Differences in tests of phenotypic colistin resistance in clinical Escherichia coli isolates from poultry and their genetic diversity

Abstract

Colibacillosis is one of the most common health problems in poultry production and is associated with high economic losses. The purpose of this study was to determine the phenotypic and genotypic colistin resistance of Escherichia coli isolates obtained from clinical cases of colibacillosis in poultry, together with determination of their phylogenetic groups, and to compare the results of three tests based on the microdilution method for phenotypic evaluation of colistin susceptibility. In addition, to determine the risk to the poultry meat consumer, further analysis of E. coli isolates phenotypically and genotypically resistant to colistin was performed, including determination of their phenotypic and genotypic resistance to other antibiotics, the presence of selected potential virulence factors, and their sequence types. A total of 91 E. coli isolates from laying hens, breeding hens, broiler chickens, and turkeys were tested. Automated test yielded 53.8 % colistin-resistant isolates, while the other two phenotypic tests and the genetic analysis (mcr-1 gene) showed 22 % resistant isolates. The 91 E. coli isolates represented phylogenetic groups D (36.2 %), A (26.4 %), B2 (26.4 %), and B1 (11 %). The mcr-1-positive E. coli isolates included 12 sequence types (ST10, ST95, ST355, ST428, ST744, ST57, ST69, ST117, ST156, ST349, ST410, and ST1196), showed the highest resistance to amoxicillin (100 %), doxycycline (100 %), enrofloxacin (85 %), chloramphenicol (75 %), and amoxicillin/clavulanic acid (55 %) and had combination of resistance genes (bla_TEM, tetA, tetB, aadA, strA/strB, aac(3)-II, aphA1, dhfrI, sul1, sul2, sul3, floR, cmlA, catA1) and potential virulence factors (iss, iucD, cvi/cva, tsh, irp2, vat, astA, and papC). Among all phylogenetic groups, the mcr-1-positive E. coli isolates representing group B2 possessed the most potential virulence factors. Notably, the ST95 E. coli isolate represented phylogenetic group B2 and contained the svg and mcr-1 genes, which could pose a real threat to humans.

Keywords: Colibacillosis; Colistin-resistance; MLST; Phylogenetic group; Poultry; mcr-1 gene.