Providencia pseudovermicola sp. nov.: redefining Providencia vermicola and unveiling multidrug-resistant strains from diabetic foot ulcers in Egypt

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.