Genomic and Pan-Genomic Characterization of Elizabethkingia meningoseptica Reveals Resistance Gene Profiles, Phylogenetic Clusters, and Functional Landscape.

Abstract

Elizabethkingia meningoseptica (E. meningoseptica) is a significant pathogen associated with various infections. This study aimed to analyze the general molecular and pan-genomic characteristics of E. meningoseptica. The 104 E. meningoseptica genomes were retrieved from NCBI, annotated using Prokka, and screened for antibiotic resistance genes via ABRicate. Core-genome single-nucleotide polymorphisms (SNPs) were identified using Parsnp, with phylogenetic trees constructed. Pan-genomic analysis employed BPGA for gene clustering at 80% identity, supplemented by COG and KEGG functional annotations. Among the 104 sequences, 86 were from human sources, 12 from nonhuman sources, and 6 had unknown origins. Phylogenetic analysis classified the strains into three clades (A, B, and C), with 95 strains (91.3%) in clade C. Nineteen resistance genes were identified, with 11 being carbapenem-resistance genes. Significant differences in the distribution of resistance genes were observed between human and non-human sources. Pan-genomic analysis revealed 8856 genes in total, including 2267 core genes, 4052 accessory genes, and 2537 unique genes. The median genomic G + C content was 36.9% (36.8%-37.0%). The pan-genome was still open but approaching closure. In COG functional classification, significant differences were found in "Information storage and processing", "cellular processes and signaling" and "Metabolism" between core genes and accessory/unique genes. Similar significant differences were also observed in KEGG functional classification, especially in Cellular Processes, Human Diseases, and Metabolism. This study provides valuable insights into the genomic characteristics of E. meningoseptica, which can contribute to understanding its evolution, pathogenicity, and drug resistance mechanisms.