Hamed Samira M, Darwish Manal M, Monir Reham, Taweel Ahmed Al, Ghanem Ayat I, Hanna Ihab N, Amer Mai A
Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt.
Medical Microbiology and Immunology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
BMC Microbiol. 2025 Apr 23;25(1):238. doi: 10.1186/s12866-025-03927-3.
Providencia species are concerning due to their intrinsic resistance to colistin and tigecycline, complicating the treatment of multidrug-resistant (MDR) infections.
In the current study, two MDR isolates, DFU6 and DFU52, 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.
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 17385 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 DFU52 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. DFU52 possessed a conjugative plasmid encoding bla, bla, rmtC, aac(6')-Ib10, sul1, aph(3')-Ia, and qacEΔ1. DFU6 carried an ISEcp1-associated bla, 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.
Following our reassessment of the taxonomic classification of all P. vermicola strains with published genomes, we propose reclassifying certain strains, including DFU6 and DFU52, into distinct species for which we propose the name Providencia pseudovermicola sp. nov. We recommend DFU52 (= 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.
普罗威登斯菌属因其对黏菌素和替加环素的固有耐药性而令人担忧，这使得耐多药（MDR）感染的治疗变得复杂。
在本研究中，2024年从埃及感染的糖尿病足溃疡中分离出两株耐多药菌株DFU6和DFU52。使用VITEK® 2和MALDI-TOF-MS初步鉴定为斯氏普罗威登斯菌后，通过DNBseq对这些菌株进行全基因组测序。
虽然16S rRNA基因与弗氏普罗威登斯菌的基因显示出100%的相似性，但在TYGS数据库中针对包括弗氏普罗威登斯菌DSM 17385在内的模式菌株进行的系统基因组分析证实，这些分离株代表了该属内的一个独特物种，总体基因组相关性指数（ORGIs）进一步支持了这一点。这种差异促使我们修订了所有已发表的弗氏普罗威登斯菌菌株（n = 59）基因组的分类学，结果显示至少56株与该物种的模式菌株无关的菌株被错误鉴定。DFU6和DFU52携带新的序列类型（ST29和ST41，已提交至PubMLST）并含有多个耐药基因。两株菌株在一个小的、不可移动的质粒上都含有qnrD1基因。DFU52拥有一个接合质粒，编码bla、bla、rmtC、aac(6')-Ib10、sul1、aph(3')-Ia和qacEΔ1。DFU6在一个2类整合子中携带一个与ISEcp1相关的bla，以及aadA、dfrA1、lnuF，在一个耐药质粒上携带armA、msrE和mphE。两株分离株还具有一个整合到pheV基因中的致病岛（PAI），带有编码菌毛的基因。
在我们重新评估了所有已发表基因组的弗氏普罗威登斯菌菌株的分类学之后，我们建议将某些菌株，包括DFU6和DFU52，重新分类为一个独特的物种，我们提议将其命名为新种假弗氏普罗威登斯菌。我们推荐DFU52（= CCASU-2024-72）作为该新物种的模式菌株。我们还揭示了这种新物种作为一种携带碳青霉烯类和氨基糖苷类耐药基因的移动遗传元件的人类病原体对公共卫生的威胁。
