Investigations and treatment
Blood tests taken at admission showed elevated C-reactive protein (CRP) (137 mg/l, normal value <8 mg/l), alkaline phosphatase (174 U/l, normal range 35-105 U/l) and plasma ferritin (311 µg/l, normal range 15-290 µg/l), whereas the white blood cell count, alanine transaminase, lactate dehydrogenase and bilirubin were within the normal range.
A standard blood culture set (two BD BACTEC™ Plus Aerobic medium and one BD BACTEC™ Lytic Anaerobic medium glass culture vials) incubated in the BACTEC FX Top instrument (Becton Dickinson AB, Stockholm, Sweden) obtained upon admission and at day three, seven and eleven were all negative after six days of incubation. Moreover, a stool sample obtained at day nine was culture-negative for enteric pathogenic bacteria, including Yersinia species.
The abovementioned CT-scan of abdomen and pelvis performed before hospital admission had revealed three liver lesions suggestive for abscesses: one in the left lobe, and two in the right lobe segment five and six, with sizes of 8 cm, 3.6 cm and 1.8 cm in diameter, respectively, see Figure 1. Moreover, choledocholithiasis with multiple small gallstones was diagnosed, but with no signs of cholecystitis or cholestasis. Ultrasound-guided percutaneous drainage of the largest abscess was performed before initiation of antibiotic therapy, and small amounts of brown-reddish pus was obtained and sent to the microbiology laboratory. Microscopy (Gram stain and wet smear) did not detect any microorganisms; however, bacterial growth was observed on both chromogenic and blood agar plates after two days incubation, and the preliminary identification of Y. pseudotuberculosis was performed by use of the matrix-assisted laser desorption ionization–time of flight (MALDI Biotyper 3.1, Bruker Daltonics Microflex LT, MBT 6903 MSP Library) with a score of 2.480. Antibiotic susceptibility testing was performed by use of McFarland standard 0.5 on Mueller-Hinton agar and ETEST (BioMérieux, Marcy l’Etoile, France) using EUCAST clinical breakpoint table for Enterobacterales , version 11.0. The isolate was sensitive to ampicillin (Minimum inhibitory concentration (MIC): 0,19 mg/L); cefotaxime (MIC: 0,016mg/L); ceftriaxone (MIC: 0,016mg/L); meropenem (MIC: 0,016mg/L); ciprofloxacin (MIC: 0,023mg/L) and gentamycin (MIC: 0,19 mg/L). No ETEST was available for piperacillin-tazobactam, but the isolate was interpreted susceptible with a disk effusion zone diameter of 40 mm.
Next, the isolate was sent to the national reference laboratory at Statens Serum Institut (SSI) and whole-genome sequencing was performed on the Illumina NextSeq instrument using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, USA) to produce paired-end reads (2 x 150 bp). Raw reads were submitted to the SSI in-house QC pipeline (https://github.com/ssi-dk/bifrost), confirming the isolate asY. pseudotuberculosis and performing genome assembly into 477 contigs representing a genome size of 4,768,263 bp and a GC content of 47.78%. No acquired resistance genes were detected in the isolate by the QC pipeline.
By use of the MLST 2.0 webtool (available at: http://www.genomicepidemiology.org) the sequence type ST-43 was assigned using the Y. pseudotuberculosis scheme. In addition, the finding of monomicrobial infection with Yersinia species was confirmed using standard 16S/18S microbiome sequencing directly from the pus aspirate, and subsequently speciated as Y. pseudotuberculosis by a species-specific PCR (data not shown) to distinguish from the closeYersinia pestis , the causative agent of plague, and previously proven to be a recently emerged clone from Y. pseudotuberculosis .