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

Mycoplasma pneumoniae detection causes excess antibiotic use in Norwegian general practice: a retrospective case-control study

BACKGROUND

The 2011 Mycoplasma pneumoniae epidemic in Norway resulted in many GP consultations and significantly increased the prescription of macrolide antibiotics.

AIM

To investigate the signs, symptoms, course, and prescription patterns of antibiotics in patients positive for M. pneumoniae compared with patients negative for M. pneumoniae.

DESIGN AND SETTING

A retrospective case-control study using questionnaires collected from GPs in a county in Norway. A total of 212 M. pneumoniae positive and 202 control patients were included.

METHOD

Descriptive statistics and logistic regression analyses were performed on the reported findings.

RESULTS

Forty-eight per cent of patients positive for M. pneumoniae received an antibiotic at first consultation. Another 45% in the same group received antibiotics after the polymerase chain reaction (PCR) result was known, although these patients were not clinically different from all other patients not receiving an antibiotic at first consultation. Logistic regression analysis to evaluate independent predictors for prescription of antibiotics at first consultation showed that the following factors were significantly associated: elevated C-reactive protein (CRP) level, temperature >38.0°C, pathological findings on pulmonary auscultation, and impaired general condition. Elevated CRP level, younger age, temperature >38.0°C, short duration of symptoms, and absence of rhinitis were found to be positive predictors for M. pneumoniae infection.

CONCLUSION

A positive PCR test for M. pneumoniae tends to trigger an antibiotic prescription, irrespective of the severity of the patient's condition at first consultation. New guidelines for treatment and possibly PCR testing should be established.

Underdiagnosing of Mycoplasma pneumoniae infections as revealed by use of a respiratory multiplex PCR panel

We compared a multiplex PCR diagnostic approach against specific PCR diagnosis for detection of Mycoplasma pneumoniae infection. Seventy-five percent of all M. pneumoniae infections were only detected "unintentionally" by the use of the multiplex PCR indicating underdiagnosing of M. pneumoniae due to absence of clinical suspicion.

Molecular detection of Mycoplasma pneumoniae by quantitative real-time PCR in patients with community acquired pneumonia

BACKGROUND & OBJECTIVES

Mycoplasma pneumoniae is the most important and common cause of community-acquired pneumonia (CAP). The conventional detection methods (culture and serology) lack sensitivity. PCR offers a better approach for rapid detection but is prone to carry over contamination during manipulation of amplification products. Quantitative real-time PCR (qRT-PCR) method offers an attractive alternative detection method. In the present study, qRT-PCR, PCR and serology methods were used to detect M. pneumoniae infection in cases of pneumonias and findings compared.

METHODS

A total of 134 samples consisting of blood (for serology) and respiratory secretions (for PCR and qRT-PCR) from 134 patients were collected. The blood samples were tested for IgG, IgM and IgA using commercially available kits. For standardization of PCR of M. pneumoniae P1 gene was cloned in pGEMTEasy vector. Specific primers and reporter sequence were designed and procured for this fragment. The qRT-PCR assay was performed to prepare the standard curve for M. pneumoniae positive control DNA template and detection in patient samples.

RESULTS

Of the 134 patients, 26 (19%) were positive for antibodies against M. pneumoniae. IgG was positive in 14.92 per cent (20) cases, IgM in 4.47 per cent (6) and IgA was positive in 5.22 per cent (7) cases. In the qRT-PCR assay 19 per cent (26) samples were positive. Of the 26 qRT-PCR positive samples, nine could be detected by serology. PCR was positive for 25 samples. An extra sample negative by PCR was detected by qRT-PCR. Thus, real-time PCR assay, PCR and serology in combination could detect M. pneumoniae infection in 43 patients.

INTERPRETATION & CONCLUSIONS

The study shows that 17 patients were detected by serology alone, 17 were detected by qRT-PCR only and nine patients were positive by both serology and real-time PCR. Of the 134 samples tested, 25 were positive by conventional PCR, but qRT-PCR could detect one more sample that was negative by PCR and serology. These results suggest that a combination of two or three methods may be required for reliable identification of CAP due to M. pneumoniae.

