Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance

Abstract

<i>Delftia tsuruhatensis</i> has become an emerging pathogen in humans. There is scant information on the genomic characteristics of this microorganism. In this study, we determined the complete genome sequence of a clinical <i>D. tsuruhatensis</i> strain, TR1180, isolated from a sputum specimen of a female patient in China in 2019. Phylogenetic and average nucleotide identity analysis demonstrated that TR1180 is a member of <i>D. tsuruhatensis</i>. TR1180 exhibited resistance to β-lactam, aminoglycoside, tetracycline and sulphonamide antibiotics, but was susceptible to phenicols, fluoroquinolones and macrolides. Its genome is a single, circular chromosome measuring 6,711,018 bp in size. Whole-genome analysis identified 17 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, as well as 24 potential virulence factors and a number of metal resistance genes. Our data showed that <i>Delftia</i> possessed an open pan-genome and the genes in the core genome contributed to the pathogenicity and resistance of <i>Delftia</i> strains. Comparative genomics analysis of TR1180 with other publicly available genomes of <i>Delftia</i> showed diverse genomic features among these strains. <i>D. tsuruhatensis</i> TR1180 harbored a unique 38-kb genomic island flanked by a pair of 29-bp direct repeats with the insertion of a novel In4-like integron containing most of the specific antibiotic resistance genes within the genome. This study reports the findings of a fully sequenced genome from clinical <i>D. tsuruhatensis</i>, which provide researchers and clinicians with valuable insights into this uncommon species.