Relevance of nucleic acid amplification techniques for diagnosis of respiratory tract infections in the clinical laboratory

First preliminary study on identification of bacterial fish pathogens with Raman spectroscopy

Accurate and rapid determination of bacterial disease agents of fish is an important step for sustainable and efficient aquaculture production. In general, biochemical and molecular methods are used for pathogen detection but they are usually time-consuming and required qualified personnel. Recently spectroscopic methods are preferred in clinical and food microbiology and declared as a promising alternative method for pathogens diagnosis with many advantages. In this study, the significant spectra of three important bacterial fish pathogens (Lactococcus garvieae, Vibrio anguillarum and Yersinia ruckeri) were determined by Raman spectroscopy. The first data of the pathogens were obtained and the distinctive differences in polysaccharides, nucleic acids, fatty acids and amino acids were identified. This preliminary study aimed to be pioneer for further studies in aquaculture and veterinary microbiology toward developing an alternative method for routine identification.

Comparison of Cell Culture with Three Conventional Polymerase Chain Reactions for Detecting Chlamydophila pneumoniae in Adult's Pharyngotonsillitis

Chlamydophila pneumoniae is an intracellular pathogen responsible for respiratory tract infections. The isolation of the microorganism from clinical specimens is essential for a diagnosis. However, the identification of C. pneumoniae by cell cultures is very difficult besides strongly depending on the sample conditions. The study aimed to investigate, in adult patients with pharyngotonsillitis, the frequency of Chlamydophila pneumoniae detection by cell cultures and three conventional PCRs (a conventional PCR targeting the 16S rRNA gene and two nested PCRs, targeting the 16S rRNA gene and the ompA gene, respectively). The presence of chlamydial inclusion in cell cultures was observed in 11/94 samples (11.70%) by IFA. C. pneumoniae DNA was detected in 12/94 (12.76%) specimens by the 16S rRNA gene nested PCR, 4/94 (4.26%) by ompA gene nested PCR, and in 2/94 (2.13%) by 16S rRNA single-step PCR. Our data show poor agreement between the three applied DNA-amplification methods; in fact, only 16S rRNA gene nested PCR showed a statistically significant difference. Moreover, this result allowed us to achieve a definitive confirmation of the previous finding and to avoid the risk of an overestimation of the C. pneumoniae as a pathogen in pharyngotonsillitis.

Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection

Background:

Analytical chemistry and biotechnology as an interdisciplinary fields of science have been developed during many years and are experiencing significant growth, to cover a wide range of microorganisms separation techniques and methods, utilized for medical therapeutic and diagnostic purposes. Currently scientific reports contribute by introducing electrophoretical and immunological methods and formation of devices applied in food protection (avoiding epidemiological diseases) and healthcare (safety ensuring in hospitals).

Methods:

Electrophoretic as well as nucleic-acid-based or specific immunological methods have contributed tremendously to the advance of analyses in recent three decades, particularly in relation to bacteria, viruses and fungi identifications, especially in medical in vitro diagnostics, as well as in environmental or food protection.

Results:

The paper presents the pathogen detection competitiveness of these methods against conventional ones, which are still too time consuming and also labor intensive. The review is presented in several parts following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis.

Discussion:

Part one, consists of elemental knowledge about microorganisms as an introduction to their characterization: descriptions of divisions, sizes, membranes (cells) components. Second section includes the development, new technological and practical solution descriptions used in electrophoretical procedures during microbes analyses, with special attention paid to bio-samples analyses like blood, urine, lymph or wastewater. Third part covers biomolecular areas that have created a basis needed to identify the progress, limitations and challenges of nucleic-acid-based and immunological techniques discussed to emphasize the advantages of new separative techniques in selective fractionating of microorganisms.

Laboratory Diagnosis of Respiratory Tract Infections in Children - the State of the Art

In the pediatric population, respiratory infections are the most common cause of physician visits. Although many respiratory illnesses are self-limiting viral infections that resolve with time and supportive care, it can be critical to identify the causative pathogen at an early stage of the disease in order to implement effective antimicrobial therapy and infection control. Over the last few years, diagnostics for respiratory infections have evolved substantially, with the development of novel assays and the availability of updated tests for newer strains of pathogens. Newer laboratory methods are rapid, highly sensitive and specific, and are gradually replacing the conventional gold standards, although the clinical utility of these assays is still under evaluation. This article reviews the current laboratory methods available for testing for respiratory pathogens and discusses the advantages and disadvantages of each approach.

A case report of Legionella and Mycoplasma pneumonia: Co-incidence or co-infection?

RATIONALE

Concurrent or sequential coinfections of Legionella pneumophila and Mycoplasma pneumoniae have been reported in the past though infrequently. Distinguishing a true co-infection from cross reactivity is often challenging as the diagnosis is mostly dependent on serological testing.

PATIENT CONCERNS

A 77-year-old male presented with worsening dyspnea, cough with yellow sputum, diarrhea and fever of 2-days duration. Patient had history of chronic obstructive pulmonary disease (COPD) on home oxygen, bronchiectasis, rheumatoid arthritis (on methotrexate and leflunomide), treated pulmonary tuberculosis and 30-pack-year smoking. Chest X-ray showed bilateral interstitial changes with left lower lobe infiltrate. On day 5, his urine antigen for L pneumophila serogroup 1 was reported positive. The following day his serum M pneumoniae IgM antibody titers were reported elevated at 6647 U/mL. Patient was started on antibiotics and placed on non-invasive positive pressure ventilation.

DIAGNOSIS

The patient was diagnosed with possible Legionella and Mycoplasma co-infection.

OUTCOMES

Sputum Mycoplasma polymerase chain reaction (PCR) and serum cold agglutinins were obtained on day 6 and later reported negative. He was treated with azithromycin for 10 days with clinical improvement.

LESSONS

Serological testing alone is an indirect measure with poor sensitivity and specificity and has its own limitations. Urine antigen detection confirms L pneumophila serogroup 1 infection in a patient with suggestive symptoms. However, diagnosis of M pneumonia should be based on combination of tests including serology and PCR to confirm true co-infection.

Rapid screening for Mycobacterium tuberculosis complex in clinical elephant trunk wash samples

Mycobacterium tuberculosis can infect and be transmitted between elephants and humans. In elephants, the 'gold standard' reference test for detection of tuberculosis is culture, which takes a minimum of eight weeks for results and has limited sensitivity. A screening test that is rapid, easily implemented, and accurate is needed to aid in diagnosis of tuberculosis in elephants. Ninety-nine clinical trunk wash samples obtained from 33 elephants were utilized to validate three molecular extraction techniques followed by a polymerase chain reaction for detection of M. tuberculosis. Diagnostic sensitivity and specificity were estimated compared to culture. Kappa coefficients were determined between molecular results and various culture categories and serological test results. An internal amplification control was developed and assessed to monitor for PCR inhibition. One molecular test (the Column method) outperformed the other two, with diagnostic sensitivity and kappa agreement estimates of 100% (CI 57-100) and 0.46 (CI 0.2-0.74), respectively, compared to culture alone. The percentage of molecular-positive/culture-negative samples was 8.4% overall. The molecular extraction technique followed by PCR provides a much-needed rapid screening tool for detection of tuberculosis in elephants. Immediate procedures can be implemented to further assess PCR-positive animals and provide personnel biosecurity. While a positive result is not a definitive test for elephant tuberculosis, the molecular test results can be used to support current diagnostic procedures applied by veterinarians for treatment decisions to prevent the spread of tuberculosis in elephants.

