Analysis of Changes in Diversity and Abundance of the Microbial Community in a Cystic Fibrosis Patient Over a Multi-Year Period. J Clin Microbiol. 2014 Nov 12, Stokell JR1, Gharaibeh RZ2, Hamp TJ3, Zapata MJ3, Fodor AA3, Steck TR4
- Department of Biological Sciences, Univ. of North Carolina at Charlotte, Charlotte, NC 28223, USA.
- 2Bioinformatics Services Division, Department of Bioinformatics and Genomics, Univ. of North Carolina at Charlotte, Kannapolis, NC 28081, USA.
- 3Department of Bioinformatics and Genomics, Univ. of North Carolina at Charlotte, Charlotte, NC 28223, USA.
- 4Department of Biological Sciences, Univ. of North Carolina at Charlotte, Charlotte, NC 28223, USA firstname.lastname@example.org.
The evolution of pulmonary disease in cystic fibrosis (CF) usually begins when bacteria get trapped in the mucus of the lungs and become established as chronic infections. While most patients experience periods of stability, pulmonary exacerbations (PE)s can occur multiple times per year and result in permanent damage to the lungs. Little is known of the shift from a period of stability to a PE but this shift is likely to be attributed to changes in the bacterial community. Here we identified changes in the lung microbiota to determine if they can reflect patient health, indicate onset of exacerbations, or are related to antibiotic treatment. Different from most bacterial studies on CF, we collected weekly from an adult CFpatient over a period of three years and performed quantitative PCR (qPCR) and Illumina sequencing on those samples. While many DNA-based studies have shown the CF microbiota to be relatively stable, we observed an increase in total bacterial abundance over time (p < .001) while the number of different taxa (bacterial richness), and the number of different taxa and their abundances (diversity), significantly decreased over time (p < .03) which was likely due to repeated antibiotic exposure. Using genus-specific primers with qPCR, we observed an increase in the abundance of Burkholderia multivorans, a CF-associated pathogen prior to the occurrence of a PE (p = .006). Combining these DNA-based techniques with frequent sampling identified a potential initiator for exacerbations and described a response of the CF microbiota to time and antibiotic treatment not observed in previous CF microbiota studies.
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