 12 in the AccuProbe test, and 11 of these 12 strains were positive in both tests. In Group 4, which consisted of 36 equivocal optochin-resistant, unencapsulated isolates, 15 strains were positive in the Ply-PCR test and 8 strains in the AccuProbe test. As a conclusion, the Ply-PCR and AccuProbe tests identified similarly typical optochin-sensitive pneumococci, but gave partly controversial results about atypical pneumococci. Thus, they did not reliably help in the identification of suspected pneumococcal isolates lacking the conventional characteristics of pneumococcus.

Detection of Streptococcus pneumoniae DNA by using polymerase chain reaction and microwell hybridization with Europium-labelled probes

The present paper describes a novel modification of polymerase chain reaction (PCR) for the detection of Streptococcus pneumoniae DNA in clinical specimens. PCR was based on the detection of a 209-base pair segment of the S. pneumoniae pneumolysin gene. For the demonstration of the amplification product, microwell hybridization with a Europium-labelled oligonucleotide probe complementary to a biotinylated strand of the PCR product was performed, and the presence of the PCR product was monitored by time-resolved fluorescence (TRF) of the Europium chelate. The sensitivity of the assay for purified S. pneumoniae DNA was 50 fg DNA corresponding to 20 genome equivalents of S. pneumoniae DNA. The efficiency of the hybridization step was monitored by using known amounts of synthetic target oligonucleotides as standards. Sensitivity of 3 x 10(8) molecules per individual reaction well was achieved with a 30-min attachment time and a 3-h hybridization time. Detection of PCR-amplified products by the microwell hybridization technique and TRF was compared to agarose gel electrophoresis in 50 middle ear fluid samples obtained from children with acute otitis media. The agarose gel and TRF detection methods identified all culture-positive samples, but both were also positive for 55% of the culture-negative samples. The results suggest that the detection of amplified PCR products by microwell hybridization using Europium-labelled oligonucleotides is a reliable method for the demonstration of the pneumolysin gene fragment. Furthermore, the method is suitable for automation and, thus, for testing high numbers of samples. The clinical significance of the PCR findings remains to be studied.

Clinical outcome of acute pneumococcal otitis media and serum antibody responses to pneumococcal pneumolysin and polysaccharides in children

Serum antibody responses to pneumococcal antigens and their relationship to the clinical outcome were determined in a prospective study of 121 children with acute otitis media (AOM). Pneumococcus positive children with a pneumolysin response more often had a recurrence and middle ear effusion (MEE) after 1 month than did the non-responders (p = 0.005 and p = 0.04, respectively). All the children who responded to pneumolysin also had clinically strong symptoms and signs of AOM. Children who responded to pneumococcal polysaccharides developed otitis media with effusion within a 6-month follow-up period more often than did the non-responders (p = 0.005). The results of this study suggest that children with pneumococcal AOM and an antibody response to the intracellular pneumococcal protein pneumolysin behave clinically differently from children with an antibody response to polysaccharides.

Factors associated with the development of recurrent acute otitis media--the significance of choosing the right and accurate dependent and independent variables in the multivariate analysis

The results of univariate and multivariate statistical analysis were compared in identifying predictive factors of the development of recurrent acuta otitis media (RAOM) after an initial episode of acute otitis media (AOM) in 121 children. Univariate correlations between the development of RAOM and potential risk factors were analysed, and variables at p < 0.10 were incorporated into the stepwise multiple logistic regression analysis. The comparisons between the univariate and multivariate analysis in identifying the predictive factors were made and the importance of changing the dependent variables in the multivariate analysis was analysed. It seems that univariate analysis is over-sensitive, but multivariate analysis is over-conservative in finding possible predictors of RAOM. Choosing the right and accurate dependent and independent variables in the multivariate analysis is extremely important, when this method is used.

