A 46-year-old man underwent resection of the right kidney in February 2020 due to a cystic variant of renal cell carcinoma complicated with a urinary fistula. Three weeks post-surgery, the patient developed a UTI. A standard microbiological laboratory test identified Enterococcus faecalis and Pseudomonas spp. In urine and, based on disk-diffusion AST, meropenem and clindamycin were prescribed. The response was insufficient and the bacteria persisted for the next two weeks, which prompted treatment with meropenem and levofloxacin (Fig. 1).
Nevertheless, the patient was still infected with E. faecalis and reinfected with Achromobacter xylosoxidans. In June 2020, E. faecalis and reinfection with Pseudomonas aeruginosa were confirmed, but due to the absence of clinical symptoms the patient was left untreated. Within a month, clinical symptoms of UTI appeared and P. aeruginosa was detected in urine; hence, the patient was administered fosfomycin, as suggested by conventional AST. However, the infection recurred and in August 2020 the patient was administered another course of fosfomycin due to persistence of P. aeruginosa along with reinfection with Escherichia coli. In February 2021, P. aeruginosa and reinfection with Klebsiella pneumoniae were identified, prompting treatment with a course of cefepime according to AST data. By April 2021, recurrence of P. aeruginosa and E. faecalis was noted and the patient was treated with ceftriaxone. During the next months, P. aeruginosa was detected in urine and, based on AST results, levofloxacin and cefepime were administered, but the infection recurred every time. Finally, in March 2022, the treating doctor prescribed a therapy based on antibiotic identification with AtbFinder.
Whereas routine AST identified only P. aeruginosa, AtbFinder detected P. aeruginosa, Staphylococcus aureus, A. xylosoxidans, and K. pneumoniae in the same urine sample. Accordingly, cefepime, moxifloxacin, cefepime + amikacin, meropenem + amikacin, and piperacillin/tazobactam + tobramycin were identified as effective by microbroth dilution, but ineffective by AtbFinder (Table 1). Instead, the latter identified ceftriaxone + amikacin, levofloxacin + azithromycin, and piperacillin/tazobactam + levofloxacin as effective (Fig. 2).
The patient was eventually treated with a combination of levofloxacin and azithromycin, which resulted in the rapid disappearance of clinical symptoms. At the check-up visit in May 2022, A. xylosoxidans was detected; however, no clinical data supported ongoing UTI. AtbFinder identified colistin, cefepime + levofloxacin, and tigecycline as effective, and the patient was treated with colistin for 5 days. At the next follow-up visits in August and October 2022, no bacterial growth in urine was detected using either conventional AST or AtbFinder.