Development and evaluation of enzyme-linked immunosorbent assay of nucleic acid sequence-based amplification for diagnosis of invasive aspergillosis

Invasive aspergillosis (IA) is a life-threatening infection in immunocompromised patients, rapid and sensitive detection of Aspergillus from clinical samples has been a major challenge in the early diagnosis of IA. An enzyme-linked immunosorbent assay of nucleic acid sequence-based amplification (NASBA-ELISA) was developed to fulfil the need for the efficient diagnosis of these infections. The primers targeting 18S rRNA were selected for the amplification of Aspergillus RNA by the isothermal digoxigenin (DIG)-labeling NASBA process. The DIG-labeled RNA amplicons were hybridized with a specific biotinylated DNA probe immobilized on streptavidin-coated microtiter plate. The hybrids were colorimetrically detected by the addition of an anti-DIG antibodies linked to ALP and substrate (disodium 4-nitrophenyl phosphate). The detection limit of the Aspergillus NABSA-ELISA system was 1 CFU and the RNA in non-target bacteria or fungus was not amplified. The performance of this NASBA-ELISA compared to RT-PCR and galactomannan (GM) was evaluated by testing blood samples from 86 patients at high risk for IA. The sensitivity of NASBA-ELISA, RT-PCR and GM-ELISA was 80.56 % (95 % CI 63.98-91.81), 72.22 % (95 % CI 54.81-85.80), 58.33 % (95 % CI 40.76-74.49), respectively, and the specificity was 80.00 % (95 % CI 66.28-89.97), 84.00 % (95 % CI 70.89-92.83), 82.00 % (95 % CI 68.56-91.42). The efficiency of the three methods in various combinations was also evaluated. Combination of NASBA-ELISA and GM-ELISA testing achieved perfect specificity (100 %; 95 % CI 92.89-100) and perfect positive predictive value (100 %; 95 % CI 83.16-100). The best sensitivity (97.22 %; 95 % CI 85.47-99.93) and the highest Youden index (0.652) were obtained by testing with both NASBA and RT-PCR in parallel. In conclusion, the NASBA-ELISA assay consists of an alternative process for large-scale samples detection with semi-quantitative results and provides good clinical performance without resorting to expensive equipment. This assay makes it possible for the NASBA based RNA diagnosis to become a routine work in laboratories in less developed countries with fewer resources.

NAIL: Nucleic Acid detection using Isotachophoresis and Loop-mediated isothermal amplification

Nucleic acid amplification tests are the gold standard for many infectious disease diagnoses due to high sensitivity and specificity, rapid operation, and low limits of detection. Despite the advantages of nucleic acid amplification tests, they currently offer limited point-of-care (POC) utility due to the need for complex instruments and laborious sample preparation. We report the development of the Nucleic Acid Isotachophoresis LAMP (NAIL) diagnostic device. NAIL uses isotachophoresis (ITP) and loop-mediated isothermal amplification (LAMP) to extract and amplify nucleic acids from complex matrices in less than one hour inside of an integrated chip. ITP is an electrokinetic separation technique that uses an electric field and two buffers to extract and purify nucleic acids in a single step. LAMP amplifies nucleic acids at constant temperature and produces large amounts of DNA that can be easily detected. A mobile phone images the amplification results to eliminate the need for laser fluorescent detection. The device requires minimal user intervention because capillary valves and heated air chambers act as passive valves and pumps for automated fluid actuation. In this paper, we describe NAIL device design and operation, and demonstrate the extraction and detection of pathogenic E. coli O157:H7 cells from whole milk samples. We use the Clinical and Laboratory Standards Institute (CLSI) limit of detection (LoD) definitions that take into account the variance from both positive and negative samples to determine the diagnostic LoD. According to the CLSI definition, the NAIL device has a limit of detection (LoD) of 1000 CFU mL(-1) for E. coli cells artificially inoculated into whole milk, which is two orders of magnitude improvement to standard tube-LAMP reactions with diluted milk samples and comparable to lab-based methods. The NAIL device potentially offers significant reductions in the complexity and cost of traditional nucleic acid diagnostics for POC applications.

Comparison of cyp141 and IS6110 for detection of Mycobacterium tuberculosis from clinical specimens by PCR

BACKGROUND

Tuberculosis is a major public health problem throughout the world. TB's worldwide patterns of prevalence coupled with the increase in incidence of HIV infection threaten the health and lives of humans worldwide. Rapid detection of TB and the rapidly initiation of the administration of medication are important strategies for stopping the transmission of this disease transmission and its resistance to anti-TB drugs. Molecular methods are advantageous relative to conventional techniques due to their greater speed and sensitivity in the detection of TB.

METHODS

In this study, we targeted the cyp141 gene for the detection of Mycobacterium tuberculosis from clinical specimens (n=123) by PCR and compared the sensitivity and specificity of this new target with those of IS6110 gene.

RESULTS

Targeting of the cyp141 gene is more sensitive (97.1% for cultured isolates and 85.7% for direct specimens) than the targeting of the commonly used IS6110 gene (95.1% for cultured isolates and 42.9% for direct specimens), and the specificities of these two target genes were equal (100%).

CONCLUSIONS

The cyp141 gene can be used as a new target for the direct detection of Mycobacterium tuberculosis that seems to be superior to IS6110.

Rapid real-time PCR for detection of Mycobacterium tuberculosis complex DNA in formalin-fixed paraffin embedded tissues: 16% of histological 'sarcoid' may contain such DNA

AIMS

To investigate the diagnostic accuracy of IS6110 real-time PCR for detection of Mycobacterium tuberculosis complex (MTBC) in DNA extracted from formalin-fixed paraffin embedded (FFPE) tissues using two different methods. In the absence of material submitted for tuberculosis (TB) culture, MTBC detection in FFPE tissue can be an important aid to diagnosis.

METHODS

We collected 144 FFPE tissue blocks (lung and lymph node) for IS6110 real-time PCR. Two DNA extraction methods (QIAamp FFPE tissue kit and NucliSENS easyMAG) were assessed within a general laboratory setting. PCR results were compared with histology and culture.

RESULTS

In the histological MTBC and culture MTBC (TB-positive) groups, 72.4% were IS6110-positive and 27.6% negative. IS6110-negative results were obtained from 98%, 61.5% and 84% of the histologically MTBC-negative (TB-negative) group, histologically TB/no culture group and sarcoidosis group, respectively. Review of 19 IS6110-positive patients in the latter three groups showed that 15 had clinical TB. Thirteen of 15 (86.7%) IS6110-positive patients in the histological TB/no culture group and 2 of 4 (50%) IS6110-positive patients in the sarcoidosis group were clinically diagnosed with TB which highlights the difficulty of a pathological diagnosis.

CONCLUSIONS

IS6110 real-time PCR using easyMAG extracted DNA is a moderately sensitive, specific and rapid method for MTBC detection in FFPE material, but must be interpreted in the overall clinical context. PCR results can be available in around 5 h from FFPE specimen receipt, with minimal hands-on time.

