We describe the case of a 73-year old male, who was referred to our tertiary referral hospital for a laparoscopic pylorus-resecting pancreatoduodenectomy because of an intraductal papillary mucinous neoplasm. Three days after surgery, the patient developed fever; a CT-scan revealed peritonitis and leakage from the hepaticojejunostomy. Multiple drains were placed and piperacillin-tazobactam 18 g/day was administered. The abdominal fluid was cultured, revealing amongst others Citrobacter freundii, which was confirmed as carbapenemase-producing using the carbapenem-inactivation method (CIM) [1]. The patient improved and piperacillin-tazobactam was stopped 10 days after drainage.

Shortly after, the patient developed fever again following the placement of a percutaneous transhepatic cholangiogram (PTC) drain. Piperacillin-tazobactam was administered again, and blood cultures revealed the carbapenemase-positive C. freundii, in addition to wildtype Raoultella planticola, Proteus mirabilis and Enterococcus faecium. A spill from the PTC-drain was suspected because of the polymicrobial nature of the blood culture and a clinically stable and quickly recovering patient.

In the next few months, the patient improved and deteriorated several times and was admitted to the Intensive care unit (ICU) twice. These clinical deteriorations were mostly caused by new intra-abdominal collections, which were drained repeatedly. Cultures revealed a carbapenemase-producing Klebsiella oxytoca and a carbapenemase-producing R. planticola. Despite the patient’s status as a known carrier of carbapenemase-producing Citrobacter freundii, he consistently was treated with piperacillin-tazobactam and drainage and improved rapidly.

Several months later, the patient developed a fever due to a new abdominal collection. Cultures showed the previously found NDM-producing C. freundii. However, it also contained carbapenemase-producing S. marcescens, which was clonal with a previously susceptible strain. Piperacillin-tazobactam and drainage did not improve the situation of the patient, thus meropenem and colistin were administered. Due to stagnation of symptoms, antibiotic treatment was eventually changed to aztreonam and ceftazidime-avibactam. Unfortunately, the patient succumbed to septic shock.

Over a period of five months, 47 Enterobacterales isolates were identified from 30 clinical cultures (of which 15 CIM positive) and 21 (of which 13 CIM positive) screening cultures of this patient using MALDI-TOF MS (Biomérieux, France) and later verified with WGS (supplemental methods). In total, four different carbapenemase-producing Enterobacterales (C. freundii, K. oxytoca, R. planticola and S. marcescens) were cultured with two of them having clustering wildtype strains. (Fig. 1) WGS and bioinformatics are described in the supplementary methods and elsewhere [2, 3]. Antimicrobial susceptibility testing is shown in Fig. 2. All C. freundii isolates cultured, belonged to sequence type 22. These isolates encoded for the following AMR genes: aac(3)-IId-like, aac(6’)-Ib-cr-like, aadA1, aadA16-like, blaCMY−48, blaNDM−7, blaTEM−1B, mph(A), QnrB6, ARR-3, sul1, sul2, tet(D), dfrA1, dfrA27 and the plasmid replicons Col440I and IncX3. The IncX3 plasmid encoded the blaNDM−7 gene and a bleomycin resistance bleMBL and was identified as conjugative, as indicated by mob suite typing. When comparing the C. freundii blaNDM−7 plasmid to internationally reported sequences, one identical plasmid (PV022885.1) in a K. pneumoniae from a Canadian study [4], and manyother highly similar plasmids with more than 99,9% sequence identity, query coverage and identical sequence orientation were identified via the web interface of BLAST, being present in E. coli, Enterobacter species, Klebsiella species, Citrobacter species, Serratia marcescens and Morganella morganii isolates (as of 22-08−2025). WGS demonstrated that the carbapenemase-producing K. oxytoca ST35, R. planticola and S. marcescens found in later cultures also carried a blaNDM−7 on an IncX3 plasmid similar to the initial C. freundii. Compared to the C. freundii resistance plasmid, K. oxytoca had 1 SNPs, S. marcescens had 1 SNPs and 1 indel and R. planticola had no SNPs or deletions. However, the blaNDM−7 plasmid of R. planticola, showed an insertion of two blaTEM−1 and IS3000 family insertion sequences at the start of the plasmid (Supplementary Figs. 1 and 2). Only the S. marcescens plasmid had a 100% exact match with a different plasmid in the NCBI database, namely LC807797.1, a K. pneumoniae isolate from food or water samples from food markets in Dhaka, Bangladesh [5]. Furthermore, WGS showed that both the wildtype and blaNDM−7positive strains of the S. marcescens in our patient clustered together and differed only 1 and 2 SNPs as inferred by split k-mer analysis (SKA).

An overview of hospital admissions, relevant cultures and antimicrobial treatment of our patient

Overview of the tested antibiotic MIC-values and interpretation of the CPE and their wildtypes if available. (EUCAST version 13.1) S: Susceptible, R: Resistant, I: Susceptible with increased exposure. *: Sensititre™ Gram Negative EUMDROXF AST Plate (Thermofisher, United States of America). **: ‘NI’ is given when no interpretation was possible based on the EUCAST clinical breakpoints when the culture was taken. ***: VITEK® 2 (Biomérieux, France). ****: ETEST® (Biomérieux, France)