Molecular methods for the detection of Mycoplasma and ureaplasma infections in humans: a paper from the 2011 William Beaumont Hospital Symposium on molecular pathology

Mycoplasma and Ureaplasma species are well-known human pathogens responsible for a broad array of inflammatory conditions involving the respiratory and urogenital tracts of neonates, children, and adults. Greater attention is being given to these organisms in diagnostic microbiology, largely as a result of improved methods for their laboratory detection, made possible by powerful molecular-based techniques that can be used for primary detection in clinical specimens. For slow-growing species, such as Mycoplasma pneumoniae and Mycoplasma genitalium, molecular-based detection is the only practical means for rapid microbiological diagnosis. Most molecular-based methods used for detection and characterization of conventional bacteria have been applied to these organisms. A complete genome sequence is available for one or more strains of all of the important human pathogens in the Mycoplasma and Ureaplasma genera. Information gained from genome analyses and improvements in efficiency of DNA sequencing are expected to significantly advance the field of molecular detection and genotyping during the next few years. This review provides a summary and critical review of methods suitable for detection and characterization of mycoplasmas and ureaplasmas of humans, with emphasis on molecular genotypic techniques.

Lower respiratory infections among hospitalized children in New Caledonia: a pilot study for the Pneumonia Etiology Research for Child Health project

We conducted a prospective pilot study over a 1-year period in New Caledonia in preparation for the Pneumonia Research for Child Health (PERCH) project. The pathogens associated with hospitalized lower respiratory infections in children were identified through the use of culture of induced sputum and blood, urinary antigen detection, polymerase chain reaction (PCR) on respiratory specimens, and serology on paired sera. Respiratory viruses were detected on respiratory specimens by immunofluorescence and PCR, and by serology on paired sera. Pathogens were detected in 87.9% of the 108 hospitalized cases. Viruses represented 81.6% of the 152 pathogens detected. Respiratory syncytial virus and rhinovirus were the most frequent, accounting for 32.2% and 24.3% of the pathogens identified, respectively. Only 26.3% of 99 induced sputum specimens collected were determined to be of good quality, which may be a consequence of the collection method used.

Single tube real time PCR for detection of Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydophila pneumoniae and Legionella pneumophila from clinical samples of CAP

We designed a multiplex real time PCR for rapid, sensitive and specific detection of Streptococcus pneumoniae, Legionella pneumophila, Chlamydophila pneumoniae and Mycoplasma pneumoniae. The study cases consisted of 129 patients with community acquired pneumonia (CAP). Bacteriological techniques were implemented for detection of the cultivable organisms. DNA were extracted from sputa, throat swabs, bronchoalveolar lavages and tracheal aspirates and used as templates in real time PCR. The primers and probes were designed for cbpA (S. pneumoniae), p1adhesin (M. pneumoniae), mip (L. pneumophila) and ompA (C. pneumoniae). After optimization of real time PCR for every organism, the experiments were continued in multiplex in a single tube. Of 129 CAP specimens, the positive cultures included 14 (10.85%) for S. pneumoniae, 9 (6.98%) for L. pneumophila and 3 (2.33%) for M. pneumoniae. Four specimens (3.10%) were positive for C. pneumoniae by real time PCR. The sensitivity of our real time PCR was 100% for all selected bacteria. The specificity of the test was 98.26%, 98.34%, 100% and 100% for S. pneumoniae, L. pneumophila, M. pneumoniae and C. pneumoniae, respectively. This is the first report on the use of multiplex real time PCR for detection of CAP patients in the Middle East. The method covers more than 90% of the bacterial pathogens causing CAP.

Development of a real time PCR assay for rapid detection of Vibrio parahaemolyticus from seafood

A real time PCR assay for the detection of Vibrio parahaemolyticus in seafood samples was developed using a novel specific target and a competitive internal amplification control (IAC). The specificity of this assay was evaluated using 390 bacterial strains including V. parahaemolyticus, and other strains belonging to Vibrio and non-Vibrio species. The real time PCR assay unambiguously distinguished V. parahaemolyticus with a detection sensitivity of 4.8 fg per PCR with purified genomic DNA or 1 CFU per reaction by counting V. parahaemolyticus colonies. The assays of avoiding interference demonstrated that, even in the presence of 2.1 μg genomic DNA or 10(7) CFU background bacteria, V. parahaemolyticus could still be accurately detected. In addition, the IAC was used to indicate false-negative results, and lower than 94 copies of IAC per reaction had no influence on the detection limit. Ninety-six seafood samples were tested, of which 58 (60.4%) were positive, including 3 false negative results. Consequently, the real time PCR assay is effective for the rapid detection of V. parahaemotyticus contaminants in seafood.

