Molecular genetic methods in the diagnosis of lower respiratory tract infections

Gram-Positive Pneumonia: Possibilities Offered by Phage Therapy

Pneumonia is an acute pulmonary infection whose high hospitalization and mortality rates can, on occasion, bring healthcare systems to the brink of collapse. Both viral and bacterial pneumonia are uncovering many gaps in our understanding of host–pathogen interactions, and are testing the effectiveness of the currently available antimicrobial strategies. In the case of bacterial pneumonia, the main challenge is antibiotic resistance, which is only expected to increase during the current pandemic due to the widespread use of antibiotics to prevent secondary infections in COVID-19 patients. As a result, alternative therapeutics will be necessary to keep this disease under control. This review evaluates the advantages of phage therapy to treat lung bacterial infections, in particular those caused by the Gram-positive bacteria Streptococcus pneumoniae and Staphylococcus aureus, while also highlighting the regulatory impediments that hamper its clinical use and the difficulties associated with phage research.

Bacterial pneumonia and its associated factors in children from a developing country: A prospective cohort study

Introduction

Pneumonia in children is a common disease yet determining its aetiology remains elusive.

Objectives

To determine the a) aetiology, b) factors associated with bacterial pneumonia and c) association between co-infections (bacteria + virus) and severity of disease, in children admitted with severe pneumonia.

Methods

A prospective cohort study involving children aged 1-month to 5-years admitted with very severe pneumonia, as per the WHO definition, over 2 years. Induced sputum and blood obtained within 24 hrs of admission were examined via PCR, immunofluorescence and culture to detect 17 bacteria/viruses. A designated radiologist read the chest radiographs.

Results

Three hundred patients with a mean (SD) age of 14 (±15) months old were recruited. Significant pathogens were detected in 62% of patients (n = 186). Viruses alone were detected in 23.7% (n = 71) with rhinovirus (31%), human metapneumovirus (HMP) [22.5%] and respiratory syncytial virus (RSV) [16.9%] being the commonest. Bacteria alone was detected in 25% (n = 75) with Haemophilus influenzae (29.3%), Staphylococcus aureus (24%) and Streptococcus pneumoniae (22.7%) being the commonest. Co-infections were seen in 13.3% (n = 40) of patients. Male gender (AdjOR 1.84 [95% CI 1.10, 3.05]) and presence of crepitations (AdjOR 2.27 [95% CI 1.12, 4.60]) were associated with bacterial infection. C-reactive protein (CRP) [p = 0.007]) was significantly higher in patients with co-infections but duration of hospitalization (p = 0.77) and requirement for supplemental respiratory support (p = 0.26) were not associated with co-infection.

Conclusions

Bacteria remain an important cause of very severe pneumonia in developing countries with one in four children admitted isolating bacteria alone. Male gender and presence of crepitations were significantly associated with bacterial aetiology. Co-infection was associated with a higher CRP but no other parameters of severe clinical illness.

Plasma cytokines eotaxin, MIP-1α, MCP-4, and vascular endothelial growth factor in acute lower respiratory tract infection

Major overlaps of clinical characteristics and the limitations of conventional diagnostic tests render the initial diagnosis and clinical management of pulmonary disorders difficult. In this pilot study, we analyzed the predictive value of eotaxin, macrophage inflammatory protein 1 alpha (MIP-1α), monocyte chemoattractant protein 4 (MCP-4), and vascular endothelial growth factor (VEGF) in 40 patients hospitalized with acute lower respiratory tract infections (LRTI). The cytokines contribute to the pathogenesis of several inflammatory respiratory diseases, indicating a potential as markers for LRTI. Patients were stratified according to etiology and severity of LRTI, based on baseline C-reactive protein and CURB-65 scores. Using a multiplex immunoassay of plasma, levels of eotaxin and MCP-4 were shown to increase from baseline until day 6 after admission to hospital. The four cytokines were unable to predict the etiology and severity. Eotaxin and MCP-4 were significantly lower in patients with C-reactive protein ≥100, and MIP-1α was significantly higher in the patients with CURB-65 > 3, but the predictive power was low. In conclusion, further evaluation, including more patients, is required to assess the full potential of eotaxin, MCP-4, MIP-1α, and VEGF as biomarkers for LRTI because of their low predictive power and a high interindividual variation of cytokine levels.

