Genomic Characterization of Multidrug-Resistant Escherichia coli BH100 Sub-strains

Abstract

The rapid emergence of multidrug-resistant (MDR) bacteria is a global health problem. Mobile genetic elements like conjugative plasmids, transposons, and integrons are the major players in spreading resistance genes in uropathogenic Escherichia coli (UPEC) pathotype. The E. coli BH100 strain was isolated from the urinary tract of a Brazilian woman in 1974. This strain presents two plasmids carrying MDR cassettes, pBH100, and pAp, with conjugative and mobilization properties, respectively. However, its transposable elements have not been characterized. In this study, we attempted to unravel the factors involved in the mobilization of virulence and drug-resistance genes by assessing genomic rearrangements in four BH100 sub-strains (BH100 MG2014, BH100 MG2017, BH100L MG2017, and BH100N MG2017). Therefore, the complete genomes of the BH100 sub-strains were achieved through Next Generation Sequencing and submitted to comparative genomic analyses. Our data shows recombination events between the two plasmids in the sub-strain BH100 MG2017 and between pBH100 and the chromosome in BH100L MG2017. In both cases, IS3 and IS21 elements were detected upstream of Tn21 family transposons associated with MDR genes at the recombined region. These results integrated with Genomic island analysis suggest pBH100 might be involved in the spreading of drug resistance through the formation of resistance islands. Regarding pathogenicity, our results reveal that BH100 strain is closely related to UPEC strains and contains many IS3 and IS21-transposase-enriched genomic islands associated with virulence. This study concludes that those IS elements are vital for the evolution and adaptation of BH100 strain.

Keywords: UPEC; antibiotic resistance; genomic sequencing; mobile genetic elements; urinary tract infection.

Figure 1

Synteny analysis between the plasmids of E. coli BH100 sub-strains. Blocks of the same colors represent homologous nucleotide matches between the plasmids pAp (BH100 MG2014), pApR (BH100 MG2017), pBH100alpha (BH100L MG2017), pBH100 (BH100 MG2017), and pBH100-1 (BH100 MG2014). White bars below each sequence represent the position of CDS. A rearrangement between pApR and pBH100-1 (BH100 MG2017) is indicated by the homologous segments in pink and orange. Other homologous segments in pAp (green and blue blocks) are also found in the plasmids pBH100-1 (BH100 MG2014) and pBH100-1 (BH100 MG2017) suggesting other recombination events. The blue block displayed below the line in pBH100-1 (BH100 MG2017) indicates a genomic inversion at the recombined region. To achieve a better visualization, the original sequences of pAp and pBH100alpha were split in a different genomic position. For the same purpose, the reverse complement sequence of pApR assembly was used and split in a different genomic position.

Figure 2

Distribution of IS elements and GEI on E. coli BH100L MG2017. An alignment between the genomic sequences of E. coli BH100 MG2017 and BH100 MG2014 is shown as indicated by the ring s in light blue (70–100% identity). GEI identified via IslandViewer4 in E. coli MG2017 are indicated by the gray bars. The IS elements and other transposases, predicted by the ISfinder tool, are indicated by arrows in green (IS21), black (IS3), blue (IS4), orange (IS110), purple (Tn3), and red (Tn21). GC content is represented by the inner ring in black.

Figure 3

Schematic representation of pBH100-1 from E. coli BH100 MG2014. The position of the main genes and features involved in mobilization of MDR in pBH100-1 are represented in the illustration generated in BRIG. The orange and purple bars represent genes involved in the conjugation and replication process, respectively. Antibiotic resistance genes are represented in dark green bars. The IS elements and other transposases, predicted by the ISfinder tool, are indicated by bars in light green (IS21), black (IS3), blue (IS4), yellow (Tn3), and red (Tn21).

Figure 4

Schematic representation of pAp from E. coli BH100 MG2014. The position and orientation of all CDS of pAp annotated in RAST Server are represented in purple arrows.

Figure 5

Distribution of IS elements in pApR from E. coli BH100 MG2017. An alignment (70–100% identity) between pApR sequence (BH100 MG2017) and the plasmids pAp (BH100 MG2014) and pBH100-1 (BH100 MG2014), performed in BRIG. is represented by the rings in emerald green and blue colors. The IS elements and other transposases, predicted by the ISfinder tool, are indicated by arrows in green (IS21), black (IS3), blue (IS4), yellow (IS110), purple (Tn3), and red (Tn21). GC content is represented by the inner ring in black.

Figure 6

Distribution of IS elements and GEI on E. coli 536. An alignment (70–100% identity) between the genomic sequences of E. coli 536 and the strains BH100 MG2014 and K12, performed in BRIG, is represented by the rings in light blue and green colors. GEI identified via IslandViewer4 in E. coli 536 are indicated by the gray bars. The IS elements, predicted by the ISfinder tool, are indicated by arrows in green (IS21), blue (IS4), and orange (IS110). GC content is represented by the inner ring in black.

Figure 7

Phylogenomic tree of E. coli BH100 and GenBank sequences inferred by PATRIC. The uppercase letters (A, B1, B2, C, D, E, and F) in the right corner indicate E. coli phylogroups. The bootstrap values ranged from 92 to 100%.