Abstract
Bacteria of the genus Elizabethkingia are emerging infectious agents that can cause infection in humans. The number of published whole-genome sequences of Elizabethkingia is rapidly increasing. In this study, we used comparative genomics to investigate the genomes of the six species in the Elizabethkingia genus, namely E. meningoseptica, E. anophelis, E. miricola, E. bruuniana, E. ursingii, and E. occulta. In silico DNA–DNA hybridization, whole-genome sequence-based phylogeny, pan genome analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, and clusters of orthologous groups were evaluated. Of the 86 whole-genome sequences available in GenBank, 21 were complete genome sequences and 65 were shotgun sequences. In silico DNA–DNA hybridization clearly delineated the six Elizabethkingia species. Phylogenetic analysis confirmed that E. bruuniana, E. ursingii, and E. occulta were closer to E. miricola than to E. meningoseptica and E. anophelis. A total of 2,609 clusters of orthologous groups were identified among the six type strains of the Elizabethkingia genus. Metabolism-related clusters of orthologous groups accounted for the majority of gene families in KEGG analysis. New genes were identified that substantially increased the total repertoire of the pan genome after the addition of 86 Elizabethkingia genomes, which suggests that Elizabethkingia has shown adaptive evolution to environmental change. This study presents a comparative genomic analysis of Elizabethkingia, and the results of this study provide knowledge that facilitates a better understanding of this microorganism.
Highlights
With advances in molecular biology and biotechnology, whole-genome sequencing has become a popular technique in microbiology research
E. miricola strain EM798-26 has been re-classified as E. bruuniana according to the whole-genome analysis[17,18]
Scaffolds and contigs were generated for the E. anophelis strain EM361-9715, and the complete whole-genome sequence of the E. bruuniana strain EM798-26 was constructed[16,17]
Summary
With advances in molecular biology and biotechnology, whole-genome sequencing has become a popular technique in microbiology research. Whole-genome sequences of microbes can provide comprehensive information on virulence factors, pathogenesis, drug resistance, metabolism, host–pathogen interaction, host–environment reaction, and others. We previously published whole-genome sequences for two Elizabethkingia species: E. anophelis (strain EM361-97; GenBank accession number, LWDS00000000)[15] and E. miricola (strain EM798-26; GenBank accession number, CP023746)[16]. E. miricola strain EM798-26 has been re-classified as E. bruuniana according to the whole-genome analysis[17,18]. Few studies have investigated the comparative genomics of the six species in the Elizabethkingia genus.
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