Comparison of tet(X4)-containing contigs from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects.

The recently discovered tigecycline-inactivating enzyme Tet(X4) can confer high-level tigecycline resistance on its hosts, which makes it a public health concern. This study focused on detection, analysis, and characterization of Tet(X4)-positive Enterobacteriaceae from the gut microbiota of a healthy cohort of individuals in Singapore using cultivation-dependent and cultivation-independent approaches. Twelve Tet(X4)-positive Enterobacteriaceae strains that were previously obtained from the cohort were fully genome-sequenced and comparatively analysed. A metagenomic sequencing (MS) dataset of the same samples was mined for contigs that harboured the tet(X4) resistance gene. The sequences of tet(X4)-containing contigs and plasmids sequences were compared. The presence of the resistance genes floR and catD (also annotated as estT) was detected in the same cassette in 10 and 12 out of the 12 tet(X4)-carrying plasmids, respectively. MS detected tet(X4)-containing contigs in two out of 109 subjects, while cultivation-dependent analysis previously reported a prevalence of 10.1%. Contig sequences are relatively short ([~]14-33 kb) but show high similarity to the respective plasmid sequences of the isolates. The frequent co-occurrence of florR and catD with tet(X4) corroborates the hypothesis that the transmission of tet(X4) may have originated from the veterinary sector. Our findings show that MS can complement efforts in the surveillance of antibiotic resistance genes for clinical samples, while it has a lower sensitivity than a cultivation-based method when the target organism have a low abundance. Further optimisation is required if MS is to be utilised in antibiotic resistance surveillance.