Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence

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.

Epidemiology and Characteristics of Elizabethkingia spp. Infections in Southeast Asia

“…Elizabethkingia isolates are frequently resistant to aminoglycosides, macrolides, tetracycline, and vancomycin but show variable susceptibility to piperacillin, piperacillin-tazobactam, fluoroquinolones, minocycline, tigecycline, and trimethoprim-sulfamethoxazole [ 3 , 38 , 41 , 44 , 45 , 46 ]; cephalosporins, monobactams, and moderate susceptibilities to piperacillin [ 47 , 48 , 49 ], ceftazidime, colistin, and meropenem [ 50 ]; and levofloxacin [ 51 ]. There are currently no established MIC breakpoints for Elizabethkingia , and susceptibilities are largely reported based on Enterobacteriaceae breakpoints of the Clinical and Laboratory Standards Institute (CLSI) M100 guidelines and/or the European Committee on Antimicrobial Susceptibility Testing (EUCAST) pharmacokinetic–pharmacodynamic (PK–PD) “non-species” breakpoints [ 37 , 38 ].…”

Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan Valley

“…Bacterial whole genome sequencing followed by comparative genomic analysis also proved to be a necessary and sufficient procedure to distinguish between closely related bacterial species. 38 - 40 This approach will help improve our understanding and increase the discovery rate of new species in environmental samples.…”

Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission

“…are high at ∼25.2% in all species ( Seong et al., 2020 ) and higher in cases of septicaemia and meningitis at 54% for E. meningoseptica ( Moore et al., 2016 ) and 28.4% for E. anophelis infections ( Lin et al., 2018b ). Elizabethkingia pathogenesis is largely unknown, though several virulence factor homologs have been reported, including capsule proteins, adhesins, iron uptake proteins and proteins contributing to biofilm formation ( Chen et al., 2015 ; Janda and Lopez, 2017 ; Li et al., 2015 ; Liang et al., 2019 ).…”