“First Reported Case of Rapidly Progressive Pyogenic Liver Abscess with Isolation of Priestia megaterium : Case Report and Literature Review”

Abstract

Priestia megaterium (formerly Bacillus megaterium) is a Gram-positive, spore-forming environmental bacillus rarely associated with human infection. In this report, we present a case of a rapidly progressive polymicrobial pyogenic liver abscess with subsequent isolation of P. megaterium in a 69-year-old woman with type II diabetes mellitus, chronic kidney disease, metabolic liver disease, and extensive antibiotic allergies. She initially presented with progressive abdominal pain and fever, with negative early imaging studies. Three weeks later, computed tomography (CT) demonstrated new hepatic abscesses. Interventional radiology drainage cultures initially grew Streptococcus intermedius, guiding targeted antimicrobial therapy; however, the patient clinically deteriorated with recurrent abscess formation despite drainage and broad-spectrum coverage. Subsequent aspirate cultures from the abscess fluid later grew P. megaterium, though this result was finalized after the patient’s death on day 12 of admission despite intensive care and source control attempts. This case suggests that P. megaterium, traditionally regarded as nonpathogenic, may be recovered in severe infections in immunocompromised hosts; however, alternative explanations—including polymicrobial infection, antibiotic-mediated suppression of co-pathogens, iatrogenic introduction during drainage procedures, or culture contamination—must be carefully considered. Contributing factors likely included her underlying comorbidities, concurrent COVID-19 infection, delayed pathogen identification, and restrictions imposed by multiple drug allergies. Diagnostic challenges underscore the importance of repeated culture sampling, careful interpretation of microbiology results, and awareness of rare organisms when standard therapy is unsuccessful. This report expands the spectrum of diseases associated with P. megaterium. It emphasizes the need for multidisciplinary collaboration and heightened clinical vigilance in cases of rapidly progressive intra-abdominal infections that are unresponsive to conventional treatment.

Introduction

Liver abscesses are serious infections of the hepatic parenchyma, most commonly classified as pyogenic or amoebic. ¹ They can deteriorate rapidly, particularly in high-risk individuals. While enteric or streptococcal pathogens cause most cases, rare environmental organisms may also be implicated. Priestia megaterium (formerly Bacillus megaterium), a soil-dwelling Gram-positive bacillus usually regarded as nonpathogenic, has only rarely been associated with human disease. ²

To our knowledge, this represents the first reported case of a rapidly progressive pyogenic liver abscess (PLA) in which P. megaterium was isolated, occurring in a 69-year-old woman with multiple comorbidities and recent COVID-19 infection. Despite early drainage and antimicrobial therapy, her course was complicated by antibiotic allergies, initial misidentification of the pathogen, and eventual progression to refractory septic shock. This case highlights essential diagnostic and therapeutic challenges, emphasizes the role of early recognition and multidisciplinary care, and raises awareness of an unusual environmental pathogen with the potential for life-threatening infection.

Case Presentation

Our patient is a 69-year-old woman with a history of type 2 diabetes, hypertension, stage 3 chronic kidney disease, and metabolic liver disease. She presented with a 1-month history of gradually progressive right upper abdominal pain, associated with intermittent fever, chills, and vomiting for 5 days before presentation. She denied previous similar episodes, unintentional weight loss, changes in bowel habits, jaundice, or abdominal distension.

Three weeks earlier, she had been admitted to another hospital with similar abdominal pain and acute hypoxic respiratory failure secondary to COVID-19. At that time, computed tomography (CT) of the abdomen revealed a nodular liver contour suspicious for cirrhotic changes in the context of fatty liver disease, without masses, and gallbladder wall thickening with pericholecystic fat stranding, possibly reactive. A hepatobiliary iminodiacetic acid scan and magnetic resonance cholangiopancreatography were negative for cholecystitis. Her symptoms improved, and she was discharged home.

At presentation to our institution, she was febrile but hemodynamically stable and nonicteric. Physical examination revealed right upper quadrant tenderness without peritoneal signs; Murphy’s sign was negative. Laboratory results were notable for leukocytosis with neutrophilia, anemia, hypokalemia, hypoalbuminemia, elevated alkaline phosphatase, which was already elevated at the prior admission, and markedly elevated procalcitonin.

CT of the abdomen with contrast demonstrated 2 new right hepatic lobe lesions measuring 11.6 and 7.4 cm, with trace pericholecystic fluid and gallbladder hyperenhancement—findings absent on imaging performed 3 weeks earlier (Figure 1). The patient was admitted with a presumptive diagnosis of liver abscess. On hospital day 1, ultrasound-guided drainage was performed, and a catheter was left in situ. Empiric eravacycline was initiated, given her history of extensive antibiotic allergies, including penicillin, beta-lactams, vancomycin, and quinolones. After confirming prior ceftriaxone tolerance, therapy was switched to ceftriaxone and metronidazole on day 3 for broader coverage—a truncal rash developed by day 5, prompting re-initiation of eravacycline. Cultures from the initial drainage grew S. intermedius but did not alter management.

