In April 2023, a 78-year-old Caucasian Swiss-born woman was admitted due to 10 kg weight loss, weakness, and intermittent night sweats that began in October 2022, progressively intensifying over subsequent months. Her medical history included a diagnosis of seronegative rheumatoid polyarthritis in November 2019, initially treated with methotrexate and subsequently leflunomide. In September 2021, leflunomide was discontinued due to persistent symptoms of polyarthritis, and adalimumab was started. Before immunosuppressive treatment in November 2019, the patient tested negative for interferon-gamma release assay (IGRA; QuantiFERON-TB-Gold plus), had a slightly reduced lymphocyte count of 700/µL and an unremarkable chest x-ray.

The work-up in April 2023 revealed heterogeneous echogenicity of the spleen. In Mai 2023, disseminated hypodense, intensely hypermetabolic splenic lesions, hypermetabolic hepatic lesions, small hypermetabolic bilateral pulmonary nodules, and intensely hypermetabolic lymph nodes at the hepatic hilus were observed in a positron emission tomography-computed tomography (PET-CT) scan (Fig. 1a). A biopsy of the hypermetabolic splenic lesions revealed non-necrotizing granulomatous splenitis (Fig. 1b). Polymerase chain reaction (PCR) targeting deoxyribonucleic acid (DNA) for mycobacteria species, M. tuberculosis and panfungal PCR from the formalin-fixed biopsy material yielded negative results.

Radiological and histopathological findings. a PET scan showing disseminated hypodense, intensely hypermetabolic splenic lesions and two focal hypermetabolic areas in segments VIII (arrow) and III (*) of the liver. b Histopathologic findings in a splenic biopsy showing a granulocyte-admixed, vague granulomatous reaction (in-between arrows) with a giant cell (*) without necrosis (100x, hematoxylin and eosin stain). c Histopathologic findings in a liver biopsy showing granulomatous hepatitis with multiple rather small non-necrotizing granulomas (in-between arrows located in portal and lobular areas, consisting of lymphocytes, epithelioid and giant cells (40x, hematoxylin and eosin stain)

In June 2023, the patient was again hospitalised due to deteriorating general condition, characterised by hypercalcaemia and acute renal failure. Upon suspicion of sarcoidosis, systemic corticosteroid therapy was initiated with subsequent clinical improvement. Further assessments for suspected sarcoidosis showed elevated angiotensin converting enzyme of 89 U/L, elevated soluble IL-2- receptor of 1996 pg/ml and elevated neopterin of 22.3 ng/ml. Due to low absolute lymphocyte numbers, the CD4:CD8 ratio from the broncho-alveolar lavage was inconclusive. Cultures for mycobacteria from the broncho-alveolar lavage were negative. Imaging showed no hilar adenopathy and biopsy of a hilar lymph node showed unspecific changes, i.e. lack of granulomas.

Serological investigations for the following infectious agents returned negative results: Treponema pallidum, human immunodeficiency virus, Bartonella henselae, Coxiella burnetii, Francisella tularensis, Brucella spp., and dimorphic fungi. A second IGRA (T-SPOT.TB) was clearly positive (ESAT-6 > 20, CFP-10 > 20). The lymphocyte count at that time was 770/µL. In May 2023, a biopsy of a hypermetabolic liver lesions seen in the PET-CT was taken to exclude a potential mycobacterial infection and revealed non-necrotizing granulomatous hepatitis (Fig. 1c). Due to the formalin fixation of the biopsy, mycobacterial culture was not performed, and PCR targeting DNA for mycobacteria species and for M. tuberculosis was negative. Blood cultures for mycobacteria were negative. Nevertheless, due to the differential diagnosis of mycobacterial infection, immunosuppression with steroids was gradually tapered and adalimumab was stopped in August 2023. Hypercalcaemia and renal failure recurred in September 2023. Treatment with steroids and adalimumab was re-initiated. One month later, in October 2023, the patient was readmitted for fever, dyspnoea, general weakness, disorientation and confusion. A computed tomography scan of the lung showed new bilateral infiltrates. Concurrently, one early-morning urine cultures for mycobacteria collected in September showed growth of MTBC. A repeated bronchoalveolar lavage showed acid-fast bacilli with PCR positive for MTBC, leading to the diagnosis of disseminated TB. Definitive culture results revealed M. bovis. Retrospectively, the patient reported that she had grown up and worked on a farm until about 30–40 years ago, where she drank unpasteurised cow milk, potentially exposing herself to M. bovis. Extensive medical history taking did not reveal any more recent potential exposures to M. bovis and the clinical course is consistent with an oral route of infection.

Standard treatment with rifampicin, isoniazid, ethambutol, and pyrazinamide was initiated. After identification of M. bovis, pyrazinamide was stopped. The patient, however, developed severe hepatitis, leading to a stop of the anti-tuberculosis therapy. After improvement of liver values, we restarted the therapy sequentially, first with rifampicin and then with isoniazid and ethambutol. Unfortunately, liver values increased again, leading us to replace isoniazid by moxifloxacin and switch rifampicin to rifabutin. However, the hepatopathy worsened, leading to complete treatment cessation after six weeks, considering the patient’s informed decision not to continue the therapy at this point. The patient passed away in November 2023.

Using validated bioinformatic pipelines [3], the whole genome sequence (Illumina based sequenced) of the cultured isolate was determined to belong to the animal lineage La1.2 (raw sequencing data are available at European Nucleotide Archive under the accession number PRJEB75913) [4]. To contextualize this finding with previously isolated M. bovis strains from Switzerland and other countries, a total of 350 genomes covering the currently known 8 lineages of M. bovis were obtained from public repositories. Figure 2 shows the overall single-nucleotide polymorphism(SNP)-based phylogenetic tree including the patient’s M. bovis sequence and five previously sequenced genomes from Swiss cattle and one human patient obtained between 2000 and 2014. Notably, all Swiss M. bovis sequences belong to the La1.2 lineage, one of the main genotypes circulating in continental Europe. However, the sequence from the present study was genetically distant (approximately 330–450 SNPs) from previously sequenced Swiss M. bovis strains from cattle [5].

Maximum-likelihood phylogenetic tree generated with the GTR-CAT substitution model including the whole genome sequence of the M. bovis isolate cultured from a urine sample of a Swiss patient, is presented. A total of 350 sequences representing the currently known 8 lineages of M. bovis are color-coded, and the country of origin of the isolates identified as La1.2 is reported. The tree was rooted using Mycobacterium caprae, and the bar scale represents the number of substitutions per site