Whole genome sequencing of an ExPEC that caused fatal pneumonia at a pig farm in Changchun, China

Abstract

Background: In recent years, highly frequent swine respiratory diseases have been caused by extraintestinal pathogenic Escherichia coli (ExPEC) in China. Due to this increase in ExPECs, this bacterial pathogen has become a threat to the development of the Chinese swine industry. To investigate ExPEC pathogenesis, we isolated a strain (named SLPE) from lesioned porcine lungs from Changchun in China, reported the draft genome and performed comparative genomic analyses.

Results: Based on the gross post-mortem examination, bacterial isolation, animal regression test and 16S rRNA gene sequence analysis, the pathogenic bacteria was identified as an ExPEC. The SLPE draft genome was 4.9 Mb with a G + C content of 51.7%. The phylogenomic comparison indicated that the SLPE strain belongs to the B1 monophyletic phylogroups and that its closest relative is Avian Pathogenic Escherichia coli (APEC) O78. However, the distribution diagram of the pan-genome virulence genes demonstrated significant differences between SLPE and APEC078. We also identified a capsular polysaccharide synthesis gene cluster (CPS) in the SLPE strain genomes using blastp.

Conclusions: We isolated the ExPEC (SLPE) from swine lungs in China, performed the whole genome sequencing and compared the sequence with other Escherichia coli (E. coli). The comparative genomic analysis revealed several genes including several virulence factors that are ExPEC strain-specific, such as fimbrial adhesins (papG II), ireA, pgtP, hlyF, the pix gene cluster and fecR for their further study. We found a CPS in the SLPE strain genomes for the first time, and this CPS is closely related to the CPS from Klebsiella pneumoniae.

Keywords: ExPEC; Genome; Pigs; Pneumonia.

Fig. 1

Histological preparation of swine lungs (haematoxylin and eosin). Note the presence of inflammatory cells in the bronchioles (a) and the surrounding alveoli (b)

Fig. 2

Phylogenomic tree of the 43 E. coli strains. Blastp, perl, mcl, clustalW and MEGA were used to reconstruct the phylogenomic tree. The phylogenomic tree of different E. coli based on the comparison of 2043 core genes. The 43 E. coli strains are divided into five monophyletic phylogroups (A, B1, B2, D and E). The SLPE strains are highlighted in blackbody. SLPE is the closest relative to APEC 078

Fig. 3

The distribution diagram of the pan-genome virulence genes among 43 E. coli strains. The right side of the vertical line shows E. coli strains that are consistent with the phylogenetic tree (Figure 2) with the following labels: (1) B1 monophyletic phylogroup, blue; (2) A monophyletic phylogroup, red; (3) E monophyletic phylogroup, green; (4) D monophyletic phylogroup, cyan and (5) B2 monophyletic phylogroup, purple. The SLPE strains are highlighted with the key symbol. The top shows the following six classified clusters: (1) fimbrial/adhesin, blue; (2) iron acquisition/exporting protein, green; (3) toxin/invasin, red; (4) capsule synthetic gene cluster, brown; (5) protectins, yellow and (6) others, purple. The red and black bodies show the distribution of the virulence genes among these strains. A red side implies that the virulence genes are present, while the black side implies that the genes are absent

Fig. 4

The genetic context for seven different types of capsular polysaccharide synthesis gene clusters. Shaded areas show conservative genes. Arrows represent the coding sequences and indicate the direction of transcription. The percentage under arrow represents the G/C content of the gene