Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin

Abstract The emergence of plasmid-mediated tigecycline-resistant strains is posing a serious threat to food safety and human health, which has attracted worldwide attention. The tigecycline resistance gene tet(X4) has been found in diverse sources, but the distribution of tet(X4) and its genetic background in the animal farming environment is not fully understood. Thirty-two tet(X)-positive Escherichia coli strains isolated from 159 samples collected from swine farms showed resistance to tigecycline. The tet(X)-positive strains were characterized by antimicrobial susceptibility testing, conjugation assay, PCR, Illumina and long-read Nanopore sequencing, and bioinformatics analysis. A total of 11 different sequence types (STs) were identified and most of them belonged to phylogroup A, except ST641. In total, 196 possible prophage sequences were identified and some of the prophage regions were found to carry resistance genes, including tet(X4). Furthermore, our results showed possible correlations between CRISPR spacer sequences and serotypes or STs. The co-existence of tigecycline-resistant tet(A) variants and tet(X4) complicates the evolution of vital resistance genes in farming environments. Further, four reorganization plasmids carrying tet(X4) were observed, and the formation mechanism mainly involved homologous recombination. These findings contribute significantly to a better understanding of the diversity and complexity of tet(X4)-bearing plasmids, an emerging novel public health concern.