Genomic features, phylogenetic relationships, and comparative genomics of Elizabethkingia anophelis strain EM361-97 isolated in Taiwan

Abstract

Elizabethkingia anophelis has become an emerging infection in humans. Recent research has shown that previous reports of E. meningoseptica infections might in fact be caused by E. anophelis. We aimed to investigate the genomic features, phylogenetic relationships, and comparative genomics of this emerging pathogen. Elizabethkingia anophelis strain EM361-97 was isolated from the blood of a cancer patient in Taiwan. The total length of the draft genome was 4,084,052 bp. The whole-genome analysis identified the presence of a number of antibiotic resistance genes, which corresponded with the antibiotic susceptibility phenotype of this strain. Based on the average nucleotide identity, the phylogenetic analysis revealed that E. anophelis EM361-97 was a sister group to E. anophelis FMS-007, which was isolated from a patient with T-cell non-Hodgkin's lymphoma in China. Knowledge of the genomic characteristics and comparative genomics of E. anophelis will provide researchers and clinicians with important information to understand this emerging microorganism.

Figure 1

Circular representation and subsystem category distribution of the genome of E. anophelis EM361-97. (A) Circles are numbered from 1 (the outermost circle) to 7 (the innermost circle). The outer four circles show the coding sequence (CDS), transfer ribonucleic acid (tRNA), ribosomal ribonucleic acid (rRNA), and open reading frame (ORF). The fifth circle represents the GC content (black). The sixth circle demonstrates the GC skew curve (positive GC skew, green; negative GC skew, violet). The genome position scaled in kb from base 1 is shown on the inner circle. (B) The genome of E. anophelis EM361-97 annotated using the Rapid Annotation System Technology (RAST) Server was classified into 356 subsystems and 27 categories. The green part in the bar chart at the leftmost position corresponds to the percentage of proteins included. The pie chart and the count of subsystem features in the right panel demonstrate the percentage distribution and category of the subsystems in E. anophelis EM361-97.

Figure 2

Proteome comparison among E. anophelis strains EM361-97 (origin, Taiwan), CSID_3015183681 (origin, USA), 3375 (origin, USA), V0378064 (E18064) (origin, Africa), and NUHP1 (origin, Singapore). The Venn diagram and bar chart represent the numbers of unique and shared orthologous genes of each strain.

Figure 3

Genomic comparison among Elizabethkingia species. (A) The genome of E. anophelis EM361-97 (center) compared to E. anophelis R26^T (the outermost circle; ring 1), E. bruuniana G0146^T (ring 2), E. meningoseptica KC1913^T (ring 3), E. miricola GTC 862 ^T (ring 4), E. occulta G4070^T (ring 5), and E. ursingii G4122^T (the innermost circle; ring 6). The genome of E. anophelis EM361-97 was highly similar to the type strain of E. anophelis R26^T. (B) The in silico DNA-DNA-hybridization (DDH) values between different strains calculated using the Genome-to-Genome Distance Calculator. The DDH value between E. anophelis EM361-97 and E. anophelis R26^T was 82%. Elizabethkingia meningoseptica KC1913^T demonstrated a relatively large phylogenetic distance from other strains of Elizabethkingia.

Figure 4

The phylogenetic tree of the 34 available strains of E. anophelis in GenBank based on average nucleotide identity (ANI) values. The phylogenetic analysis revealed that E. anophelis EM361-97 was a sister group to E. anophelis FMS-007, which was a clade sister of strains Po0527107 (E27017) and V0378064 (E18064) isolated in the Central African Republic.