Chlamydia psittaci Infection in nongastrointestinal extranodal MALT lymphomas and their precursor lesions

Extranodal marginal zone lymphomas of mucosa-associated lymphoid tissue (MALT) are associated with various infectious pathogens. We analyzed the presence of Chlamydia psittaci, Chlamydia pneumoniae, and Chlamydia trachomatis DNA in 47 nongastrointestinal and 14 gastrointestinal MALT lymphomas, 37 nonmalignant control samples, and 27 autoimmune precursor lesions by polymerase chain reaction amplification and direct sequencing. In 47 nongastrointestinal MALT lymphomas, 13 (28%) were positive for C psittaci DNA compared with 4 (11%) of 37 nonmalignant control samples (P = .09). C psittaci was detected at variable frequencies in MALT lymphomas of different sites: lung, 100% (5/5; P < .01); thyroid gland, 30% (3/10; P > .05); salivary gland, 13% (2/15; P > .05); ocular adnexa, 15% (2/13); and skin, 25% (1/4). Of 27 autoimmune precursor lesions (11 Hashimoto thyroiditis and 16 Sjögren syndrome), 11 (41%) contained C psittaci DNA. Only 1 (7%) of 14 gastrointestinal MALT lymphomas was positive for C psittaci. All specimens were negative for C trachomatis and C pneumoniae. Besides ocular adnexal lymphomas, C psittaci infection is associated with nongastrointestinal MALT lymphomas and autoimmune precursor lesions, suggesting possible involvement of C psittaci-induced antigenic-driven MALT lymphomagenesis.

Aetiology of community-acquired pneumonia in hospitalized adult patients in New Caledonia

OBJECTIVE

To describe the aetiology of community-acquired pneumonia (CAP) in hospitalized adult patients in New Caledonia, a French archipelago in the South Pacific.

METHODS

Confirmed CAP patients (n=137) were enrolled prospectively. Pathogens were detected by culture, molecular methods, serology on paired sera, immunofluorescence on nasopharyngeal swabs and antigen detection in urine.

RESULTS

The aetiology of CAP was determined in 82 of 137 cases (59.8%), of which 31 exhibited two or more pathogens (37.8%). Hundred and seventeen pathogens were detected: Streptococcus pneumoniae was the most common one (41.0%), followed by influenza virus A (22.1%) and Haemophilus influenzae (10.2%). The frequency of atypical bacteria was low (6.0%). The most frequent and significant coinfection was S. pneumoniae with influenza A virus (P=0.004). Influenza virus was detected from nasopharyngeal swabs in four patients (15.4% of patients tested for influenza) and by PCR from pulmonary specimens in 15 patients (57.7%). CONCLUSIONS : Pneumoniae is the leading cause of CAP in New Caledonian adults. Viral-bacterial co-infections involving S. pneumoniae and influenza virus are very common during the winter. Such adult patients hospitalized with CAP are a clear sentinel group for surveillance of influenza. Vaccination against influenza and S. pneumoniae should be strengthened when risk factors are identified.

Acute respiratory infection due to Mycoplasma pneumoniae: current status of diagnostic methods

Because of the absence of well-standardized both in-house and FDA-approved commercially available diagnostic tests, the reliable diagnosis of respiratory infection due to Mycoplasma pneumoniae remains difficult. In addition, no formal external quality assessment schemes which would allow to conclude about the performance of M. pneumoniae diagnostic tests exist. In this review, the current state of knowledge of M. pneumoniae-associated respiratory infections in the context of epidemiological studies published during the past 5 years is discussed, with particular emphasis on the diagnostic strategies used and their impact on results. The role of M. pneumoniae as a cause of respiratory tract infections (RTIs) differs from study to study due to geographical and epidemiological differences, as well as to the application of different diagnostic techniques and criteria used.

