We describe a 73-year-old patient who presented with progressively increasing lower back pain for the previous 1 month and fever for the last 1 week in October 2019. The medical history included surgery for coronary artery disease 13 years previously and hypertension under treatment. Radiographs showed multilevel degeneration in the lumbar spine and collapse of the L2-3 disc space with some local kyphosis (Fig. 1). Lumbar magnetic resonance imaging (MRI) showed paradiscal signal changes at L2-3 consistent with infection, in addition to a right-sided psoas abscess (Fig. 2). A clinical diagnosis of infective spondylodiscitis was made, and a CT-guided biopsy was performed (Fig. 3). The material was sent for aerobic and anaerobic culture. Further, Gene Xpert TB PCR was negative for Mycobacterium tuberculosis, while aspirate smears were also negative for acid-fast bacilli (AFB). Additionally, investigation of inflammatory markers showed C-reactive protein of 126 mg l-1, which is significantly higher than the normal level (<6 mg l-1).
The patient was followed up to 6 weeks. In view of the above, the patient was treated for suspected pyogenic spondylodiscitis by starting intravenous cloxacillin 2 g 6 hourly for 1 week. Consequently, after 48 h, scanty growth of fine colonies was seen in a blood agar plate (7 % defibrinated sheep blood used) incubated at 37  C. A Gram stain showed Gram-negative thin bacilli. A further organism sub-cultured on Campy BAP selective medium under microaerophilic conditions at 42  C for 24 h showed fine translucent colonies (Fig. 4). A Gram stain performed from the selective media showed Gram-negative thin bacilli with seagull appearance. The colonies were further subjected to matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) (,VITEK MS version 3.2, bioMerieux, Inc., Durham, NC, USA) and identified as C. fetus. Antimicrobial susceptibility testing could not be performed in this study as a viable isolate could not be cultured. After 1 week of treatment, the lower back pain reduced and the patient was able to sit and stand with support. Intravenous cloxacillin was given 2 g 6 hourly for another week. The patient was discharged on day 14 and advised to continue oral antibiotic cloxacillin 1 g 6 hourly for 4 weeks.
The isolate was subsequently subjected to whole-genome sequencing (WGS) to study the rare pathogen characteristics from the unusual site. Genomic DNA was purified from Campy BAP medium using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). WGS was performed with 400 bp read chemistry using an IonTorrent Personal Genome Machine (PGM) (Life Technologies, Carlsbad, CA, USA) as per the manufacturer's instructions. The reads were assembled and annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The genomic features of C. fetus sequenced in this study are given in Table 1. The species was confirmed as C. fetus subsp fetus using KmerFinder 3.2 (https://cge.cbs.dtu.dk/services/KmerFinder/) available at the Center for Genomic Epidemiology. Analysis of antimicrobial resistance mechanisms using ResFinder 4.1 (https://cge.cbs.dtu.dk/services/ResFinder/) showed that the isolate does not harbour any acquired genes or point mutation that confers resistance. Notably, mobile genetic elements were not found when screened using MobileElementFinder (https://cge.cbs.dtu.dk/services/MobileElementFinder/). The isolate was also negative for the cytolethal distending toxin (cdtA/B/C) gene when analysed. Further, multilocus sequence typing (MLST) analysis using MLSTFinder 2.0 (https://cge.cbs.dtu.dk//services/ MLST/) revealed that the isolate belongs to ST25.