Developments for improved diagnosis of bacterial bloodstream infections

Bloodstream infections (BSIs) are associated with high mortality and increased healthcare costs. Optimal management of BSI depends on several factors including recognition of the disease, laboratory tests and treatment. Rapid and accurate identification of the etiologic agent is crucial to be able to initiate pathogen specific antibiotic therapy and decrease mortality rates. Furthermore, appropriate treatment might slow down the emergence of antibiotic resistant strains. Culture-based methods are still considered to be the "gold standard" for the detection and identification of pathogens causing BSI. Positive blood cultures are used for Gram-staining. Subsequently, positive blood culture material is subcultured on solid media, and (semi-automated) biochemical testing is performed for species identification. Finally, a complete antibiotic susceptibility profile can be provided based on cultured colonies, which allows the start of pathogen-tailored antibiotic therapy. This conventional workflow is extremely time-consuming and can take up to several days. Furthermore, fastidious and slow-growing microorganisms, as well as antibiotic pre-treated samples can lead to false-negative results. The main aim of this review is to present different strategies to improve the conventional laboratory diagnostic steps for BSI. These approaches include protein-based (MALDI-TOF mass spectrometry) and nucleic acid-based (polymerase chain reaction [PCR]) identification from subculture, blood cultures, and whole blood to decrease time to results. Pathogen enrichment and DNA isolation methods, to enable optimal pathogen DNA recovery from whole blood, are described. In addition, the use of biomarkers as patient pre-selection tools for molecular assays are discussed.

Comparison of four DNA extraction methods for detecting Mycobacterium tuberculosis by real-time PCR and its clinical application in pulmonary tuberculosis

OBJECTIVES

China is one of the countries with a high burden of Mycobacterium tuberculosis (MTB) infection. One challenge for the earlier diagnosis of tuberculosis is the DNA extraction of MTB. This study was to compare four MTB DNA extraction methods, and use the best one in the diagnosis of pulmonary tuberculosis.

METHODS

A total of 43 serum and 94 plasma samples were collected from 124 clinical diagnosed pulmonary tuberculosis patients. Four different MTB DNA extraction methods, including phenol-chloroform method, Qiagen kit, Omega kit and magnetic bead method, were compared to determine which method displayed the highest sensitivity. A quantitative fluorescent PCR assay was also designed for the detection of MTB DNA.

RESULTS

The highest DNA extraction efficiency (52.8%) and the best reproducibility (coefficient of variance =26.7%) were observed using the magnetic bead method. For 39 of the 124 (31.5%) pulmonary tuberculosis patients, MTB DNA was detected in their plasma or serum samples. Interestingly, 35.3% (12/34) of smear-negative cases were MTB DNA positive.

CONCLUSIONS

In conclusion, magnetic bead method is the best one for the DNA extraction of MTB. The detection of MTB DNA may provide valuable information for the diagnosis of acid-fast bacilli (AFB) negative pulmonary tuberculosis patients.

Frequency of different human mollicutes species in the mucosa of the oropharynx, conjunctiva, and genitalia of free-ranging and captive capuchin monkeys (Cebus spp.)

This study is the first to evaluate the occurrence of several Mollicutes species in Brazilian capuchin monkeys (Cebus spp.). Mollicutes were detected by culture and polymerase chain reaction (PCR) in samples of the oropharyngeal, conjuctiva, and genital mucosae of 58 monkeys. In the oropharynx, Mollicutes in general (generic PCR to the Class), and those of the genus Ureaplasma (genus PCR), were detected in 72.4% and 43.0% of the samples, respectively. The identified species in this site included: Mycoplasma arginini (43.1%), M. salivarium (41.4%), and M. pneumoniae (19.0%). Both Ureaplasma and Mycoplasma are genera of the order Mycoplasmatales. In the preputial/vaginal mucosa, PCR detected Mollicutes in general in 27.58% of the samples, the genus Ureaplasma in 32.7%, the species M. arginini in 8.6%, and Acholeplasma laidlawii of the order Acholeplasmatales in 1.7% In the conjunctiva, Mollicutes in general were detected in 29.3% of the samples, with 1.7% being identified as A. laidlawii. Culturing was difficult due to contamination, but two isolates were successfully obtained. The Mollicutes species of this study provided new insights into these bacteria in Brazilian Cebus. Studies are lacking of the actual risk of Mollicutes infection or the frequency at which primates serve as permanent or temporary reservoirs for Mollicutes. In the present study, the samples were collected from monkeys without clinical signs of infection. The mere presence of Mollicutes, particularly those also found in humans, nevertheless signals a need for studies to evaluate the impact of these microorganisms on the health of non-human primates (NHPs) and the possibility of cross-species transmission between NHPs and humans.

Evaluation of 10 serological assays for diagnosing Mycoplasma pneumoniae infection

In this study, the performance of 10 serological assays for the diagnosis of Mycoplasma pneumoniae infection was evaluated. A total of 145 sera from 120 patients were tested. They were obtained from patients who were serologically positive for M. pneumoniae infection as well as from patients who were infected with micro-organisms that may cause interstitial pneumonia. The following assays were utilized: SeroMP IgM and IgG, SeroMP recombinant IgM, IgA and IgG, Liaison M. pneumoniae IgM and IgG and M. pneumoniae IgM, IgA and IgG ELISA Medac. The SeroMP Recombinant and Liaison assays both showed low IgM specificity, and crossreactivity was mainly observed in groups of patients with acute cytomegalovirus and Epstein-Barr virus infections. For IgA, the Medac assay was less specific than the SeroMP Recombinant assay. Discrepancies between the four tests were observed in IgG analyses, and due to the lack of a gold standard, 22 results were removed prior to determining the sensitivity and specificity. Therefore, the overall performance of IgG assays may be overstated; nevertheless, the SeroMP assay demonstrated a lack of sensitivity. The seroprevalence of IgG appears to be very low, raising concerns regarding whether the serological techniques can detect IgG levels over time. Serology remains a biological tool of choice for diagnosing M. pneumoniae infection, but improvement and standardization of the assays are needed, particularly for the determination of IgG.

Application of three uniplex polymerase chain reaction assays for the detection of atypical bacteria in asthmatic patients in Kuwait

BACKGROUND

Respiratory infections are known to exacerbate wheezing in many asthmatic patients. We aimed to use molecular methods for the fast detection of Mycoplasma pneumoniae, Chlamydia pneumoniae and Legionella pneumophila in respiratory specimens from asthmatic patients in Kuwait.

METHODS

We used uniplex PCR assays to detect the three atypical bacteria in clinical specimens from 235 asthmatic and non-asthmatic patients in Kuwait. A regression analysis was used to identify the risk factors related to the bacterial type. Group comparisons for similarity were conducted and correlation coefficients were calculated using SPSS statistical software.

RESULTS

The detection limits using uniplex PCR for C. pneumoniae, L. pneumophila and M. pneumoniae were approximately 1pg, 2.4fg and 12pg of DNA, respectively. M. pneumoniae PCR positivity was more common in asthmatic patients (15%) than in non-asthmatic subjects (9%) (P<0.05). A marked difference was observed between patients with acute asthma exacerbation (11%) and patients with chronic (stable) asthma (7%) among Kuwaiti patients; these percentages were 16% for non-Kuwaiti acute asthma patients and 14% for non-Kuwaiti chronic asthma patients (P<0.201). There was a weak positive correlation between asthma severity and PCR positivity for M. pneumoniae. The PCR results for C. pneumoniae and L. pneumoniae were found to be statistically insignificant.

CONCLUSIONS

The results of this study suggest that infection with M. pneumoniae may be related to the exacerbation of asthma symptoms and could possibly be a factor that induces wheezing.