Current applications and future trends of molecular diagnostics in clinical bacteriology

Molecular diagnostics of infectious diseases, in particular, nucleic-acid-based methods, are the fastest growing field in clinical laboratory diagnostics. These applications are stepwise replacing or complementing culture-based, biochemical, and immunological assays in microbiology laboratories. The first-generation nucleic acid assays were monoparametric such as conventional tests, determining only a single parameter. Improvements and new approaches in technology now open the possibility for the development of multiparameter assays using microarrays, multiplex nucleic acid amplification techniques, or mass spectrometry, while the introduction of closed-tube systems has resulted in rapid microbial diagnostics with a subsequently reduced contamination risk. Whereas the first assays were focused on the detection and identification of microbial pathogens, these new technologies paved the way for the parallel determination of multiple antibiotic resistance determinants or to perform microbial epidemiology and surveillance on a genetic level.

Epidemiology, clinical manifestations, pathogenesis and laboratory detection of Mycoplasma pneumoniae infections

Since its initial description in the 1940s and eventual elucidation as a highly evolved pathogenic bacterium, Mycoplasma pneumoniae has come to be recognized as a worldwide cause of primary atypical pneumonia. Beyond its ability to cause severe lower respiratory illness and milder upper respiratory symptoms it has become apparent that a wide array of extrapulmonary infectious and postinfectious events may accompany the infections in humans caused by this organism. Autoimmune disorders and chronic diseases such as asthma and arthritis are increasingly being associated with this mycoplasma, which frequently persists in individuals for prolonged periods. The reductive evolutionary process that has led to the minimal genome of M. pneumoniae suggests that it exists as a highly specialized parasitic bacterium capable of residing in an intracellular state within the respiratory tissues, occasionally emerging to produce symptoms. This review includes discussion of some of the newer aspects of our knowledge on this pathogen, characteristics of clinical infections, how it causes disease, the recent emergence of macrolide resistance, and the status of laboratory diagnostic methods.

Multiple Chlamydiaceae species in trachoma: implications for disease pathogenesis and control

BACKGROUND

Chlamydia trachomatis is a unique obligate intracellular bacterium that remains the leading cause of sexually transmitted bacterial diseases and preventable blindness worldwide. Chronic ocular infections are referred to as trachoma, and predominate in developing countries. Since 2001, the World Health Organization has promoted control strategies including antibiotics, improved hygiene, and environmental measures with limited success. Consequently, a vaccine is urgently needed. Integral to vaccine design is an understanding of the interactions of the pathogen and host immune response. Various animal models of trachoma show that urogenital C. trachomatis strains and other species of the family Chlamydiaceae produce severe conjunctival inflammation and scarring similar to that of the ocular C. trachomatis strains. However, we do not know the extent of organisms that may be involved in human trachoma. Furthermore, C. trachomatis heat shock protein 60 (Hsp60) has been implicated in inflammation and conjunctival scarring but the role of other Chlamydiaceae Hsp60 in disease pathogenesis has not been examined. In this study, we set out to identify whether other Chlamydiaceae species are present in trachoma, and determine their association with severity of clinical disease and with mucosal and systemic immune responses to Chlamydiaceae species-specific Hsp60 to further investigate the immunopathogenesis of this blinding disease.

METHODS AND FINDINGS

We randomly selected nine of 49 households in a trachoma-endemic region of Nepal. Trachoma was graded, and real-time, quantitative (k)PCR was used to detect genomic DNA and cDNA (from RNA) for Chlamydiaceae ompA and 16S rRNA genes, respectively, from conjunctival swabs. IgG antibody responses to recombinant (r) Chlamydiaceae species-specific Hsp60 were determined for tears and sera. Surprisingly, all three species-C. trachomatis, Chlamydophila psittaci, and Chlamydophila pneumoniae-were detected in eight (89%) study households; one household had no members infected with C. pneumoniae. Of 80 (63%; n = 127) infected individuals, 28 (35%) had infection with C. psittaci, or C. pneumoniae, or both; single and dual infections with C. psittaci and C. pneumoniae were significantly associated with severe conjunctival inflammation (OR 4.25 [95% confidence interval (CI), 2.9-11.3], p = 0.009] as were single infections with C. trachomatis (OR 5.7 [95% CI, 3.8-10.1], p = 0.002). Of the 80 infected individuals, 75 (93.8%) were also positive for 16S rRNA by kPCR for the same organism identified by ompA. Individuals with tear IgG immunoreactivity to Chlamydiaceae rHsp60 were eight times more likely than individuals without tear immunoreactivity to be infected (95% CI 6.4-15.1; p = 0.003), 6.2 times more likely to have severe inflammation (95% CI 4.4-12.6; p = 0.001), and 5.7 times more likely to have scarring (95% CI 3.9-11.1; p = 0.019) while individuals with serum IgG immunoreactivity were 4.1 times more likely to be infected (95% CI 3.1-10.1; p = 0.014).

