Characterization of qnrB-carrying plasmids from ESBL- and non-ESBL-producing Escherichia coli

Abstract

Background: Escherichia coli carrying clinically important antimicrobial resistances [i.e., against extended-spectrum-beta-lactamases (ESBL)] are of high concern for human health and are increasingly detected worldwide. Worryingly, they are often identified as multidrug-resistant (MDR) isolates, frequently including resistances against quinolones/fluoroquinolones.

Results: Here, the occurrence and genetic basis of the fluoroquinolone resistance enhancing determinant qnrB in ESBL-/non-ESBL-producing E. coli was investigated. Overall, 33 qnrB-carrying isolates out of the annual German antimicrobial resistance (AMR) monitoring on commensal E. coli (incl. ESBL-/AmpC-producing E. coli) recovered from food and livestock between 2013 and 2018 were analysed in detail. Whole-genome sequencing, bioinformatics analyses and transferability evaluation was conducted to characterise the prevailing qnrB-associated plasmids. Furthermore, predominant qnrB-carrying plasmid-types were subjected to in silico genome reconstruction analysis. In general, the qnrB-carrying E. coli were found to be highly heterogenic in their multilocus sequence types (STs) and their phenotypic resistance profiles. Most of them appeared to be MDR and exhibited resistances against up to ten antimicrobials of different classes. With respect to qnrB-carrying plasmids, we found qnrB19 located on small Col440I plasmids to be most widespread among ESBL-producing E. coli from German livestock and food. This Col440I plasmid-type was found to be highly conserved by exhibiting qnrB19, a pspF operon and different genes of unassigned function. Furthermore, we detected plasmids of the incompatibility groups IncN and IncH as carriers of qnrB. All qnrB-carrying plasmids also exhibited virulence factors and various insertion sequences (IS). The majority of the qnrB-carrying plasmids were determined to be self-transmissible, indicating their possible contribution to the spread of resistances against (fluoro)quinolones and other antimicrobials.

Conclusion: In this study, a diversity of different plasmid types carrying qnrB alone or in combination with other resistance determinants (i.e., beta-lactamase genes) were found. The spread of these plasmids, especially those carrying antimicrobial resistance genes against highest priority critically important antimicrobial agents, is highly unfavourable and can pose a threat for public health. Therefore, the dissemination pathways and evolution of these plasmids need to be further monitored.

Keywords: E. coli; Fluoroquinolone; Inc-group; Plasmids; qnrB.

Fig. 1

Phylogenetic tree of the Col-plasmids carrying qnrB19. The phylogenetic tree was visualised with iTOL v6.3 after creating a nexus file with a multiple Clustal Omega alignment. All tools were used with default parameters

Fig. 2

Arrow graph of annotated plasmids assigned to the Col plasmid group, visualised with the ggplot2 package gggenes in RStudio. Genes were aligned according to the position of qnrB19. The schematic illustration provides no information on the actual plasmid size but the size and position of the annotated genes. The ruler given below the gene map represents an artificial indicator for the size of the region

Fig. 3

IncN plasmid contigs mapped against the best matching reference NC_019098 with BRIG

Fig. 4

Organization of the qnrB1 coding region on the IncH plasmids. The region represents the contig as detected for the four investigated qnrB1 carrying E. coli of our study. This contig, bioinformatically mapped to the reference plasmids containing the IncH replicon sequence, did always consist of the same structure as presented here