New directions in diagnostics

An integrated flow cytometry-based system for real-time, high sensitivity bacterial detection and identification

Foodborne illnesses occur in both industrialized and developing countries, and may be increasing due to rapidly evolving food production practices. Yet some primary tools used to assess food safety are decades, if not centuries, old. To improve the time to result for food safety assessment a sensitive flow cytometer based system to detect microbial contamination was developed. By eliminating background fluorescence and improving signal to noise the assays accurately measure bacterial load or specifically identify pathogens. These assays provide results in minutes or, if sensitivity to one cell in a complex matrix is required, after several hours enrichment. Conventional assessments of food safety require 48 to 56 hours. The assays described within are linear over 5 orders of magnitude with results identical to culture plates, and report live and dead microorganisms. This system offers a powerful approach to real-time assessment of food safety, useful for industry self-monitoring and regulatory inspection.

Quality in diagnostic microbiology: experiential note to emphasize value of internal control programs

Background:

Quality control (QC) in diagnostic microbiology is a matter of effective, efficient, accurate reporting in the expected turnaround time. Major stages of the analytical “standard operational procedures” where QC could be easily affected include organism identification and antibacterial susceptibility testing.

Aim:

The objective of this experiential technical note is to provide an evidence base to highlight the value of internal QC program in evaluating the effectiveness and efficiency of a laboratory's standard operational procedures; and the competences of individual scientific/technical staff.

Materials and Methods:

This report is based on four different scenarios requiring internal QC, including cases that are not reported within the turnaround time of standard operational procedures. Small-scale evaluations of (i) internal QC program, (ii) ciprofloxacin vs. moxifloxacin susceptibilities, and (iii) calibrated dichotomous susceptibility vs. directed susceptibility testing were performed.

Results:

The internal QC program identified sources of discrepancies in laboratory results. Evidence base for decision on new methodology and antibiotic testing were developed. For instance, it is observed that calibrated dichotomous susceptibility gives greater annular radius than directed susceptibility (P < 0.01).

Conclusions:

Internal QC program continues to be valuable means of identifying discrepancies, and vetting new ideas. This report presents evidence base to reaffirm that the need for internal QC is ever present.

Constrictive pericarditis secondary to infection with Mycoplasma pneumoniae

Pericardial effusions can be insidious, variable in presentation, and may result from a wide variety of causes. We report here a rare case of pericardial effusion in a pediatric patient secondary to infection with Mycoplasma pneumoniae that progressed to cardiac tamponade and constrictive pericarditis. The differential diagnosis of pericardial effusion is reviewed as well as current treatments for pericardial effusions and constrictive pericarditis.

Rapid multiplex nested PCR for detection of respiratory viruses

Respiratory tract infections can be caused by a heterogeneous group of viruses and bacteria that produce similar clinical presentations. Specific diagnosis therefore relies on laboratory investigation. This study developed and evaluated five groups of multiplex nested PCR assays that could simultaneously detect 21 different respiratory pathogens: influenza A virus (H1N1, H3N2, and H5N1); influenza B virus; parainfluenza virus types 1, 2, 3, 4a, and 4b; respiratory syncytial virus A and B; human rhinoviruses; human enteroviruses; human coronaviruses OC43 and 229E; severe acute respiratory syndrome coronavirus; human metapneumoviruses; Mycoplasma pneumoniae; Chlamydophila pneumoniae; Legionella pneumophila; and adenoviruses (A to F). These multiplex nested PCRs adopted fast PCR technology. The high speed of fast PCR (within 35 min) greatly improved the efficiency of these assays. The results show that these multiplex nested PCR assays are specific and more sensitive (100- to 1,000-fold) than conventional methods. Among the 303 clinical specimens tested, the multiplex nested PCR achieved an overall positive rate of 48.5% (95% confidence interval [CI], 42.9 to 54.1%), which was significantly higher than that of virus isolation (20.1% [95% CI, 15.6 to 24.6%]) and that of direct detection by immunofluorescence assay (13.5% [95% CI, 9.7 to 17.4%]). The improved sensitivity was partly due to the higher sensitivity of multiplex nested PCR than that of conventional methods in detecting cultivatable viruses. Moreover, the ability of the multiplex nested PCR to detect noncultivatable viruses, particularly rhinoviruses, coronavirus OC43, and metapneumoviruses, contributed a major gain (15.6%) in the overall positive rate. In conclusion, rapid multiplex nested PCR assays can improve the diagnostic yield for respiratory infections to allow prompt interventive actions to be taken.

