*2.1. Sample Collection*

A total of 150 ESBL-producing *Escherichia coli* were selected from a wide collection of ESBL-producing Enterobacteriaceae, isolated in Navarra from different environments: food products (*n* = 48), farms and feeds (*n* = 20), rivers and wastewater treatment plants (WWTPs) (*n* = 33) and human origins, including healthy volunteers (*n* = 13) and hospital inpatients (*n* = 36). Clinical isolates from hospital inpatients were provided by Clínica Universidad de Navarra, and were collected from January 2009 to December 2012 [5]. Food and environmental samples were collected from different locations in Navarra in two sampling periods (2010–2013 [5,28,29]; 2015–2016 [30]) and, finally, isolates from healthy people were collected from September 2015 to September 2016 (data not published). All samples were already identified, and phenotypically and genotypically characterized, in order to know the antimicrobial susceptibility pattern, the types of β-lactamase genes, and the phylogenetic group [28–30]. Isolates were selected according to the following criteria: they must show multidrug-resistant phenotype (to at least three different classes of antimicrobials) and must carry at least one ESBL gene. The main characteristics of the selected isolates, regarding type of ESBL, is shown in Table 1. Resistance profiles and complete information of each isolate is presented in the Supplementary Material, Tables S1–S6).


**Table 1.** Genotypic characteristics of extended-spectrum β-lactamase (ESBL)-producing *E. coli* according to their origin [5,28–30].

NA: Not analyzed.
