Antimicrobial Resistance Traits of Escherichia coli Isolated from Dairy Manure and Freshwater Ecosystems Are Similar to One Another but Differ from Associated Clinical Isolates

Abstract

Antimicrobial resistance (AMR) is a prevalent global health problem across human and veterinary medicine. The One Health approach to AMR is necessary to mitigate transmission between sources of resistance and decrease the spread of resistant bacteria among humans, animals, and the environment. Our primary goal was to identify associations in resistance traits between Escherichia coli isolated from clinical (n = 103), dairy manure (n = 65), and freshwater ecosystem (n = 64) environments within the same geographic location and timeframe. Clinical E. coli isolates showed the most phenotypic resistance (47.5%), followed by environmental isolates (15.6%) and manure isolates (7.7%), with the most common resistances to ampicillin, ampicillin-sulbactam, and cefotaxime antibiotics. An isolate subset was screened for extended spectrum beta-lactamase (ESBL) production resulting in the identification of 35 ESBL producers. The most common ESBL gene identified was bla_TEM-1. Additionally, we found nine different plasmid replicon types including IncFIA-FIB, which were frequently associated with ESBL producer isolates. Molecular phylotyping revealed a significant portion of clinical E. coli were associated with phylotype B2, whereas manure and environmental isolates were more diverse. Manure and environmental isolates were significantly different from clinical isolates based on analyzed traits, suggesting more transmission occurs between these two sources in the sampled environment.

Keywords: E. coli; ESBL; One Health; antimicrobial resistance; isolate association; phylotyping; plasmid replicon typing.

Figure 1

Percentage of resistant and intermediate resistant Escherichia coli isolates from clinical (blue), environmental (yellow), and manure (grey) environments. Antibiotic abbreviations: CFZ = cefazolin, FOX = cefoxitin, CAZ = ceftazidime, FEP = cefepime, CAX = ceftriaxone, ERT = ertapenem, MER = meropenem, AMP = ampicillin, A/S = ampicillin-sulbactam, P/T = piperacillin-tazobactam, T/S = trimethoprim-sulfamethoxazole, NIT = nitrofurantoin, CIP = ciprofloxacin, LEV = levofloxacin, TOB = tobramycin, GEN = gentamicin, AZT = aztreonam.

Figure 2

Multiple antibiotic resistance index (MAR) of clinical, environmental, and manure E. coli isolates. Isolates are presented as individual values with the mean and standard error of each source plotted. MAR indices >0.2 indicate that isolates likely originate from areas of high antibiotic use or a high risk source [30].

Figure 3

Biofilm formation strength of E. coli isolates as measured by absorbance of crystal violet staining. Isolates are presented as individual values with the mean and standard error of each source plotted. Strong, intermediate, and weak biofilm former classification is defined in Section 2.7, Materials and Methods.

Figure 4

Relative percentage of E. coli isolate phylotype within clinical, environmental, and manure isolation sources.

Figure 5

Principal coordinate analysis of all measured traits of E. coli isolates in this study based on Gower distance. Measured traits with a correlation strength of >0.5 are displayed on the plot.