Diagnosis of Streptococcus pneumoniae infections in adults with bacteremia and community-acquired pneumonia: clinical comparison of pneumococcal PCR and urinary antigen detection

Performance Characteristics of a Real-Time PCR Assay for Direct Detection of Streptococcus pneumoniae in Clinical Specimens

Community-acquired pneumonia and complications, such as bacteremia and meningitis due to Streptococcus pneumoniae infection, still occur in at-risk populations, despite the availability of effective vaccines. Laboratory confirmation of S. pneumoniae remains challenging despite advances in blood culture techniques and the availability of nucleic acid-amplification tests. The goal of this study was to determine the performance characteristics of a molecular assay designed as a diagnostic test using primary clinical specimens for invasive pneumococcal disease. The molecular assay adapted for the Luminex Aries instrument targets an S. pneumoniae-specific gene (autolysin, lytA) in clinical specimens. Using real-time PCR MultiCode technology, four different clinical specimen types were evaluated. Specimen types included bronchoalveolar lavage, whole blood, cerebrospinal fluid, and urine to cover the various presentations and appropriate specimen types for invasive pneumococcal infections. The lower limit of detection in urine was 10 colony forming units (CFU)/mL, while in bronchoalveolar lavage, cerebrospinal fluid, and whole blood, it was 100 CFU/mL. Accuracy and specificity were both 100%, and all specimen types were stable for 8 days at 4°C. Finally, 38 clinical specimens were tested to further evaluate the assay. The performance characteristics met Clinical Laboratory Improvement Amendments standards for a clinical diagnostic assay, and the assay offers a sensitive and specific real-time PCR test for direct detection of S. pneumoniae in relevant clinical specimens.

Will Antigen Testing Remain Relevant in the Point-of-Care Testing Environment?

Before the molecular age, cell culture was the gold standard for confirmatory diagnosis of viral and atypical infectious diseases. Typical cell culture methodologies are costly, require days (or weeks) for results, and require significant technical expertise. As a result, cell culture is impractical for timely diagnostic testing in most of the health care environments. Traditional bacterial culture methods, also have disadvantages due to the need for incubation, subsequent identification of pathogens, and significant technical expertise. This article discusses the general considerations of antigen and molecular assays and the merits and factors to consider when implementing diagnostic assays for several common pathogens.

Nuclease activity: an exploitable biomarker in bacterial infections

INTRODUCTION

In the increasingly challenging field of clinical microbiology, diagnosis is a cornerstone whose accuracy and timing are crucial for the successful management, therapy, and outcome of infectious diseases. Currently employed biomarkers of infectious diseases define the scope and limitations of diagnostic techniques. As such, expanding the biomarker catalog is crucial to address unmet needs and bring about novel diagnostic functionalities and applications.

AREAS COVERED

This review describes the extracellular nucleases of 15 relevant bacterial pathogens and discusses the potential use of nuclease activity as a diagnostic biomarker. Articles were searched for in PubMed using terms: "nuclease", "bacteria", "nuclease activity" or "biomarker". For overview sections, original and review articles between 2000 and 2019 were searched for using terms: "infections", "diagnosis", "bacterial", "burden", "challenges". Informative articles were selected.

EXPERT OPINION

Using the catalytic activity of nucleases offers new possibilities compared to established biomarkers. Nucleic acid activatable reporters in combination with different transduction platforms and delivery methods can be used to detect disease-associated nuclease activity patterns in vitro and in vivo for prognostic and diagnostic applications. Even when these patterns are not obvious or of unknown etiology, screening platforms could be used to identify new disease reporters.

Micro/nanotechnology-inspired rapid diagnosis of respiratory infectious diseases

Humans have suffered from a variety of infectious diseases since a long time ago, and now a new infectious disease called COVID-19 is prevalent worldwide. The ongoing COVID-19 pandemic has led to research of the effective methods of diagnosing respiratory infectious diseases, which are important to reduce infection rate and help the spread of diseases be controlled. The onset of COVID-19 has led to the further development of existing diagnostic methods such as polymerase chain reaction, reverse transcription polymerase chain reaction, and loop-mediated isothermal amplification. Furthermore, this has contributed to the further development of micro/nanotechnology-based diagnostic methods, which have advantages of high-throughput testing, effectiveness in terms of cost and space, and portability compared to conventional diagnosis methods. Micro/nanotechnology-based diagnostic methods can be largely classified into (1) nanomaterials-based, (2) micromaterials-based, and (3) micro/nanodevice-based. This review paper describes how micro/nanotechnologies have been exploited to diagnose respiratory infectious diseases in each section. The research and development of micro/nanotechnology-based diagnostics should be further explored and advanced as new infectious diseases continue to emerge. Only a handful of micro/nanotechnology-based diagnostic methods has been commercialized so far and there still are opportunities to explore.

Identifying pneumococci in parapneumonic pleural effusion: Is there a role for culture-independent methods?

OBJECTIVE

To evaluate culture-independent procedures (immunochromatography and quantitative polymerase chain reaction [qPCR]) in the detection and susceptibility of Streptococcus pneumoniae directly from culture-negative pleural fluid (PF) in children.

METHOD

Detection of S. pneumoniae in PF of children with parapneumonic effusion and/or empyema by using two culture-independent methods: an immunochromatographic membrane test (IMT) which identifies the pneumococcal C antigen, and a real-time PCR test to detect pneumococcal genes lytA and pbp2b, a marker of susceptibility of β-lactam agents, in PF samples.

RESULTS

We tested 36 PF specimens and recorded the previous use of antimicrobials. In the final analysis, 34 samples were included. IMT and qPCR presented positive results in 23 (67.6%) and 24 (70.6%) of the samples, respectively, showing a moderate agreement (k = 0.518) between the two methods. From the 36 children included, 34 (94.4%) had antibiotic data available by the time when PFs were collected. Thirty-four (100%) children had been given treatment before PF sampling, with 33 (97%) receiving β-lactam antibiotics administered empirically. Of the 24 lytA real-time positive samples, 21 (87.5%) were also positive for pbp2b, a marker of β-lactam susceptibility.

CONCLUSION

The reduced sensitivity of culture for pneumococcal detection can be improved through the addition of IMT and qPCR analysis. The utility of qPCR combining detection of lytA and a marker of β-lactam susceptibility should be explored further.

