Ancestral lineages of human enterotoxigenic Escherichia coli

Abstract

Enterotoxigenic Escherichia coli (ETEC) is a common cause of diarrhea among children living in and among travelers visiting developing countries. Human ETEC strains represent an epidemiologically and phenotypically diverse group of pathogens, and there is a need to identify natural groupings of these organisms that may help to explain this diversity. Here, we sought to identify most of the important human ETEC lineages that exist in the E. coli population, because strains that originate from the same lineage may also have inherited many of the same epidemiological and phenotypic traits. We performed multilocus sequence typing (MLST) on 1,019 ETEC isolates obtained from humans in different countries and analyzed the data against a backdrop of MLST data from 1,250 non-ETEC E. coli and eight ETEC isolates from pigs. A total of 42 different lineages were identified, 15 of which, representing 792 (78%) of the strains, were estimated to have emerged >900 years ago. Twenty of the lineages were represented in more than one country. There was evidence of extensive exchange of enterotoxin and colonization factor genes between different lineages. Human and porcine ETEC have probably emerged from the same ancestral ETEC lineage on at least three occasions. Our findings suggest that most ETEC strains circulating in the human population today originate from well-established, globally widespread ETEC lineages. Some of the more important lineages identified here may represent a smaller and more manageable target for the ongoing efforts to develop effective ETEC vaccines.

Figures

FIG. 1.

Distribution of human ETEC clonal groups in the E. coli population structure. The maximum-likelihood tree is based on 394 different MLST STs from 1,019 human ETEC, 8 porcine ETEC, and 1,250 non-ETEC E. coli isolates. Each bubble represents a unique ST, centered on its tree node. The area of each bubble is proportional to the number of human ETEC strains that had the given ST. Bubbles representing the same clonal group (CT) have the same color and, unless they overlap with each other, are connected by dotted lines. The long connector lines seen in CG4 and CG11 are probably effects of recombination. The numbers 1 to 42 indicate each of the 42 ETEC CGs. Known non-ETEC E. coli CGs indicated in the drawing are EHEC 1 (enterohemorrhagic E. coli O157:H7, e.g., strains EDL933 and Sakai), EHEC 2 (e.g., strains 11128 and 11368), EPEC 1 (typical enteropathogenic E. coli, e.g., strain E2348/69), EPEC 2 (e.g., strain B171), Shigella 1 (Shigella group 1, e.g., strains Sb227 and CDC3083-94), Shigella 2, Shigella 3 (e.g., strains Sf2457T, 301, and Sf8401), S. dysenteriae 1 (Shigella dysenteriae type 1, e.g., strain Sd197), S. sonnei (e.g., strain Ss046), and UTI 1 (uropathogenic E. coli, e.g., strain CFT073).

FIG. 2.

Composition of human ETEC clonal groups 1 to 8. Each clonal group (CG) comprises ≥10 strains that do not originate from Guinea-Bissau. The CGs were identified through a combination of eBURST analyses and maximum-likelihood bootstrap analyses. In each CG, strains with different MLST ST-toxin/colonization factor (CF) combinations are listed separately. Each bubble represents a unique ST-toxin/CF-origin combination, and the area of each bubble is proportional to the number of strains that have this ST-toxin/CF-origin combination. Different colored bubbles are used for depicting different CGs, and each CG color combination matches those used in Fig. 1. The topology is taken from the maximum-likelihood bootstrap consensus tree, where connected entries share a ≥50% bootstrap support (≥80% for entries flagged with an asterisk). The legend for the bubble sizes is found in Fig. 1. ETEC origin: 1, Guinea-Bissau; 2, Saudi Arabia and Egypt; 3, India; 4, all other countries.

FIG. 3.

Composition of human ETEC clonal groups 9 to 42. Each clonal group comprises