Examination of bacteria/host cell interactions is important for understanding the aetiology of many infectious diseases. The colony-forming-unit (CFU) has been the standard for quantifying bacterial burden for the past century, however, this suffers from low sensitivity and is dependent on bacterial culturability in vitro. Our data demonstrate the discrepancy between the CFU and bacterial genome copy number in an osteomyelitis-relevant co-culture system and we confirm diagnosis and quantify bacterial load in clinical bone specimens. This study provides insight into improving the quantification of bacterial burden in such cases.

The DNA sequences were generated by Oxford Nanopore sequencing platform, using the PCR amplicons following the enrichment of bacterial signal from total DNA isolated from clinical bone specimens.