Diagnosis of the pulmonary tuberculosis by polymerase chain reaction: a comparative study between HIV-positive and -negative individuals

This study was performed to assess the efficiency of polymerase chain reaction (PCR) directly from sputum for the diagnosis of pulmonary tuberculosis by comparison between HIV-positive and HIV-negative individuals. Sputum samples were collected from hospitalized patients admitted with a clinical diagnosis of pulmonary tuberculosis, and subjected to smear microscopy, culture on LJ medium and detection of M. tuberculosis by PCR. Sensitivity, specificity, and predictive values (positive and negative) were calculated using smear and/or culture at day 42 as the gold standard, by comparing the yield in HIV-positive and HIV-negative individuals. Regardless of serostatus, the technique’s yield had 62% sensitivity, 70% specificity, 79% positive predictive value, 50% negative predictive value, and 65% accuracy. HIV-negative had 64% sensitivity, 74% specificity, 75% positive predictive value, 63% negative predictive value, and 68% accuracy. HIV-positive had 59% sensitivity, 33% specificity, 87% positive predictive value, 10% negative predictive value, and 56% accuracy. The PCR showed a higher yield in HIV-negative individuals compared to HIV-positive individuals.

Evaluation of processing methods to equitably aliquot sputa for mycobacterial testing

We compared bacillary loads after splitting sputum specimens by chemical (N-acetyl-l-cysteine [NALC]) and mechanical homogenization by vortexing with sterile glass beads. NALC and vortexing with glass beads were equally effective at homogenizing sputum specimens, resulting in an equal distribution of tubercle bacilli in the aliquots.

Can tissue PCR augment the diagnostic accuracy in genitourinary tract tuberculosis?

PURPOSE

Conventional methods like smear and culture for Mycobacterium tuberculosis are of limited sensitivity and specificity. Histopathological examination (HPE) for the tissues obtained gives inconclusive diagnosis in the absence of caseous necrosis or stained acid-fast bacilli. This study was conducted to determine the utility of tissue PCR for diagnosing tuberculosis of the genitourinary tract (GUTB) and its comparative evaluation with HPE.

PATIENTS AND METHODS

A prospective study was conducted from January 2006 to August 2009 with 78 tissue specimens (renal, prostate, epididymis, penile and soft tissue) from patients with clinically suspected GUTB. All the samples were processed for both PCR and histopathology.

RESULTS

In 68 (87.1%) samples, results for both PCR and HPE were coinciding. False positivity and false negativity was observed in 5.1% (4/78) and 7.6% (6/78) samples, respectively. With HPE as the gold standard, PCR has shown sensitivity of 87.5% (95% CI 80.1; 91.9) and specificity of 86.7% (95% CI 74.9; 93.8) and positive agreement between two tests was observed as significant (0.7). PCR results were obtained within a mean period of 3.4 days while those of HPE were obtained in 7.2 days.

CONCLUSIONS

Tissue PCR is a sensitive and specific method for obtaining early and timely diagnosis of GUTB. Application of tissue PCR results can augment the diagnostic accuracy in histopathologically labelled granulomatous inflammations.

Cytochrome CYP141: a new target for direct detection of Mycobacterium tuberculosis from clinical specimens

Cytochrome P450 CYP141 is an intermediary metabolic and respiratory protein that interferes with oxidation reduction in Mycobacterium tuberculosis. This conserved protein has also been debated as a hypothetical target for therapeutics. We used the sequences of CYP141 gene to develop a PCR for rapid detection of Mycobacterium tuberculosis from respiratory specimens. The sensitivity of this PCR for culture positive-smear positive and culture positive-smear negative samples were 92% and 62.5%, respectively. The overall sensitivity and specificity of this PCR was 85.7% and 97.8%. As compared with other studies, it appears that the CYP141 gene is a good target for direct detection of M. tuberculosis from respiratory specimens.

Comparison of two laboratory-developed PCR methods for the diagnosis of pulmonary tuberculosis in Brazilian patients with and without HIV infection

BACKGROUND

Direct smear examination with Ziehl-Neelsen (ZN) staining for the diagnosis of pulmonary tuberculosis (PTB) is cheap and easy to use, but its low sensitivity is a major drawback, particularly in HIV seropositive patients. As such, new tools for laboratory diagnosis are urgently needed to improve the case detection rate, especially in regions with a high prevalence of TB and HIV.

OBJECTIVE

To evaluate the performance of two in house PCR (Polymerase Chain Reaction): PCR dot-blot methodology (PCR dot-blot) and PCR agarose gel electrophoresis (PCR-AG) for the diagnosis of Pulmonary Tuberculosis (PTB) in HIV seropositive and HIV seronegative patients.

METHODS

A prospective study was conducted (from May 2003 to May 2004) in a TB/HIV reference hospital. Sputum specimens from 277 PTB suspects were tested by Acid Fast Bacilli (AFB) smear, Culture and in house PCR assays (PCR dot-blot and PCR-AG) and their performances evaluated. Positive cultures combined with the definition of clinical pulmonary TB were employed as the gold standard.

RESULTS

The overall prevalence of PTB was 46% (128/277); in HIV+, prevalence was 54.0% (40/74). The sensitivity and specificity of PCR dot-blot were 74% (CI 95%; 66.1%-81.2%) and 85% (CI 95%; 78.8%-90.3%); and of PCR-AG were 43% (CI 95%; 34.5%-51.6%) and 76% (CI 95%; 69.2%-82.8%), respectively. For HIV seropositive and HIV seronegative samples, sensitivities of PCR dot-blot (72% vs 75%; p=0.46) and PCR-AG (42% vs 43%; p=0.54) were similar. Among HIV seronegative patients and PTB suspects, ROC analysis presented the following values for the AFB smear (0.837), Culture (0.926), PCR dot-blot (0.801) and PCR-AG (0.599). In HIV seropositive patients, these area values were (0.713), (0.900), (0.789) and (0.595), respectively.

CONCLUSION

Results of this study demonstrate that the in house PCR dot blot may be an improvement for ruling out PTB diagnosis in PTB suspects assisted at hospitals with a high prevalence of TB/HIV.

Usefulness of the polymerase chain reaction dot-blot assay, used with Ziehl-Neelsen staining, for the rapid and convenient diagnosis of pulmonary tuberculosis in human immunodeficiency virus-seropositive and -seronegative individuals

There are scarce data regarding the value of molecular tests, when used in parallel with classical tools, for the diagnosis of tuberculosis (TB) under field conditions, especially in regions with a high burden of TB-human immunodeficiency virus (HIV) co-infection. We evaluated the usefulness of the polymerase chain reaction dot-blot assay (PCR) used in parallel with Ziehl-Neelsen staining (ZN) for pulmonary tuberculosis (PTB) diagnosis, in a TB-HIV reference hospital. All sputum samples from 277 patients were tested by ZN, culture, and PCR. Performances were assessed individually, in parallel, for HIV status, history of anti-TB treatment, and in different simulated TB prevalence rates. Overall, the PTB prevalence was 46% (128/277); in HIV-seropositive (HIV⁺) individuals, PTB prevalence was 54% (40/74); the ZN technique had a lower sensitivity (SE) in the HIV⁺ group than in the HIV-seronegative (HIV⁻) group (43% vs. 68%; Fisher test, P<0.05); and the SE of PCR was not affected by HIV status (Fisher test; P=0.46). ZN, in parallel with PCR, presented the following results: i) among all PTB suspects, SE of 90%, specificity (SP) of 84%, likelihood ratio (LR)⁺ of 5.65 and LR⁻ of 0.12; ii) in HIV⁻ subjects: SE of 92%, LR⁻ of 0.10; iii) in not previously treated cases: SE of 90%, LR⁻ of 0.11; iv) in TB, prevalence rates of 5–20%; negative predictive values (NPV) of 98–99%. ZN used in parallel with PCR showed an improvement in SE, LR⁻, and NPV, and may offer a novel approach in ruling out PTB cases, especially in not previously treated HIV⁻ individuals, attended in hospitals in developing nations.

