Global distribution and genomic characteristics of tet(X)-positive Escherichia coli among humans, animals, and the environment

Abstract

In recent years, the plasmid-mediated transmission of the tigecycline resistance gene tet(X) in Escherichia coli has received considerable attention. However, studies on the global distribution of tet(X)-positive E. coli remain scarce. Herein, we performed a systematic genomic analysis of 864 tet(X)-positive E. coli isolates from humans, animals and the environment around the world. These isolates were reported in 25 countries and isolated from 13 different hosts. China reported the most tet(X)-positive isolates (71.76 %), followed by Thailand (8.45 %) and Pakistan (5.9 %). Pigs (53.93 %), humans (17.41 %), and chickens (17.41 %) were determined to be important reservoirs of these isolates. The sequence types (STs) of E. coli were highly diverse, with the ST10 clone complex (Cplx) being the most prevalent clone. Correlation analysis revealed a positive association between the antibiotic resistance genes (ARGs) in ST10 E. coli and the presence of insertion sequences and plasmid replicons; however, we found no significant correlation between ARGs and virulence genes. Furthermore, the ST10 tet(X)-positive isolates from multiple sources displayed a high degree of genetic similarity (<200 single-nucleotide polymorphisms [SNPs]) to the mcr-1-positive but tet(X)-negative human-derived isolates, suggesting clonal transmission. The most prevalent tet(X) variant in the E. coli isolates was tet(X4), followed by tet(X6)-v. Genome-wide association study (GWAS) indicated that compared to tet(X4), tet(X6)-v harbored more significantly different resistance genes. Notably, certain tet(X)-positive E. coli isolates from different geographical locations or hosts shared a few SNPs (<200 SNPs), indicating cross-contamination. Therefore, continuous global surveillance of tet(X)-positive E. coli is imperative in the future.