First Report and Characterization of the mcr-1 Positive Multidrug-Resistant Escherichia coli Strain Isolated from Pigs in Croatia

Abstract

The emergence and rapid spread of the plasmid-mediated colistin-resistant mcr-1 gene introduced a serious threat to public health. In 2021, a multi-drug resistant, mcr-1 positive Escherichia coli EC1945 strain, was isolated from pig caecal content in Croatia. Antimicrobial susceptibility testing and whole genome sequencing were performed. Bioinformatics tools were used to determine the presence of resistance genes, plasmid Inc groups, serotype, sequence type, virulence factors, and plasmid reconstruction. The isolated strain showed phenotypic and genotypic resistance to nine antimicrobial classes. It was resistant to colistin, gentamicin, ampicillin, cefepime, cefotaxime, ceftazidime, sulfamethoxazole, chloramphenicol, nalidixic acid, and ciprofloxacin. Antimicrobial resistance genes included mcr-1, bla_TEM-1B, bla_CTX-M-1, aac(3)-IId, aph(3')-Ia, aadA5, sul2, catA1, gyrA (S83L, D87N), and parC (A56T, S80I). The mcr-1 gene was located within the conjugative IncX4 plasmid. IncI1, IncFIB, and IncFII plasmids were also detected. The isolate also harbored 14 virulence genes and was classified as ST744 and O101:H10. ST744 is a member of the ST10 group which includes commensal, extraintestinal pathogenic E. coli isolates that play a crucial role as a reservoir of genes. Further efforts are needed to identify mcr-1-carrying E. coli isolates in Croatia, especially in food-producing animals to identify such gene reservoirs.

Keywords: Escherichia coli; MDR; antimicrobial resistance; mcr-1; pigs.

Figure 1

Structural comparison between mcr-1 plasmids. The alignment includes three references (OK642378.1, KX236309.1, and KU761327.1) and IncX4 mcr-1-bearing plasmid found in our study (EC1945_IncX4).

Figure 2

Dendrogram showing relationship of identified strain to the most related strains present in database used in this study according to MLST 7 Achtman scheme. Strains are also identified according to ST, source, country of origin species, and year of isolation. STs are designated by different colors. Isolate from this study is in rectangle.

Figure 3

Dendrogram showing relationship of identified strain to the most related strains present in database used in this study calculated from cgMLST results. cgMLST profiles were generated using the 2513 core genes. Strains are also identified according to ST, source and country of origin species, and year of isolation. Complete linkage cluster analysis was used in the calculation with scaling factor of 100. Numbers indicated on the branches correspond to the number of allelic differences between strains multiplied by 100. Different colors indicate similarities between strains within same linkage cluster. Isolate from this study is in rectangle.