Sepsis caused by two Phytobacter species: clinical cases and polyphasic characterization of an emerging Enterobacteriaceae

Background Phytobacter spp., a recently recognized human pathogen, presents significant diagnostic challenges. Conventional biochemical and automated identification methods often fail to distinguish Phytobacter from other Enterobacterales , which hinders accurate diagnosis and may potentially delay appropriate treatment. Since 2018, our state public health laboratory (LACEN-PR) has adopted a polyphasic identification strategy, integrating matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, API 20E, targeted quantitative PCR, and whole-genome sequencing to investigate closely related Enterobacterales isolates that were initially misidentified and subsequently confirmed as Phytobacter spp. This study reports three cases of Phytobacter -associated sepsis, including a putative novel Phytobacter species and the first documented case of bla NDM -positive Phytobacter ursingii . Case Summary Case 1: A 31-year-old man living with HIV developed sepsis following respiratory failure. Initial testing misidentified the isolate as Leclercia adecarboxylata , but the polyphasic approach revealed the potential for a novel Phytobacter species. The patient showed clinical improvement following targeted antimicrobial therapy. Case 2: A 50-year-old trauma patient developed sepsis caused by a Phytobacter spp. The isolate was closely related to that of Case 1. Despite treatment, he succumbed to the infection. Case 3: A 68-year-old woman with multiple comorbidities who developed septic shock. Blood cultures identified bla NDM -positive Phytobacter ursingii . The patient did not survive. Conclusion These cases underscore the clinical significance of Phytobacter spp. as an emerging pathogen and highlight the challenges posed by their misidentification. The discovery of a novel species and multidrug-resistant P. ursingii highlights the need for improved diagnostic accuracy and effective treatment to enhance surveillance and improve patient outcomes.