Comparative genomics of quinolone-resistant Escherichia coli from broilers and humans in Norway

Abstract

Background: The usage of fluoroquinolones in Norwegian livestock production is very low, including in broiler production. Historically, quinolone-resistant Escherichia coli (QREC) isolated from Norwegian production animals rarely occur. However, with the introduction of a selective screening method for QREC in the Norwegian monitoring programme for antimicrobial resistance in the veterinary sector in 2014; 89.5% of broiler caecal samples and 70.7% of broiler meat samples were positive. This triggered the concern if there could be possible links between broiler and human reservoirs of QREC. We are addressing this by characterizing genomes of QREC from humans (healthy carriers and patients) and broiler isolates (meat and caecum).

Results: The most frequent mechanism for quinolone resistance in both broiler and human E. coli isolates were mutations in the chromosomally located gyrA and parC genes, although plasmid mediated quinolone resistance (PMQR) was also identified. There was some relatedness of the isolates within human and broiler groups, but little between these two groups. Further, some overlap was seen for isolates with the same sequence type isolated from broiler and humans, but overall, the SNP distance was high.

Conclusion: Based on data from this study, QREC from broiler makes a limited contribution to the incidence of QREC in humans in Norway.

Keywords: Escherichia coli; Antimicrobial resistance; Broiler; Core genome phylogeny; Human; Quinolone resistance.

Fig. 1

eBURST analysis. Minimum Spanning Tree of all MLSTs using PHYLOViZ v 2.0 showing the clonal relationship of broiler (n = 100) and human (n = 90) quinolone-resistant Escherichia coli isolates. Size of the circle corresponds to the number of isolates. The colour of the circle borders corresponds to group founder (light green) and common node (light blue)

Fig. 2

Maximum likelihood SNP tree of 100 broiler and 90 human quinolone-resistant Escherichia coli isolates. Branch supports (ultrafast bootstrap approximation) are denoted with black or white nodes. The coloured tips and shapes on the tree denote species of origin and material. The tip labels denote the sequence types from the MLST scheme hosted by EnteroBase. The colouring on the outer rings denotes the presence/absence of mutations leading to amino acid (AA) substitutions in chromosomal genes and the presence/absence of plasmid-mediated genes leading to quinolone resistance. The grey shades denote groups of STs that contains isolates from both hosts, and which contains five or more isolates in total, ST10, ST117, ST131, ST155, ST162, and ST453. The tree was generated with IQTree from SNPs in core genes from Roary aligned with MAFFT. The evolutionary model used was GTRFASCR9 - GTRGAMMA. The tree is midpoint rooted for better visualization

Fig. 3

Maximum likelihood core gene midpoint rooted SNP trees for clades ST10, ST117, ST131, ST155, ST162 and ST453. These six clades comprise quinolone-resistant Escherichia coli isolates from both humans and broiler. Core genome SNPs were identified with ParSNP, and recombinant sites were removed with Gubbins. ST - sequence type. Genotypes explaining the quinolone resistance mechanism are represented in the heat map