Fig. 3

Time course SIQ analyses compared with conventional clinical microbiology data for two patients. a Time course of patient S10. A 68-year-old male patient presented with a tumor of his stomach with the need for a gastrectomy. Following the surgical procedure the patient suffered from septic shock due to severe pneumonia without any evidence of an anastomosis insufficiency. Staphylococcus aureus was shown to be the dominant organism in different secretions (e.g., tracheal secretion, abdominal wound swab, blood culture, etc.). In addition, pneumonia was shown to be accompanied (respectively boosted) by reactivation of herpes simplex virus type 1 (HSV1) in tracheal secretions. Following a prolonged weaning phase, the patient was then able to be discharged to the normal ward 6 weeks after the onset of septic shock. In this figure, the antibiotic treatment regime, SIQ scores for species identified via NGS/SEPseq, and cfDNA concentrations of the respective plasma samples are plotted for the trial period of 28 days. 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, HSV herpes simplex virus, CIP ciproflocaxine, MTZ metronidazole, MEM meropenem, VAN vancomycin, CFG caspofungin, FLX flucloxacillin, FLC fluconazole, ACV aciclovir, AFG anidulafungin, TGC tigecycline. Anti-infectives are displayed as antibacterial antibiotics, antimycotics, and antivirals in light grey, black, and dark grey, respectively. 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 Table S5.) b Time course of patient S60. Following a complicated course of perforated sigmoid diverticulitis, a 70-year-old female patient presented for reconstruction of bowel continuity. In the postoperative phase the patient developed septic shock due to bowel leakage with the need for surgical revision. Abdominal wound swabs were shown to be positive for Escherichia coli and Enterococcus faecium. One day later the patient suffered from a second septic hit due to perforation of the colon with the need for surgical colectomy and construction of a stump by Hartmann. Afterwards the patient suffered from another septic hit due to an insufficiency of the stump by Hartmann. Accordingly, one further explorative laparotomy was performed and an intensive abdominal lavage was initiated. In the further course of the septic disease the patient developed a fourth septic hit due to ventilator-associated pneumonia triggered by E. coli, Stenotrophomonas maltophilia, and Klebsiella pneumoniae. Following a prolonged weaning phase the patient was then able to be transferred to the intermediate care ward after 3 months of ICU treatment. Ultimately, the patient could be discharged from hospital another 2 weeks later. 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, BAL bronchoalveolar lavage, HSV1 herpes simplex virus 1, IPM imipenem, LZD linezolid, CFG caspofungin, ACV aciclovir, TZP piperacillin-tazobactam, CTX cotrimoxazol, CAZ ceftazidime. Antibacterial antibiotics are colored 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)