CONCLUSIONS

We provide substantial evidence for the involvement of C. psittaci and C. pneumoniae, in addition to C. trachomatis, in trachoma. The distribution of Chlamydiaceae species by household and age suggests that these infections are widespread and not just sporadic occurrences. Infection with multiple species may explain the failure to detect chlamydiae among active trachoma cases, when only C. trachomatis is assayed for, and the failure of clinically active cases to resolve their disease following what would be considered effective C. trachomatis treatment. The evidence for viable (RNA-positive) organisms of all three species in single and coinfections, the significant association of these infections with severe inflammation, and the significant association of tear and serum IgG responses to Chlamydiaceae Hsp60 with inflammation and scarring, support the role of all three species in disease pathogenesis. Thus, while our findings should be confirmed in other trachoma-endemic countries, our data suggest that a reevaluation of treatment regimens and vaccine design may be required. Understanding the full impact of Chlamydiaceae species on the epidemiology, immunopathology, and disease outcome of trachoma presents a new challenge for Chlamydiaceae research.

Simultaneous detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae by use of molecular beacons in a duplex real-time PCR

A real-time PCR was designed for detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae such that each pathogen could be detected in a single tube and differentiated using molecular beacons marked with different fluorochromes. This duplex PCR, targeting the P1 adhesion gene for M. pneumoniae and the ompA gene for C. pneumoniae, was compared with two conventional PCR assays targeting the 16S rRNA gene and the ompA gene. A total of 120 clinical throat and nasopharyngeal swab samples were tested. DNA extraction was performed using an alkali denaturation/neutralization method, and real-time amplification, detection, and data analysis were performed using a Rotor-Gene 2000 real-time rotary analyzer (Corbett Life Science, Sydney, Australia). Using conventional PCR as a reference in an analysis of 120 samples, 13 of 14 samples positive for C. pneumoniae were detected by the novel real-time PCR. In an analysis of M. pneumoniae, 22 samples were positive in the conventional PCR and the novel assay detected 24 positive samples. When using the conventional PCR as a reference, sensitivity and specificity were 93% and 100%, respectively, for C. pneumoniae and 100% and 98%, respectively, for M. pneumoniae. With an overall agreement of 98.8%, this suggests that performance of the new duplex real-time PCR is comparable to that of conventional PCR.

Chlamydia psittaci in MALT lymphomas of ocular adnexals: the Austrian experience

The presence of Chlamydia (C.) psittaci, C. pneumoniae and C. trachomatis DNAs in MALT lymphomas of ocular adnexals from 13 Austrian patients were studied. Gastrointestinal MALT lymphomas and gastritis specimens served as controls. Of 13 MALT lymphomas of the ocular adnexals, seven were positive for C. psittaci DNA. In contrast, one of 17 gastrointestinal specimens tested positive. All specimens were negative for C. trachomatis and C. pneumoniae DNAs. In conclusion, C. psittaci infection was observed in the majority of MALT lymphomas of ocular adnexals in Austrian patients.

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.

Molecular typing of a Legionella pneumophila outbreak in Ontario, Canada

An outbreak of Legionnaires' disease at a long-term care facility in Ontario, Canada from September to October 2005 resulted in the death of 23 residents and the illness of 112 other people. In response, molecular methods were developed to detect Legionella pneumophila in clinical lung samples and to subtype isolates from clinical and environmental samples. The targeted genetic loci included Legionella-specific virulence determinants (mip, icmO, sidA and lidA) and core bacterial determinants (ftsZ, trpS and dnaX). An established amplified fragment length polymorphism typing method provided the first indication of genetic relatedness between strains recovered from clinical samples and strains cultured from environmental samples taken from the outbreak site. These associations were verified using the European Working Group for Legionella Infections sequence-based typing protocol targeting the flaA, pilE, asd, mip, mompS and proA loci. These molecular typing methods confirmed the outbreak source as a contaminated air conditioning cooling tower.

