Atypical bacterial pathogens in community-acquired pneumonia in children: a hospital-based study

Agarwal, Jyotsna; Awasthi, Sanjay; Rajput, Anuradha; Tiwari, Manoj Kumar; Jain, Amita

doi:10.1258/td.2008.080248

Cited by 11 publications

(22 citation statements)

References 8 publications

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“…species of these two genera are described as atypical pathogens for pneumonia [35], other studies have identified ''atypical pathogens'' as the predominant species in respiratory tract infections [15]. These findings are similar to previously published data for comparisons of traditional culture and culture-independent methods [6].…”

Section: Discussionsupporting

confidence: 85%

Examination with Next-Generation Sequencing Technology of the Bacterial Microbiota in Bronchoalveolar Lavage Samples after Traumatic Injury

Huebinger

Liu

Dowd³

et al. 2013

Surgical Infections

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Background: We examined the microbiota of bronchoalveolar lavage (BAL) samples with next-generation sequencing (NGS) technology to determine whether its results correlate with those of standard culture methods or affect patient outcome or both. Methods: We collected BAL samples in the surgical intensive care unit (SICU) as part of the standard of care for intubated individuals who had a Clinical Pulmonary Infection Score (CPIS) ‡ 6 points. A portion of the BAL fluid was sequenced for the 16S region of ribosomal deoxyribonucleic acid (rDNA) with the Roche 454 FLX Titanium sequencer. Sequences were analyzed through a data-analysis pipeline to identify the appropriate taxonomic designation (*species) of each 16s sequence. The bacterial microbiota of each BAL sample was compared with the bacteria identified in the sample through standard culture methods. Correlations between the taxonomic diversity of the microbiota and clinical outcome were examined through linear regression and Pearson correlation. Results: Bronchoalveolar lavage samples from 12 individuals in the SICU who had a CPIS ‡ 6 points were examined through 454 pyrosequencing. The number of phylotypes (*species) in the samples ranged from 15 to 129. The number of phyla in the BAL samples ranged from 3 to 14. There was little correlation between the bacteria identified by NGS and those identified with standard culture methods. The same predominant bacterial strain was identified by both culture and sequencing in only a single sample. The correlation between patient days on a ventilator and the number of species in BAL samples was significant (r = 0.7435, p = 0.0056; r 2 = 0.5528). Conclusions: Increasing diversity of the bacterial microbiota in BAL samples correlates with the duration of mechanical ventilation. Bacteria identified through standard culture methods were not well correlated with the findings of NGS.

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Section: Discussionsupporting

confidence: 85%

Examination with Next-Generation Sequencing Technology of the Bacterial Microbiota in Bronchoalveolar Lavage Samples after Traumatic Injury

Huebinger

Liu

Dowd³

et al. 2013

Surgical Infections

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“…Several genera of important possible pathogens were detected by the 454 platform but were absent from the list obtained by the clinical method. According to our knowledge and published articles, Mycoplasma, Haemophilus, and Moraxella are referred to as atypical pathogens of pneumonia [5,[26][27][28]. Compared with clinical reports, these potential pathogens were only found sporadically by our method in sputum samples.…”

Section: This Indicates That Althoughmentioning

confidence: 81%

Analysis of the microbiota of sputum samples from patients with lower respiratory tract infections

Zhou¹,

Lin²,

Li³

et al. 2010

ABBS

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Sputum is the most common sample collected from patients suffering from lower respiratory tract infections and it is crucial for the bacterial identification of these infections. In this study, we enrolled 101 sputum samples from 101 patients with lower respiratory tract infections. Initially, pyrosequencing of the 16S rDNA V3 hypervariable regions of the bacteria contained in the sputum was utilized as a culture-independent approach for microbiota analysis. For comparison, clinical laboratory tests using a culture-dependent automated bacterial identification system for the same cohort of sputum samples were also done. By pyrosequencing, >70,000 DNA fragments were found and classified into 129 bacterial genera after being analyzed by the Ribosomal Database Project (RDP) process. Most sequences belonged to several predominant genera, such as Streptococcus and Staphylococcus, indicating that these genera play an important role in lower respiratory tract infections. In addition, some sequences belonging to potential causative agents, such as Mycoplasma, Haemophilus, and Moraxella, were also found, but these sequences were not found by clinical laboratory tests. For the nine genera detected by both methods, the methods' sensitivities were compared and the results showed that pyrosequencing was more sensitive, except for Klebsiella and Mycobacterium. Significantly, this method revealed much more complicated bacterial communities and it showed a promising ability for the detection of bacteria.

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“…The most common concern was unclear reporting of baseline study population characteristics. We had concerns about the spectrum of patients recruited and the validity of the reference standard in one study (Agarwal 2009) Summary of findings 2. Diagnostic value of clinical symptoms and signs -pooled results with 95% confidence intervals Somer 2006).…”

Section: Quality Concernsmentioning

confidence: 99%

Clinical symptoms and signs for the diagnosis of Mycoplasma pneumoniae in children and adolescents with community-acquired pneumonia

Gill

Perera

Thomson

et al. 2012

Cochrane Database of Systematic Reviews

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Atypical bacterial pathogens in community-acquired pneumonia in children: a hospital-based study

Cited by 11 publications

References 8 publications

Examination with Next-Generation Sequencing Technology of the Bacterial Microbiota in Bronchoalveolar Lavage Samples after Traumatic Injury

Examination with Next-Generation Sequencing Technology of the Bacterial Microbiota in Bronchoalveolar Lavage Samples after Traumatic Injury

Analysis of the microbiota of sputum samples from patients with lower respiratory tract infections

Clinical symptoms and signs for the diagnosis of Mycoplasma pneumoniae in children and adolescents with community-acquired pneumonia

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