Community-acquired pneumonia

Community-acquired pneumonia (CAP) remains a leading cause of morbidity and mortality worldwide and has significant financial implications for health-care systems. The epidemiology and fundamental biology of the disease has evolved, reflecting the human immunodeficiency virus pandemic, increasing world travel, and, as always, poverty. The promise held out by molecular diagnostic technology has yet to deliver in this arena, and antibiotic resistance continues to drive the quest for new antimicrobial agents. The emergence of multidrug-resistant Streptococcus pneumoniae, the microorganism most often implicated as a cause of CAP, continues to threaten treatment options. The evolution of this organism, the persistently high mortality rate associated with CAP, and increasing health-care costs have prompted the publication of guidelines by various authorities that can be used to assist in the initial assessment of the patient and then guide empirical antimicrobial therapy. It is unclear whether these guidelines will have significant impact on cost and mortality, although the trend toward a rational and evidence-based approach to antimicrobial therapy must be a goal to aspire to.

Horizontal transfer of parC and gyrA in fluoroquinolone-resistant clinical isolates of Streptococcus pneumoniae

We have analyzed genetically three clinical isolates (3180, 3870, and 1244) of Streptococcus pneumoniae with high-level ciprofloxacin resistance. Isolates 3180 and 3870 were atypical because of their insolubility in deoxycholate. However, they hybridized specifically with pneumococcal autolysin and pneumolysin gene probes and have typical pneumococcal atpC and atpA gene sequences. Analysis of the complete sequences of the parC and gyrA genes revealed total variations of 8 and 8.7% (isolate 3180) and 7.4 and 3.6% (isolate 3870), respectively, compared to the wild-type strain R6 sequence. The variations observed between the sequences of R6 and isolate 1244 were less than 0.9%. The structure of the gyrA and parC genes from isolates 3180 and 3870 was organized in sequence blocks that show different levels of divergence, suggesting a pattern of recombination. These results are evidence for recombination at the fluoroquinolone target genes in clinical isolates of S. pneumoniae. The genetically related viridans group streptococci could act as a reservoir for fluoroquinolone resistance genes.

Viral-Bacterial Synergy in Otitis Media: Implications for Management

Despite the extensive use of broad-spectrum antibiotics, poor clinical response to the treatment of acute otitis media is common. Evidence derived from numerous studies during the past two decades supports a crucial role for respiratory viruses in the etiology and pathogenesis of acute otitis media, and recent studies indicate that viruses may also have a profound adverse effect on the resolution of this disease. Viruses seem to interact with bacteria and enhance the local inflammatory process in the middle ear. Effective adjuvant therapies are needed to improve outcome in children with otitis media. Increasing knowledge of the role of viruses, viral-bacterial interaction, and host inflammatory mechanisms in otitis media may lead to major improvements in the management of this disease.

Quantitative analysis of the effect of xylitol on pneumococcal nasal colonisation in rats

Xylitol possesses anti-bacterial effects on pneumococci in vitro. To study the effect in vivo, the nostrils of 80 rats were inoculated with pneumococci. Intervention groups (n = 20) received either a xylitol diet or xylitol nasal sprays. The control groups were on a normal diet or had saline sprays. After 3 days, a quantitative bacterial culture and a PCR were done from the mucosal suspension. Neither the mean colony-forming unit counts nor the PCR counts differed statistically significant between the xylitol and control groups. Thus, we found that xylitol had no significant effect on pneumococcal mucosal colonisation.

Expression of intercellular adhesion molecule-1 in rat inner ear due to bacterial otitis media

Expressions of anti-Streptococcus pneumoniae antibody and anti-intercellular adhesion molecule-1 (ICAM-1) antibody in the inner ear were studied immunohistochemically in rats following inoculation of S pneumoniae type 6A into the middle ear cavity. Positive staining with anti-S pneumoniae antibody was detected in the marginal cells of the stria vascularis of rats sacrificed 3 days after S pneumoniae inoculation, but almost no staining was detected in those sacrificed at 14 days. Strong ICAM-1 expression was detected in the basal cell layer of the stria vascularis of rats sacrificed 3 days after inoculation, but the intensity of the staining had decreased by 14 days. These results suggest that the stria vascularis may be a site of the inner ear damage that follows bacterial inoculation into the middle ear cavity. The up-regulated expression of ICAM-1 in the basal cell layer may represent a reaction of the inner ear to the bacterial otitis media.