Risk Factors for Detection, Survival, and Growth of Antibiotic-Resistant and Pathogenic Escherichia coli in Household Soils in Rural Bangladesh

Abstract

Soil may represent a direct source or act as an intermediary for the transmission of antibiotic-resistant and pathogenic Escherichia coli strains, particularly in low-income and rural settings. Thus, determining risk factors associated with detection, growth, and long-term survival of E. coli in soil environments is important for public health. Here, we demonstrate that household soils in rural Bangladesh are reservoirs for antibiotic-resistant and potentially pathogenic E. coli strains and can support E. coli growth and survival, and defined soil physicochemical characteristics are drivers of E. coli survival in this environment. In contrast, we found no evidence that household-level factors, including water, sanitation, and hygiene indicators, were associated with E. coli contamination of household soils.

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

“…The placement of soil E. coli in terminal lineages of the phylogeny with fecal E. coli suggests the fluidity and lack of phylogenetic structure based on source. Humans and animals are suggested as likely contributors to the E. coli population in soils (28,35), but clonality or an estimate of the time of diversification between E. coli in soil and E. coli from the input source has not yet been established. Mutation rates are routinely used to establish time of diversification (36,37).…”

“…First, the pathogenicity potential and acquired antibiotic resistance of environmental strains reaffirm the need for interventions that effectively reduce E. coli across different environmental reservoirs. This represents a major challenge, as multiple previous studies showed no significant impact of sanitation (16), household-level water, sanitation, and hygiene infrastructure (17,28) or an integrated water, sanitation, and hygiene intervention (54) on E. coli concentrations in soils in and around households. Second, the lack of core phylogenetic signal based on source and apparent fluidity of E. coli strains across human, animal, and environmental reservoirs reaffirms the need for integrated interventions that address both human and animal fecal sources (One Health approaches) (55).…”

“…Bacterial isolates and antibiotic susceptibility testing. A subset of 60 isolates, part of a 175-isolate collection that was previously recovered in a study conducted in households in rural villages of Mirzapur, Bhatgram, Gorai, and Jamurki in Tangail district of Bangladesh (28), were selected for this study (Table 1). These isolates were phenotypically identified as E. coli using the API-20E (bioMérieux, Marcy-l'Étoile, France).…”

“…The nomenclature indicates the household (HH) from which the isolate was collected, followed by the source: "S" for soil, "H" for human fecal, "CH" for chicken fecal, and "C" for cattle fecal (i.e., HH03C is an E. coli isolate from cattle feces in household 03). Disk diffusion against 16 different antibiotic disks was previously performed (28). In addition, susceptibility against azithromycin (AZM) (Oxoid, Basingstoke, UK) was evaluated for selected isolates and interpreted using the Clinical and Laboratory Standards Institute (CLSI) guidelines and interpretation standards (58).…”

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.…”