High Genomic Diversity and Heterogenous Origins of Pathogenic and Antibiotic-Resistant Escherichia coli in Household Settings Represent a Challenge to Reducing Transmission in Low-Income Settings

Abstract

Escherichia coli is present in multiple hosts and environmental compartments as a normal inhabitant, temporary or persistent colonizer, and as a pathogen. Transmission of E. coli between hosts and with the environment is considered to occur more often in areas with poor sanitation. We performed whole-genome comparative analyses on 60 E. coli isolates from soils and fecal sources (cattle, chickens, and humans) in households in rural Bangladesh. Isolates from household soils were in multiple branches of the reconstructed phylogeny, intermixed with isolates from fecal sources. Pairwise differences between all strain pairs were large (minimum, 189 single nucleotide polymorphisms [SNPs]), suggesting high diversity and heterogeneous origins of the isolates. The presence of multiple virulence and antibiotic resistance genes is indicative of the risk that E. coli from soil and feces represent for the transmission of variants that pose potential harm to people. Analysis of the accessory genomes of the Bangladeshi E. coli relative to E. coli genomes available in NCBI identified a common pool of accessory genes shared among E. coli isolates in this geographic area. Together, these findings indicate that in rural Bangladesh, a high level of E. coli in soil is likely driven by contributions from multiple and diverse E. coli sources (human and animal) that share an accessory gene pool relatively unique to previously published E. coli genomes. Thus, interventions to reduce environmental pathogen or antimicrobial resistance transmission should adopt integrated One Health approaches that consider heterogeneous origins and high diversity to improve effectiveness and reduce prevalence and transmission.IMPORTANCEEscherichia coli is reported in high levels in household soil in low-income settings. When E. coli reaches a soil environment, different mechanisms, including survival, clonal expansion, and genetic exchange, have the potential to either maintain or generate E. coli variants with capabilities of causing harm to people. In this study, we used whole-genome sequencing to identify that E. coli isolates collected from rural Bangladeshi household soils, including pathogenic and antibiotic-resistant variants, are diverse and likely originated from multiple diverse sources. In addition, we observed specialization of the accessory genome of this Bangladeshi E. coli compared to E. coli genomes available in current sequence databases. Thus, to address the high level of pathogenic and antibiotic-resistant E. coli transmission in low-income settings, interventions should focus on addressing the heterogeneous origins and high diversity.

Keywords: Escherichia coli; accessory genes; genomic diversity; household settings; soils.

FIG 1

Phylogeny of 60 E. coli isolates collected from soils and fecal sources in rural Bangladesh. The core genome phylogenetic tree, based on SNPs and indels, was constructed by maximum likelihood using IQ tree and visualized using the iTOL online tool. The genome of Escherichia fergusonii was used as the outgroup. The household (HH) where the isolate was collected and the source (“S” for soil, “H” for human fecal, “CH” for chicken fecal, and “C” for cattle fecal) correspond to the isolate name. The source is additionally indicated by colored circles; E. coli phylogroups are indicated on the right.

FIG 2

Intestinal virulence markers, antibiotic resistance genes, and plasmid replicon profiles for the 60 E. coli isolates collected from soils and fecal sources in households in rural Bangladesh. Distribution of virulence genes associated with intestinal pathotypes, antibiotic resistance gene determinants, and plasmid replicons with identity and coverage >90% against the Virulence Factor, ResFinder, and PlasmidFinder databases, respectively. The virulence genes are grouped by intestinal pathotype, the antibiotic resistance genes are grouped by antibiotic class, and the plasmid replicons are grouped by plasmid groups (x axis). The isolates are grouped by source, household, union, and village (Mirzapur: S.P., Sreehori Para; Sr., Sarishadair; An., Andhora; Ba., Baimhati; Ka., Kanthalia; Bhatgram: D.B., Dulla Begum; Si., Sinjuri; Gorai: K.D., K. Deohata; Jamurki [Ja]: Sa., Satiachara) (y axis). The source of isolation is also indicated by the colors.

FIG 3

Phylogenetic distance and accessory genome analyses of soil and fecal E. coli isolates from rural Bangladesh against representative and nearest E. coli genomes available in NCBI. Mash distance hierarchical dendrogram of the 60 Bangladeshi E. coli isolates against 199 representative (A) and 265 nearest-neighbor (C) E. coli genomes available in NCBI (see Table S5 in the supplemental material for the list of the genomes used for comparison). Accessory-genome bipartite network generated by AcCNET with the 199 representative (B) and 265 nearest-neighbor (D) accessory genomes. Proteins with a P value of <0.001 and frequency in Bangladesh data set of >50% are represented.

FIG 4

Venn diagram indicating the distribution of the accessory genome proteins found in Bangladeshi E. coli isolates. Proteins coded by the accessory genomes of the Bangladeshi isolates include proteins that are putative or hypothetical with unknown function (47.4%), statistically significantly enriched relative to their nearest neighbors in the NCBI database (16.7%), and/or present in at least half of the Bangladeshi isolates (3.7%).