Genomic insights of Pannonibacter phragmitetus strain 31801 isolated from a patient with a liver abscess

Abstract

Pannonibacter phragmitetus is a bioremediation reagent for the detoxification of heavy metals and polycyclic aromatic compounds (PAHs) while it rarely infects healthy populations. However, infection by the opportunistic pathogen P. phragmitetus complicates diagnosis and treatments, and poses a serious threat to immunocompromised patients owing to its multidrug resistance. Unfortunately, genome features, antimicrobial resistance, and virulence potentials in P. phragmitetus have not been reported before. A predominant colony (31801) was isolated from a liver abscess patient, indicating that it accounted for the infection. To investigate its infection mechanism(s) in depth, we sequenced this bacterial genome and tested its antimicrobial resistance. Average nucleotide identity (ANI) analysis assigned the bacterium to the species P. phragmitetus (ANI, >95%). Comparative genomics analyses among Pannonibacter spp. representing the different living niches were used to describe the Pannonibacter pan-genomes and to examine virulence factors, prophages, CRISPR arrays, and genomic islands. Pannonibacter phragmitetus 31801 consisted of one chromosome and one plasmid, while the plasmid was absent in other Pannonibacter isolates. Pannonibacter phragmitetus 31801 may have a great infection potential because a lot of genes encoding toxins, flagellum formation, iron uptake, and virulence factor secretion systems in its genome. Moreover, the genome has 24 genomic islands and 2 prophages. A combination of antimicrobial susceptibility tests and the detailed antibiotic resistance gene analysis provide useful information about the drug resistance mechanisms and therefore can be used to guide the treatment strategy for the bacterial infection.

Keywords: Pannonibacter phragmitetus; antibiotic resistance mechanism; comparative genomic analysis; genomic sequencing; pathogenesis.

Figure 1

Representation of the completed chromosome and plasmid of Pannonibacter phragmitetus 31801. Concentric rings, from outer to inner rings, represent the following features: in the clockwise or counterclockwise direction, the coding sequences (CDS) in light blue, rRNAs in pink, tRNAs brown; GC content (percentage) as a peak to valley profile in black; GC‐skew graph in purple and green

Figure 2

Phylogenetic placement of Pannonibacter phragmitetus strain 31801. (a) The genetic placement of P. phragmitetus strain 31801 (identity with *) based on 16S rRNA. Alignment of 16S rRNA sequences was conducted using ClustalW (Thompson, Higgins, & Gibson, 1994), and the tree was generated using the neighbor‐joining algorithm with 1,000 bootstraps, using MEGA 6.0. The corresponding GenBank accession numbers were indicated in parentheses. Rhodobacteraceae bacterium SH22‐2a was used as out‐group. (b) Phylogenetic tree inferred from concatenated genes. The tree is calculated from 1,125 core amino acids sequences per genome (15,750 core amino acid sequences). The accession numbers for selected genomes are P. phragmitetus 31801 (CP013068), P. phragmitetus CGMCC9175 (LGSQ01000001.1), P. phragmitetus DSM 14782 (NZ_KB908215.1), P. indicus 23407 (NZ_LIPT01000001.1), Polymorphum gilvum SL003B‐26A1 (NC_015259), Labrenzia aggregata IAM 12614 (NZ_AAUW00000000.1), and Brucella melitensis bv. 1 str. 16M (NZ_AHWC01000000)

Figure 3

Venn diagram and ANI analysis of representative Pannonibacter spp. and their relatives. (a) Heat map of ANI values among Pannonibacter spp. and their relatives. 31801 represents P. phragmitetus 31801 (CP013068), CGMCC9175 represents P. phragmitetus CGMCC9175 (LGSQ01000001.1), DSM 14782 represents P. phragmitetus DSM 14782 (NZ_KB908215.1), and DSM 23407 represents P. indicus 23407 (NZ_LIPT01000001.1), P.gil represents Polymorphum gilvum SL003B‐26A1 (NC_015259), L.agg represents Labrenzia aggregata IAM 12614 (NZ_AAUW00000000.1), and B.mel represents Brucella melitensis bv. 1 str. 16M (NZ_AHWC01000000). (b) Four representative genomes, P. phragmitetus 31801 (CP013068) and P. phragmitetus CGMCC9175 (LGSQ01000001.1), P. phragmitetus DSM 14782 (NZ_KB908215.1) and P. indicus (NZ_LIPT01000001.1) were selected to illustrate the Venn diagram. The Venn diagram was not drawn in proportion; its sole purpose is to illustrate the shared CDSs between the selected strains. The overlapping regions represent CDSs shared with respective strains. The number outside the overlapping regions indicates the number of CDSs in each genome without homologs in other genomes. ANI, average nucleotide identity

Figure 4

Subsystem distribution in different categories of Pannonibacter phragmitetus 31801. Subsystem coverage shows the total genes in the subsystems (49% in subsystems and 51% not in subsystems). Each part of the pie graph indicates different functions and proportions of genes. The numbers in parentheses show the counts of genes with specific functions

Figure 5

The gene organization of the predicted prophages in Pannonibacter phragmitetus 31801 chromosome. (a) The prophage 1 locates between 5,071,359 and 5,089,611 bp (18,253 bp); the GC content is 66.19%. The different colored rectangles indicate the different phage elements. (b) The prophage 2 locates between 622,766 and 633,573 bp (10,807 bp); the GC content is 64. 09%

Figure 6

Genomic islands predicted by IslandViewer 3 and the type IV secretion system in Pannonibacter phragmitetus 31801 chromosome. (a) Twenty‐four genome islands were predicted with the sizes ranging from 4,202 to 12,259 bp; the “conjugative plasmid”‐like regions (551,959–612,947 bp) span GI and GI4. (b) The putative genetic elements in T4SS shown on the top are Tra I, G, F, L, J, E, C, B, G; virB3 and virD2 are shown below. Their relative positions are shown