Rapid Detection of Respiratory Pathogens for Community-Acquired Pneumonia by Capillary Electrophoresis-Based Multiplex PCR

Community-acquired pneumonia (CAP) is a common infectious disease linked to high rates of morbidity and mortality. Fast and accurate identification of the pathogens responsible for CAP will aid in diagnosis. We established a capillary electrophoresis-based multiplex PCR (CEMP) panel to enable the detection of viral and bacterial pathogens associated with CAP. The assay simultaneously detects and identifies the 13 common unculturable CAP viral and bacterial pathogens within 4 h. We evaluated the performance of a commercially available panel with 314 samples collected from CAP patients. We compared the results to those obtained with the liquid chip-based Luminex xTAG Respiratory Viral Panel (RVP) Fast Kit (for viruses) and the agarose gel-based Seegene PneumoBacter ACE Detection Kit (for atypical bacteria). All positive samples were further verified by the Sanger sequencing method. The sensitivity, specificity, positive predictive value, and negative predictive value of CEMP were 97.31%, 100%, 100%, and 99.85%, respectively. CEMP provides a rapid and accurate method for the high-throughput detection of pathogens in patients with CAP.

lytA Quantitative PCR on Sputum and Nasopharyngeal Swab Samples for Detection of Pneumococcal Pneumonia among the Elderly

Real-time quantitative PCR (qPCR) assay of sputum or nasopharyngeal specimens has shown promising results in the detection of pneumococcal community-acquired pneumonia (PncCAP). We applied qPCR for the autolysin gene (lytA) and compared sputum and nasopharyngeal swab (NPS) pneumococcal loads in elderly patients with community-acquired pneumonia (CAP), and specifically in patients with PncCAP, to those in patient groups with other respiratory diseases. We studied patients aged ≥65 years with radiologically confirmed CAP, clinical CAP not retrospectively radiologically confirmed, other acute respiratory infections, or stable chronic lung disease. Pneumococcal etiology of CAP was ascertained by using a combination of multiple diagnostic methods. We analyzed sputum and NPS specimens by lytA qPCR with 10⁴ pneumococcal genome equivalents (GE)/ml as a cutoff for positivity. Among PncCAP patients, lytA qPCR detected pneumococci in 94% of the sputum samples and in large quantities (mean, 6.82 ± 1.02 log₁₀ GE/ml) but less frequently in NPS (44%) and in smaller quantities (5.55 ± 0.92 log₁₀ GE/ml). In all other patient groups, ≤10% of the sputum samples and <5% of the NPS samples were lytA qPCR positive; but when they were positive, the sputum pneumococcal loads were similar to those in the PncCAP patients, suggesting a pneumococcal etiology in these patients. This was supported by other pneumococcal assay results. Overall, sputum lytA qPCR positivity was more common in PncCAP patients than in the other patient groups, but the quantitative results were mainly similar. NPS lytA qPCR was less sensitive than sputum lytA qPCR in detecting PncCAP.

Pneumococcal conjugate vaccine use in adults - Addressing an unmet medical need for non-bacteremic pneumococcal pneumonia

Streptococcus pneumoniae is a frequent cause of community acquired pneumonia (CAP), with the largest burden of disease attributed to non-bacteremic pneumonia. Due to the high persistent burden of disease, pneumococcal pneumonia, particularly non-bacteremic pneumococcal pneumonia, continues to be a major public health concern. There are currently two pneumococcal vaccines approved for use in adults in the United States (US) and other countries worldwide: a 23-valent pneumococcal simple polysaccharide vaccine (PPV23), and a 13-valent pneumococcal conjugate vaccine (PCV13). The capsular polysaccharides included in PPV23 induce antibodies primarily by a T-cell independent mechanism, thus the immune response is short lived and lacks the ability to elicit an anamnestic response. PCV13, on the other hand, has the bacterial polysaccharides covalently conjugated to an immunogenic carrier protein resulting in the formation of memory B lymphocytes, thus proving long-acting immunologic memory and an anamnestic response. Despite 30years of use, the question of PPV23 vaccine efficacy, particularly with respect to efficacy for non-bacteremic pneumonia, has been extensively debated and investigated; whereas PCV13 efficacy against vaccine-type pneumococcal CAP, both bacteremic and non-bacteremic, was confirmed in a large randomized controlled trial in older adults. PCV13 was approved under the US Food and Drug Administration's accelerated pathway, which allows for earlier approval of products that provide meaningful benefit over existing treatments - in this case, protection of adults from non-bacteremic pneumococcal pneumonia. Its use is now increasingly recommended globally. This article summarizes the history and use of PPV23 and PCV13 in adults and how vaccination of adults with PCV13 addresses an unmet medical need.

Respiratory Infections

The majority of respiratory tract infections (RTIs) are community acquired and are the single most common cause of physician office visits and among the most common causes of hospitalizations. The morbidity and mortality associated with RTIs are significant and the financial and social burden high due to lost time at work and school. The scope of clinical symptoms can significantly overlap among the respiratory pathogens, and the severity of disease can vary depending on patient age, underlying disease, and immune status, thereby leading to inaccurate presumptions about disease etiology. The rapid and accurate diagnosis of the causative agent of RTIs improves patient care, reduces morbidity and mortality, promotes effective hospital bed utilization and antibiotic stewardship, and reduces length of stay. This chapter focuses on the clinical utility, advantages, and disadvantages of viral and bacterial tests cleared by the Food and Drug Administration (FDA), and new promising technologies for the detection of bacterial agents of pneumonia currently in development or in US FDA clinical trials are briefly reviewed.

Usefulness of pneumococcal antigen urinary testing in the intensive care unit?

OBJECTIVES

The use of pneumococcal antigen urinary tests is substantially increasing and is associated with a significant cost. The relevant use of this test in the intensive care unit (ICU) should be better defined. Our aim was to define the role of this test in relation to other microbiological tests. We described a series of patients admitted to the ICU for an invasive pneumococcal disease (IPD).

PATIENTS AND METHODS

We conducted a retrospective and descriptive study of the microbiological tests used to diagnose IPD in patients admitted to the ICU of the University Hospital in Bordeaux. Our aim was to measure the sensitivity of these bacteriological tests and of the BinaxNOWS. pneumoniae test.

RESULTS

Between 2009 and 2013, 148 patients were admitted for an IPD. A lower respiratory tract infection was diagnosed in 96.6% of them (143 patients). The overall ICU case fatality rate was 17.6%. The sensitivity of the pneumococcal antigen urinary test, sputum bacteriological examination, and blood cultures was respectively 83%, 37.6%, and 29.7%. S. pneumoniae was isolated from at least one bacteriological sample in 48.6% of patients, but in 51.4%, the diagnosis was only based on the results of the pneumococcal antigen urinary test.

