Culture versus polymerase chain reaction for the etiologic diagnosis of community-acquired pneumonia in antibiotic-pretreated pediatric patients

Development and validation of a multiplex real-time PCR assay for detection and quantification of Streptococcus pneumoniae in pediatric respiratory samples

IMPORTANCE

Streptococcus pneumoniae (Spn) is the world's leading cause of lower respiratory tract infection morbidity and mortality in children. However, current clinical microbiological methods have disadvantages. Spn can be difficult to grow in laboratory conditions if a patient is pre-treated, and Spn antigen testing has unclear clinical utility in children. Syndromic panel testing is less cost-effective than targeted PCR if clinical suspicion is high for a single pathogen. Also, such testing entails a full, expensive validation for each panel target if used for multiple respiratory sources. Therefore, better diagnostic modalities are needed. Our study validates a multiplex PCR assay with three genomic targets for semi-quantitative and quantitative Spn molecular detection from lower respiratory sources for clinical testing and from upper respiratory sources for research investigation.

Performance of TEM-PCR vs Culture for Bacterial Identification in Pediatric Musculoskeletal Infections

Improved diagnostics are needed for children with musculoskeletal infections (MSKIs). We assessed the performance of target-enriched multiplex polymerase chain reaction (TEM-PCR) in children with MSKI. TEM-PCR was concordant with culture in pathogen identification and antibiotic susceptibility testing, while increasing the overall yield of pathogen detection. This technology has the potential to inform judicious antimicrobial use early in the disease course.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past 25 years due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation in the clinical microbiology laboratory as well as user-friendly software and robust laboratory informatics systems have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting [3, 4]. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, has benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods continues to lag behind. The purpose of this chapter is to review, update, and discuss the interpretation and relevance of results produced by these advanced molecular techniques.

Mycoplasma pneumoniae from the Respiratory Tract and Beyond

Mycoplasma pneumoniae is an important cause of respiratory tract infections in children as well as adults that can range in severity from mild to life-threatening. Over the past several years there has been much new information published concerning infections caused by this organism. New molecular-based tests for M. pneumoniae detection are now commercially available in the United States, and advances in molecular typing systems have enhanced understanding of the epidemiology of infections. More strains have had their entire genome sequences published, providing additional insights into pathogenic mechanisms. Clinically significant acquired macrolide resistance has emerged worldwide and is now complicating treatment. In vitro susceptibility testing methods have been standardized, and several new drugs that may be effective against this organism are undergoing development. This review focuses on the many new developments that have occurred over the past several years that enhance our understanding of this microbe, which is among the smallest bacterial pathogens but one of great clinical importance.

Impact of bronchoalveolar lavage multiplex polymerase chain reaction on microbiological yield and therapeutic decisions in severe pneumonia in intensive care unit

PURPOSE

The purpose of the study is to evaluate the impact of adding bronchoalveolar lavage multiplex polymerase chain reaction (M-PCR) to conventional cultures (CC) on microbiological yield and therapeutic decisions in adult intensive care unit patients with pneumonia and severe sepsis or septic shock.

MATERIAL AND METHODS

In this retrospective case-control study, bronchoalveolar lavage cultures were taken for control (58 patients, 58 admissions) and study arms (57 patients, 58 admissions). Bronchoalveolar lavage M-PCR was sent simultaneously for the latter.

RESULTS

A total of 267 microorganisms were identified (M-PCR alone, 211; CC alone, 15; both, 41) in the study arm vs 64 in controls. Concordance between M-PCR and culture was complete in 32 (55.17%), partial in 4 (6.9%), and discordant in 22 (37.93%) including 17 with positive M-PCR but negative CC. Time to antibiotic therapy modification was significantly less (P < .001) in M-PCR group compared to controls (32.40 ± 14.41 vs 41.74 ± 45.61 hours). There was no significant difference in index episode resolution (48.3% vs 50%; P = 1), intensive care unit mortality (57.4% vs 51.2%; P = .67), and hospital mortality (59.6% vs 61.5%; P = 1) in study and control arms, respectively, despite more septic shock patients in the study arm (89.7% vs 75.9%; P = .05).

