Providencia pseudovermicola sp. nov.: redefining Providencia vermicola and unveiling multidrug-resistant strains from diabetic foot ulcers in Egypt
Date
2025-04-23
Journal Title
Journal ISSN
Volume Title
Type
Article
Publisher
BioMed Central Ltd
Series Info
BMC Microbiology ; Volume 25, Issue 1, December 2025 , Article number 238
Scientific Journal Rankings
Abstract
Background Providencia species are concerning due to their intrinsic resistance to colistin and tigecycline,
complicating the treatment of multidrug-resistant (MDR) infections.
Methods In the current study, two MDR isolates, DFU6 and DFU52T
, were recovered from infected diabetic foot
ulcers in Egypt in 2024. Following their initial identification as Providencia stuartii using VITEK® 2 and MALDI-TOF-MS,
the isolates were subjected to whole-genome sequencing via DNBseq.
Results While the 16S rRNA gene showed 100% similarity to that of Providencia vermicola, phylogenomic analysis
against the type strains in the TYGS database, including P. vermicola DSM 17385T
confirmed that these isolates
represent a distinct species within the genus, further supported by overall genome-relatedness indices (ORGIs).
This discrepancy prompted us to revise the taxonomy of all published genomes of P. vermicola strains (n=59) which
revealed misidentification of at least 56 strains that are unrelated to the type strain of this species. DFU6 and DFU52T
carried novel sequence types (ST29 and ST41, submitted to PubMLST) and harbored multiple resistance genes. Both
strains contained the qnrD1 gene on a small, non-mobilizable plasmid. DFU52T
possessed a conjugative plasmid
encoding blaCMY−6, blaNDM−1, rmtC, aac(6’)-Ib10, sul1, aph(3’)-Ia, and qacEΔ1. DFU6 carried an ISEcp1-associated
blaCTX−M−14, along with aadA, dfrA1, lnuF in a class 2 integron, and armA, msrE, and mphE on a resistance plasmid. Both
isolates also featured a pathogenicity island (PAI) integrated into the pheV gene with fimbriae-encoding genes.
Conclusion Following our reassessment of the taxonomic classification of all P. vermicola strains with published
genomes, we propose reclassifying certain strains, including DFU6 and DFU52T
, into distinct species for which we
propose the name Providencia pseudovermicola sp. nov. We recommend DFU52T
(=CCASU-2024-72) as the type strain
for the novel species. We also shed light on the public health threat of this novel species as a human pathogen that
harbours carbapenem and aminoglycoside resistance genes on mobile genetic elements.
Description
SJR 2024
1.032 Q1
H-Index
147
Keywords
ANI, dDDH, Diabetic foot ulcer, Multidrug resistance, OGRIs, Providencia pseudovermicola, Providencia vermicola, Providenciaspp, Taxonogenomics, Whole genome sequencing
Citation
Hamed, S. M., Darwish, M. M., Monir, R., Taweel, A. A., Ghanem, A. I., Hanna, I. N., & Amer, M. A. (2025). Providencia pseudovermicola sp. nov.: redefining Providencia vermicola and unveiling multidrug-resistant strains from diabetic foot ulcers in Egypt. BMC Microbiology, 25(1). https://doi.org/10.1186/s12866-025-03927-3