CONCLUSION

We suggest performing a pneumococcal antigen urinary test when an IPD is suspected, only if the bacteriological tests are still negative after 48hours. This strategy would result in a substantial cost saving. Patients would not face any additional risks as the result of the pneumococcal antigen urinary test does not have any impact on the initially prescribed antibiotic therapy.

Methodological criticisms in the evaluation of Pneumococcal Conjugate Vaccine effectiveness

Globally, lower respiratory tract infections (LRTIs), including community-acquired pneumonia (CAP), cause considerable of morbidity and mortality in adults, especially in the elderly. In addition to age, underlying medical conditions are associated with an increased risk of CAP. From an aetiological point of view, Streptococcus pneumoniae is the leading cause of adult CAP throughout the world. Two types of vaccine are available for the prevention of pneumococcal diseases: the pneumococcal polysaccharide vaccine (PPV23) and the pneumococcal conjugate vaccine (PCV7, PCV10 and PCV13). An accurate understanding of the LRTIs burden and the types of subjects at risk of CAP, allow to find an appropriately targeted immunization strategy and provide baseline data to evaluate pneumococcal vaccine effectiveness. Given the high variability in available estimates of LRTIs burden and associated risk factors, the objective of the study was to discuss the methodological criticism in its evaluation, in the light of the gradual introduction of PCV13 immunization strategy targeted to elderly and risk groups in middle-high income countries.

Use of an automated PCR assay, the GenomEra S. pneumoniae, for rapid detection of Streptococcus pneumoniae in blood cultures

BACKGROUND

Streptococcus pneumoniae is recognized as a major cause of pneumonia, meningitis, and bacteremia. Since the mortality rate for pneumococcal bacteremia remains high, the reliable detection of the bacterium in blood samples is important. In this study, the performance of a new automated PCR assay, the GenomEra(™) S. pneumoniae, for direct detection of S. pneumoniae in blood cultures was investigated.

METHODS

In total, 200 samples were analyzed, including 90 previously identified culture collection isolates and 110 blood culture specimens. The species identification was confirmed with routine diagnostic methods including MALDI-TOF or 16S rDNA sequencing.

RESULTS

From culture collection, the GenomEra S. pneumoniae assay correctly identified all 37 S. pneumoniae isolates consisting of 18 different serotypes, while all 53 non-S. pneumoniae isolates yielded negative test results. Of 110 blood culture specimens, 46 grew S. pneumoniae and all were positive by the GenomEra assay direct from bottle. The detection sensitivity and specificity of the GenomEra assay for direct analysis of S. pneumoniae in signal positive blood culture bottles was 100%, respectively. With a straightforward sample preparation protocol of blood cultures the results were available within 55 min, thus being significantly quicker than by the routinely used identification methods (18-48 h). The two-step, time-resolved fluorometric measurement mode employed by the GenomEra CDX(™) instrument showed no interference from blood or charcoal.

CONCLUSION

The GenomEra S. pneumoniae assay is a tool that performs well for the rapid and reliable detection of S. pneumoniae in blood cultures.

Respiratory Infections in the U.S. Military: Recent Experience and Control

This comprehensive review outlines the impact of military-relevant respiratory infections, with special attention to recruit training environments, influenza pandemics in 1918 to 1919 and 2009 to 2010, and peacetime operations and conflicts in the past 25 years. Outbreaks and epidemiologic investigations of viral and bacterial infections among high-risk groups are presented, including (i) experience by recruits at training centers, (ii) impact on advanced trainees in special settings, (iii) morbidity sustained by shipboard personnel at sea, and (iv) experience of deployed personnel. Utilizing a pathogen-by-pathogen approach, we examine (i) epidemiology, (ii) impact in terms of morbidity and operational readiness, (iii) clinical presentation and outbreak potential, (iv) diagnostic modalities, (v) treatment approaches, and (vi) vaccine and other control measures. We also outline military-specific initiatives in (i) surveillance, (ii) vaccine development and policy, (iii) novel influenza and coronavirus diagnostic test development and surveillance methods, (iv) influenza virus transmission and severity prediction modeling efforts, and (v) evaluation and implementation of nonvaccine, nonpharmacologic interventions.

Detection and serotyping of pneumococci in community acquired pneumonia patients without culture using blood and urine samples

Background

Treatment of community acquired pneumonia (CAP) patients with antibiotics before laboratory-confirmed diagnosis leads to loss of knowledge on the causative bacterial pathogen. Therefore, an increasing number of pneumococcal infections is identified using non-culture based techniques. However, methods for serotyping directly on the clinical specimen remain scarce. Here we present three approaches for detection and serotyping of pneumococci using samples from patients with CAP.

Methods

The first approach is quantitative PCR (qPCR) analysis on blood samples (n = 211) followed by capsular sequence typing (CST) to identify the serotype. The second approach, a urinary antigen assay (n = 223), designated as inhibition multiplex immunoassay (IMIA), is based on Luminex technology targeting 14 serotypes. The third approach is a multiplex immunoassay (MIA) (n = 171) also based on Luminex technology which detects serologic antibody responses against 14 serotypes. The three alternative assays were performed on samples obtained from 309 adult hospitalized CAP patients in 2007–2010 and the results were compared with those obtained from conventional laboratory methods to detect pneumococcal CAP, i.e. blood cultures, sputum cultures and BinaxNOW® urinary antigen tests.

Results

Using qPCR, MIA and IMIA, we were able to detect the pneumococcus in samples of 56% more patients compared to conventional methods. Furthermore, we were able to assign a serotype to the infecting pneumococcus from samples of 25% of all CAP patients, using any of the three serotyping methods (CST, IMIA and MIA).

Conclusion

This study indicates the usefulness of additional molecular methods to conventional laboratory methods for the detection of pneumococcal pneumonia. Direct detection and subsequent serotyping on clinical samples will improve the accuracy of pneumococcal surveillance to monitor vaccine effectiveness.

Clinical factors associated with negative urinary antigen tests implemented for the diagnosis of community-acquired pneumococcal pneumonia in adult patients

OBJECTIVE

This study investigated clinical factors associated with negative urinary antigen tests (UAT) implemented for the diagnosis of pneumococcal community-acquired pneumonia (CAP) in adult patients.