Pneumococcal Disease in the Era of Pneumococcal Conjugate Vaccine

Universal immunization of infants and toddlers with pneumococcal conjugate vaccines over the last 15 years has dramatically altered the landscape of pneumococcal disease. Decreases in invasive pneumococcal disease, all-cause pneumonia, empyema, mastoiditis, acute otitis media, and complicated otitis media have been reported from multiple countries in which universal immunization has been implemented. Children with comorbid conditions have higher rates of pneumococcal disease and increased case fatality rates compared with otherwise healthy children, and protection for the most vulnerable pediatric patients will require new strategies to address the underlying host susceptibility and the expanded spectrum of serotypes observed.

Prevalence of Pulmonary Infections Caused by Atypical Pathogens in non-HIV Immunocompromised Patients

Although atypical bacteria are important causes of lower airway infections, data on their role in immunocompromised patients are scarce. The aim of the study was to evaluate the prevalence of atypical pulmonary infections in patients with various types of immunosuppression, and to analyze clinical characteristics of these infections. Eighty non-HIV immunocompromised patients with different underlying diseases and clinical and radiological signs of pulmonary infection were enrolled. Due to incomplete data on eight patients, 72 patients were eligible for final analysis (median age 58 years). All patients underwent fiberoptic bronchoscopy and bronchoalveolar lavage. Bronchoalveolar lavage fluid (BALF) fluid samples were sent for direct microscopy, cultures, and fungal antigen detection, when appropriate. Commercial qualitative amplification assay (PNEUMOTRIS oligomix Alert Kit(®)), based on nested PCR method, was used to detect specific DNA sequences of L. pneumophila, C. pneumoniae, and M. pneumoniae in BALF. There were 61 (84.7 %) patients with hematologic diseases, 3 (4.2 %) after solid organ transplantation, and 8 (11.1 %) with miscellaneous diseases affecting immune status. Specific sequences of M. pneumoniae, C. pneumoniae, and L. pneumophila DNA were found in 7 (9.7 %), 2 (2.8 %), and 0 patients, respectively. In 8 of these patients co-infections with different microorganisms were demonstrated. Co-infection with A. baumanii and P. aeruginosa was diagnosed in three patients who died. We conclude that atypical lower airway infections are uncommon in immunocompromised patients. The majority of these infections are co-infections rather than single pathogen infections.

How recent advances in molecular tests could impact the diagnosis of pneumonia

Molecular diagnostic tests have been the single major development in pneumonia diagnostics over recent years. Nucleic acid detection tests (NATs) have greatly improved the ability to detect respiratory viruses and bacterial pathogens that do not normally colonize the respiratory tract. In contrast, NATs do not yet have an established role for diagnosing pneumonia caused by bacteria that commonly colonize the nasopharynx due to difficulties discriminating between pathogens and coincidental carriage strains. New approaches are needed to distinguish infection from colonization, such as through use of quantitative methods and identification of discriminating cut-off levels. The recent realization that the lung microbiome exists has provided new insights into the pathogenesis of pneumonia involving the interaction between multiple microorganisms. New developments in molecular diagnostics must account for this new paradigm.

Rapid and sensitive detection of lower respiratory tract infections by stuffer-free multiplex ligation-dependent probe amplification

Lower respiratory tract infection is one of the most common infectious diseases. However, conventional methods for detecting infectious pathogens are time-consuming, and generally have a limited impact on early therapeutic decisions. We previously reported a rapid and sensitive method for detecting such pathogens using stuffer-free multiplex ligation-dependent probe amplification coupled with high-resolution CE-SSCP. In this study, we report an application of this method to the detection of respiratory pathogens. As originally configured, this method was capable of simultaneously detecting seven bacterial species responsible for lower respiratory tract infections, but its detection limit and assay time were insufficient to provide useful information for early therapeutic decisions. To improve sensitivity and shorten assay time, we added a target-specific preamplification step, improving the detection limit from 50 pg of genomic DNA to 500 fg. We further decreased time requirements by optimizing the hybridization step, enabling the entire assay to be completed within 7 h while maintaining the same detection limit. Taken together, these improvements enable the rapid detection of infectious doses of pathogens (i.e. a few dozen cells), establishing the strong potential of the refined method, particularly for aiding early treatment decisions.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past two decades due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation and user-friendly software have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, have benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods has lagged somewhat behind. The purpose of this chapter is to review and discuss the interpretation and relevance of results produced by these advanced molecular techniques. Moreover, this chapter will address the “myths” of NAATs, as these myths can markedly influence the interpretation and relevance of these results.

