Table_3_Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance.docx

Delftia tsuruhatensis 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 D. tsuruhatensis 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 D. tsuruhatensis. 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 Delftia possessed an open pan-genome and the genes in the core genome contributed to the pathogenicity and resistance of Delftia strains. Comparative genomics analysis of TR1180 with other publicly available genomes of Delftia showed diverse genomic features among these strains. D. tsuruhatensis 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 D. tsuruhatensis, which provide researchers and clinicians with valuable insights into this uncommon species.

德尔菲亚菌（Delftia tsuruhatensis）已成为人类新兴病原体。关于该微生物的基因组特征信息稀缺。在本研究中，我们确定了2019年从中国一名女性患者的痰液中分离出的临床菌株TR1180的完整基因组序列。通过系统发育和平均核苷酸同源性分析，证实了TR1180为德尔菲亚菌的一员。TR1180表现出对β-内酰胺类、氨基糖苷类、四环素和磺胺类抗生素的耐药性，但对苯酚类、氟喹诺酮类和宏环素类抗生素敏感。其基因组为单一、环状染色体，大小为6,711,018碱基对。全基因组分析鉴定出17个与抗生素耐药性相关的基因，这与该菌株的抗菌敏感性谱相匹配，以及24个潜在的毒力因子和多个金属耐药基因。我们的数据显示，德尔菲亚菌具有开放的全基因组，核心基因组中的基因有助于德尔菲亚菌株的致病性和耐药性。与公开可用的其他德尔菲亚菌基因组进行比较基因组学分析，这些菌株之间展现出多样化的基因组特征。德尔菲亚菌TR1180携带一个独特的38-kb基因组岛，该岛被一对29-bp直接重复序列所夹持，并插入了一个包含基因组中大部分特定抗生素耐药基因的新型In4样整合子。本研究报告了对临床德尔菲亚菌TR1180的完整基因组测序结果，为研究人员和临床医生提供了关于这一罕见物种的宝贵见解。