SUBJECTS AND METHODS

We reviewed the medical records of 755 adult patients who completed the UAT in our hospital between 2009 and 2012. Of these, we evaluated 63 patients with bacteriologically confirmed definite pneumococcal CAP (33 were UAT-positive, and 30 were UAT-negative).

RESULTS

There was no significant difference between the UAT-positive and the UAT-negative patients regarding age, dehydration, respiratory failure, orientation, blood pressure (ADROP) score (the CAP severity score proposed by the Japanese Respiratory Society), gender, white blood cell counts, liver/kidney function tests, or urinalysis. However, serum C-reactive protein (CRP) concentrations were 31% lower in the UAT-negative patients than in the UAT-positive patients (p = 0.02). Furthermore, the prothrombin time-international normalized ratio was 50% higher in the UAT-negative patients than in the UAT-positive patients, although the difference did not reach statistical significance (p = 0.06). The prevalence of comorbidities was similar in both UAT-positive and UAT-negative patients. However, warfarin had been prescribed in 8 (27%) of the UAT-negative patients compared to only 1 (3%) of the UAT-positive patients (odds ratio = 11.6; p = 0.01).

CONCLUSIONS

These results suggested that low serum CRP concentrations and the use of warfarin increased the possibility with which false-negative UAT results occurred in these patients with pneumococcal CAP.

[Which samples to obtain in the emergency department for the microbiological diagnosis of community-acquired pneumonia in the immunocompetent patient?]

Current diagnostic methods allow microbial identification in 50% of patients admitted with severe community-acquired pneumonia (CAP). Guidelines derived from epidemiological data help physicians to start empirical antimicrobial therapy. Definitive microbial diagnosis is useful to guide further pathogen-directed therapy. Blood cultures, cultures of respiratory specimens and urine antigen tests are recommended to determine the causative bacterial pathogen. Positive blood cultures range from 15 to 25% of CAP patients according to severity. Whether sputum specimens represent or not lower respiratory secretions determines its accuracy in CAP microbial diagnosis. In intubated patients, endotracheal aspirates are often of interest. Detection of positive pneumococcal or legionella urinary antigen is often associated with CAP severity. The sensitivity of this test is not decreased in patients who have received antibiotics prior to sampling. Viral pneumonia account for 10 to 40% of severe CAP. Nasal swabs are recommended for influenza identification using polymerase chain reaction (PCR) in order to deliver oseltamivir treatment. In the emergency department, atypical pneumonia serology is less useful than respiratory specimens obtained using fiberoptic bronchoscopy. Serum PCR to diagnose bacterial CAP is not superior to the other usual methods.

Streptococcus pneumoniae antigen in urine: diagnostic usefulness and impact on outcome of bacteraemic pneumococcal pneumonia in a large series of adult patients

BACKGROUND AND OBJECTIVE

Urinary pneumococcal antigen detection provides good results in the diagnosis of pneumococcal pneumonia but has rarely been used in bacteraemic pneumococcal pneumonia and it is not known whether it is associated with outcome in this type of pneumonia. Our objectives were to assess the usefulness of an immunochromatographic technique for detecting the pneumococcal antigen in urine in a large prospective study of patients with bacteraemic pneumococcal pneumonia and explore any potential association with outcomes.

METHODS

This study, carried out over 8 years, included all adult immunocompetent patients admitted for bacteraemic pneumococcal pneumonia. An immunochromatographic test for the Streptococcus pneumoniae antigen in urine was performed in the first 24 h. The sensitivity of test was assessed and patients were divided into two groups according to test results to explore differences on admission and during the course of the illness using logistic regression models.

RESULTS

Of the 350 patients with bacteraemic pneumococcal pneumonia included, 261 (74.6%) were positive for the antigen. Patient characteristics were very similar on admission and differences in severity (Pneumonia Severity Index) were not statistically significant. In the adjusted analysis, antigen-positive patients had a higher risk of intensive care unit admission, treatment failure and adverse outcome.

CONCLUSIONS

The sensitivity of the immunochromatographic urinary antigen test was 74.6% and positive results were associated with poorer clinical outcome. We therefore recommend systematic use of this test when pneumonia is diagnosed in the emergency department.

Clinical evaluation of a disposable amperometric magneto-genosensor for the detection and identification of Streptococcus pneumoniae

A disposable PCR-based amperometric magneto-genosensor for detection and identification of Streptococcus pneumoniae was evaluated. ROC curve analysis used to determine optimal signal cutoff values yielded a sensitivity of 91% and a specificity of 90%. The method was also tested for the direct detection of pneumococci in clinical samples.

Urine antigen tests for the diagnosis of respiratory infections: legionellosis, histoplasmosis, pneumococcal pneumonia

Urinary antigen testing has grown in popularity for several significant respiratory infections, particularly Legionella pneumophila, Streptococcus pneumoniae, and Histoplasma capsulatum. By capitalizing on the concentration of shed antigen from a variety of pathogens in the kidneys for excretion in the urine, urinary antigen testing can be used to obtain rapid test results related to respiratory infection, independent of an invasive collection such as a bronchoalveolar lavage. This article describes the 3 aforementioned organisms, their role in respiratory disease, and the current status of urinary antigen testing in their respective diagnosis.

Pneumococcal urinary antigen positivity in healthy colonized children: is it age dependent?

BACKGROUND

Pneumococcal urinary antigen test is a valuable tool for diagnosing pneumococcal pneumonia and meningitis in adults. Its use in children is generally not accepted because of nonspecificity at this age. It is frequently positive in asymptomatic nasopharyngeal carriers. The aim of our study was to assess the age limit from which the test is no longer positive in asymptomatic healthy carriers.

METHODS

A total of 197 children aged 36-83 months attending 9 day care centers in Prague were enrolled during February and March 2010. Nasopharyngeal swab specimens were collected from each participant and selectively cultivated. The presence of pneumococcal antigen in urine was detected by BinaxNOW® S. pneumoniae kit.

RESULTS

Streptococcus pneumoniae was cultivated in 53.3 % of healthy children with the highest colonization rate (59.3 %) in children aged 48-59 months. The most frequently colonizing serotypes were: 19F, 23F, 3, 19A, 6B and 4. The presence of pneumococcal antigen in urine decreased with age from 39.0 % in 36-47 months to 17.9 % in 72-83 months old (p = 0.031). The antigen positivity was serotype-dependent and more frequent in nonvaccinated children.