[The role of atypical microorganisms and viruses in severe acute community-acquired pneumonia]

Usually, intensivists do not focus on atypical bacteria and viruses in severe community-acquired pneumonia (CAP). Only Legionella pneumophila and influenza virus, following the recent H1N1 influenza pandemic, are routinely suggested as responsible agents. However, CAP due to atypical bacteria may represent up to 44% of all CAP. Viral CAP is considered less severe than the usual bacterial ones, although 25% of them warrant hospitalization and 15% result in severe sepsis. Even though L. pneumophila is the most frequently atypical pathogen involved in severe cases, Mycoplasma pneumoniae may be responsible for multiorgan failure. To date, tools including detection of Legionella antigen in urine and Mycoplasma using polymerase chain reaction (PCR) allow rapid and accurate diagnosis. The treatment is based on macrolides and fluoroquinolones that can be associated in severe Legionnaire diseases. The presence of virus in CAP, either alone or in association with bacteria, has been demonstrated using molecular biology tests. These techniques also allowed the identification of several new viruses in CAP. However, the exact role of these detected viruses in CAP as well as the efficiency of antiviral therapy still represent major unsolved concerns.

Laboratory methods for determining pneumonia etiology in children

Laboratory diagnostics are a core component of any pneumonia etiology study. Recent advances in diagnostic technology have introduced newer methods that have greatly improved the ability to identify respiratory pathogens. However, determining the microbial etiology of pneumonia remains a challenge, especially in children. This is largely because of the inconsistent use of assays between studies, difficulties in specimen collection, and problems in interpreting the presence of pathogens as being causally related to the pneumonia event. The laboratory testing strategy for the Pneumonia Etiology Research for Child Health (PERCH) study aims to incorporate a broad range of diagnostic testing that will be standardized across the 7 participating sites. We describe the current status of laboratory diagnostics for pneumonia and the PERCH approach for specimen testing. Pneumonia diagnostics are evolving, and it is also a priority of PERCH to collect and archive specimens for future testing by promising diagnostic methods that are currently under development.

Comparison of sputum and nasopharyngeal swab specimens for molecular diagnosis of Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Legionella pneumophila

Background

Differentiation of atypical pathogens is important for community-acquired pneumonia (CAP). In this study, we compared sputum and nasopharyngeal swabs (NPS) for use in detection of Mycoplasma pneumoniae (MP), Chlamydophila pneumoniae (CP), and Legionella pneumophila (LP), using Seeplex PneumoBacter ACE Detection Assay (PneumoBacter; Seegene).

Methods

Sputum and NPS specimens were collected from patients in 15 hospitals. DNA was extracted from sputum using QIAamp DNA Stool Mini Kit (Qiagen) and from NPS using easyMAG (bioMérieux). Both types of specimens were evaluated by multiplex PCR using PneumoBacter. To determine the diagnostic performance of this assay, sputum samples were also tested using BD ProbeTec ET Atypical Pneumonia Assay (APA; Becton Dickinson).

Results

Among 217 sputum and NPS, 20 (9.2%), 2 (0.9%), and 0 sputum were positive for MP, LP, and CP, respectively, whereas 8 (3.7%) NPS were positive for MP. The sputum APA test yielded 186, 206, and 204 interpretable results for MP, LP, and CP, respectively. Of these, 21 (11.3%) were positive for MP, 2 (1.0%) were positive for LP, and 0 samples were positive for CP. Compared to APA, the sensitivity and specificity of the sputum assay for MP were 95.2% and 100.0%, respectively, whereas for the NPS assay, these were 38.1% and 93.9%. Sputum testing was more sensitive than NPS testing (P=0.002). For LP and CP diagnosis, PneumoBacter and APA tests agreed 100%.