The interaction between respiratory viruses and pathogenic bacteria in the upper respiratory tract of asymptomatic Aboriginal and non-Aboriginal children

BACKGROUND

Associations between respiratory viruses and the bacterial pathogens Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis may be important in the pathogenesis of otitis media (OM). However, data on asymptomatic identification rates of respiratory viruses are limited, particularly in Indigenous populations, who suffer a high burden of OM.

METHODS

We describe the identification of respiratory viruses alone and in combination with pathogenic OM bacteria in 1006 nasopharyngeal aspirates collected from asymptomatic Aboriginal and non-Aboriginal children in a longitudinal community-based cohort study in rural Western Australia.

RESULTS

Viruses were identified in 42% of samples from Aboriginal and 32% from non-Aboriginal children. Rhinoviruses were the most frequently identified virus with higher identification rates in Aboriginal (23.6%) than non-Aboriginal children (16.5%; P = 0.003). Rhinoviruses were associated with H. influenzae (odds ratio [OR], 2.24; 95% CI, 1.24-4.07 for Aboriginal children) and M. catarrhalis (OR, 1.94; 95% CI, 1.05-3.57 for Aboriginal children). Adenoviruses were positively associated with H. influenzae in Aboriginal children (OR, 3.30; 95% CI, 1.19-9.09) and M. catarrhalis in non-Aboriginal children (OR, 5.75; 95% CI, 1.74-19.23), but negatively associated with S. pneumoniae in Aboriginal children (OR, 0.39; 95% CI, 0.18-0.84).

CONCLUSIONS

We found a high identification rate of rhinoviruses and adenoviruses in asymptomatic children. The associations between these viruses and OM bacteria have implications for preventive strategies targeted at specific pathogens.

Microfluidic platform versus conventional real-time polymerase chain reaction for the detection of Mycoplasma pneumoniae in respiratory specimens

Rapid, accurate diagnosis of community-acquired pneumonia (CAP) due to Mycoplasma pneumoniae is compromised by low sensitivity of culture and serology. Polymerase chain reaction (PCR) has emerged as a sensitive method to detect M. pneumoniae DNA in clinical specimens. However, conventional real-time PCR is not cost-effective for routine or outpatient implementation. Here, we evaluate a novel microfluidic real-time PCR platform (Advanced Liquid Logic, Research Triangle Park, NC) that is rapid, portable, and fully automated. We enrolled patients with CAP and extracted DNA from nasopharyngeal wash (NPW) specimens using a biotinylated capture probe and streptavidin-coupled magnetic beads. Each extract was tested for M. pneumoniae-specific DNA by real-time PCR on both conventional and microfluidic platforms using Taqman probe and primers. Three of 59 (5.0%) NPWs were positive, and agreement between the methods was 98%. The microfluidic platform was equally sensitive but 3 times faster and offers an inexpensive and convenient diagnostic test for microbial DNA.

A prospective study of the diagnostic utility of sputum Gram stain in pneumonia

INTRODUCTION

Sputum Gram stain and culture have been said to be unreliable indicators of the microbiological diagnosis of bacterial pneumonia. The etiological diagnosis of pneumonia is surrounded by great degree of uncertainty. This uncertainty should be and can be calculated and incorporated in the diagnosis and treatment.

STUDY OBJECTIVES

To determine the diagnostic accuracy and diagnostic value of sputum Gram stain in etiological diagnosis and initial selection of antimicrobial therapy of bacterial community acquired pneumonia (CAP). DESIGN-METHOD: Prospective study of 1390 patients with CAP admitted January 2002-June 2008, to our institutions. Of the 1390 patients, 178 (12.8%) fulfilled the criteria for inclusion into this study (good-quality sputa and presence of the same microorganism in blood and sputum cultures which was used as gold standard for assessing the diagnostic accuracy and diagnostic value of sputum Gram stain).

RESULTS

The sensitivity of sputum Gram stain was 0.82 for Pneumococcal pneumonia, 0.76 for Staphylococcal pneumonia, 0.79 for Haemophilus influenzae pneumonia and 0.78 for Gram-negative bacilli pneumonia. The specificity of sputum Gram stain was 0.93 for Pneumococcal pneumonia, 0.96 for Staphylococcal pneumonia, 0.96 for H. influenzae pneumonia and 0.95 for Gram-negative bacilli pneumonia. The positive likelihood ratio (LR+) was 11.58 for Pneumococcal pneumonia, 19.38 for Staphylococcal pneumonia, 16.84 for H. influenzae pneumonia, 14.26 for Gram-negative bacilli pneumonia. The negative likelihood ratio (LR-) was 0.20 for Pneumococcal pneumonia, 0.25 for Staphylococcal pneumonia, 0.22 for H. influenzae pneumonia, and 0.23 for Gram-negative bacilli pneumonia.

CONCLUSIONS

Sputum Gram stain is a dependable diagnostic test for the early etiological diagnosis of bacterial CAP that helps in choosing orthological and appropriate initial antimicrobial therapy.

Evaluation of different primer sets for the rapid diagnosis of tuberculosis

Pleural fluid samples from patients with exudative effusion who were diagnosed with tuberculous pleuritis are examined using a new designed primer set based on IS1081 gene (IS1081-PCR) and rpoB-PCR. The PCR results are compared with the results of the sample cultures, using Loewenstein-Jensen (LJ) medium and Ziehl-Neelsen (ZN) staining. Of 78 cases that were confirmed as tuberculous pleuritis by histopathology, supported by sputum culture, biochemical markers (adenosine deaminase, gamma interferon and tumor necrosis factor), radiographic and clinical data, 61 (78.2%) were positive by IS1081-PCR, 43 (55.1%) by rpoB-PCR, 17 (21.7%) by culture and 3 (3.8%) by ZN stain. When IS1081-PCR test results were compared with the confirmed culture, the sensitivity, specificity, positive predictive value and negative predictive value for the IS1081-PCR were 94.1, 55.7, 37.2 and 97.1%, respectively. The corresponding values for the rpoB-PCR were 94.1, 26.2, 26.2 and 94.1%, respectively. When tests results were compare with the confirmed radiographic, histopathology, biochemical markers and clinical diagnosis of tuberculous pleuritis, the IS1081-PCR assay is more sensitive, specific and reliable than both rpoB-PCR assay and culture.

Métodos convencionais e moleculares para o diagnóstico da tuberculose pulmonar: um estudo comparativo

OBJETIVO: Comparar quatro métodos laboratoriais no diagnóstico de tuberculose pulmonar. MÉTODOS: Foram realizadas pesquisa direta pelas colorações de Ziehl-Neelsen e auramina, cultura para micobactérias em meio Löwenstein-Jensen (LJ) e polymerase chain reaction (PCR, reação em cadeia da polimerase) para Mycobacterium tuberculosis em 160 amostras de secreção respiratória de pacientes com suspeita de tuberculose pulmonar. As cepas isoladas foram identificadas por método radiométrico utilizando-se p-nitro-alfa-acetilamino-beta-hidroxipropiofenona (NAP) e métodos clássicos. A sensibilidade dos métodos foi comparada com o padrão ouro para o diagnóstico da tuberculose pulmonar, definido por critérios clínicos, radiológicos e microbiológicos. RESULTADOS: Dos 160 pacientes, 142 foram diagnosticados com tuberculose pulmonar de acordo com o padrão ouro. As técnicas de Ziehl-Neelsen e auramina, cultura em meio LJ e PCR apresentaram sensibilidade de 54,2%, 58,4%, 67,6% e 77,5%, respectivamente, quando comparados ao critério diagnóstico adotado. A especificidade dos quatro métodos foi de 100%. A concordância na identificação da micobactéria entre PCR e o método radiométrico utilizando NAP foi alta (96,8%). A sensibilidade da PCR foi de 50,8% nas amostras com baciloscopia negativa e de 98,8% naquelas com baciloscopia positiva. Nas amostras com resultados negativos na baciloscopia e cultura, a sensibilidade da PCR foi menor que nas com resultados positivos (25,6% e 99,0%, respectivamente). CONCLUSÕES: A PCR é método promissor no diagnóstico da tuberculose pulmonar, mesmo em amostras paucibacilares. Além disso, apresenta a vantagem da identificação simultânea e rapidez do resultado.