CONCLUSION

We demonstrated age-dependent linear decrease of pneumococcal antigen excretion into urine in healthy children. The positivity rate of the test in children aged 72-83 months was similar to that referred in healthy adults, irrespective of colonization. To confirm this age limit for use of this test in diagnostics of pneumococcal diseases, further study in school-age children is justified.

What is the role of newer molecular tests in the management of CAP?

Community-acquired pneumonia (CAP) accounts for major morbidity and mortality in the United States. With improved broad-spectrum antibiotics, the implementation of diagnostic studies has declined and most patients do not have an etiologic pathogen of CAP identified. To enhance the appropriate use of antiviral agents and prevent overuse of antibiotics, the successful management of CAP requires rapid and accurate diagnosis of the etiologic agent of CAP. This article provides an overview of the new rapid molecular tests for the diagnosis of influenza, other respiratory viruses, and bacteria compared with nonmolecular tests and how their use for directed therapy can enhance and improve the management of CAP.

Systematic review and meta-analysis of a urine-based pneumococcal antigen test for diagnosis of community-acquired pneumonia caused by Streptococcus pneumoniae

Standard culture methods for diagnosis of Streptococcus pneumoniae pneumonia take at least 24 h. The BinaxNOW urine-based test for S. pneumoniae (BinaxNOW-SP) takes only 15 min to conduct, potentially enabling earlier diagnosis and targeted treatment. This study was conducted to assess whether the use of BinaxNOW-SP at the time of hospital admission would provide adequate sensitivity and specificity for diagnosis of community-acquired pneumonia (CAP) in adult patients. We searched PubMed, EMBASE/OVID, Cochrane Collaboration, Centre for Reviews and Dissemination, INAHTA, and CADTH for diagnostic or etiologic studies of hospitalized predominately adult patients with clinically defined CAP that reported the diagnostic performance of BinaxNOW-SP versus cultures. Two authors independently extracted study details and diagnostic two-by-two tables. We found that 27 studies met our inclusion criteria, and three different reference standards were used between them. A bivariate meta-analysis of 12 studies using a composite of culture tests as the reference standard estimated the sensitivity of BinaxNOW-SP as 68.5% (95% credibility interval [CrI], 62.6% to 74.2%) and specificity as 84.2% (95% CrI, 77.5% to 89.3%). A meta-analysis of all 27 studies, adjusting for the imperfect and variable nature of the reference standard, gave a higher sensitivity of 74.0% (CrI, 66.6% to 82·3%) and specificity of 97.2% (CrI, 92.7% to 99.8%). The analysis showed substantial heterogeneity across studies, which did not decrease with adjustment for covariates. We concluded that the higher pooled sensitivity (compared to culture) and high specificity of BinaxNOW-SP suggest it would be a useful addition to the diagnostic workup for community-acquired pneumonia. More research is needed regarding the impact of BinaxNOW-SP on clinical practice.

HIV-associated bacterial pneumonia

Community-acquired bacterial pneumonia (CAP) remains one of the most common opportunistic infections in patients who are infected with the human immunodeficiency virus (HIV). The risk of CAP increases as the CD4 cell count decreases. The common bacterial pathogens that cause CAP in HIV-infected persons are similar to those in HIV-uninfected individuals, with the pneumococcus being the most common pathogen. Prevention of CAP remains critical and necessitates a comprehensive approach addressing, among many other factors, cigarette smoking cessation strategies, antiretroviral therapy adherence, and immunization against those infections for which effective vaccinations are available.

Diagnostics for community-acquired and atypical pneumonia

PURPOSE OF REVIEW

After decades of neglect, the importance of establishing an aetiological diagnosis for community-acquired and atypical pneumonias has increased dramatically in recent years--driven by the movement towards more rational use of antibiotics, the further spread of antimicrobial resistance, and advances in point-of-care assays that circumvent the diagnostic delays that result from the centralization of laboratories.

RECENT FINDINGS

There have been very few developments in patient sampling, or the direct visualization, culture, and serological detection of respiratory pathogens. There has, however, been significant interest in the development of improved and more clinically useful assays for the detection of pathogen nucleic acids and proteins, and also in the potential utility of the assessment of host response for tailoring therapy.

SUMMARY

The majority of patients have yet to benefit from any advances. However, nucleic acid, newer protein, and possibly host-response assays have significant potential to influence patient care in the near future.

Can an etiologic agent be identified in adults who are hospitalized for community-acquired pneumonia: results of a one-year study

INTRODUCTION

Determining the cause of community-acquired pneumonia (CAP) remains problematic. In this observational study, we systematically applied currently approved diagnostic techniques in patients hospitalized for CAP in order to determine the proportion in which an etiological agent could be identified.

METHODS

All patients admitted with findings consistent with CAP were included. Sputum and blood cultures, urine tests for pneumococcal and Legionella antigens, nasopharyngeal swab for viral PCR, and serum procalcitonin were obtained in nearly every case. Admission-related electronic medical records were reviewed in entirety.

RESULTS

By final clinical diagnosis, 44 patients (17.0%) were uninfected. A causative bacterium was identified in only 60 (23.2%) cases. PCR identified a respiratory virus in 42 (16.2%), 12 with documented bacterial coinfection. In 119 (45.9%), no cause for CAP was found; 69 (26.6%) of these had a syndrome indistinguishable from bacterial pneumonia. Procalcitonin was elevated in patients with bacterial infection and low in uninfected patients or those with viral infection, but with substantial overlap.

CONCLUSIONS

Only 23.2% of 259 patients admitted with a CAP syndrome had documented bacterial infection; another 26.6% had no identified bacterial etiology, but findings closely resembled those of bacterial infection. Nevertheless, all 259 received antibacterial therapy. Careful attention to the clinical picture may identify uninfected patients or those with viral infection, perhaps with reassurance by a non-elevated procalcitonin. Determining an etiologic diagnosis remains elusive. Better discriminators of bacterial infection are sorely needed.

Rapid diagnosis of invasive pneumococcal disease in pediatric population

The aim of this study was to evaluate the Binax NOW immunochromatographic pneumococcal antigen test for the identification of Streptococcus pneumoniae in pleural and cerebrospinal fluids from children with suspected invasive pneumococcal disease. The results were compared with those obtained by PCR. Binax NOW was applied to these samples as recommended by the manufacturer for urine and cerebrospinal samples. Detection of pneumococcal DNA was performed by real-time PCR assay targeting the autolysin gene (lytA). Of the 199 samples analyzed, 131 were positive by both Binax NOW and lytA PCR, and 36 samples were negative by both techniques. Using the real-time PCR as a comparative method to the Binax for the detection of S. pneumoniae, the sensitivity and specificity of Binax NOW was 88% and 72.5%, respectively. Of the 145 positive samples analyzed by Binax NOW, 119 showed intense coloring of the sample line and 26 showed weak intensity. Conventional culture is the most common method in clinical settings, but Binax NOW is an easier and faster test for identifying S. pneumoniae in pleural and cerebrospinal fluids from children with suspected invasive pneumococcal disease.