Conclusions

Specimen type is crucial and sputum is preferred over NPS for simultaneous detection of MP, LP, and CP using multiplex PCR in CAP.

A real-time PCR for the detection and characterisation of Aspergillus species

An early diagnosis of an invasive fungal infection is essential for the initiation of a specific antifungal therapy and to avoid unnecessary discontinuation of a baseline therapy for haematological or oncological diseases. A real-time PCR assay for the detection and strain identification of Aspergillus species from culture strains was evaluated. DNA preparation was evaluated in contaminated culture media, urine and serum. A LightCycler PCR to differentiate various Aspergillus species was established. A real-time PCR assay for the detection of Aspergillus species was improved and was able to detect and differentiate medically important Aspergillus spp. The sensitivity of the test was <10 plasmid equivalents/assay. The real-time PCR assay is a useful tool for the rapid identification of Aspergillus species and might be useful as an early diagnostic tool to detect an invasive fungal infection. A real-time PCR protocol was improved by generating plasmid standards, additional generation of melting curves for species identification and the correlation between the melting temperature and the nucleotide exchanges within the used 18S rRNA gene region.

Emerging advances in rapid diagnostics of respiratory infections

Recent developments in rapid diagnostics for respiratory infections have mostly occurred in the areas of antigen and nucleic acid detection. Nucleic acid amplification tests have improved the ability to identify respiratory viruses in clinical specimens and have played pivotal roles in the rapid characterization of new viral pathogens. Antigen-detection assays in immunochromatographic or similar formats are most easily developed as near-patient tests, although they have been developed commercially only for a limited range of respiratory pathogens. New approaches for respiratory pathogen detection are needed, and breath analysis is an exciting area with enormous potential.

An integrated, self-contained microfluidic cassette for isolation, amplification, and detection of nucleic acids

A self-contained, integrated, disposable, sample-to-answer, polycarbonate microfluidic cassette for nucleic acid-based detection of pathogens at the point of care was designed, constructed, and tested. The cassette comprises on-chip sample lysis, nucleic acid isolation, enzymatic amplification (polymerase chain reaction and, when needed, reverse transcription), amplicon labeling, and detection. On-chip pouches and valves facilitate fluid flow control. All the liquids and dry reagents needed for the various reactions are pre-stored in the cassette. The liquid reagents are stored in flexible pouches formed on the chip surface. Dry (RT-)PCR reagents are pre-stored in the thermal cycling, reaction chamber. The process operations include sample introduction; lysis of cells and viruses; solid-phase extraction, concentration, and purification of nucleic acids from the lysate; elution of the nucleic acids into a thermal cycling chamber and mixing with pre-stored (RT-)PCR dry reagents; thermal cycling; and detection. The PCR amplicons are labeled with digoxigenin and biotin and transmitted onto a lateral flow strip, where the target analytes bind to a test line consisting of immobilized avidin-D. The immobilized nucleic acids are labeled with up-converting phosphor (UCP) reporter particles. The operation of the cassette is automatically controlled by an analyzer that provides pouch and valve actuation with electrical motors and heating for the thermal cycling. The functionality of the device is demonstrated by detecting the presence of bacterial B.Cereus, viral armored RNA HIV, and HIV I virus in saliva samples. The cassette and actuator described here can be used to detect other diseases as well as the presence of bacterial and viral pathogens in the water supply and other fluids.

Routine using pattern and performance of diagnostic tests for tuberculosis on a university hospital

INTRODUCTION

Nucleic acid amplification tests to detect Mycobacterium tuberculosis in clinical specimens are used increasingly as a laboratory tool. We aimed to investigate the routine using pattern and the effects on therapeutic decision of diagnostic tests for tuberculosis in our hospital.

METHODS

In this descriptive study, we investigated retrospectively the routine using pattern and the effects on therapeutic decision of diagnostic tests for tuberculosis. Patients with discordant results were clinically evaluated retrospectively by a chest physician. Samples were tested for the presence of M. tuberculosis by a smear technique, M. tuberculosis culture growth technique (Löwenstein-Jensen and/or BACTEC-960), and IS6110 polymerase chain reaction (PCR).

