Genome-wide association reveals host-specific genomic traits in Escherichia coli

Abstract

Background Escherichia coli is an opportunistic pathogen which colonizes various host species. However, to what extent genetic lineages of E. coli are adapted or restricted to specific hosts and the genomic determinants of such adaptation or restriction is poorly understood. Results We randomly sampled E. coli isolates from four countries (Germany, UK, Spain, and Vietnam), obtained from five host species (human, pig, cattle, chicken, and wild boar) over 16 years, from both healthy and diseased hosts, to construct a collection of 1198 whole-genome sequenced E. coli isolates. We identified associations between specific E. coli lineages and the host from which they were isolated. A genome-wide association study (GWAS) identified several E. coli genes that were associated with human, cattle, or chicken hosts, whereas no genes associated with the pig host could be found. In silico characterization of nine contiguous genes (collectively designated as nan-9) associated with the human host indicated that these genes are involved in the metabolism of sialic acids (Sia). In contrast, the previously described sialic acid regulon known as sialoregulon (i.e. nanRATEK-yhcH, nanXY, and nanCMS) was not associated with any host species. In vitro growth experiments with a Δnan-9 E. coli mutant strain, using the sialic acids 5-N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) as sole carbon source, showed impaired growth behaviour compared to the wild-type. Conclusions This study provides an extensive analysis of genetic determinants which may contribute to host specificity in E. coli. Our findings should inform risk analysis and epidemiological monitoring of (antimicrobial resistant) E. coli.

Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes

“…The predominant bacterial phyla in the caecal mucosal epithelium samples were Firmicutes , Actinobacteria , Proteobacteria and Bacteroidota , which is consistent with previous studies of swine caecal microbiomes [9, 19, 40]. Escherichia coli was the predominant pathogen found in the caecal microbiome, which is a common pathogen in both humans and animals [41–43]. This pathogen is associated with post-weaning diarrhoea and oedema disease in swine, which can have an enormous economic impact.…”

Genomic insights into ESBL-producing Escherichia coli isolated from non-human primates in the Peruvian Amazon

“…The most prevalent lineage in our dataset was the ST10 clone, a well-known high-risk pandemic lineage associated with infections in humans and has been found in livestock and meat in Peru ( 43 , 44 ) Other STs identified in this study, such as ST117, have been found in emerging ExPEC strains of foodborne E. coli , posing a risk to human health ( 45 , 46 ). ST752 has been associated with poultry in Europe and the United States and is considered predominant in chicken populations ( 47 , 48 ). ST7176 has been detected in porcine E. coli strains carrying the bla CTX-M-55 variant ( 49 ).…”

Unveiling Antibiotic Resistance, Clonal Diversity, and Biofilm Formation in E. coli Isolated from Healthy Swine in Portugal

“…MDR traits can spread from contaminated animal products to humans or be introduced directly into the natural environment through fecal matter [ 13 , 14 ]. E. coli has become a repository of antibiotic-resistant genes, making it a key indicator for monitoring the prevalence of antibiotic resistance, a role recognized by the World Organization for Animal Health (OIE) [ 2 , 15 , 16 ]. In addition, E. coli also has the ability to transfer genes to other bacterial species, including pathogens [ 15 ].…”