Microbial diagnostics in patients with presumed severe infection in the emergency department

INTRODUCTION

Sepsis in the early stage is a common disease in emergency medicine, and rapid diagnosis is essential. Our aim was to compare pathogen diagnosis using blood cultures (BC) and the multiplex polymerase chain reaction (PCR) test.Methods. At total of 211 patients admitted to the multidisciplinary emergency department of our university hospital between 2006 and 2009 with suspected severe infection from any origin were studied. Blood samples for BC (aerobic and anaerobic) and multiplex PCR were taken for identification of infectious microorganisms immediately after hospital admission. Results of the BC and PCR correlated with procalcitonin concentration (PCT) and clinical diagnosis of sepsis (≥2 positive SIRS criteria) as well as with severity of disease at admission and with clinical outcome measures.

RESULTS

Results of the BC were available in 200 patients (94.8%) and PCR were available in 119 patients (56.3%), respectively. In total, 87 BC (43.5%) were positive and identified 94 pathogens. In 45 positive PCRs, 47 pathogens (37.8%) were found. Identical results were obtained in 81.4%. In addition, BC identified 9 Gram-positive and 3 Gram-negative bacteria, while PCR added 5 Gram-negative pathogens. Coagulase-negative staphylococci were detected in blood cultures only (n=20, 21.3%), whereas PCR identified significantly more Gram-negative bacteria than BC. In patients with positive PCR results, the PCT level was significantly higher than in patients with negative PCR (15.0±23.3 vs. 8.8±32.8 ng/ml, p<0.001). This difference was not observed for BC (10.6±25.7 vs. 11.6±44.9 ng/ml, p=0.075). The APACHE II score correlated with PCR (19.2±9.1 vs. 15.8±8.9, p<0.05) and was also higher in positive BC (18.7±8.7 vs. 14.4±8.0, p<0.01). Positive PCR and BC were correlated with negative clinical outcomes (e.g., transfer to ICU, mechanical ventilation, renal replacement therapy, death).

CONCLUSION

In patients admitted with suspected severe infection, a high percentage of positive BC and PCR were observed. Positive findings in the PCR correlate with elevated levels of PCT and high APACHE II scores.

Evaluation of a rapid test for the diagnosis of pneumococcal pneumonia

We evaluated the usefulness of a rapid immunochromatographic pneumococcal urinary antigen test (UAT) for the diagnosis of pneumonia over a period of five years. The UAT was positive in 32 (2.3%) urine samples obtained from 1414 patients. In 46 of these 1414 patients results of UAT and/or sputum/pleural fluid culture and/or blood culture and/or procalcitonin levels were available and therefore the study was concentrated on these patients. A concordance between UAT positivity and the presence of Streptococcus pneumoniae in the sputum was observed in only 4 of 46 (8.7%) patients for which both urine and sputum samples were analyzed. A discordant result (UAT positive and absence of S. pneumoniae in sputum samples) was recorded in 8 of 46 (17.4 %) patients. UAT negative results with sputum culture positive for S. pneumoniae were recorded in 28.3% of patients. In 20 patients, UAT tested positive but sputum culture was not performed. A concordance between UAT positivity and the isolation of S. pneumoniae from blood was seen in 2 of 46 patients whereas a discordant result (UAT positive and blood culture negative) was seen in 12 (26.1%) patients. A concordance between the UAT and high levels (≥2ng/ml) of procalcitonin was observed in 4 out of 46 patients, whereas a positive UAT result and a procalcitonin negative result were observed in 2 patients. In our experience the UAT allows the detection of the etiological agent of pneumonia, and also when sputum and/or blood cultures are negative for S. pneumoniae, when the clinical picture is suggestive of alveolar pneumonia.

Etiology and Incidence of viral and bacterial acute respiratory illness among older children and adults in rural western Kenya, 2007-2010

BACKGROUND

Few comprehensive data exist on disease incidence for specific etiologies of acute respiratory illness (ARI) in older children and adults in Africa.

METHODOLOGY/PRINCIPAL FINDINGS

From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0 °C or oxygen saturation <90% or hospitalization). We also collected swabs from asymptomatic controls, from which we calculated pathogen-attributable fractions, adjusting for age, season, and HIV-status, in logistic regression. We calculated incidence by pathogen, adjusting for health-seeking for ARI and pathogen-attributable fractions. Among 3,406 ARI patients >5 years old (adjusted annual incidence 12.0 per 100 person-years), influenza A virus was the most common virus (22% overall; 11% inpatients, 27% outpatients) and Streptococcus pneumoniae was the most common bacteria (16% overall; 23% inpatients, 14% outpatients), yielding annual incidences of 2.6 and 1.7 episodes per 100 person-years, respectively. Influenza A virus, influenza B virus, respiratory syncytial virus (RSV) and human metapneumovirus were more prevalent in swabs among cases (22%, 6%, 8% and 5%, respectively) than controls. Adenovirus, parainfluenza viruses, rhinovirus/enterovirus, parechovirus, and Mycoplasma pneumoniae were not more prevalent among cases than controls. Pneumococcus and non-typhi Salmonella were more prevalent among HIV-infected adults, but prevalence of viruses was similar among HIV-infected and HIV-negative individuals. ARI incidence was highest during peak malaria season.

CONCLUSIONS/SIGNIFICANCE

Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings.

