DataSheet_3_Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance.pdf

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.

查氏戴尔福特菌（Delftia tsuruhatensis）现已成为一种新型人类致病菌。目前针对该微生物的基因组特征研究信息尚较为匮乏。本研究针对2019年从中国一名女性患者痰液标本中分离得到的临床查氏戴尔福特菌菌株TR1180，完成了全基因组测序。系统发育分析与平均核苷酸一致性（average nucleotide identity, ANI）分析结果显示，TR1180属于查氏戴尔福特菌。TR1180对β-内酰胺类、氨基糖苷类、四环素类及磺胺类抗生素具有耐药性，但对酰胺醇类、氟喹诺酮类及大环内酯类抗生素敏感。该菌株的基因组为一条长度6711018 bp的环状单染色体。全基因组分析共鉴定出17个与抗生素耐药相关的基因，其结果与该菌株的抗菌药敏表型一致；同时还鉴定出24个潜在毒力因子以及多个金属耐药基因。本研究数据表明，戴尔福特菌属（Delftia）拥有开放泛基因组，其核心基因组中的基因参与了该属菌株的致病过程与耐药机制。将TR1180与其他已公开的戴尔福特菌属基因组进行比较基因组学分析后发现，不同菌株间存在多样的基因组特征。查氏戴尔福特菌TR1180携带一段独特的38 kb基因组岛，该基因组岛两侧各有一对29 bp正向重复序列，且其基因组内插入了一个新型类In4整合子，该整合子包含了绝大多数特异性抗生素耐药基因。本研究报道了临床分离查氏戴尔福特菌的完整基因组序列，其研究结果可为科研人员与临床工作者深入了解这一罕见菌种提供宝贵参考。