Crohn’s disease (CD) can involve any portion of the gastrointestinal tract, from the mouth to the anus. CD is also linked with extraintestinal manifestations (EIMs) beyond its mere gastrointestinal symptoms, which can involve the musculoskeletal system and other organ systems [¹]. Musculoskeletal symptoms are seen in more than half of the IBD patients and stand as one of the most frequent EIMs [²]. Arthralgia, i.e., pain in the joints, and peripheral arthritis, which more frequently affect large joints such as the knees and ankles, can be among them, as can axial involvement in the form of spondyloarthritis [⁴,⁵]. The shoulder can also be affected less frequently [³]. Although the exact pathophysiology of the majority of musculoskeletal EIMs is unknown, it is thought to include immunological dysregulation, genetics, and the interaction of systemic inflammation with gut microbiota [⁷]. In this case, the patient’s shoulder pain was initially misattributed to CD-related arthralgia, highlighting how immunosuppression can mask typical signs of infection, thereby delaying suspicion of osteomyelitis. Musculoskeletal manifestations in CD patients can have a significant negative impact on their quality of life and typically require a multidisciplinary management strategy.

Osteomyelitis is an infectious disease that results in an inflammatory bone and bone marrow condition induced by bacterial infection, leading to progressive bone destruction [⁶]. It can be either acute or chronic, and it is typically diagnosed based on a constellation of clinical symptoms, imaging studies (such as X-rays, MRIs, and CT scans), and laboratory results (including elevated inflammatory markers and positive blood cultures) [⁸]. In this case, diagnosis relied on MRI (T1 hypointensity, T2-STIR hyperintensity, post-contrast enhancement) and clinical course, as bone biopsy was deferred due to surgical risk in an immunocompromised patient [⁸,⁹]. A definitive diagnosis is the gold standard and typically includes a bone biopsy, histological study, and microbiological culture [⁹]. Osteomyelitis treatment is typically long-term and involves surgical debridement to remove infected or necrotic bone, along with long-term antibiotic treatment [¹⁰]. The antibiotics are chosen based on culture findings, as well as the patient’s specific characteristics. Here, vancomycin (1 g IV every 12 hours) was administered for 6 weeks based on MSSA susceptibility (MIC < 1 µg/mL), followed by oral levofloxacin for 4 weeks. In some instances, particularly in chronic osteomyelitis, surgery is necessary for the definitive removal of the infection [¹¹]. The duration of antibiotic treatment may vary, but it typically lasts weeks to months, depending on the seriousness and type of infection [¹²].

Staphylococcus aureus (S. aureus) is a common skin and nasal bacterium that is the leading cause of osteomyelitis [¹³]. S. aureus can produce infection of the bone by a variety of mechanisms, including hematogenous spread, direct inoculation (like trauma, surgery, or, in our patient, an unsterile injection), and contiguous spread from an infective overlying soft tissue infection [¹⁴]. Here, a contiguous spread from an injection-site abscess (MSSA, as indicated by wound culture collected prior to antibiotics) was likely, given the low local MRSA prevalence per hospital epidemiology. The ability of S. aureus to form biofilms on bone and medical devices, as well as its capacity to survive intracellularly within host cells, contributes to the recurrence and chronicity of osteomyelitis, making treatment challenging [¹⁵,¹⁶]. Initial antibiotic failure was likely due to inadequate duration and bone penetration, underscoring the need for early imaging. The presence of S. aureus in an abscess, especially in close proximity to bone, should raise a high suspicion of underlying osteomyelitis, particularly if this does not respond to standard treatment or if it is recurrent.