Validation of an immunodiagnostic assay for detection of 13 Streptococcus pneumoniae serotype-specific polysaccharides in human urine

To improve the clinical diagnosis of pneumococcal infection in bacteremic and nonbacteremic community-acquired pneumonia (CAP), a Luminex technology-based multiplex urinary antigen detection (UAD) diagnostic assay was developed and validated. The UAD assay can simultaneously detect 13 different serotypes of Streptococcus pneumoniae by capturing serotype-specific S. pneumoniae polysaccharides (PnPSs) secreted in human urine. Assay specificity is achieved by capturing the polysaccharides with serotype-specific monoclonal antibodies (MAbs) on spectrally unique microspheres. Positivity for each serotype was based on positivity cutoff values calculated from a standard curve run on each assay plate together with positive- and negative-control urine samples. The assay is highly specific, since significant signals are detected only when each PnPS was paired with its homologous MAb-coated microspheres. Validation experiments demonstrated excellent accuracy and precision. The UAD assay and corresponding positivity cutoff values were clinically validated by assessing 776 urine specimens obtained from patients with X-ray-confirmed CAP. The UAD assay demonstrated 97% sensitivity and 100% specificity using samples obtained from patients with bacteremic, blood culture-positive CAP. Importantly, the UAD assay identified Streptococcus pneumoniae (13 serotypes) in a proportion of individuals with nonbacteremic CAP, a patient population for which the pneumococcal etiology of CAP was previously difficult to assess. Therefore, the UAD assay provides a specific, noninvasive, sensitive, and reproducible tool to support vaccine efficacy as well as epidemiological evaluation of pneumococcal disease, including CAP, in adults.

Elderly patients with community-acquired pneumonia: optimal treatment strategies

Community-acquired pneumonia (CAP) is a common infectious disease that still causes substantial morbidity and mortality. Elderly people are frequently affected, and several issues related to care of this condition in the elderly have to be considered. This article reviews current recommendations of guidelines with a special focus on aspects of the care of elderly patients with CAP. The most common pathogen in CAP is still Streptococcus pneumoniae, followed by other pathogens such as Haemophilus influenzae, Mycoplasma pneumoniae, Chlamydophila pneumoniae and Legionella species. Antimicrobial resistance is an increasing problem, especially with regard to macrolide-resistant S. pneumoniae and fluoroquinolone-resistant strains. With regard to β-lactam antibacterials, resistance by H. influenzae and Moraxella catarrhalis is important, as is the emergence of multidrug-resistant Staphylococcus aureus. The main management decisions should be guided by the severity of disease, which can be assessed by validated clinical risk scores such as CURB-65, a tool for measuring the severity of pneumonia based on assessment of confusion, serum urea, respiratory rate and blood pressure in patients aged ≥65 years. For the treatment of low-risk pneumonia, an aminopenicillin such as amoxicillin with or without a β-lactamase inhibitor is frequently recommended. Monotherapy with macrolides is also possible, although macrolide resistance is of concern. When predisposing factors for special pathogens are present, a β-lactam antibacterial combined with a β-lactamase inhibitor, or the combination of a β-lactam antibacterial, a β-lactamase inhibitor and a macrolide, may be warranted. If possible, patients who have undergone previous antibacterial therapy should receive drug classes not previously used. For hospitalized patients with non-severe pneumonia, a common recommendation is empirical antibacterial therapy with an aminopenicillin in combination with a β-lactamase inhibitor, or with fluoroquinolone monotherapy. With proven Legionella pneumonia, a combination of β-lactams with a fluoroquinolone or a macrolide is beneficial. In severe pneumonia, ureidopenicillins with β-lactamase inhibitors, broad-spectrum cephalosporins, macrolides and fluoroquinolones are used. A combination of a broad-spectrum β-lactam antibacterial (e.g. cefotaxime or ceftriaxone), piperacillin/tazobactam and a macrolide is mostly recommended. In patients with a predisposition for Pseudomonas aeruginosa, a combination of piperacillin/tazobactam, cefepime, imipenem or meropenem and levofloxacin or ciprofloxacin is frequently used. Treatment duration of more than 7 days is not generally recommended, except for proven infections with P. aeruginosa, for which 15 days of treatment appears to be appropriate. Further care issues in all hospitalized patients are timely administration of antibacterials, oxygen supply in case of hypoxaemia, and fluid management and dose adjustments according to kidney function. The management of elderly patients with CAP is a challenge. Shifts in antimicrobial resistance and the availability of new antibacterials will change future clinical practice. Studies investigating new methods to detect pathogens, determine the optimal antimicrobial regimen and clarify the duration of treatment may assist in further optimizing the management of elderly patients with CAP.

Guidelines for the management of adult lower respiratory tract infections--summary

This document is an update of Guidelines published in 2005 and now includes scientific publications through to May 2010. It provides evidence-based recommendations for the most common management questions occurring in routine clinical practice in the management of adult patients with LRTI. Topics include management outside hospital, management inside hospital (including community-acquired pneumonia (CAP), acute exacerbations of COPD (AECOPD), acute exacerbations of bronchiectasis) and prevention. The target audience for the Guideline is thus all those whose routine practice includes the management of adult LRTI.

Guidelines for the management of adult lower respiratory tract infections--full version

This document is an update of Guidelines published in 2005 and now includes scientific publications through to May 2010. It provides evidence-based recommendations for the most common management questions occurring in routine clinical practice in the management of adult patients with LRTI. Topics include management outside hospital, management inside hospital (including community-acquired pneumonia (CAP), acute exacerbations of COPD (AECOPD), acute exacerbations of bronchiectasis) and prevention. Background sections and graded evidence tables are also included. The target audience for the Guideline is thus all those whose routine practice includes the management of adult LRTI.

Should patients with chronic obstructive pulmonary disease be vaccinated against pneumococcal diseases?

Over the past 15 years, no fewer than ten meta-analyses or systematic literature reviews of the efficacy of pneumococcal polysaccharide vaccine in adults have been conducted, including one specifically in chronic obstructive pulmonary disease patients. Their general conclusion is that it is effective in preventing invasive infections, but no conclusions can be drawn for high-risk patients (owing to a highly polymorphic population). Opinions are divided as to its efficacy in pneumonia, with the studies being too heterogeneous to carry sufficient statistical weight. Most conclude that there is no impact on mortality. Chronic obstructive pulmonary disease patients are frequently described as an at-risk population, but controlled studies in such patients are very limited, leaving only case-control or cohort studies to provide information on which to base any decision. The aim of this article is first to discuss the place of pneumococcal polysaccharide vaccination in this risk population, which is increasing in prevalence and in which pneumococcal infections play a considerable role. Pending other vaccines, the polysaccharide vaccine is currently the only preventive approach that has demonstrated an effect, even if it does not match up to expectations. The possibilities of alternative vaccines, such as conjugate vaccines in the near future and perhaps protein vaccines at a later date, will be considered.

