Jesser, K. J. | bioRxiv Science

bioRxiv2026

Genomovar-level resolution reveals rapid pathotype switching and genomovar-specific disease potential in diarrheagenic Escherichia coli populations in northern Ecuador

Diarrheagenic Escherichia coli (DEC) pathotypes are commonly defined by molecular detection of discrete virulence genes, yet how quickly these diagnostic genes emerge and move among co-circulating lineages remain unclear. Here, we classified 248 whole-genome-sequenced E. coli isolates from the EcoZUR case-control study in northern Ecuador into intra-species genomovar units using the recently described 99.5% ANI threshold. This framework exposed cryptic population structure, revealing that single sequence types, representing identical multilocus sequence types (MLST), can harbor multiple distinct genomovars. Within individual genomovars, we observed a few cases of different pathotypes among isolates showing ~99.7% ANI (and many such cases between genomovars). Coupled with synteny and phylogeny analyses that revealed pervasive incongruences between pathotype-diagnostic virulence genes and the core genome, these findings suggest recent horizontal gene transfer as the primary driver of pathotype evolution. Virulence gene profiling further revealed that accessory virulence repertoires are hierarchically structured by phylogroup across pathotypes, with genomovars assigned to phylogroups B2 and D exhibiting more conserved virulence architectures than those in phylogroup A and B1. Among DAEC isolates specifically, the B2- and D-associated genomovars showed elevated diarrhea-association rates relative to their phylogroup A counterparts. Rare virulence genes, including Type VI secretion systems, further distinguished diarrhea-associated from asymptomatic genomovars. These findings demonstrate that, although there seems to be within-lineage (phylogroup) conservation of virulence, pathotype identity is a labile state defined by horizontally acquired virulence genes at the genomovar level, and that the genomovar framework provides a biologically meaningful unit for linking intra-species diversity to pathogenic potential and outbreaks.

genomics↗

bioRxiv2025

Microbial source tracking of human and animal fecal contamination in Ecuadorian households

Exposures to both human and animal feces pose human health risks, particularly for young children in low- and middle-income country (LMIC) settings where domestic animals are common, water and sanitation infrastructure is often limited, and enteropathogen transmission is high. Microbial source tracking (MST) markers specific to feces from humans and particular animal types can be used to identify the provenance of microbial contamination, yet most MST studies explore few household environmental sample types, limiting understanding of how marker utility varies by matrix. We validated qPCR assays for six MST markers and quantified their prevalence in 585 samples from 59 households spanning an urban-rural gradient in northwestern Ecuador. We used GenBac3 to test for general fecal contamination, and HF183, Rum2Bac, Pig2Bac, DG37, and GFD to test for human, ruminant, swine, dog, and avian contamination, respectively. Approximately 10 sample types were collected per household, including: rinses of child and adult hands, swabs of floors and surfaces, soil, domestic and drinking water, and food. GenBac3 and HF183 were detected in 77.82% and 15.36% of samples, respectively. Animal-associated markers were detected less frequently, in 0.5-4.1% of samples. However, when present, animal marker concentrations were comparable to HF183. Host-associated markers were most often detected in adult and child hand rinse and floor samples, and GenBac3 concentrations were highest in hand rinses. HF183 detection on adult caregiver hands was associated with increased odds of HF183 detection on childrens hands and floors. ImportanceUnderstanding the sources and pathways of detectable household environmental fecal contamination is critical for identifying how exposures occur and for developing targeted interventions to reduce risk of enteric infection By linking contamination on caregiver hands to that on childrens hands and floors, we highlight a likely route for pathogen transfer in the home. The inclusion of multiple host-associated markers across a wide range of sample types reveals patterns that narrower studies may miss, offering new insights into the complex ecology of fecal contamination. These findings can inform sampling strategies, guide risk assessments, and support the design of interventions aimed at reducing child exposure to enteric pathogens in similar high-risk settings.

microbiology↗