Diverse commensal E. coli clones and plasmids disseminate antimicrobial resistance genes in domestic animals and children in a semi-rural community in Ecuador

Abstract

The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts in human medicine. Many of the multi-drug resistant (MDR) Enterobacteriaceae found in humans are community-acquired and linked to food animals (i.e. livestock raised for meat and dairy products). In this study, we examined whether numerically dominant, commensal Escherichia coli strains from humans (n=63 isolates) and domestic animals (n=174 isolates) in the same community and with matching phenotypic AMR patterns, were clonally related or shared the same plasmids. We identified 25 multi-drug resistant isolates (i.e. resistant to 3 or more antimicrobial classes) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes and plasmids carrying the AMR genes using conjugation, replicon typing and whole genome sequencing. None of the MDR E. coli isolates (from children and domestic animals) analyzed were clonal. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. Our findings suggest that nonclonal resistance gene dissemination is common in this community and that diverse plasmids carrying AMR genes presents a significant challenge for understanding the movement of AMR in a community.IMPORTANCEEven though Escherichia coli strains may share nearly identical AMR profiles, AMR genes, and overlap in space and time, the diversity of clones and plasmids challenges to research that aims to identify sources of AMR. Horizontal gene transfer appears to play a much larger role than clonal expansion in the spread of AMR in the community.

Prevalence, Risk Factors, and Genetic Characterization of Extended-Spectrum Beta-Lactamase Escherichia coli Isolated From Healthy Pregnant Women in Madagascar

“…Plasmid content analysis revealed an unusually prevalent IncY plasmid compared to other studies (Lyimo et al, 2016;Salinas et al, 2019), suggesting a dissemination in the country of an IncY type plasmid harboring a resistance genes island containing bla CTX−M−15 and six other resistant genes of different antibiotic classes. To our knowledge, this is the first report of such a high prevalence of an IncY plasmid in ESBL-E. coli isolates.…”

Presence and abundance of antibiotic resistance genes at an organic goat dairy farm

“…Compared to the non-agricultural soil control, there was a greater occurrence of ARGs in the organic goat dairy farm samples (Table 1). This was expected based on results from a study in Ecuador (Salinas et al, 2019). ARG prevalence can occur in non-agricultural soils such as pastureland, residential, recreational, and forest soils though at lower levels than cropland (Dungan et al, 2019).…”

“…The use of antibiotics in animal agriculture has spread to rural areas of the world, such as farming communities in Ecuador (Salinas et al, 2019). Unlike the majority of animal agriculture in the United States and China, some of the people who are raising livestock in Ecuador live in close proximity to their animals.…”

“…As a result, settings such as these are important to help us understand how horizontal gene transfer could contribute to the spread of ARGs between bacteria isolated from humans and animals. Based on one study that has been done on this system, it was found that ARGs are spread between bacteria isolated from humans and animals as they found shared ARGs (Salinas et al, 2019). Results such as these present a clear picture that the impacts antibiotic use have on the microbiomes of livestock animals are not isolated from the human microbiome.…”

Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer

“…In 2018, Salinas et al 66 performed a study that included E. coli isolated from faecal samples from children and domestic animals. Even though the bacteria presented similar antibiotic resistance genes, they were genotypically diverse.…”