CONICET | Buscador de Institutos y Recursos Humanos

Escherichia coli has not been considered as a typical Cystic Fibrosis pathogen and its clinical significance has been underestimated, though the impact of its colonization in lung function and patients outcome is diverse and still uncertain. In 2013, in a local reference center for adults with CF, a patient died due to an abscess caused by an E. coli strain that was previously recovered from her sputum samples. Then, the rapid decline of the outcome of a child attended at Children Hospital at La Plata city who was chronically colonized by E. coli prompted us to undertake a deep analysis of her respiratory samples and encouraged us to do an epidemiological study of E. coli at this CF Reference Center. Airways samples of 160 patients with CF were screened for E. coli over a 5-year period (2014?2019). Diverse phenotypic characteristics of the isolates recovered from 12 patients were analyzed (colony morphology, mucoid phenotype, biofilm formation capacity, bacterial motility, antimicrobial susceptibility and production of curli and cellulose in Congo-red agar plates). Five isolates consecutively recovered along the infection of one patient chronically colonized only by E. coli were sequenced using an Illumina HiSeq platform; assemblies were subjected to gene prediction and annotation using PROKKA v1.10. The genomic content was analyzed by the Center for Genomic Epidemiology Services and Get homologues software. In 12 patients (7.5 %) E. coli was cultured at least once, and in 3 of them (25 %), it was chronically colonizing the patient?s lungs. Phenotypic analysis of the first isolates of all patients showed relatively very low motility and almost all of them produced biofilm matrix components. Their antimicrobial profile showed sensitivity to colistin, meropenem and ceftazidime, but resistance to ciprofloxacin. Genomic analysis of the 5 sequenced strains demonstrated that the patient has been persistently colonized by a single extraintestinal pathogenic E. coli (ExPEC) clone O25b:H4-ST131, which belongs to a widespread pandemic clonal group known to produce antimicrobial-resistant urinary tract infections. After 3 years of chronicity, a small colony variant (SCV) was recovered, presenting a low growth rate and resistance to a greater number of antimicrobials. The Congo red staining showed that alterations in the biofilm matrix composition might be involved in the long-term adaptation. The genomic analysis showed that isolates have a low genome-wide mutation rate and some plasmid mobility along the 5 years of chronic infection. In conclusion, this investigation revealed that a virulent lineage of E. coli can be a persistent colonizer of CF lungs and that E. coli can adapt to this particular niche by undergoing phenotypic changes as traditional CF pathogens. These results showed that we should continue with the screening of E. coli and also study its impact on the decline of lung function and the evolution of the disease.