Abstract: Methods are provided for detecting non-human candidate DNA within a plasma sample from a human subject. A method of diagnosing and characterizing a bacterial infection may include the steps of obtaining a plasma sample from a subject suspected of having a bacterial infection, extracting cell-free DNA (cfDNA) from the plasma sample, performing whole genome sequencing on the cfDNA to obtain sequencing data, aligning the sequencing data with a human genome to identify human DNA and non-human DNA, removing the human DNA from the sequencing data, assigning the non-human DNA to a candidate pathogen DNA, selecting a subset of the non-human DNA based on a fragment length of the non-human DNA, and determining the presence of the candidate pathogen DNA within the subset of the non-human DNA.