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 .