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Published on: December 23, 2022
Genomic insights of the emerging human pathogen Proteus appendicitidis sp. nov
Yao Peng1, Yanting Wang2, Xingxing Kang3
1Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, 518055, China.
Objectives:
Proteus are known as opportunistic human pathogens that can cause a variety of infections. Proteus appendicitidis is a novel Proteus species associated with appendicitis, whereas their genomic characteristics and virulence potential remain understudied. This study aims to compare the genomic features of P. appendicitidis to that of the close Proteus species, and to assess its virulence-factor encoding capacity as an emerging pathogen.
Methods:
Genomes similar to that of P. appendicitidis HZ0627T were retrieved from the PATRIC-v3.6.10 web-server using the implanted Similar Genome Finder tool. Average nucleotide identity (ANI) between HZ0627T and the retrieved genomes was calculated using FastANI-v1.33. Core-genome sequences were extracted using Roary-v3.13.0, and core-genomic tree was constructed using FastTree-v2.1.11. Virulence-factor encoding capacity was predicted using PathoFact-v1.0.
Results:
Two previously unclassified Proteus sp. strains were reclassified as P. appendicitidis. Strains phylogenomically close to P. appendicitidis were clustered into five species, three of which were previously categorized under P. vulgaris biogroup 3. Remarkably, Proteus genomosp. 6 was identified as the closest species to P. appendicitidis, exhibiting ANI values ranging from 94.45 % to 94.95 % against HZ0627T. Genome annotation revealed shared genomic features and antimicrobial resistance (AMR) genes between P. appendicitidis and its phylogenetic neighbors. Additionally, P. appendicitidis is hypothesized to share infection mechanisms with Proteus genomosp. 6, as evidenced by the encoding of numerous virulence factors implicated in cell lysis and membrane pore-formation in the genome of both species.
Conclusions:
This study provides genomic insights of P. appendicitidis sp. nov. and its taxonomic relatives, shedding light on their evolutionary relationships, pathogenic mechanisms, and AMR profiles. The findings are significant for the development of targeted therapeutic interventions against infections caused by this emerging pathogen.
Insights
This study reclassifies Proteus appendicitidis, revealing its close genomic relationship to Proteus genomosp. 6. Findings highlight shared virulence factors and antimicrobial resistance genes, crucial for understanding this emerging pathogen.
Area of Science:
- Microbiology
- Genomics
- Pathogen Discovery
Background:
- Proteus species are opportunistic human pathogens.
- Proteus appendicitidis is a novel species linked to appendicitis, but its genomics and virulence are understudied.
Purpose of the Study:
- To compare the genomic features of P. appendicitidis with related Proteus species.
- To assess the virulence-factor encoding capacity of P. appendicitidis as an emerging pathogen.
Main Methods:
- Genome retrieval and comparison using Similar Genome Finder and FastANI.
- Core-genome analysis and phylogenetic tree construction using Roary and FastTree.
- Virulence factor prediction using PathoFact.
Main Results:
- Two unclassified Proteus strains were reclassified as P. appendicitidis.
- Proteus genomosp. 6 was identified as the closest species to P. appendicitidis (94.45-94.95% ANI).
- Shared genomic features, AMR genes, and virulence factors (cell lysis, pore-formation) were identified between P. appendicitidis and Proteus genomosp. 6.
Conclusions:
- Genomic insights into P. appendicitidis and its relatives illuminate evolutionary paths, pathogenic mechanisms, and AMR profiles.
- Findings are vital for developing targeted therapies against P. appendicitidis infections.
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