Time course of patient S11. A 62-year-old male patient presented with a multilocular hepatocellular carcinoma with the need for a left-sided hemihepatectomy. Following the surgical procedure the patient suffered from septic shock due to severe pneumonia with Klebsiella pneumoniae as the dominant organism in blood cultures as well as tracheal secretions. Empiric antibiotic therapy was performed with imipenem, which was then switched to moxifloxacin based on the susceptibility findings. In the further course of the disease, K. pneumoniae was shown to be multidrug resistant. Although antibiotic therapy was adapted according to the findings of susceptibility testing, the pulmonary septic focus could not be removed sufficiently. In the end, the patient died from ongoing septic shock due to pneumonia with K. pneumonia 2Â months after study inclusion. In addition, septic disease was shown to be accompanied by a reactivation of herpes simplex virus type 1 (HSV1) as well as cytomegalovirus (CMV) in different secretions as assessed by a PCR-based diagnostic procedure. These findings were in good agreement with next generation sequencing (NGS) of plasma. In this figure, the antibiotic treatment regime, SIQ scores for species identified via NGS, and cfDNA concentrations of the respective plasma samples are plotted over the timeline of the trial period for patient S11. Pertinent (clinical microbiology) laboratory results are marked using arrows to indicate the day the clinical specimen was obtained. Abbreviations: BC blood culture, CVC central venous catheter, TS tracheal secretion, GNST Gram-negative staphylococci, HSV1 herpes simplex virus 1, IPM imipenem, VAN vancomycin, MXF moxiflocaxin, CIP ciprofloxacin, TGC tigecycline, CAZ ceftazidime. Antibacterial antibiotics are displayed in light grey. The relative amount of bacteria found by conventional clinical microbiology is indicated with plenty (p), medium (m), or scarce (s). (For a detailed list of the anti-infective abbreviations, see Additional file 9: Table S5) (PDF 16 kb
