Prevalence of Streptococci and Increased Polymicrobial Diversity Associated with Cystic Fibrosis Patient Stability

Filkins, Laura; Hampton, Thomas H.; Gifford, Alex H.; Gross, Maegan J.; Hogan, Deborah A.; Sogin, Mitchell L.; Morrison, Hilary G.; Paster, Bruce J.; O’Toole, George A.

doi:10.1128/jb.00566-12

Cited by 171 publications

(219 citation statements)

References 31 publications

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“…In patients with cystic fibrosis, increased lung microbial diversity has been suggested to be beneficial for overall health status improvement (60). In the present study, we hypothesized that immunocompromise resulting from HIV infection can significantly disrupt the normally constituted commensal bacterial colonization in the oral microbiota.…”

Section: Discussionmentioning

confidence: 91%

HIV Infection and Microbial Diversity in Saliva

et al. 2014

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f Limited information is available about the effects of HIV and subsequent antiretroviral treatment on host-microbe interactions. This study aimed to determine the salivary microbial composition for 10 HIV-seropositive subjects, before and 6 months after highly active antiretroviral therapy (HAART), compared with that for 10 HIV-seronegative subjects. A conventional culture and two culture-independent analyses were used and consistently demonstrated differences in microbial composition among the three sets of samples. HIV-positive subjects had higher levels of total cultivable microbes, including oral streptococci, lactobacilli, Streptococcus mutans, and Candida, in saliva than did HIV-negative subjects. The total cultivable microbial levels were significantly correlated with CD4 ؉ T cell counts. Denaturing gradient gel electrophoresis (DGGE), which compared the overall microbial profiles, showed distinct fingerprinting profiles for each group. The human oral microbe identification microarray (HOMIM) assay, which compared the 16S rRNA genes, showed clear separation among the three sample groups. Veillonella, Synergistetes, and Streptococcus were present in all 30 saliva samples. Only minor changes or no changes in the prevalence of Neisseria, Haemophilus, Gemella, Leptotrichia, Solobacterium, Parvimonas, and Rothia were observed. Seven genera, Capnocytophaga, Slackia, Porphyromonas, Kingella, Peptostreptococcaceae, Lactobacillus, and Atopobium, were detected only in HIVnegative samples. The prevalences of Fusobacterium, Campylobacter, Prevotella, Capnocytophaga, Selenomonas, Actinomyces, Granulicatella, and Atopobium were increased after HAART. In contrast, the prevalence of Aggregatibacter was significantly decreased after HAART. The findings of this study suggest that HIV infection and HAART can have significant effects on salivary microbial colonization and composition.

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Section: Discussionmentioning

confidence: 91%

HIV Infection and Microbial Diversity in Saliva

et al. 2014

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“…However, 16S sequence data have a limited ability to resolve taxonomy identification to the species level (30) and may introduce biases during the primer-binding step of PCR (31). For example, different species of Pseudomonas or Streptococcus were distinguished using this method, and Staphylococcus aureus that was detected by culturing was not detected by sequencing (29,30).…”

Section: Discussionmentioning

confidence: 99%

Clinical Insights from Metagenomic Analysis of Sputum Samples from Patients with Cystic Fibrosis

et al. 2014

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f As DNA sequencing becomes faster and cheaper, genomics-based approaches are being explored for their use in personalized diagnoses and treatments. Here, we provide a proof of principle for disease monitoring using personal metagenomic sequencing and traditional clinical microbiology by focusing on three adults with cystic fibrosis (CF). The CF lung is a dynamic environment that hosts a complex ecosystem composed of bacteria, viruses, and fungi that can vary in space and time. Not surprisingly, the microbiome data from the induced sputum samples we collected revealed a significant amount of species diversity not seen in routine clinical laboratory cultures. The relative abundances of several species changed as clinical treatment was altered, enabling the identification of the climax and attack communities that were proposed in an earlier work. All patient microbiomes encoded a diversity of mechanisms to resist antibiotics, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in CF patients. The metabolic potentials of these communities differed by the health status and recovery route of each patient. Thus, this pilot study provides an example of how metagenomic data might be used with clinical assessments for the development of treatments tailored to individual patients.

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“…In addition to "typical" CF pathogens, "nonpathogenic oral bacteria," including many obligate and facultative anaerobic species, are often present in densities that well exceed those of the traditional opportunists associated with CF (4). Although most of these studies analyzed expectorated sputum samples that would be expected to be "contaminated" with bacteria residing in the nonsterile oropharynx during expectoration, several lines of evidence indicate that this has only a marginal impact on measures of airway microbiota (17,24,25).…”

Section: The Lung Microbiome In Cfmentioning

confidence: 99%

Antibiotic Management of Lung Infections in Cystic Fibrosis. I. The Microbiome, Methicillin-Resistant Staphylococcus aureus, Gram-Negative Bacteria, and Multiple Infections

et al. 2014

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Despite significant advances in treatment strategies targeting the underlying defect in cystic fibrosis (CF), airway infection remains an important cause of lung disease. In this two-part series, we review recent evidence related to the complexity of CF airway infection, explore data suggesting the relevance of individual microbial species, and discuss current and future treatment options. In Part I, the evidence with respect to the spectrum of bacteria present in the CF airway, known as the lung microbiome is discussed. Subsequently, the current approach to treat methicillin-resistant Staphylococcus aureus, gram-negative bacteria, as well as multiple coinfections is reviewed. Newer molecular techniques have demonstrated that the airway microbiome consists of a large number of microbes, and the balance between microbes, rather than the mere presence of a single species, may be relevant for disease pathophysiology. A better understanding of this complex environment could help define optimal treatment regimens that target pathogens without affecting others. Although relevance of these organisms is unclear, the pathologic consequences of methicillin-resistant S. aureus infection in patients with CF have been recently determined. New strategies for eradication and treatment of both acute and chronic infections are discussed. Pseudomonas aeruginosa plays a prominent role in CF lung disease, but many other nonfermenting gram-negative bacteria are also found in the CF airway. Many new inhaled antibiotics specifically targeting P. aeruginosa have become available with the hope that they will improve the quality of life for patients. Part I concludes with a discussion of how best to treat patients with multiple coinfections.

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Prevalence of Streptococci and Increased Polymicrobial Diversity Associated with Cystic Fibrosis Patient Stability

Cited by 171 publications

References 31 publications

HIV Infection and Microbial Diversity in Saliva

HIV Infection and Microbial Diversity in Saliva

Clinical Insights from Metagenomic Analysis of Sputum Samples from Patients with Cystic Fibrosis

Antibiotic Management of Lung Infections in Cystic Fibrosis. I. The Microbiome, Methicillin-Resistant Staphylococcus aureus, Gram-Negative Bacteria, and Multiple Infections

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