Figure 1.

CT abdomen and pelvis with contrast. Panels (B and D) show evidence of liver abscesses, which were not visible on panels (A and C) from the CT obtained 3 weeks earlier.

The patient was worked up for hepatic abscesses secondary to perforation due to acute/chronic cholecystitis. Clinical and laboratory findings were consistent with cholecystitis; however, ultrasonography revealed no findings suggestive of cholecystitis. The HIDA scan was also negative for acute cholecystitis. Repeat ultrasonography on day 7 was suspicious for recurrence of hepatic abscess. Triple phase CT scan of the abdomen was performed on day 8 of admission, which showed 2 new collections—subfascial in the anterior right lobe of liver, 2 cm × 5 cm × 4 cm, and an ill-defined lobulated collection in the medial aspect of the gallbladder, 3.4 cm × 3.5 cm, neither of which was covered by an in situ surgical drain. Drainage of the abscess was deferred due to the small size of the collections and the challenging anatomical location.

The patient acutely deteriorated with hemodynamic instability and worsening respiratory distress, necessitating transfer to the intensive care unit. Tobramycin and micafungin were added empirically, and vasopressor support was initiated. She subsequently required intubation. Repeat CT imaging demonstrated enlarging hepatic and perihepatic collections. On day 11, CT-guided drainage of the new collections was performed. Cultures from this procedure later grew P. megaterium, while all other cultures remained negative.

Despite maximal supportive care, including broad-spectrum antimicrobials, vasopressors, and renal replacement therapy, the patient progressed to refractory septic shock and ultimately succumbed to the disease the day following the second culture.

Discussion

Liver abscesses are defined as localized collections of pus within the hepatic parenchyma, typically arising from direct hepatic injury or the dissemination of intra-abdominal infections. ¹ They are conventionally classified as pyogenic or amoebic, with pyogenic abscesses representing the majority of cases. ¹ Entamoeba histolytica most commonly causes amoebic abscesses, whereas pyogenic abscesses are usually polymicrobial. ¹ The pathogens most frequently implicated in PLAs include Escherichia coli, Klebsiella spp., Streptococcus spp., Staphylococcus spp., and various anaerobic bacteria. ¹ Understanding the microbial spectrum is essential for guiding empiric therapy and optimizing patient outcomes.

To date, there are no published reports describing P. megaterium (formerly, Bacillus megaterium) as a primary or contributing organism in PLA, a bacterium commonly found in soil and other environmental sources. Nonetheless, P. megaterium has been implicated in other clinical infections, including soft tissue infections and brain abscesses.^2,3

PLAs can be life-threatening, with reported case fatality rates ranging from 3% to 30% globally. ⁴ In a 12-year retrospective study of 1572 patients with PLAs in China, 47% achieved complete recovery, 48.4% demonstrated clinical improvement, 3.2% remained uncured, and 1.3% died during hospitalization. ⁵ Prognosis depends on multiple factors, including patient demographics, underlying comorbidities, and initial clinical presentation. Nevertheless, with timely recognition and appropriate treatment, rapid progression to septic shock remains uncommon.

Here, we report a rapidly progressive PLA in which P. megaterium was isolated on repeat aspiration following initial growth of S. intermedius, highlighting diagnostic challenges related to polymicrobial infection, delayed organism identification, and antimicrobial limitations.

Priestia megaterium is a large, Gram-positive, rod-shaped, spore-forming aerobic bacillus that inhabits diverse environments but is most commonly associated with soil. ⁶ It is considered an essential industrial microorganism in enzyme production and biotechnology due to its ability to utilize various carbon sources and grow over a wide temperature range (3°C-45°C). ⁶ Although generally regarded as nonpathogenic, P. megaterium demonstrates notable resilience under environmental stress and antimicrobial pressure. A genome-wide transcriptome analysis in 2018 revealed that P. megaterium can withstand acidic stress through multiple adaptive mechanisms. More recently, a 2025 study identified “primed cells” in P. megaterium—subpopulations preadapted to enter a persisted state before exposure to lethal antibiotic stress—mirroring a phenomenon previously described in the Gram-negative bacterium E. coli. ⁷ These findings suggest that P. megaterium may persist under selective pressure and, in susceptible hosts, may contribute to opportunistic infection rather than acting as a primary pathogen.

