Circulating Bacteriophage DNA Distinguishes Staphylococcal Infection from Commensal Colonization.

Background: Diagnosing periprosthetic joint infections (PJI) is challenging. We previously reported on using bacteriophage sequences in cell-free DNA (cfDNA) in plasma to diagnose bacterial pathogens in sepsis. Here, we hypothesized that plasma bacteriophage cfDNA can serve as a serological biomarker to monitor staphylococcal PJI.

Methods: Using a previously described computational pipeline, bacteriophage sequences were identified in cfDNA from 35 plasma samples from three distinct patient cohorts: patients who had a current Staphylococcal PJI (n=10), patients with a prior PJI (n=12), and patients with no PJI (n=13). The overall phageome and the proportion of Staphylococcus bacteriophage was described and compared among the three cohorts. The presence of Staphylococcus bacteriophage as a binary variable was also analyzed for its diagnostic performance in identifying Staphylococcal PJI.

Results: There were no differences in the distribution of bacterial cfDNA among the three cohorts (P = 0.597). The current PJI cohort had a significantly higher proportion of Staphylococcus bacteriophage compared to no PJI (median, 2.6 versus 0%, P = 0.013), and the prior PJI cohort had a significantly higher proportion of Staphylococcus bacteriophage compared to no PJI (median, 1.0 versus 0%, P = 0.049). Of note, there was no difference in the proportion of Staphylococcus bacteriophage between current PJI and prior PJI (median, 2.6 versus 1.0%, P = 0.554). Staphylococcus bacteriophage was present in six of 10 samples in the current PJI, seven of 12 samples in the prior PJI, and one of 13 samples in the no PJI groups. The presence of Staphylococcus bacteriophage had a sensitivity of 60% and specificity of 92% for a Staphylococcal PJI.

Conclusions: These findings suggest that plasma bacteriophage cfDNA offers a promising approach to detect and monitor staphylococcal PJI. The persistence of these Staphylococcus bacteriophages in prior PJI may reflect subclinical infection or residual microbial DNA undetectable by standard culture-based diagnostics.