Bacterial Infections

In Osier’s time, bacterial pneumonia was a dreaded event, so important that he borrowed John Bunyan’s characterization of tuberculosis and anointed the pneumococcus, as the prime pathogen, “Captain of the men of death.”1 One hundred years later much has changed, but much remains the same. Pneumonia is now the sixth most common cause of death and the most common lethal infection in the United States. Hospital-acquired pneumonia is now the second most common nosocomial infection.2 It was documented as a complication in 0.6% of patients in a national surveillance study,3 and has been reported in as many as 20% of patients in critical care units.4 Furthermore, it is the leading cause of death among nosocomial infections.5 Leu and colleagues6 were able to associate one third of the mortality in patients with nosocomial pneumonia to the infection itself. The increase in hospital stay, which averaged 7 days, was statistically significant. It has been estimated that nosocomial pneumonia produces costs in excess of $500 million each year in the United States, largely related to the increased length of hospital stay.

Legionella in clinical specimens and hospital water supply facilities: molecular detection and genotyping of the isolates

OBJECTIVE

To evaluate genus- and species-specific polymerase chain reactions (PCRs) for the detection of the genus Legionella and the species Legionella pneumophila in clinical specimens and hospital water supplies, and to establish a simple and reproducible random amplification of polymorphic DNA (RAPD)-PCR technique for genotyping of Legionella.

MATERIALS AND METHODS

A total of 70 respiratory tract specimens(bronchoalveolar lavage: n = 46; endotracheal secretions: n = 9; sputum: n = 15) from patients with atypical pneumonia, and 283 environmental samples (water: 20; swabs: 263) collected from water storage and supply facilities of the Mubarak Al-Kabeer Hospital, Kuwait, were tested by culture and genus-specific PCR for the detection of Legionella. The L. pneumophila isolates were subsequently typed by serology and RAPD-PCR using serotype-specific sera and arbitrary primers, respectively.

RESULTS

Of the 70 clinical samples, culture yielded 2 (2.9%) whereas genus-specific PCR detected Legionella in 20 (28.6%) samples. The 2 culture-positive specimens were also positive for L.-pneumophila-specific PCR. Testing of swab and water samples by culture and genus-specific PCR yielded 61 (21.6%) and 67 (23.7%) positive samples, respectively. All of the 61 culture-positive samples were also positive by genus-specific PCR and 45 of them were positive for L.-pneumophila-specific PCR. Serological typing of 43 L. pneumophila isolates showed that 8 of these belonged to serotype 1 and 35 to serotype 3; however, RAPD-PCR analyses demonstrated polymorphisms among the isolates of both serotypes.

CONCLUSION

A higher association between PCR and culture was observed for the environmental samples than for the clinical samples. The application of genus- and species-specific PCRs and RAPD is useful in the detection and typing of Legionella in clinical and environmental samples.

Effect of Sample Aliquot Size on the Limit of Detection and Reproducibility of Clinical Assays

Background: Nucleic acid amplification technologies significantly improved the limit of detection (LOD) for diagnostic assays. The ability of these assays to amplify fewer than 10 target copies of DNA or RNA imposes new requirements on the preparation of clinical samples. We report a statistical method to determine how large of an aliquot is necessary to reproducibly provide a detectable number of cells.

Methods: We determined the success probability (p) based on aliquot size and sample volume. The binomial distribution, based on p and the concentration of cells in sample, was used to calculate the probability of getting no target objects in an aliquot and to determine the minimum number of objects per aliquot necessary to generate a reproducible clinical assay.

Results: The described method was applied to find a minimum aliquot volume required for a set LOD, false-negative rate (FNR), and %CV. For example, to keep FNR &lt;0.01% for 0.5%, 1% and 2% aliquots (minimum 2000, 1000, and 500 cells per sample) are required. Comparison between experimental and predicted FNR demonstrated good correlation for the small volume aliquots and/or low concentration of target. When 4 μL of 200 copies/mL of plasmid is amplified, predicted and experimental FNRs are 47.2% and 44.9%.

Conclusion: This probability model is a useful tool to predict the impact of aliquot volume on the LOD and reproducibility of clinical assays. Even for samples for which pathogens are homogeneously distributed, it is theoretically impossible to collect a single pathogen consistently if the concentration of pathogen is below a certain limit.

Comparison of polymerase chain reaction and the indirect particle agglutination antibody test for the diagnosis of Mycoplasma pneumoniae pneumonia in children during two outbreaks

BACKGROUND

Diagnosis of Mycoplasma pneumoniae pneumonia is challenging because of the lack of standardized rapid tests. Many serologic tests and polymerase chain reaction (PCR) based methods are used with different diagnostic criteria.

METHODS

This retrospective study was conducted to compare the diagnostic values of the indirect particle agglutination test and nested PCR of nasopharyngeal aspirates for the diagnosis of M. pneumoniae pneumonia in children. These assays were evaluated in 234 hospitalized children with community-acquired lower respiratory tract infections during 2 outbreaks of M. pneumoniae pneumonia in 2000 and 2003.

RESULTS

The cumulative PCR positive rate was 26.7% in patients with maximum antibody titers of < or =1:320 and 78.2% in those with titers of > or =1:640. Based on these data, a positive PCR, a 4-fold increase in antibody titer, or a single titer > or =1:640 were considered to indicate acute M. pneumoniae infection. Overall, 152 children were diagnosed to have M. pneumoniae pneumonia; 27 (18%) by serology only, 26 (17%) by PCR only, and 99 (65%) by both methods. Children who were diagnosed by PCR only were significantly younger (P = 0.003) and were more often immunocompromised (P = 0.019) than those that were PCR negative. Duration of cough before PCR diagnosis was shorter in cases diagnosed by PCR only than those that were PCR negative (P = 0.045).

CONCLUSIONS

In conclusion, during the 2 outbreaks of M. pneumoniae infection, we found that the PCR test may be useful for the rapid diagnosis of M. pneumoniae pneumonia, particularly in young children and in immunocompromised patients and in early stage disease.

Epidemiological evidence for Mycobacterium avium subspecies paratuberculosis as a cause of Crohn's disease

Mycobacterium avium subspecies paratuberculosis is the causative agent of Johne's disease, a chronic enteritis in ruminants including cattle, sheep, goats, and farmed deer. Recently, this bacterium has received an increasingly wide interest because of a rapidly growing body of scientific evidence which suggests that human infection with this microorganism may be causing some, and possibly all, cases of Crohn's disease. Recent studies have shown that a high percentage of people with Crohn's disease are infected with M. avium subsp. paratuberculosis; whether the association of this bacterium and Crohn's disease is causal or coincidental is not known. Crohn's disease is a gastrointestinal disease in humans with similar histopathological findings to those observed in the paucibacillary form of Johne's disease in cattle. The search for risk factors in Crohn's disease has been frustrating. However, epidemiologists have gathered enough information that points to an association between M. avium subsp. paratuberculosis and Crohn's disease. This paper reviews epidemiological models of disease causation, the major philosophical doctrines about causation, the established epidemiological criteria for causation, and the currently known epidemiological evidence of M. avium subsp. paratuberculosis as a possible cause of Crohn's disease.