Although rare, human infections have been documented. A 2020 case report described a soft tissue infection likely acquired through injury or wound penetration, which resolved completely following appropriate surgical intervention and antibiotic therapy. ² Additional reports include lamellar keratitis following ocular surgery in 2006 and primary cutaneous infection after skin microabrasions in 2011.^8,9 A brain abscess in 2015 secondary to chronic P. megaterium infection was reported in a patient with a history of psoriasis and syphilis. ³ More recently, a 2024 report documented pulmonary alveolar proteinosis associated with P. megaterium in a 58-year-old woman. ¹⁰

The microbiologic findings in this case raise important considerations regarding causality. The initial abscess aspirate grew S. intermedius, a well-established pathogen in PLA, while P. megaterium was isolated only on subsequent drainage after several days of targeted antimicrobial therapy. This temporal sequence suggests several plausible explanations: (1) the abscess was polymicrobial from the outset, with P. megaterium unmasked following suppression of Streptococcus spp.; (2) P. megaterium emerged as a secondary pathogen under antibiotic selection pressure; (3) the organism was introduced iatrogenically during percutaneous drainage or other invasive care; or (4) the isolate represented contamination rather than a true pathogen. Unfortunately, gram stain data and quantitative colony counts from the aspirates were unavailable, limiting definitive differentiation among these possibilities.

The exact route of P. megaterium dissemination leading to the development of PLA in this patient remains uncertain. Limited information regarding the patient’s social history precludes a definitive assessment of potential environmental exposures. By analogy to previously reported brain abscess cases, it is possible that P. megaterium entered the bloodstream via skin abrasions or penetrating injuries and subsequently seeded the liver.^2,3

In our patient, an alternative route of infection may have involved the gastrointestinal tract, supported by the concurrent COVID-19 infection, which is known to cause intestinal damage and hepatic injury.^11,12 The rapid progression from an unremarkable liver imaging study to a fully developed abscess within 3 weeks is atypical in the absence of common triggers such as intra-abdominal perforation or severe peritonitis. Previous reports classify PLAs developing within 3 months as rapidly progressive. ¹³ Thus, COVID-19-associated immune dysregulation, combined with diabetes, advanced age, and chronic kidney disease, may have facilitated rapid abscess evolution and impaired host defense, regardless of the specific microbial contributors. Immunosuppression is a significant predisposing factor for the persistence of P. megaterium within the host, as both the present case and the previously documented brain abscess occurred in immunocompromised individuals. ³

This case was particularly challenging due to the interplay of delayed diagnosis, recurrent collections, antimicrobial restrictions related to multiple drug allergies, and evolving microbiologic data. Repeated drainage and culture sampling were essential in reassessing the microbiologic landscape, notably when the clinical course failed to improve as expected. The identification of an uncommon environmental organism on repeat culture underscores the importance of cautious interpretation of culture results within a clinical context.

As a novel report of P. megaterium isolated from a PLA, culminating in septic shock and death, this case holds educational value by illustrating the complexity of polymicrobial intra-abdominal infections and the diagnostic uncertainty surrounding rare organisms. Rather than establishing P. megaterium as a definitive etiologic agent, this case emphasizes its potential role as a contributing or opportunistic organism in a vulnerable host.

This case illustrates that P. megaterium, though usually regarded as nonpathogenic, may be recovered in severe infections in immunocompromised individuals and should be interpreted cautiously rather than dismissed outright. It underscores the importance of early imaging, prompt source control, and close interdisciplinary collaboration among infectious disease, interventional radiology, and critical care teams. Clinicians should maintain a high index of suspicion for polymicrobial disease, reassess microbiologic data when clinical response is suboptimal, and remain mindful of rare organisms that may emerge under antimicrobial pressure.

Conclusion

This case broadens the understanding of P. megaterium by demonstrating that this common environmental organism may be associated with severe hepatobiliary sepsis in the setting of a complex, likely polymicrobial infection. In an elderly patient with diabetes, chronic kidney disease, liver disease, and concurrent COVID-19, a rapidly progressive PLA developed, initially yielding S. intermedius and later P. megaterium on repeat aspiration. The clinical course suggests a polymicrobial process, with the possibility that P. megaterium emerged under antibiotic pressure, was introduced during invasive procedures, or represented a true opportunistic pathogen rather than a sole causative agent. Diagnostic challenges included sequential isolation of different organisms, evolving radiographic findings, and restricted antimicrobial options due to extensive drug allergies. The rapid progression to fatal septic shock underscores the importance of cautious interpretation of culture results, recognition of potential polymicrobial disease, and consideration of rare or environmental organisms in patients who fail to improve with standard therapy. Timely identification, aggressive source control, repeat microbiologic evaluation, and prompt re-assessment are essential to improving outcomes in rapidly progressive PLAs.