CONCLUSION

Bronchoalveolar lavage M-PCR with culture leads to higher microbiological yield and earlier modification of antibiotics compared to conventional culture.

Blood culture isolates in neonatal sepsis and their sensitivity in Anand District of India

OBJECTIVES

To study prevalent organisms in neonatal sepsis, their sensitivity to antibiotics and outcome in neonates with culture proven sepsis.

METHODS

This was a retrospective study of hospital records of 4 y. From 276 culture positive reports of 226 newborns, organisms, their sensitivity to different antibiotics were studied and their outcome was compared to 571 culture negative newborns. Growth detection was done by BacT/ALERT®PF system.

RESULTS

Most common isolates were Klebsiella (42.4 %), Coagulase-negative staphylococci (11.2 %), Enterobacter (9.4 %), Escherichia coli (9.1 %), Pseudomonas (5.4 %) and Acinetobacter (4.7 %). Gram negative organisms were predominant both in early-onset and late-onset neonatal sepsis as well as in inborn and outborn newborns and most of them were resistant to commonly used first line antibiotics like ampicillin, gentamicin and cephalosporins. Extended Spectrum Beta Lactamase producing Klebsiella and Escherichia coli were 94.87 % and 92 %, respectively. Methicillin resistant Staphylococci were 33 %. Vancomycin resistance among the Enterococci was 20 %. Most effective first line antibiotic combinations were amikacin with levofloxacin and amikacin with piperacillin-tazobactam. Survival in culture positive newborns (43.36 %, 95 % CI 37.07 to 49.88) was poor than culture negative newborns (53.06 %, 95 % CI 48.96 to 57.12).

CONCLUSIONS

Gram negative organisms were most common cause of neonatal sepsis and were resistant to first line antibiotics. Blood culture positive newborns had poor outcome than culture negative newborns.

Diagnostic features of community-acquired pneumonia in children: what's new?

AIM

To critically summarise the available data on diagnosis of CAP in children, focusing on the newest findings and on the need for new studies.

METHODS

Eighty studies on the diagnosis of paediatric community-acquired pneumonia were scrutinised.

RESULTS

We found no significant associations between the signs or symptoms and aetiology of pneumonia and concluded that chest radiographs remain controversial and real-time polymerase chain reaction appears more sensitive than blood cultures.

CONCLUSION

Antibiotic overuse could make it difficult to differentiate viral and bacterial causes. Molecular methods provide promising tools for diagnosing infection by atypical bacteria, but are expensive and should be used selectively.

Interpretation and Relevance of Advanced Technique Results

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

Vaccine preventable community-acquired pneumonia in hospitalized children in Northwest China

BACKGROUND

Community-acquired pneumonia (CAP) is a major cause of morbidity in industrialized countries and morbidity/mortality in developing countries. In China, comprehensive studies of the etiology of CAP in children aged between 2 months and 14 years who are serious enough to require hospitalization are lacking. Previous studies have been limited in child age range, focused on fatal cases, and/or limited in etiologies sought. An understanding of the etiologies is needed for development of best prevention and management practices.

OBJECTIVE

The aim of this study was to prospectively determine during a 12-month period the etiology of CAP in hospitalized children in a center in Northwest China.

DESIGN/METHODS

A prospective 12-month study (2004-2005) of CAP cases in children who were 2 months to 14 years of age admitted to the Second Hospital of Lanzhou University, China. Testing included admission and 1-month postdischarge serum for viral and bacterial serologic analyses (respiratory syncytial virus, influenza A and B, paraflu 1-3, adenovirus; Streptococcus pneumoniae, Haemophilus influenza B, Mycoplasma, and Moraxella. catarrhalis), blood culture, a nasopharyngeal aspirate for viral antigen testing, and a chest radiograph on admission and 1 month postdischarge. The study was funded by Lanzhou University. The study was performed in compliance with the guidelines of the institutional review board of the Second Hospital of Lanzhou University.

