Diversity of Environmental Escherichia coli in Subtropical Freshwater Systems of South Africa

TL;DR

This study explores the diversity of Escherichia coli in South African freshwater systems, revealing unexpected phylogroup B2 isolates that may have disease-causing potential.

Contribution

The study identifies a significant presence of phylogroup B2 E. coli in environmental samples, which is novel for this region.

Findings

Phylogroup B2 E. coli isolates formed a distinct phylogenetic cluster, independent of niche or geographic origin.

Environmental E. coli isolates harbored virulence factors associated with extraintestinal disease.

Phylogroup B1 was the most dominant, but B2 was unexpectedly the second most dominant.

Abstract

Escherichia coli is widely used as an indicator of faecal contamination, as it is assumed that faeces from warm-blooded animals is the primary source of E. coli in the environment. However, various studies have shown that E. coli can survive and multiply in environmental niches, including soil, sand and sediment. E. coli can be assigned to eight main phylogroups but environmental E. coli are associated primarily with phylogroups A and B1. In this study, 410 E. coli were isolated from different niches within two peri-urban catchments in the Gauteng province of South Africa. To represent the E. coli circulating within the human population, E. coli was also isolated from sewage before treatment and released into these reservoirs. To capture the diversity of E. coli among these isolates, the β-D-glucuronidase (uidA) and mismatch repair (mutS) genes were sequenced. While isolates linked to phylogroup B1 dominated as was expected, the recovery of many isolates linked to phylogroup B2, the second most dominant group, was unanticipated. To further investigate this observation, the genomes of representative phylogroup B2 isolates were sequenced and subjected to phylogenetic and functional analyses. The results showed that phylogroup B2 isolates formed a distinct phylogenetic cluster, apparently independent of niche or geographic origin. Our findings also showed that while isolates seem to be associated with environmental samples, they could have the ability to colonize the gut and cause disease as they harboured several virulence factors associated with extraintestinal E. coli.

The online version contains supplementary material available at 10.1007/s00284-025-04402-y.

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