Comparative genomic analysis of malaria mosquito vector-associated novel pathogen Elizabethkingia anophelis

Abstract

Acquisition of Elizabethkingia infections in intensive care units (ICUs) has risen in the past decade. Treatment of Elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. Elizabethkingia infections have long been attributed to Elizabethkingia meningoseptica. Recently, we used whole-genome sequencing to reveal that E. anophelis is the pathogenic agent for an Elizabethkingia outbreak at two ICUs. We performed comparative genomic analysis of seven hospital-isolated E. anophelis strains with five available Elizabethkingia spp. genomes deposited in the National Center for Biotechnology Information Database. A pan-genomic approach was applied to identify the core- and pan-genome for the Elizabethkingia genus. We showed that unlike the hospital-isolated pathogen E. meningoseptica ATCC 12535 strain, the hospital-isolated E. anophelis strains have genome content and organization similar to the E. anophelis Ag1 and R26 strains isolated from the midgut microbiota of the malaria mosquito vector Anopheles gambiae. Both the core- and accessory genomes of Elizabethkingia spp. possess genes conferring antibiotic resistance and virulence. Our study highlights that E. anophelis is an emerging bacterial pathogen for hospital environments.

Keywords: Elizabethkingia; comparative genomics; pan/core-genomes.

Fig. 1.—

A phylogenetic tree showing the 12 Elizabethkingia spp. This phylogenetic tree was produced by pair-wise genome comparisons by Progressive Mauve.

Fig. 2.—

SNP distance matrix among the 12 Elizabethkingia spp. SNP difference between each pair of Elizabethkingia spp. was calculated by using the snpTree web server.

Fig. 3.—

Sequence comparison by alignment. The Elizabethkingia anophelis NUHP1 strain (red arc) was aligned against: E. anophelis R26 strain (blue arc), E. anophelis Ag1 (orange arc), E. meningoseptica ATCC 12535 (NITE) (yellow arc), and E. meningoseptica 502 (light green arc). Colored links between contigs represent homologous regions spanning: 10²–10³ bp (green), 10³–10⁴ bp (blue), and above 10⁴ bp (red). The presence of red links between the NUHP1 strain and E. anophelis R26, Ag1 contigs, and E. meningoseptica 502 contigs indicate a high degree of similarity between these genomes.

Fig. 4.—

Curves for the core-genomes, pan-genomes, and numbers of new genes of the 12 Elizabethkingia spp.

Fig. 5.—

The identified EM-only and EA-only proteins were assigned to Clusters of Orthologous Groups (COGs). The y axis indicates the percentage of genes in a specific function cluster out of the total numbers of EM-only and EA-only proteins, respectively. *The abundances of specific function clusters were compared statistically as described in Rodriguez-Brito et al. (2006) and Allen et al. (2009) using a subsample size of 500 and 1,000 bootstrap replicates at a statistical confidence of 99%.