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Urban river pollution by multidrug-resistant (MDR) bacteria constitutes an important public health concern. Epidemiologically important strains of MDR Escherichia coli transmissible at the human–animal–environment interfaces are especially worrying. Quantifying and characterizing MDR E. coli at a molecular level is thus imperative for understanding its epidemiology in natural environments and its role in the spread of resistance in precise geographical areas. Cefotaxime-resistant E. coli was characterized along the watercourse of the major urban river in Quito. Our results showed high quantities of cefotaxime-resistant E. coli (2.7 × 103–5.4 × 105 CFU/100 mL). The antimicrobial resistance index (ARI) revealed the exposure of the river to antibiotic contamination, and the multiple antibiotic resistance index indicated a high risk of contamination. The blaCTX-M-15 gene was the most prevalent in our samples. Isolates also had class 1 integrons carrying aminoglycoside-modifying enzymes and folate pathway inhibitors. The isolates belonged to phylogroups A, B1 and D. Clonal complex 10 was found to be the most prevalent (ST10, ST44 and ST 167), followed by ST162, ST394 and ST46. Our study provides a warning about the high potential of the major urban river in Quito for spreading the epidemiologically important MDR E. coli.

Mycobacterium timonense is a non-tuberculous mycobacteria (NTM) described in southern France in 2009, and to our knowledge, not reported again as a human pathogen in indexed literature. The aim of this work was to characterize the first clinical isolate of M. timonense in Ecuador. Time of growth, biochemical tests, thin layer growth test, PCR-RFLP analysis of the hsp65 gene and MALDI-TOF spectra analysis were not able to identify the species. The species identification was achieved through sequencing of rrs, hsp65 and rpoB genes. The results highlight the necessity to set up a sequencing method to identify emerging NTM in Ecuadorian clinical facilities.