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. 2020 Jun 1;96(6):fiaa088.
doi: 10.1093/femsec/fiaa088.

Whole genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter

Ingvild Falkum Ullmann  1 , Anders Benteson Nygaard  1 , Hege Smith Tunsjø  1   2 , Colin Charnock  1
Affiliations

Whole genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter

Ingvild Falkum Ullmann et al. FEMS Microbiol Ecol. .

Abstract

A total of four strains of the 'environmental superbug' Pedobacter isolated from sludge produced at Norwegian drinking water treatment plants, were characterized by whole genome sequencing and antibiotic susceptibility assays. As with previous studies on members of this genus, we found that the isolates were multi-drug resistant, and that this resistance included clinically important beta-lactams, aminoglycosides and the fluoroquinolone ciprofloxacin. Using the minION sequencing platform (Oxford Nanopore Technologies) combined with HiSeq PE150 Illumina sequencing data, the four isolates were assembled into genomes of single contigs. Analysis of the genomes revealed potential genetic factors possibly underlying some of the specific resistances observed. Metallo-beta-lactamase activity was detected in one isolate, and the same isolate contained a putative metallo-betalactamase gene resembling pedo-2. Furthermore, several genes related to multidrug efflux systems were found using the resistance database CARD. Additionally, the present study extends our knowledge on the phylogeny of this genus, adding four new genomes to the existing 50.

Keywords: Pedobacter spp; antimicrobial resistance; drinking water; environmental microbiology; minION sequencing.

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Figures

Figure 1.
Figure 1.
Phylogenetic tree of Pedobacter spp. Using the online tool PATRIC, the phylogeny of 32 different Pedobacter genomes was produced with RAxML and Jackknife (50%). One minor clade and two major clades are indicated. The four isolates investigated in this study spread out on two different clades and are given in red. Isolates B7_64 and B6_2 have a similar phylogeny and group together in the proposed Clade 2. Isolate B8_22 is closely related to Pedobacter antarcticus, while isolate B8_47 branches with Pedobacter cryoconitis. The tree was rooted using two strains of Sphingobacterium.
Figure 2.
Figure 2.
Bit score vs. identity distribution of resistance gene sequences identified in minION draft genomes by RGI in the CARD database according to resistance mechanism with a 50% cut-off on the identity score.
Figure 3.
Figure 3.
Bit score vs. identity distribution of resistance gene sequences identified in Illumina draft genomes by RGI in the CARD database according to resistance mechanism with a 50% cut-off on the identity score.
Figure 4.
Figure 4.
Bit score vs. identity distribution of resistance gene sequences identified in minION-Illumina-hybrid genomes by RGI in the CARD database according to resistance mechanism with a 50% cut-off on the identity score.
Figure 5.
Figure 5.
Bit score vs. identity distribution of resistance gene sequences identified in minION, Illumina and hybrid genomes draft genomes by RGI in the CARD database according to resistance mechanism with a 50% cut-off on the identity score. For the three panels, data from all four isolates are combined to illustrate the accuracy of the three assembly methods in resistance profile search.
See this image and copyright information in PMC

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