RESULTS

CAP was the admitting diagnosis for 29% of all admissions during the 12-month study. Of the 884 CAP cases, 821 (93%) were enrolled and completed the study. The age range was 2 months to 14 years; mean age was 2.3 years; 40% were <1 year. The average length of stay was 9.2 days (range, 6-20) but varied by age and etiology. Fourteen percent had received antibiotics before admission and 14% had underlying illnesses; 12% required intensive care unit treatment and 5 died. A microbial etiology for CAP was identified in 547 (67%); viral 535 (43%), bacterial 228 (27%), mixed viral bacterial 107 (13%), mixed viral in 1%, and mixed bacterial in 1%. The etiology varied by age; respiratory syncytial virus was most common in <1 year, S. pneumoniae and Hib 1-3 years, and Mycoplasma 5 years. Three potentially vaccine preventable etiologies accounted for 35% of the cases: influenza 9%, Hib 12%, and S. pneumonia 14%.

CONCLUSIONS

CAP is a major cause of childhood admission in China. Given the etiologic findings in this study, potentially 25% to 35% of cases could be prevented if seasonal influenza vaccine and conjugated H. influenza b and conjugated pneumococcal vaccines were introduced into routine practice.

Emerging molecular assays for detection and characterization of respiratory viruses

This article describes several emerging molecular assays that have potential applications in the diagnosis and monitoring of respiratory viral infections. These techniques include direct nucleic acid detection by quantum dots, loop-mediated isothermal amplification, multiplex ligation-dependent probe amplification, amplification using arbitrary primers, target-enriched multiplexing amplification, pyrosequencing, padlock probes, solid and suspension microarrays, and mass spectrometry. Several of these systems already are commercially available to provide multiplex amplification and high-throughput detection and identification of a panel of respiratory viral pathogens. Further validation and implementation of such emerging molecular assays in routine clinical virology services will enhance the rapid diagnosis of respiratory viral infections and improve patient care.

Basic concepts of microarrays and potential applications in clinical microbiology

The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform's advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles.

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

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

Identification and differentiation of clinically relevant mycobacterium species directly from acid-fast bacillus-positive culture broth

Mycobacterium species cause a variety of clinical diseases, some of which may be species specific. Therefore, it is clinically desirable to rapidly identify and differentiate mycobacterial isolates to the species level. We developed a rapid and high-throughput system, MycoID, to identify Mycobacterium species directly from acid-fast bacillus (AFB)-positive mycobacterial culture broth. The MycoID system incorporated broad-range PCR followed by suspension array hybridization to identify 17 clinically relevant mycobacterial complexes, groups, and species in one single reaction. We evaluated a total of 271 AFB-positive culture broth specimens, which were identified by reference standard methods in combination with biochemical and molecular tests. The overall identification agreement between the standard and the MycoID system was 89.7% (perfect match) or 97.8% (one match in codetection). In comparison to the standard, the MycoID system possessed an overall sensitivity of 97.1% and specificity of 98.8%. The 159 Mycobacterium avium-M. intracellulare complex isolates were further identified to the species level by MycoID as being M. avium (n = 98; 61.1%), M. intracellulare (n = 57; 35.8%), and mixed M. avium and M. intracellulare (n = 2; 1.3%). M. avium was recovered more frequently from sterile sites than M. intracellulare (odds ratio, 4.6; P = 0.0092). The entire MycoID procedure, including specimen processing, can be completed within 5 h, providing rapid and reliable identification and differentiation of mycobacterium species that is amenable to automation. Additional differentiation of Mycobacterium avium-M. intracellulare complex strains into M. avium and M. intracellulare may provide a tool to better understand the role of Mycobacterium avium-M. intracellulare complex isolates in human disease.