RESULTS

Culture positivity was 7.2% (83 of 1159 patients). In total, 198 (62.4%) were tested with PCR, acid-fast bacilli, and culture. On the basis of culture results as a gold standard, sensitivity, specificity, positive predictive value, and negative predictive value of PCR were 46%, 89%, 23%, and 93.5%, respectively.

CONCLUSIONS

Selection of appropriate patients for further testing and exclusion of low-risk patients from microbiologic testing by experienced clinicians may help to optimize the positive predictive value of PCR.

PCR using blood for diagnosis of invasive pneumococcal disease: systematic review and meta-analysis

The use of molecular-based methods for the diagnosis of bacterial infections in blood is appealing, but they have not yet passed the threshold for clinical practice. A systematic review of prospective and case-control studies assessing the diagnostic utility of PCR directly with blood samples for the diagnosis of invasive pneumococcal disease (IPD) was performed. A broad search was conducted to identify published and unpublished studies. Two reviewers independently extracted the data. Summary estimates for sensitivity and specificity with 95% confidence intervals (CIs) were calculated by using the hierarchical summary receiver operating characteristic method. The effects of sample processing, PCR type, the gene-specific primer, study design, the participants' age, and the source of infection on the diagnostic odds ratios were assessed through meta-regression. Twenty-nine studies published between 1993 and 2009 were included. By using pneumococcal bacteremia for case definition and healthy people or patients with bacteremia caused by other bacteria as controls (22 studies), the summary estimates for sensitivity and specificity were 57.1% (95% CI, 45.7 to 67.8%) and 98.6% (95% CI, 96.4 to 99.5%), respectively. When the controls were patients suspected of having IPD without pneumococcal bacteremia (26 studies), the respective values were 66.4% (95% CI, 55.9 to 75.6%) and 87.8% (95% CI, 79.5 to 93.1%). With lower degrees of proof for IPD (any culture or serology result and the clinical impression), the sensitivity of PCR decreased and the specificity increased. All analyses were highly heterogeneous. The use of nested PCR and being a child were associated with low specificity, while the use of a cohort study design was associated with a low sensitivity. The lack of an appropriate reference standard might have caused underestimation of the performance of the PCR. Currently available methods for PCR with blood samples for the diagnosis of IPD lack the sensitivity and specificity necessary for clinical practice.

Usefulness of real-time PCR for lytA, ply, and Spn9802 on plasma samples for the diagnosis of pneumococcal pneumonia

In the present study, we evaluated rapid real-time PCR assays for ply, Spn9802, and lytA applied to plasma samples for the detection of Streptococcus pneumoniae in patients with community-acquired pneumonia (CAP). In a prospective study of CAP aetiology, an EDTA plasma sample was collected together with blood culture in 92 adult CAP patients and 91 adult controls. Among the 92 CAP patients, lytA PCR was positive in eight (9%), Spn9802 PCR was positive in 11 (12%) and ply PCR was positive in 19 (21%) cases. Of 91 controls, the ply PCR was positive in eight cases (9%), but no positive cases were noted by Spn9802 or lytA PCRs. Ten CAP patients had pneumococcal bacteraemia. Compared to blood culture, PCR for lytA, Spn9802 and ply had sensitivities of 70% (7/10), 60% (6/10) and 70% (7/10), and specificities of 96% (79/82), 94% (77/82) and 85% (70/82) respectively. With blood culture and/or culture of representative sputum, and/or urinary antigen detection, S. pneumoniae was identified in 31 CAP patients. Compared to these tests in combination, PCR for lytA, Spn9802 and ply showed sensitivities of 26% (8/31), 32% (10/31) and 42% (13/31), and specificities of 100% (61/61), 98% (60/61) and 90% (55/61) respectively. We conclude that Spn9802 and lytA PCRs may be useful for the rapid detection of bacteraemic pneumococcal pneumonia, whereas ply PCR is not specific enough for routine use and blood PCR with small plasma volumes is not useful for the detection of nonbacteraemic pneumococcal pneumonia.

Atypical pneumonia--time to breathe new life into a useful term?

