enomic characterization of multidrug-resistant extraintestinal pathogenic Escherichia coli isolated from grain culture soil

Author(s)

Rueda Furlan, Joao Pedro ^[1] ; Lage Gallo, Inara Fernanda ^[1] ; Stehling, Eliana Guedes ^[1]

Affiliation

^[1] Univ Sao Paulo, Dept Anal Clin Toxicol & Bromatol, Fac Ciencias Farmaceut Ribeirao Preto, BR-14040903 Ribeirao Preto, SP - Brazil

• Document type: Journal article
• Source: Pedosphere; v. 32, n. 3, p. 495-502, JUN 2022.
• Web of Science Citations: 0

Abstract

Multidrug-resistant (MDR) Escherichia coli, mainly extraintestinal pathogenic E. coli (ExPEC), has been widely reported in infections worldwide. In agricultural soils, manure is a hotspot for the dissemination of antimicrobial resistance genes (ARGs) and pathogenic bacteria; however, MDR bacteria have also been reported in soils with no history of manure use. In addition, cross-resistance and co-resistance have been described as responsible for the metal-driven selection of bacteria resistant to antimicrobials. Therefore, the aim of this study was to analyze three MDR E. coli isolates obtained from Brazilian grain culture soil samples with no history of manure use by whole-genome sequencing. The MDR E. coli isolates were recovered from soils from corn and coffee fields, and presented resistance to ,9-lactams, quinolones, aminoglycosides, tetracyclines, sulphonamides, and dihydrofolate reductase inhibitor. Resistome analysis showed ARGs to several antimicrobials (i.e., ,9-lactams, tetracyclines, aminoglycosides, sulphonamides, trimethoprim, phenicols, fosfomycin, and macrolides) as well as several metal resistance genes and antibacterial biocide resistance genes. In addition, known mutations in quinolone-resistance-determining regions of GyrA (Ser83Leu and Asp87Asn), ParE (Ser458Thr), and ParC (Ser80Ile) were also detected. Virulome analysis showed the presence of virulence genes (lpfA, mcmA, gad, mchF, iroN, cma, and iss) associated with ExPEC. Multidrug-resistant ExPEC isolates were assigned to phylogenetic group B1. The presence of MDR B1-ExPEC in soil samples shows the ability of these isolates to survive in soils. This study reports for the first time some sequence types (i.e., ST345, ST448, and ST1146) of MDR E. coli in Brazilian soils. Therefore, these findings contribute to the monitoring of antimicrobial resistance and surveillance studies based on whole-genome sequencing worldwide. (AU)

• FAPESP's process: 18/19539-0 - Molecular characterization of Escherichia coli isolates from the environment
• Grantee: Eliana Guedes Stehling
• Support Opportunities: Regular Research Grants
• FAPESP's process: 18/01890-3 - Study of resistance, virulence and epidemiological profile of Escherichia coli isolated from environment
• Grantee: João Pedro Rueda Furlan
• Support Opportunities: Scholarships in Brazil - Doctorate