The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone

Abstract

The ST131 multilocus sequence type (MLST) of Escherichia coli is a globally successful pathogen whose dissemination is increasing rates of antibiotic resistance. Numerous global surveys have demonstrated the pervasiveness of this clone; in some regions ST131 accounts for up to 30% of all E. coli isolates. However, many regions are underrepresented in these published surveys, including Africa, South America, and Asia. We collected consecutive bloodstream E. coli isolates from three countries in Southeast Asia; ST131 was the most common MLST type. As in other studies, the C2/H30Rx clade accounted for the majority of ST131 strains. Clinical risk factors were similar to other reported studies. However, we found that nearly all of the C2 strains in this study were closely related, forming what we denote the SEA-C2 clone. The SEA-C2 clone is enriched for strains from Asia, particularly Southeast Asia and Singapore. The SEA-C2 clone accounts for all of the excess resistance and virulence of ST131 relative to non-ST131 E. coli. The SEA-C2 strains appear to be locally circulating and dominant in Southeast Asia, despite the intuition that high international connectivity and travel would enable frequent opportunities for other strains to establish themselves.

Figure 1

Flow chart of study samples. A flow chart for study enrollment and reasons for sample exclusion is shown.

Figure 2

Phylogenomic analysis of ST131 strains (with removal of recombination). (A) Overview of all ST131 strains analyzed in this study. The tree on the left is an approximately maximum-likelihood tree, with mutations indicated on the x-axis at the bottom. Colored boxes indicate different subsets of the ST131 strains. From left to right, bars indicate the new strains contributed by this study (black boxes), the hospital from which the strains in this study were obtained (colored boxes below the “Hospital” label), the WHO region from which the strain was isolated (if available), resistance gene predictions for selected beta-lactamase genes, and the strains included from the GASREC and MERINO studies (with country of origin for MERINO strains). At the far right, the bar graph represents the percentage of the pTTSH16 plasmid that is covered by the assembly for each strain (based on blastn). Average plasmid coverage values for selected subsets of strains are indicated. (B) Expanded view of the SEA-C2 clone. Strains from this study, MERINO, or GASREC are indicated by font size and color; gray labels indicate other public data sets. Country of origin is indicated by the colored circles, with strains from Asia on the left with black outlines and strains from non-Asian areas on the right. Resistance gene predictions for each strain are indicated on the right with colored boxes; each class of resistance gene is in a separate color, with the gene indicated at the top.

Figure 3

Phylogenomic analysis of ST131 strains (without removing recombination). A neighbor joining tree with all SNP positions is shown. Major clades of ST131 are highlighted by colored boxes. The SEA-C2 clone is highlighted in purple. From left to right, bars indicate the new strains contributed by this study (black boxes), the hospital from which the strains in this study were obtained (colored boxes below the “Hospital” label), and the WHO region from which the strain was isolated (if available). The SEA-C2 clone is still monophyletic in this analysis.

Figure 4

Similarity of SEA-C2 plasmids to the pEC958 ST131 plasmid. From inner to outer circle, the following are indicated: GC content, GC skew, pTTSH10, pEC958, gene annotation, and labels of selected genes/loci. The rings representing pTTSH10 and pEC958 consist of a colored bar indicating the sequence identity to pTTSH16 (used as the reference). Areas with less than 50% identity are considered not present and indicated by the absence of a colored bar in that section of the ring, as indicated by the legend at the top right. Genes with certain functional annotations are indicated in color, as indicated by the legend at the bottom right. Gene names for resistance genes and plasmid replication genes are indicated; loci containing conjugation-related genes and clusters of replication genes are annotated with a colored line and a boxed label.