[Etiology of acute viral respiratory tract infections in children from Gran Canaria, the Canary Islands (Spain)]

Objetivo

Las infecciones respiratorias agudas (IRA) de origen vírico son una causa frecuente de consulta y hospitalización pediátrica. El objetivo de este estudio fue conocer la etiología de dichas infecciones en la isla de Gran Canaria.

Métodos

Durante 3 años (de mayo de 2002 a mayo de 2005) se recogieron 1957 lavados nasofaríngeos de 1.729 niños atendidos en Urgencias con síntomas compatibles con IRA. En todas las muestras se realizó una técnica rápida de detección de antígeno de virus respiratorio sincitial (VRS) y, en las que se obtuvo resultado negativo, inmunofluorescencia (IF) y cultivo celular (CC).

Resultados

La mediana de edad fue de 2 meses (intervalo: 0,03-119). Se identificó el agente causal del cuadro respiratorio en 1.032 niños (59,7%). El VRS se detectó en 769 niños (74,5%). Los demás virus identificados, por orden de frecuencia, fueron: virus parainfluenza, rinovirus, adenovirus, virus de la gripe, enterovirus y coronavirus. Se encontraron diferencias estadísticamente significativas al comparar la edad y el tipo de virus detectado: los adenovirus fueron responsables de cuadros en niños de mayor edad (mediana: 6 meses; intervalo: 1-74). Hubo 6 casos de infección mixta. La sensibilidad de la IF en relación con el CC fue del 55,8%, y la especificidad del 99,2%.

Conclusiones

Los virus respiratorios son responsables de un alto número de casos de IRA, principalmente el VRS. Su identificación es determinante en el tratamiento clínico de los pacientes y en el empleo adecuado de antibacterianos y antivirales.

Evaluation of in situ methods used to detect Mycobacterium avium subsp. paratuberculosis in samples from patients with Crohn's disease

In common with other diagnostic tests, detection of mycobacteria in tissue by microscopic examination is susceptible to spectrum bias. Since Crohn's disease is defined by the absence of detectable pathogenic organisms, the use of in situ techniques to search for Mycobacterium avium subsp. paratuberculosis in Crohn's disease samples requires validation of methods in a paucibacillary setting. To generate paucibacillary infection, C57BL/6 mice were artificially infected with Mycobacterium avium subsp. paratuberculosis strain K10 and M. tuberculosis H37Rv, yielding tissues harboring fewer than one bacillus per oil immersion field. Serial sections of organs were then studied by cell wall-based staining techniques (Ziehl-Neelsen and auramine rhodamine) and nucleic acid-based staining techniques (in situ hybridization [ISH] and indirect in situ PCR [IS PCR]). Microscopic examination and measurement of morphometric parameters of bacilli revealed that for all methods, Mycobacterium avium subsp. paratuberculosis bacilli were observed to be shorter, smaller, and less rod shaped than M. tuberculosis bacilli. Ziehl-Neelsen, auramine rhodamine stains, ISH targeting rRNA, and IS-PCR targeting the IS900 element afforded comparable sensitivities, but for all methods, visualization of individual bacterial forms required magnification x1,000. Auramine rhodamine staining and IS-PCR generated positive signals in negative controls, indicating the nonspecificity of these assays. Together, our results indicate that detection of Mycobacterium avium subsp. paratuberculosis bacilli in tissue requires oil immersion microscopy, that rRNA-ISH provides sensitivity and specificity comparable to those of Ziehl-Neelsen staining, and that the microscopic detection limit for Mycobacterium avium subsp. paratuberculosis in tissue is governed more by bacterial burden than by staining method.

Evaluation of the GenoType Mycobacteria Direct assay for detection of Mycobacterium tuberculosis complex and four atypical mycobacterial species in clinical samples

We evaluated GenoType Mycobacteria Direct (GTMD), a novel commercial assay based on nucleic acid sequence-based amplification technology, for the detection of Mycobacterium tuberculosis complex, M. avium, M. intracellulare, M. kansasii, and M. malmoense directly from clinical specimens. A total of 134 respiratory and extrapulmonary samples from 65 patients were processed. Sensitivity, specificity, positive predictive, and negative predictive values for GTMD were 92, 100, 100, and 77%, respectively. The GMTD technique is useful, reliable, and rapid when used during the normal routine of a clinical laboratory.

Modern approaches to a rapid diagnosis of tuberculosis: promises and challenges ahead

The limitations of the conventional methods for diagnosing tuberculosis have spurred multi-faceted research activities in this field throughout the world. Chromatographic methods appear promising but may not be widely available in the developing countries. Immuno-diagnostic methods using combinations ("cocktails") of antigens have high sensitivity and specificity and can easily be applied in the peripheral laboratories and in the field settings. Though expensive, molecular methods for diagnosis of tuberculosis have advantages of speed, sensitivity, and specificity. Adequate training of the eligible personnels in molecular methods and prevention of laboratory-dependent contamination may help reduce false positive results. Although, there are no clear guidelines, so far on how to make out the best from the gene amplification methods, yet their use may be encouraged with adequate quality controls, because of the inherent ingenuity and promises of these methods. Phage-based molecular methods provide rapid results in susceptibility tests for anti-tubercular drugs. In future, many sophisticated techniques are expected to hit the market for a rapid diagnosis of tuberculosis. In the developing countries, it is necessary to evaluate availability of suitable infrastructure and trained personnels before adopting modern diagnostic methods.

[Performances of the "Amplified Mycobacterium tuberculosis Direct Test" in respiratory and non-respiratory specimens]

From March 1998 to December 2004, 3641 specimens (2427 respiratory samples and 1214 non-respiratory samples) collected from 2079 patients, were tested using the "Gen-Probe Amplified Mycobacterium tuberculosis Direct Test" (AMTD). After decontamination procedure every sample was testing by AMTD and by culture on solid and liquid media. The "Gold-standard" was considered by the combination of culture results and clinical diagnosis. Respiratory tuberculosis was present in 9.7% (127 patients), and non-respiratory tuberculosis was present in 18.9% (170 patients, mostly originated from Africa). Among the 2427 respiratory samples (197 culture positive samples, 211 AMTD positive) 225 corresponded to tuberculosis; for the 1214 non-respiratory samples (184 culture positive samples, 213 AMTD positive) 231 corresponded to tuberculosis. After resolving the discordant results, the sensitivity, specificity, positive and negative predictive values were 93.8, 100, 100, 99.4% respectively for respiratory samples and 92.2, 99.9, 99.5, 98% for non respiratory samples.

Enzyme-linked immunosorbent assay of nucleic acid sequence-based amplification for molecular detection of M. tuberculosis

An enzyme-linked immunosorbent assay of nucleic acid sequence-based amplification (NASBA-ELISA) was developed for molecular detection of Mycobacterium tuberculosis. The primers targeting 16S rRNA were used for the amplification of bacterial RNA by the isothermal digoxigenin (DIG)-labeling NASBA process, resulting in the accumulation of DIG-labeled RNA amplicons. The amplicons were hybridized with a specific biotinylated DNA probe which was non-covalently immobilized on streptavidin-coated microtiter plate. The RNA-DNA hybrids were colorimetrically detected by the addition of an anti-DIG antibody HRP conjugate and 2,2-azino-di-(3-ethylbenzthiazolinsulfonate) substrate. Using this method, as little as 1 x 10(2) CFU ml(-1) of M. tuberculosis was detected within less than 5h. Results obtained from the clinical specimens showed 85.7% and 96% sensitivity and specificity, respectively. No interference was encountered in the amplification and detection of M. tuberculosis in the presence of non-target bacteria, confirming the specificity of the method.