The term atypical pneumonia was originally used to describe an unusual presentation of pneumonia. It is now more widely used in reference to either pneumonia caused by a relatively common group of pathogens, or to a distinct clinical syndrome the existence of which is difficult to demonstrate. As such, the use of atypical pneumonia is often inaccurate, potentially confusing, and of dubious scientific merit. We need to return to the original meaning of atypical pneumonia and restrict its use to describe pneumonia that is truly unusual in clinical presentation, epidemiology, or both.

Evaluation of five commercial real-time PCR assays for detection of Mycoplasma pneumoniae in respiratory tract specimens

The performances of five commercial TaqMan real-time PCR assays for the detection of Mycoplasma pneumoniae in respiratory tract specimens were evaluated in comparison with an in-house real-time PCR. All kits allowed prompt and specific results, validated by the use of an internal control. The Nanogen kit showed the best clinical sensitivity.

Is quantitative PCR for the pneumolysin (ply) gene useful for detection of pneumococcal lower respiratory tract infection?

The pneumolysin (ply) gene is widely used as a target in PCR assays for Streptococcus pneumoniae in respiratory secretions. However, false-positive results with conventional ply-based PCR have been reported. The aim here was to study the performance of a quantitative ply-based PCR for the identification of pneumococcal lower respiratory tract infection (LRTI). In a prospective study, fibreoptic bronchoscopy was performed in 156 hospitalized adult patients with LRTI and 31 controls who underwent bronchoscopy because of suspicion of malignancy. Among the LRTI patients and controls, the quantitative ply-based PCR applied to bronchoalveolar lavage (BAL) fluid was positive at >or=10(3) genome copies/mL in 61% and 71% of the subjects, at >or=10(5) genome copies/mL in 40% and 58% of the subjects, and at >or=10(7) genome copies/mL in 15% and 3.2% of the subjects, respectively. Using BAL fluid culture, blood culture, and/or a urinary antigen test, S. pneumoniae was identified in 19 LRTI patients. As compared with these diagnostic methods used in combination, quantitative ply-based PCR showed sensitivities and specificities of 89% and 43% at a cut-off of 10(3) genome copies/mL, of 84% and 66% at a cut-off of 10(5) genome copies/mL, and of 53% and 90% at a cut-off of 10(7) genome copies/mL, respectively. In conclusion, a high cut-off with the quantitative ply-based PCR was required to reach acceptable specificity. However, as a high cut-off resulted in low sensitivity, quantitative ply-based PCR does not appear to be clinically useful. Quantitative PCR methods for S. pneumoniae using alternative gene targets should be evaluated.

Novel approaches to the identification of Streptococcus pneumoniae as the cause of community-acquired pneumonia

Current diagnostic tests lack sensitivity for the identification of the bacterial etiology of pneumonia. Attempts during the past 2 decades to improve sensitivity of detection of bacterial constituents in blood by use of antibody-antigen complexes and polymerase chain reaction have been disappointing. Recent data using pneumococcal conjugate vaccines as probes suggest that increased levels of both C-reactive protein and procalcitonin may be useful adjuncts to chest radiographs in the selection of patients with presumed bacterial pneumonia for inclusion in clinical trials. Among pneumococcal diagnostics currently under investigation, quantitative real-time polymerase chain reaction of respiratory secretions, as well as urinary antigen detection and pneumococcal surface adhesin A serological analysis for adults, are candidates for use in future clinical trials of antibiotics.

Integrated microfluidic systems for sample preparation and detection of respiratory pathogen Bordetella pertussis

An integrated microfluidic system for combined manipulation, pre-concentration, and lysis of samples containing Bordetella pertussis by dielectrophoresis and electroporation has been developed and implemented. The microfluidic device was able to pre-concentrate the amount of B. pertussis cells present in 200 microl of a B. pertussis suspension stock into a 20 microl volume. The device exhibited optimal sample pre-concentration of 6.7x at a stock value of 10(3) cfu/ml and at a flow rate of 250 microl/h. Electro-disruption experiments showed that on-chip-based electroporation is an effective solution for lysis of B. pertussis cells that is easily integrated with dielectrophoresis assisted pre-concentration procedures. Pulsed voltage applied, number of pulses, and presence of potassium chloride in a B. pertussis suspension showed a reduction in B. pertussis cell viability by electroporation; and transmission electron microscopy confirmed B. pertussis cell disruption by electroporation. Genetic amplification and detection of the pre-concentrated sample employing an integrated chip-based system demonstrated a complete chip approach for pathogen detection.

