(478) Evaluation of Bacterial Detection by Microbial Cell Free DNA Using Plasma Collected During Admission for CF Pulmonary Exacerbation

Background: Pulmonary exacerbation treatment targets bacterial pathogens detected from airway samples. Spontaneously expectorated sputum is the preferred sample for culture, however, some people with CF may be unable to spontaneously expectorate particularly younger patients or those on highly effective CFTR modulator therapy. Non-invasive diagnostic approaches that provide rapid results and reflect lower airway pathogens even in non-expectorating patients are needed for pathogen identification during pulmonary exacerbations. Microbial cell-free DNA (mcf-DNA) detection of bacterial and viral pathogens has been demonstrated in sepsis and pneumonia. We sought to determine whether CF pathogens are detected using mcf-DNA analysis of peripheral blood specimens collected at admission for treatment of a pulmonary exacerbation. We compared mcf-DNA results to airway microbiologic culture and molecular sequencing.

Methods: Residual frozen aliquots of blood specimens collected from a previously completed prospective study of pulmonary exacerbations in people with CF ages 12 – 22 years of age were used for this study. Sputum was collected spontaneously or by induction on admission and at the end of treatment. Microbiologic culture and microbiome analysis with 16S rRNA gene sequencing were performed at the time of the study.

Results: Thirty-five stored admission blood specimens from 35 patients were available and sent to Karius, Inc. for analysis. Sputum culture on admission was positive for Pseudomonas aeruginosa (Pa) in 11/35 (31%), Staphylococcus aureus (18/35, 51%), Stenotrophomonas (Sm, 6/35, 17%), Haemophilus (Hi, 1/35, 3%). mcf-DNA results were concordant with sputum culture results in 32/35 (91%) for Pa, and (20/35, 57%) for S. aureus. Mcf-DNA failed to identify Sm, Hi and Achromobacter in a small number of patients. The twelve Pa not identified by mcf-DNA included eight with quantities < 10⁵ CFU/ml, only one of the twelve was also not detected by 16S, the remaining had RA < 2%. The 15 Sa not identified by mcf-DNA included 12 with quantities ≤10⁵ CFU/ml. Concordance was similar at end of treatment with more individuals negative by culture and mcf-DNA.

In addition to traditional CF pathogens, mcf-DNA identified atypical bacteria that we are in the process of comparing to molecular sequencing data from sputum. These additional microbes may allow identification of other important organisms in CF and provide insight into atypical organisms identified by molecular approaches.


Conclusions: Detection of Pa appears promising, but additional work is required to understand the poor sensitivity for other CF pathogens. Additionally, further studies are needed particularly in non-expectorating patients and those on modulator who may have a lower bacterial burden.

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