Interpreting assays for the detection of Streptococcus pneumoniae

Streptococcus pneumoniae is both an aggressive pathogen and a normal part of the human respiratory microbiome. Clinicians and microbiologists have struggled to develop tests that can identify pneumococcal respiratory infection and accurately distinguish colonization from invasive disease. Molecular methods hold the promise of an improved ability to rapidly detect microorganisms in respiratory secretions and to make an accurate diagnosis; however, interpretation of diagnostic testing for S. pneumoniae remains problematic. Molecular assays, such as those targeting the pneumolysin gene, may cross-react with other streptococcal species, confounding detection and quantification. Assays that target the autolysin gene appear to be more specific. Even when accurately identified, however, the significance of S. pneumoniae DNA detected in clinical samples is difficult to determine. Here we will discuss the challenges faced in the interpretation of molecular testing for S. pneumoniae, and some strategies that might be used to improve our ability to diagnose pneumococcal respiratory infection.

Diagnostic tests for agents of community-acquired pneumonia

Lower respiratory infections are the major cause of death due to infectious disease in the United States and worldwide. Most forms of community-acquired pneumonia (CAP) are treatable, and there is consensus that the selection of antimicrobial agents is notably simplified if the pathogen is defined. The rich history of CAP studies in the prepenicillin era showed that an etiologic diagnosis was established in >90% of cases, but the 2009 data from Medicare indicate that a probable pathogen is now detected in <10% according to a review of the records of >17,000 patients hospitalized with CAP. This review addresses the issue of the state of the art of microbiological studies of CAP in terms of the realities of current-day practice. Unfortunately, the desire for better data to achieve pathogen-directed treatment clashes with a multitude of harsh realities, including cost, Centers for Medicare and Medicaid Services (CMS) requirements for antibiotics to be administered within 6 h of disease onset, guidelines that discourage any microbiological studies in most cases, belief in empiricism that is well supported by at least 1 prospective study, the decline of microbiological analysis standards in most laboratories, and the devastating impact of the Clinical Laboratory Improvement Amendments (CLIA) regulations that led to the demise of "the house staff laboratory" and the distancing of microbiological analysis from the site of care. Microbiological principles are reviewed, with emphasis on specimen source, pathogenic potential of isolates, concentrations, impact of antecedent antibiotics, and the "Washington criteria" for expectorated sputum. The recommendation is that the high-quality microbiological analysis that is still achieved in some places should be retained but that to advance the field on the basis of the contemporary realities, two goals should be adopted: First is the broad use of antigen tests for Streptococcus pneumoniae and Legionella pneumophila with interpretation by clinical staff under the CLIA waiver for low-complexity tests. The second and more ambitious recommendation is the adoption of molecular techniques, with particular emphasis on nucleic acid detection, which is rapid and sensitive and has already been developed for virtually all recognized pulmonary pathogens. This may be the ultimate solution for many laboratories, and it is likely to have selected use.

New modalities in treating pneumococcal pneumonia

Despite the availability of effective antibiotics and intensive medical care, pneumococcal pneumonia is still associated with substantial mortality. Early diagnosis is becoming increasingly possible. This article reviews several adjunctive measures that might be instituted at or soon after admission in patients who are hospitalized for community-acquired pneumonia that is found to be due to Streptococcus pneumoniae. Available data favor the use of a macrolide together with a β-lactam antibiotic for treatment, based largely on immunomodulatory activity of macrolides. Two large subgroup analyses from a single major study suggest that activated protein C (eg, drotrecogin) should be considered for patients with severe sepsis, organ failure, and an Acute Physiology and Chronic Health Evaluation II score > 25 due to pneumococcal pneumonia. Statins exert an anti-inflammatory effect and several retrospective studies suggest that their use might ameliorate the adverse effects of pneumonia. Because inflammation elsewhere in the body is associated with inflammation in coronary arteries and because pneumococcal pneumonia has been shown to precipitate myocardial infarction, statins might be of further benefit by decreasing the likelihood of associated myocardial infarction. Aspirin, which inhibits platelet aggregation in inflamed coronary arteries, might also be considered for initial therapy. One reason that the association between myocardial infarction and pneumonia was not previously recognized is that aspirin was widely used in the past when people had acute febrile conditions. The literature on the benefits of corticosteroids in pneumonia is not convincing, and a particularly well-done, very recent study shows no benefit with corticosteroid use in patients with pneumococcal pneumonia, and perhaps even a worse outcome. No clinical data favor the use of platelet-activating factor antagonists.

Pneumococcal DNA is not detectable in the blood of healthy carrier children by real-time PCR targeting the lytA gene

The diagnosis of invasive pneumococcal disease (IPD) is currently based on culture methods, which lack sensitivity, especially after antibiotic therapy. Molecular methods have improved sensitivity and do not require viable bacteria; however, their use is complicated by reports of low specificity with some assays. The present study investigated the specificity of a real-time PCR targeting lytA for the detection of IPD. A group of 147 healthy children, aged 6 months to 16 years (mean 6.4 years, median 4.9 years, interquartile range 6.4 years), who were in hospital for routine examinations, were tested for pneumococcal carrier status and for the presence of detectable pneumococcal DNA in their blood by real-time PCR targeting the pneumococcal lytA gene. In addition, 35 culture-positive biological samples were analysed. Urine was examined for the presence of pneumococcal DNA and C-polysaccharide antigen. Carriage was detected in 77 of the 147 subjects (52.4 %); however, regardless of carrier status, none of the subjects had a positive result from blood. Analysis of the culture-positive biological samples yielded positive results in 100 % (15/15) of cerebrospinal fluid samples and 95 % (19/20) of blood samples. All urine samples from healthy carriers were negative for DNA, whilst antigenuria was detected in 44/77 carriers (57.1 %). In conclusion, real-time PCR is both sensitive and specific and can be a useful tool in the routine diagnosis of IPD. Its sensitivity, which surpasses that of other methods for this purpose, does not come at the cost of reduced specificity.

recA-based PCR assay for accurate differentiation of Streptococcus pneumoniae from other viridans streptococci

Proper identification of Streptococcus pneumoniae by conventional methods remains problematic. The discriminatory power of the 16S rRNA gene, which can be considered the "gold standard" for molecular identification, is too low to differentiate S. pneumoniae from closely related species such as Streptococcus pseudopneumoniae, Streptococcus mitis, and Streptococcus oralis in the routine clinical laboratory. A 313-bp part of recA was selected on the basis of variability within the S. mitis group, showing <95.8% interspecies homology. In addition, 6 signature nucleotides specific for S. pneumoniae were identified within the 313-bp recA fragment. We show that recA analysis is a useful tool for proper identification to species level within the S. mitis group, in particular, for pneumococci.