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

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

FTIR microscopy as a method for identification of bacterial and fungal infections

Fourier-transform infrared (FTIR) microscopy is considered to be a comprehensive and sensitive method for detection of molecular changes in cells. The advantage of FTIR microspectroscopy over conventional FTIR spectroscopy is that it facilitates inspection of restricted regions of the examined sample. In the present study, we examined the potential of FTIR microscopy as an easy, rapid and reliable technique for discrimination between bacteria and fungi both of which are involved in various human and other animal infections. In many cases, there is no easy and rapid technique for identifying the cause of such infections whether it is bacteria, fungi or both. Knowing such information in a rapid way could be highly important for effective therapy. Our results proved detectable and significant spectral differences between bacterial and fungal samples. Representative peaks of bacteria and fungi appeared clearly in the spectra of a mixture of bacteria and fungi. It seems that this technique could be used for rapid discrimination between bacterial and fungal infections and contaminations.

Clinical and epidemiologic characteristics of viral infections in a neonatal intensive care unit during a 12-year period

BACKGROUND

The incidence of viral infections in patients treated in the neonatal intensive care unit (NICU) is not well-known. We summarized the data of all patients with laboratory-confirmed viral infections admitted at the NICU of our hospital during the period of 1992-2003.

OBJECTIVES

To determine the incidence of viral infections among infants hospitalized in a NICU, the associated clinical manifestations and their outcome.

METHODS

Retrospective analysis of epidemiologic, virologic and clinical data from infants with proven viral infection. The diagnosis viral infection was confirmed by positive viral culture and/or polymerase chain reaction from clinical samples.

RESULTS

Viral infection was confirmed in 51 of 5396 infants (1%) admitted to the NICU; 20 (39%) had an enterovirus and parechovirus (EV/PEV) infection, 15 (29%) a respiratory syncytial virus (RSV) infection, 5 (10%) a rotavirus infection, 3 (6%) a cytomegalovirus (CMV) infection, 2 (4%) an adenovirus infection, 2 (4%) a parainfluenza virus infection, 2 (4%) a herpes simplex virus infection, 1 (2%) a rhinovirus infection and 1 (2%) a rubella virus infection. Three of the infants presented at birth with symptomatic rubella virus, CMV or herpes simplex virus infection. RSV infection developed mostly in hospitalized infants (60%), and 93% of infections occurred during the winter (November-March). The clinical presentations of EV/PEV disease were sepsis-like illness, prolonged seizures in term infants and gastrointestinal disease in preterm infants. RSV, parainfluenza virus, rhinovirus and CMV caused respiratory disease, predominantly in preterm infants. Gastrointestinal disease was seen only in preterm infants with adenovirus, rotavirus or EV/PEV infection. Mortality and serious sequelae were high in patients infected with EV/PEV (10 and 15%, respectively).

CONCLUSIONS

The incidence of viral infection in the NICU was 1%. Enteroviral infections were the most frequently diagnosed infections, occurred often in term infants born at home and presented with sepsis-like illness or seizures. Preterm infants hospitalized from birth mainly developed gastrointestinal disease caused by rotavirus and adenovirus infection or respiratory disease caused by RSV, parainfluenza and CMV infection. Enteroviruses were responsible for the highest mortality and development of serious sequelae.

Chlamydia pneumoniae and Mycoplasma pneumoniae in young children from China with community-acquired pneumonia

Eighty-five cases community-acquired pneumonia (CAP) in children 5 years or younger, confirmed by chest X-ray, and 185 age-matched control patients with diarrhea or dermatitis from the Outpatient Department at Beijing Children's Hospital were enrolled into this study. Nasopharyngeal swab specimens were obtained from all subjects. Real-time PCR-based fluorescence assays were performed for Chlamydia pneumoniae and Mycoplasma pneumoniae. A nested PCR was also run for C. pneumoniae for comparison of assays. C. pneumoniae was found in 3 (3.5%) of CAP cases and in 4 (2.1%) of controls (P = 0.51). M. pneumoniae was found in 6 (7.1%) of CAP cases and in none of the controls (P = 0.001). The agreement rate of the 2 applied PCR methods used for C. pneumoniae detection was 98.5%. Our study demonstrates that M. pneumoniae may play a significant role in CAP affecting children up to 5 years in China, whereas C. pneumoniae in nasopharyngeal specimens was not associated with CAP in this age group.

Diagnosis of parapneumonic pleural effusion by polymerase chain reaction in children

PURPOSE

Most pleural effusions are associated with bacterial pneumonia, and the identification of the pathogen will assist the therapeutic decision. A specific method that is not affected by previous antibiotic therapy is sought to detect the main causative agents of pneumonia in infants and children (Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus). The aim of the present study was to compare the polymerase chain reaction (PCR) technique with standard culture methods in identifying bacterial infections in infants' and children's pleural effusion.

METHODS

Samples obtained from pediatric patients (n = 37) with a diagnosis of pneumonia associated to pleural effusion, submitted to thoracentesis, were analyzed by PCR with specific primers.

RESULTS

The PCR technique identified the presence of bacterial infection in a larger proportion (95.2%) than the standard culture method (33.3%) on complicated pleural effusion samples. The microorganism detection on uncomplicated pleural effusion samples was positive only by the PCR method (31.3%). The frequencies of microorganisms identified on complicated pleural effusion were 57.1% of all patients for methicillin-resistant Staphylococcus; 52.4%, S pneumoniae; 28.6%, S aureus; and 23.8%, H influenzae. The previous use of antibiotics interferes with standard culture method, but it did not interfere with the PCR results.

CONCLUSIONS

The molecular diagnosis by PCR method could improve the etiologic diagnosis and might help to guide the treatment of parapneumonic effusion in children.

Single-run, parallel detection of DNA from three pneumonia-producing bacteria by real-time polymerase chain reaction

A molecular assay for parallel detection of three bacteria, Chlamydia (C.) pneumoniae, Legionella (L.) spp., and Mycoplasma (M.) pneumoniae, in clinical specimens by a set of real-time polymerase chain reactions (PCRs) in a single run was evaluated. Bacterial DNAs were extracted by an automated DNA extraction protocol on the MagNA Pure LC System. Amplification and detection were done by real-time PCR on the LightCycler (LC) instrument. For amplification, specific oligonucleotides derived from the 16s rRNA genes of C. pneumoniae, L. spp., and M. pneumoniae were used. The three assays were complemented with an internal control (IC), a specially designed DNA fragment which contains the specific primer binding sites for the three PCRs. The IC was added to the samples, co-extracted, and co-amplified. Primers and hybridization probes were designed to suit one LC PCR program. LC PCRs were established, detection limits were determined, and clinical samples were tested. The detection limits were found between 5.0 and 0.5 IFU/CFU per PCR reaction for each of the bacteria. A total number of 100 clinical specimens were tested for validation of the molecular assay. Tested samples included 63 bronchoalveolar lavages (BALs) and 37 induced sputa specimens. The internal control was detected in all negative and low-positive samples; no inhibition was found throughout the whole study. Additionally, samples underwent testing by culture for L. spp., and M. pneumoniae; for C. pneumoniae, the serological microimmunofluorescence (MIF) test was used. In conclusion, the developed set of LC PCR assays permits parallel detection of C. pneumoniae, L. spp., and M. pneumoniae in a single LC run. This molecular assay may lead to accurate and early diagnosis of pneumonia produced by these three types of bacteria. The assay proved to be suitable for the high-throughput routine diagnostic laboratory.