Medical microbiology: laboratory diagnosis of invasive pneumococcal disease

The laboratory diagnosis of invasive pneumococcal disease (IPD) continues to rely on culture-based methods that have been used for many decades. The most significant recent developments have occurred with antigen detection assays, whereas the role of nucleic acid amplification tests has yet to be fully clarified. Despite developments in laboratory diagnostics, a microbiological diagnosis is still not made in most cases of IPD, particularly for pneumococcal pneumonia. The limitations of existing diagnostic tests impact the ability to obtain accurate IPD burden data and to assess the effectiveness of control measures, such as vaccination, in addition to the ability to diagnose IPD in individual patients. There is an urgent need for improved diagnostic tests for pneumococcal disease--especially tests that are suitable for use in underresourced countries.

Electro-disruption of Escherichia coli bacterial cells on a microfabricated chip

A miniaturized system for sample preparation of relevant bacterial pathogens has been developed using a variety of microfabrication techniques. The system manipulates and disrupts Eschericha coli bacterial cells using dielectrophoresis, electroporation and enzymes. The microchip consisted of circular gold electrodes patterned on glass using standard photolithography housed in a PDMS chamber. The bacterial lysis efficiency by electroporation and enzymatic degradation was evaluated on the microchip. The miniaturized system was capable of concentrating and aligning bacterial cells in regions of high electric field by dielectrophoresis. The miniaturized sample preparation system had a lysis efficiency of 17% when the bacterial cells were suspended in a 0.25 M sucrose solution and increased to 80% when the bacterial cells were suspended in a solution containing 0.25 M sucrose and 10 KU/ml lysozyme. Sample preparation is a limiting factor for the successful application of molecular pathogen detection methods. Therefore, the development of miniaturized systems useful for sample preparation will improve molecular detection methods of bacterial pathogens.

Currently used nucleic acid amplification tests for the detection of viruses and atypicals in acute respiratory infections

For the detection of respiratory viruses conventional culture techniques are still considered as the gold standard. However, results are mostly available too late to have an impact on patient management. The latest developments include appropriate DNA- and RNA-based amplification techniques (both NASBA and PCR) for the detection of an extended number of agents responsible for LRTI. Real time amplification, the latest technical progress, produces, within a considerable shorter time, results with a lower risk of false positives. As results can be obtained within the same day, patient management with appropriate therapy or reduction of unnecessary antibiotic therapy in LRTI will be possible. A number of technical aspects of these amplification assays, and their advantages are discussed.

The availability and use of these new diagnostic tools in virology has contributed to a better understanding of the role of respiratory viruses in LRTI. The increasing importance of the viral agents, Mycoplasma pneumoniae and Chlamydophila pneumoniae in ARI is illustrated. A great proportion of ARI are caused by viruses, but their relative importance depends on the spectrum of agents covered by the diagnostic techniques and on the populations studied, the geographical location and the season. The discovery of new viruses is ongoing; examples are the hMPV and the increasing number of coronaviruses. Indications for the use of these rapid techniques in different clinical situations are discussed. Depending on the possibilities, the laboratory could optimize its diagnostic strategy by applying a combination of immunofluorescence for the detection of RSV an IFL, and a combination of real-time amplification tests for other respiratory viruses and the atypical agents. When implementing a strategy, a compromise between sensitivity, clinical utility, turn around time and cost will have to be found.

Increased detection of respiratory syncytial virus, influenza viruses, parainfluenza viruses, and adenoviruses with real-time PCR in samples from patients with respiratory symptoms

Respiratory samples (n = 267) from hospitalized patients with respiratory symptoms were tested by real-time PCR, viral culture, and direct immunofluorescence for respiratory syncytial virus, influenza virus, parainfluenza viruses, and adenoviruses. Compared with conventional diagnostic tests, real-time PCR increased the diagnostic yields for these viruses from 24% to 43% and from 3.5% to 36% for children and adults, respectively.