High sensitivity and specificity of the Pastorex® latex agglutination test for Neisseria meningitidis serogroup A during a clinical trial in Niger

There is a great need for a rapid diagnostic test to guide vaccine choice during outbreaks of meningococcal meningitis in resource-poor countries. During a randomised clinical trial conducted during an epidemic of Neisseria meningitidis serogroup A in Niger in 2003, the sensitivity and specificity of the Pastorex latex agglutination test for this serogroup under optimal field conditions were assessed, using culture and/or PCR as the gold standard. Results from 484 samples showed a sensitivity of 88% (95% CI 85-91%) and a specificity of 93% (95% CI 90-95%). Pastorex could be a good alternative to current methods, as it can be performed in a local laboratory with rapid results and is highly specific. Sensitivity can be improved with prior microscopy where feasible. A study specifically to evaluate the Pastorex test under epidemic conditions, using laboratories with limited resources, is recommended.

Practical implementation of a multiplex PCR for acute respiratory tract infections in children

Molecular testing for acute respiratory infections (ARIs) has documented value but limited implementation due to questions that typically slow the acceptance of new tests. This study sought to address these questions and achieve implementation. Rhinovirus was added to a nested multiplex PCR (M-PCR), increasing its diagnostic yield. Over one winter, three hospital pediatric departments used the M-PCR to complement their direct fluorescent-antibody assay (DFA) for respiratory syncytial virus (RSV). Clinicians recorded "pretest probability estimates" (using continuous scales for various pathogen groups) for comparison with test results; treatments and test turnaround times were also recorded. Transnasal and throat swabs, with or without nasopharyngeal aspirate (NPA), were M-PCR tested. NPA-containing sample sets found to be RSV positive by DFA were not further tested. Single PCR for human metapneumovirus (hMPV) was performed retrospectively. Of 178 ARI episodes representing 172 patients, NPA was included in 97 sample sets; 54 (56%) were determined to be RSV positive. The other NPA-containing sample sets (n = 43) yielded 27 findings (63%), and the swab-only sets (n = 81) yielded 47 findings (58%); rhinovirus was found most often. Testing for hMPV yielded seven positive results. M-PCR median turnaround times were 4 days in swab-only samples and 5 days with NPA. Antibiotics were prescribed in 50 episodes, at rates similar for RSV and rhinovirus. Pretest probability estimates of a viral cause were lower in episodes caused by rhinovirus than in episodes caused by RSV. The hospitals continued to use M-PCR for NPA-containing samples found to be RSV negative by DFA. Test implementation is more likely with higher diagnostic yield and a protocol that reflects day-to-day clinical and laboratory operations.

Studies on acute human infections using FTIR microspectroscopy and cluster analysis

A novel methodology for the diagnosis of acute infections using FTIR microspectroscopy (FTIR-MSP) data on blood components and cluster analysis is presented. Blood samples were collected from 11 patients suffering from various infections and 16 age-matched healthy human controls. Blood components such as white blood cells, red blood cells, and plasma were isolated using standard procedures and FTIR-MSP of these components was utilized. A cluster analysis of the FTIR spectra was performed. The spectra obtained from the three blood components of patients were different from those of controls. The FTIR spectra of white blood cells from patients suffering infections were significantly different from the controls. Cluster analyses of averaged FTIR-MSP spectra of white blood cells provided 100% classification between patients and healthy controls.

