Development of a Providencia stuartii multilocus sequence typing scheme

Gabriele Arcari; Alice De Francesco; Riccardo Polani; Alessandra Carattoli; Valerio Capitani

doi:10.3389/fmicb.2024.1493621

Development of a Providencia stuartii multilocus sequence typing scheme

Front Microbiol. 2024 Oct 31:15:1493621. doi: 10.3389/fmicb.2024.1493621. eCollection 2024.

Authors

Gabriele Arcari^{1

2}, Alice De Francesco³, Riccardo Polani³, Alessandra Carattoli³, Valerio Capitani⁴

Affiliations

¹ Department of Medicine and Technological Innovation, University of Insubria, Varese, Italy.
² Ospedale di Circolo e Fondazione Macchi, Laboratory of Medical Microbiology and Virology, Varese, Italy.
³ Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.
⁴ Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.

Abstract

Introduction: The Providencia genus is assuming greater clinical relevance among infections caused by Enterobacterales also because of its intrinsic and acquired resistance to last-resort antibiotics. However, despite having been known and studied for over 50 years, genomics and taxonomy of the Providencia genus are currently undergoing a deep rearrangement. In this study we aim to outline and characterized the P. stuartii species.

Methods: We retrieved from the GenBank database all genomes labelled as Providencia and performed a comprehensive genome-based species definition founded on average nucleotide identity (ANI) and on alignment-free approaches.

Results: After defining the genomes assuredly identifiable as P. stuartii, we devised a MultiLocus Sequence Typing (MLST) and a core-genome MLST (cgMLST) schemes, based on 7 and 2,296 loci respectively.

Discussion: This work hence provides a framework for understanding the role of P. stuartii and of other members of this genus, which should be considered as emerging multidrug-resistant pathogens.

Keywords: MLST; Providencia stuartii; allele; gene; phylogenomics.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This research was supported by the European Union funding A. C. from the NextGeneration EU-MUR PNRR Extended Partnership Initiative on Emerging Infectious Diseases (project no. PE00000007, PE13 INF-ACT, Spoke 3). R. P. was supported by the PNRR PHD scholarship (EX M.D. 351/22) financed by the Rome Technopole project.