Development of a multiple internal control for clinical diagnostic real-time amplification assays

A major pitfall in most published genomic amplification methods for the detection and identification of human pathogens is that they do not include an internal amplification control in order to achieve an acceptable level of confidence for the absence of false-negative results. By applying composite primer technology, a single multiple internal amplification control DNA molecule was constructed to detect and quantify the hepatitis B virus, human polyomavirus, Epstein-Barr virus, Toxoplasma gondii and cytomegalovirus using real-time PCR. The multiple internal amplification control contains all forward and reverse primer binding regions targeted in the five distinct duplex PCRs, but with a unique probe hybridization site. Multiple internal amplification control detection sensitivity, assessed by Probit analysis, was 58 copies per PCR, associated with an extremely wide dynamic range (8 log(10) units). Moreover, in testing 614 patient samples, PCR inhibition occurred at a frequency of 0-8.8%. Similar multiple internal amplification controls for quantitative PCR-based assays could be designed to accommodate any infectious profiles in a particular institution as they are easy to make and inexpensive.

Spectrum of viruses and atypical bacteria in intercontinental air travelers with symptoms of acute respiratory infection

Respiratory infections after air travel are frequent, but epidemiological data are incomplete. Using sensitive polymerase chain reactions, we studied the spectrum of atypical bacteria and respiratory viruses in travelers fulfilling the case definition of severe acute respiratory syndrome. A pathogen was identified in 67 travelers (43.2%). Influenza and parainfluenza viruses were most prevalent, at 14.2% and 15.5%, respectively. Prevalences of adenoviruses, human metapneumovirus, coronaviruses, and rhinoviruses ranged between 2.6% and 4.8%. Human bocavirus, respiratory syncytial virus, and Legionella, Mycoplasma, and Chlamydophila species were absent or appeared at frequencies of <1%. To our knowledge, these are the first specific baseline data for the mentioned agents in the context of air travel.

Development of an internal positive control for rapid diagnosis of avian influenza virus infections by real-time reverse transcription-PCR with lyophilized reagents

We developed an internal positive control (IPC) RNA to help ensure the accuracy of the detection of avian influenza virus (AIV) RNA by reverse transcription (RT)-PCR and real-time RT-PCR (RRT-PCR). The IPC was designed to have the same binding sites for the forward and reverse primers of the AIV matrix gene as the target amplicon, but it had a unique internal sequence used for the probe site. The amplification of the viral RNA and the IPC by RRT-PCR were monitored with two different fluorescent probes in a multiplex format, one specific for the AIV matrix gene and the other for the IPC. The RRT-PCR test was further simplified with the use of lyophilized bead reagents for the detection of AIV RNA. The RRT-PCR with the bead reagents was more sensitive than the conventional wet reagents for the detection of AIV RNA. The IPC-based RRT-PCR detected inhibitors in blood, kidney, lungs, spleen, intestine, and cloacal swabs, but not allantoic fluid, serum, or tracheal swabs The accuracy of RRT-PCR test results with the lyophilized beads was tested on cloacal and tracheal swabs from experimental birds inoculated with AIV and compared with virus isolation (VI) on embryonating chicken eggs. There was 97 to 100% agreement of the RRT-PCR test results with VI for tracheal swabs and 81% agreement with VI for cloacal swabs, indicating a high level of accuracy of the RRT-PCR assay. The same IPC in the form of armored RNA was also used to monitor the extraction of viral RNA and subsequent detection by RRT-PCR.

Real-time detection of Mycoplasma pneumoniae in respiratory samples with an internal processing control

Real-time PCR was employed to detect a region of the P1 cytadhesin gene of Mycoplasma pneumoniae in clinical samples. An internal processing control was included that could be co-amplified simultaneously in the same reaction tube. The assay could reproducibly detect 1 x 10(3) M. pneumoniae organisms ml(-1) in clinical samples. There was no amplification of DNA or signal production from 15 other species of human mycoplasmas and 19 other bacterial species. Using a panel of 175 respiratory samples taken from patients with pneumonia of proven aetiology, the sensitivity was found to be 60 % and the specificity of the assay 96.7 % when compared with serology. This assay is suitable for same-day diagnosis of M. pneumoniae infection and batch processing of respiratory samples for clinical screening.