[Investigations for etiologic causes in community-acquired pneumonia in children (besides imagery)]

The aim of laboratory investigations in acute lower respiratory tract infections in children is mainly to help to differentiate bacterial from viral infections. While blood cell counts and C reactive protein have good negative predictive value and specificity. Blood cultures are at the best positive in 10% of bacterial pneumonia. Immunofluorescence bacterial antigen detection in nasopharyngeal secretions are useful for the etiological diagnosis of viral pneumonia while polymerase chain reaction technique remains at the present time too expensive to be routinely used. Bronchoalveolar lavage is only indicated in respiratory infections that resist a first line well conducted treatment.

Heteroduplex mobility assay for rapid, sensitive and specific detection of mycobacteria

We report an improved method for the detection and identification of mycobacteria using PCR and the heteroduplex mobility shift assay (HMA). The HMA for detection of mycobacteria was based on the microheterogeneity within the DNA coding sequences for 16S rRNA. A remarkable shift between single-stranded, heteroduplex and homoduplex bands in PAGE was observed among the Mycobacterium spp. tested. The Mycobacteria HMA (MHMA) of amplified PCR products from mycobacteria DNA coding for 16S rDNA derived from culture showed a specific heteroduplexes formed among different Mycobacterium species. Other bacterium species were distinguished from Mycobaterium due to slow migrating heteroduplexes mobility bands observed when M. bovis (BCG), M. avium, or M. fortuitum were used as a standard. The specific heteroduplexes were detected when as little as 1 etag of DNA template was used, although better results were obtained with 5 etag and when PCR products of sample test and mycobacterium standard were mixed at a ratio of 1.8. To correctly evaluate the feasibility of using MHMA to detect and identify mycobacteria, 15 clinical sample patients were tested. All MTB-positive clinical samples were identified by MHMA as well as the negative samples. In addition, MHMA will, in principle, be applicable to the detection and classification of any microorganism showing differences within the 16S rRNA as well as to the identification of new and unrecognized bacterial species.

Value of cerebrospinal fluid leukocyte aggregation in distinguishing the causes of meningitis in children

BACKGROUND

Current laboratory tests often cannot distinguish between bacterial and aseptic meningitis rapidly and accurately. The ability to make a prompt diagnosis has important implications for the management and outcome of children with meningitis. The observation that leukocytes aggregate in the cerebrospinal fluid (CSF) has been previously reported, and it has been advocated as a reliable method to distinguish the causes of meningitis in children.

OBJECTIVE

To investigate the utility of CSF leukocyte aggregation as a screening test to distinguish between bacterial and aseptic meningitis.

METHODS

We compared the clinical and laboratory indices of 109 prospectively enrolled patients with meningitis (67 bacterial, 23 viral, 19 undefined etiology) and evaluated the validity of the CSF leukocyte aggregation test. The predefined leukocyte aggregation scores (LAS) were compared among the types of meningitis, and correlations with other markers of inflammation were calculated.

RESULTS

The median LAS was significantly higher (P < 0.001) in the bacterial (32.1%; range, 0 to 84.1%) than in the viral (0%; range, 0 to 16.6%) or undefined (0%; range, 0 to 20.7%) groups. The optimal sensitivity of the leukocyte aggregation test, 98.5 to 92.5%, was demonstrated with LAS values of 0 to 3%. The corresponding specificity was 64.3 to 88.1%. The peripheral white blood cell (WBC) count, serum C-reactive protein, CSF WBC count, blood culture, CSF Gram stain and CSF culture were inferior to the LAS as screening tests when compared individually. The LAS was as effective as CSF protein, TNF-alpha, IL-1-beta, IL-6 and IL-8 to predict bacterial meningitis. In a logistic regression model that included routine laboratory tests, the best predictor of bacterial meningitis was the LAS (odds ratio, 1.6 to 3.7). Significant correlations were demonstrated between the LAS and CSF protein, CSF WBC count, IL-1-beta, IL-6 and IL-8. Duration of symptoms before diagnosis, pretreatment with antibiotics, HIV-1 infection status and CSF red blood cell count did not significantly alter the LAS.

