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. IMPORTANCE Escherichia 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.

The utility of Escherichia coli as a contamination indicator for rural drinking water: Evidence from whole genome sequencing

“…In households like those in our study area, with low levels of access to sanitation and hygiene facilities, E . coli and other faecal indicators and pathogens are widespread on surfaces and in food produce [ 77 ] and it is likely that strains circulate between humans, animals, and the domestic environment [ 8 , 78 ]. Large-scale randomised control trials investigating the impact of water, sanitation, and hygiene interventions on health outcomes for communities in Kenya, Bangladesh and elsewhere have demonstrated the importance of considering multiple faecal exposure pathways [ 79 ].…”

Genomic and Phenotypic Analysis of an ESBL-Producing E. coli ST1159 Clonal Lineage From Wild Birds in Mongolia

“…Determined plasmid incompatibility (Inc.) types were IncFIC(FII) and IncI1. Both IncF- as well as IncI-type plasmids have been previously associated with the spread of ESBL-producing E. coli ( Coque et al, 2008 ; Branger et al, 2018 ; Montealegre et al, 2020 ). Group 3 genomes showed only small plasmid analogies with the Mongolian representatives and did not carry any ESBL-genes.…”

Digital multiplex ligation assay for highly multiplexed screening of β-lactamase-encoding genes in bacterial isolates

“…2). The bacterial isolates included 60 isolates hosting known β-lactamase genes previously characterized by Patrice Nordmann's lab (University of Fribourg, Fribourg, Switzerland, personal communication) and 14 Escherichia coli isolates from Bangladesh 27,28 . The bacterial genomic DNA was extracted by boiling at 100°C for 1 h. Ligation and PCR proceeded as described, with a probe pair mix totalling 1 μM, and 2 probe pairs per cluster for 18 clusters.…”