doi: 10.3967/bes2023.040
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Abstract:
Objective A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in Proteus mirabilis. Methods In this work, we propose a publicly available cgMLST scheme for P. mirabilis using chewBBACA. In total 72 complete P. mirabilis genomes, representing the diversity of this species, were used to set up a cgMLST scheme targeting 1,842 genes, 635 unfinished (contig, chromosome, and scaffold) genomes were used for its validation. Results We identified a total of 205 CGs from 695 P. mirabilis strains with regional distribution characteristics. Of these, 159 unique CGs were distributed in 16 countries. CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes. Nine virulence genes (papC, papD, papE, papF, papG, papH, papI, papJ, and papK) related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20. These CGs require attention due to potential risks. Conclusion This research innovatively performs high-resolution molecular typing of P. mirabilis using whole-genome sequencing technology combined with a bioinformatics pipeline (chewBBACA). We found that the CGs of P. mirabilis showed regional distribution differences. We expect that our research will contribute to the establishment of cgMLST for P. mirabilis. -
Key words:
- Proteus mirabilis /
- CgMLST /
- Genotyping /
- Clonal evolution /
- ChewBBACA
注释:1) CONFLICT OF INTEREST: -
Figure 1. Characterization of the P. mirabilis isolates included in this study. (A) Hosts of isolated P. mirabilis. “Others” represents host types with only one strain. (B) Geographic distribution of available genomes. “Others” represents countries with less than five strains. (C) Isolation source distribution of isolates. “Others” represents sources with less than eight strains. (D) Temporal distribution of P. mirabilis isolates. “Others” represents years when less than two strains were collected.
Figure 4. Minimum spanning tree (MST) of CGs generated using the 695 P. mirabilis strains based on the cgMLST scheme. Due to the limitation of the visualization of the MST, only the CG types containing the top 30 strains are displayed. “Others” represents the CG types containing less than five strains.
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22263Supplementary Materials.pdf