CONCLUSIONS

There is no single test to diagnose the etiology of meningitis in children promptly and accurately. The finding of leukocyte aggregation in CSF might be of value as a sensitive adjunctive screening tool for the timely diagnosis of bacterial meningitis, recognizing that it has low specificity and potential practical limitations.

Oral tuberculosis: a clinical evaluation of 42 cases

OBJECTIVES

A retrospective review of a large series of oro-facial cases of tuberculosis to analyse clinical, histopathological, and radiological aspects, as well as those of chemotherapy.

MATERIALS AND METHODS

A total of 42 cases of tuberculosis of the oro-facial region were examined. Thirteen patients had a primary form and 29 a secondary form of the disease. Diagnosis was based on careful clinical examination, Mantoux reaction, histopathological examination, microbiological cultures and immunological investigation with the detection of antibodies against Mycobacteria in the patients' serum (ELISA).

RESULTS

Cases examined consisted of 27 males and 15 females. The age range was 3 to 73 years (mean age 31 years). Clinical manifestations comprised oral ulcers in 69.1%, bone involvement in 21.4%, and salivary gland and/or lymph node involvement in 14.3%. A total of 79.4% patients with secondary disease had pulmonary lesions, 15 of whom showed clinical and radiological signs of activity; there was one case of bilateral renal lesions and two of skin lesions.

CONCLUSIONS

Oro-facial tuberculosis is often difficult to diagnose and it should be an important consideration in the differential diagnosis of lesions that appear in the oral cavity. The most important diagnostic tools remain a careful clinical evaluation, biopsy for histologic study, as well as acid-fast stains, culture, and immunological assays, and skin testing.

Simplified preparation of human arterial sections for PCR analysis of Chlamydia pneumoniae and human DNA

AIMS

To investigate multiple techniques for the preparation of solid tissue for polymerase chain reaction (PCR) analysis, and to identify the most simple techniques for routine use in the laboratory.

METHODS

Techniques for the preparation of arterial tissue samples including homogenisation, ultrafiltration, and treatments involving proteinase K, Gene Clean, lectin, and Fe3+ specific chelators were evaluated using the PCR to amplify both Chlamydia pneumoniae and human DNA.

RESULTS

Treatment with either Gene-Clean or lectin and the Fe3+ specific chelator deferoxamine mesylate removed PCR inhibitors from tissue homogenates. Homogenisation followed by GeneClean treatment resulted in the amplification of C pneumoniae DNA from within a section of atherosclerotic carotid artery, implying that C pneumoniae elementary bodies had been disrupted. In eight further clinical samples from patients not known to have C pneumoniae infection, human DNA was amplified and no cross contamination was observed between samples. These samples contained no evidence of C pneumoniae by PCR.

CONCLUSIONS

A simple preparation of solid tissue for PCR analysis, involving homogenisation followed by GeneClean treatment has been developed, and is effective for the amplification of both C pneumoniae and human DNA.

Toward an integrated program for patient care in pediatric infections

BACKGROUND

Clinicians and scientists have important and complementary roles to play in improving the management of pediatric infectious diseases. The clinician's role is to provide optimal care for the individual patient, whereas the scientist is closely involved in teaching and research.

OBJECTIVES

To review the current challenges in the management of childhood infections and the contributions of different groups to meeting these challenges.

DISCUSSION

The pattern of infectious diseases in children is constantly changing, emphasizing the importance of microbiologic research in meeting these challenges. In the clinical setting the research results must be applied and integrated in routine practice. The development and successful clinical use of new diagnostic techniques, new antibiotics and new vaccines provide good examples of the teamwork between scientists and clinicians, which is essential for progress in the field of common childhood infectious diseases. The most urgent challenges in this area that now face physicians are the increasing prevalence of antibiotic-resistant bacteria, especially the spread of penicillin-resistant Streptococcus pneumoniae, and the growing numbers of immunocompromised children. Devising and implementing strategies to meet these demands will require a continuing commitment from pediatricians and microbiologists.