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.