Patients with Crohn’s disease frequently require immunosuppressive medications, such as biologics and immunomodulators, to control their chronic inflammation [¹⁷]. While these medications are quite efficient at controlling disease activity, they do increase the patient’s vulnerability to infections from bacterial, viral, and fungal pathogens [¹⁸]. The nature and severity of immunosuppression vary depending on the drug and combination therapy used. For example, anti-tumor necrosis factor (TNF) medications, which are routinely used in CD, can impede the immune system’s ability to generate an effective response to infections, including those caused by S. aureus [¹⁹]. In this case, adalimumab was paused after the diagnosis of an abscess and restarted 3 months after antibiotic completion, following consultations with infectious disease and gastroenterology specialists who confirmed resolution of the infection (CRP <10 mg/L, no fever). This increased risk of infection necessitates careful monitoring and a heightened awareness of potential infectious complications, as infections in immunocompromised patients can present atypically and progress rapidly. The interruption of immunotherapy, as occurred in this case, is a common practice when an infection is suspected or confirmed. Still, it also highlights the delicate balance between controlling the underlying disease and mitigating the risk of infection.

The spread from soft tissue infection, i.e., abscess, to osteomyelitis is a well-documented process when infection is not managed or is managed improperly, or if it occurs in very close proximity to bone [²⁰]. An abscess at the deltoid injection site likely seeded the humerus via contiguous spread, exacerbated by immunosuppression. In immunocompromised individuals, this can be even quicker and insidious due to a weakened immune response. An abscess, which is a localized collection of pus, can exert pressure on adjacent bone, leading to local ischemia and creating an environment conducive to bacterial invasion of the bone tissue. Furthermore, bacteria from the abscess can directly spread into the bone through microtrauma or through pre-existing vascular channels. The acute management of the abscess, although mandatory, may not always eradicate all of the bacteria, especially if the infection has already begun to involve the bone. Red flags (persistent pain for more than 72 hours, CRP 80 mg/L, and new numbness) were ignored, delaying the MRI; a safety-net checklist should have prompted faster imaging [²¹] (Table 3).

Persistent pain and new neurological symptoms of numbness are critical red flag signs that should be further investigated with further workup for deeper, more serious infections such as osteomyelitis, even if imaging was initially negative or inconclusive. This case exemplifies how a seemingly localized infection can escalate to a severe bone infection, especially in a vulnerable patient population.

This case exemplifies the complexity of clinical reasoning, as well as the crucial role of medical education in teaching critical thinking and a willingness to question assumptions. Clinical reasoning is an interactive process of data collection, hypothesis generation, and hypothesis testing, which is typically conducted under conditions of uncertainty [²²]. Although experience is beneficial, it can also lead to cognitive biases, such as anchoring bias (overreliance on initial information) and confirmation bias (seeking information that confirms preconceived views) [²³]. In this case, the attending physician, perhaps fixated on the initial diagnosis of a soft tissue infection and subsequent abscess drainage, may have overlooked the possibility of a deeper, more severe infection, blaming the patient’s persistent symptoms on expected post-surgical complications. Anchoring on post-operative complications and confirmation bias delayed MRI; diagnostic time-outs and trainee escalation pathways could mitigate such errors [²³]. This demonstrates a typical weakness in medical practice: the tendency to prematurely stop a diagnostic investigation when a plausible explanation is available, even if it does not fully account for all of the patient’s symptoms. The medical student with a fresh perspective was able to synthesize the evolving clinical picture—the patient’s immunocompromised state, the S. aureus infection, the persistent and worsening pain despite antibiotic treatment, and the new neurological symptoms—to propose an alternative, more severe diagnosis. This highlights the importance of creating an environment in medical school where students feel empowered to express their findings and hypotheses, even if they disagree with those of their superiors. Effective medical education entails more than just imparting knowledge; it also includes cultivating diagnostic curiosity, supporting a systematic approach to problem solving, and developing the courage to challenge. Although the student’s suggestion was initially rejected, it ultimately proved accurate, highlighting the possibility that insightful information can come from all levels of the medical hierarchy. This instance supports the ideas that responsiveness to different viewpoints is crucial for the best possible patient outcomes and that learning in medicine is an ongoing, team-based process.