Genetic variability of Shiga toxin-producing Escherichia coli strains isolated from Paraguayan cattle

Abstract

Escherichia coli is a commensal of the intestinal microbiota; however, there are pathogenic strains associated with both intestinal and extraintestinal conditions. One of these pathotypes is Shiga toxin-producing E. coli (STEC), which can cause diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome and has cattle as one of its main reservoirs. This study aimed to characterize genomes of STEC strains isolated from rectal swabs of cattle from ranches in the departments of San Pedro, Cordillera, Caaguazú, Paraguarí, and Villa Hayes in Paraguay. The previous characterization of the isolates and their classification as STEC were carried out by conventional PCR to identify the presence of the stx1 and stx2 genes. Here, whole genome sequencing was performed on 40 strains in total (38 STEC and 2 non-STEC) using the Illumina MiSeq platform. The presence of 27 different virulence profiles and 34 different serotypes was detected. Regarding antibiotic resistance, the fosA7 gene related to fosfomycin resistance was detected in 10% of the strains (n = 4), and the sitABCD gene related to hydrogen peroxide resistance in 2.5% (n = 1). Twenty-nine sequence types were detected, with ST58 (n = 3) and ST11729 (n = 3) being the most frequent. Most of the strains belong to phylogroup B1. This is the first report on the genetic variability of STEC strains isolated from cattle in Paraguay. Given the importance of livestock in the country’s economy, epidemiological surveillance of pathogenic strains should continue to be carried out.