Evaluation of real-time PCR for the detection and quantification of bacteria in chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) embraces a number of pathological processes including chronic bronchitis, chronic bronchiolitis and emphysema. The chronic and progressive course of COPD is often aggravated by short periods of increasing symptoms. Respiratory tract infections (RTIs) are the most common causes of COPD exacerbations. Detection and enumeration of respiratory bacteria are important techniques in diagnosing RTIs and in the validation of new treatment methods. We describe here the development and evaluation of real-time PCR assays for the simultaneous direct detection and quantification of a range of respiratory bacteria in individuals with COPD during stable periods and during acute exacerbations of the disease. Sputum samples from 30 subjects in a COPD study were analysed, and results compared with the current gold standard of culture. Real-time PCR assays proved highly sensitive, with no cross-reactivity with other species. The prevalence of bacteria detected by real-time PCR compared with that by culture was substantially higher for Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus spp. and Moraxella catarrhalis. Multiple pathogens were also found with real-time PCR but were not detected by culture. This study demonstrates the potential of such methods in the detection and enumeration of respiratory bacteria.

[Contribution of microbiological investigations to the diagnosis of lower respiratory tract infections]

The diagnosis of community-acquired pneumonia is usually based on clinical and radiological criteria. The identification of a causative organism is not required for the diagnosis. Although numerous microbiological techniques are available, their sensitivity and specificity are not high enough to guide first-line antimicrobial therapy. Consequently, this treatment remains most often empiric. If the causative organism is identified, the antimicrobial treatment is adapted. Sputum analysis may be proposed as a diagnostic tool for patients with an acute exacerbation of chronic obstructive pulmonary disease, in specific cases (prior antibiotherapy, hospitalization, failure of the empiric antimicrobial treatment).

Quantitative detection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in lower respiratory tract samples by real-time PCR

The limitation of polymerase chain reaction (PCR) in diagnosis of lower respiratory tract infections (LRTIs) caused by Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis has been a distinguishing colonization from infection. We assess here the usefulness of real-time quantitative PCR (RQ-PCR) performed on lower respiratory tract samples to overcome this problem. Consecutive respiratory tract samples from patients with and without signs of infection (n = 203) were subjected to RQ-PCR, targeting the genes pneumolysin (S. pneumoniae), fumarate reductase (H. influenzae), and outer membrane protein B (M . catarrhalis). DNA from positive controls with predefined colony forming units (CFUs) per milliliter were included to allow estimation of CFU per milliliter for the test samples. In parallel, assessment of quantitative cultures from all samples was performed. In the group of patients with LRTI, significant pathogens (>/=10(5) CFU/mL) were found in 32/135 samples (23.7%) with culture, in 51/135 (37.7%) with RQ-PCR, and in 59/135 (43.7%) when combining the methods.

Swedish guidelines for the management of community-acquired pneumonia in immunocompetent adults

This document presents the evidence-based guidelines of the Swedish Society of Infectious Diseases for the management of adult immunocompetent patients with community-acquired pneumonia (CAP), who are assessed at hospital. The prognostic score 'CURB-65' is recommended for all CAP patients in the emergency room. The score provides an assessment tool for the decision regarding outpatient treatment or level of hospital supervision, the choice of microbiological investigations, and empirical antibiotic treatment. In patients with non-severe CAP (CURB-65 score 0-2) we recommend initial narrow-spectrum antibiotic treatment, orally or intravenously, primarily directed at Streptococcus pneumoniae. In those with CURB-65 score 3, penicillin G or a cephalosporin intravenously is recommended. For CURB-65 score 0-3 atypical pathogens should be covered only when they are suspected on clinical or epidemiological grounds. In patients with CURB-65 score 4-5 intravenous combination therapy with either cephalosporin/macrolide or penicillin G/fluoroquinolone is recommended. Efforts should be made to identify the CAP aetiology in order to support the ongoing antibiotic treatment or to suggest treatment alterations. Recommended measures for prevention of CAP include influenza -- and pneumococcal -- vaccination to risk groups and efforts for smoking cessation.