Abstract
Since the discovery of the urinary microbiome, including the identification of Escherichia coli in healthy hosts, its involvement in UTI development has been a subject of high interest. We explored the population diversity and antimicrobial resistance of E. coli (n = 22) in the urogenital microbiome of ten asymptomatic women (representing 50% of the sample tested). We evaluated their genomic relationship with extraintestinal pathogenic E. coli (ExPEC) strains from healthy and diseased hosts, including the ST131 lineage. E. coli prevalence was higher in vaginal samples than in urine samples, and occasionally different lineages were observed in the same individual. Furthermore, B2 was the most frequent phylogenetic group, with the most strains classified as ExPEC. Resistance to antibiotics of therapeutic relevance (e.g., amoxicillin-clavulanate conferred by blaTEM-30) was observed in ExPEC widespread lineages sequence types (ST) 127, ST131, and ST73 and ST95 clonal complexes. Phylogenomics of ST131 and other ExPEC lineages revealed close relatedness with strains from gastrointestinal tract and diseased host. These findings demonstrate that healthy urogenital microbiome is a source of potentially pathogenic and antibiotic resistant E. coli strains, including those causing UTI, e.g., ST131. Importantly, diverse E. coli lineages can be observed per individual and urogenital sample type which is relevant for future studies screening for this uropathogen.
Highlights
Most Urinary tract infections (UTIs) are caused by a subset of Extraintestinal pathogenic E. coli (ExPEC) strains [e.g., sequence type (ST) 131, ST95, ST69, ST73, ST127, ST12] that are highly disseminated across different continents and populations and represent great clinical challenges because they are often resistant to the main therapeutic choices and because of their extended reservoirs [11–16]
We provided a detailed strain-level analysis of the E. coli isolates idenin the female urogenital microbiome, revealing that the urogenital tract of healthy women tified in the female urogenital microbiome, revealing that the urogenital tract of healthy is an additional reservoir of pandemic ExPEC clones with the potential to cause UTI
We demonstrated that E. coli strains identified in the urogenital microbiome of healthy women frequently belong to international, pandemic, and occasionally antibiotic resistant B2 clones
Summary
Urinary tract infections (UTIs) are reported to be one of the most common infections worldwide, and occur more frequently in women than in men due to anatomical differences, and its incidence increases with age or sexual activity [1–4]. Several bacterial species are reported as causative agents of UTIs (e.g., Escherichia coli, Klebsiella sp., Proteus sp., Staphylococcus saprophyticus), E. coli is responsible for the majority (up to 75%) of both uncomplicated and complicated UTIs [2,5–7]. Extraintestinal pathogenic E. coli (ExPEC) strains are most frequently responsible for these infections, with this pathotype associated with genetic characteristics that seem to favor the pathogenicity of particular strains, and E. coli persistence in the urinary tract [8–10]. Most UTIs are caused by a subset of ExPEC strains [e.g., sequence type (ST) 131, ST95, ST69, ST73, ST127, ST12] that are highly disseminated across different continents and populations and represent great clinical challenges because they are often resistant to the main therapeutic choices and because of their extended reservoirs (human and animal gastrointestinal tract and the environment) [11–16]
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