Table_3_Whole-genome sequencing reveals high-risk clones of Pseudomonas aeruginosa in Guangdong, China.XLSX

The ever-increasing prevalence of infections produced by multidrug-resistant or extensively drug-resistant Pseudomonas aeruginosa is commonly linked to a limited number of aptly-named epidemical ‘high-risk clones’ that are widespread among and within hospitals worldwide. The emergence of new potential high-risk clone strains in hospitals highlights the need to better and further understand the underlying genetic mechanisms for their emergence and success. P. aeruginosa related high-risk clones have been sporadically found in China, their genome sequences have rarely been described. Therefore, the large-scale sequencing of multidrug-resistance high-risk clone strains will help us to understand the emergence and transmission of antibiotic resistances in P. aeruginosa high-risk clones. In this study, 212 P. aeruginosa strains were isolated from 2 tertiary hospitals within 3 years (2018–2020) in Guangdong Province, China. Whole-genome sequencing, multi-locus sequence typing (MLST) and antimicrobial susceptibility testing were applied to analyze the genomic epidemiology of P. aeruginosa in this region. We found that up to 130 (61.32%) of the isolates were shown to be multidrug resistant, and 196 (92.45%) isolates were Carbapenem-Resistant Pseudomonas aeruginosa. MLST analysis demonstrated high diversity of sequence types, and 18 reported international high-risk clones were identified. Furthermore, we discovered the co-presence of exoU and exoS genes in 5 collected strains. This study enhances insight into the regional research of molecular epidemiology and antimicrobial resistance of P. aeruginosa in China. The high diversity of clone types and regional genome characteristics can serve as a theoretical reference for public health policies and help guide measures for the prevention and control of P. aeruginosa resistance.

多重耐药（multidrug-resistant）或泛耐药（extensively drug-resistant）铜绿假单胞菌（Pseudomonas aeruginosa）引起的感染患病率持续攀升，这类感染通常与少数命名贴切的流行性‘高风险克隆株’相关——这类克隆株在全球各级医院内部及医院之间广泛传播。医院中新型潜在高风险克隆株的出现，凸显了深入解析其出现与流行背后潜在遗传机制的必要性。此前国内仅零星检出与铜绿假单胞菌相关的高风险克隆株，且相关基因组序列的报道极为匮乏。因此，对多重耐药高风险克隆株开展大规模基因组测序，将有助于解析铜绿假单胞菌高风险克隆株中抗生素耐药性的出现与传播机制。本研究于2018至2020年三年间，从中国广东省的2家三级医院分离得到212株铜绿假单胞菌。研究采用全基因组测序、多位点序列分型（multi-locus sequence typing, MLST）以及抗菌药物敏感性试验，对该区域铜绿假单胞菌的基因组流行病学特征进行分析。结果显示，共计130株（占比61.32%）分离株为多重耐药株，196株（占比92.45%）为碳青霉烯类耐药铜绿假单胞菌（Carbapenem-Resistant Pseudomonas aeruginosa）。多位点序列分型分析表明，该区域菌株的序列型别具有高度多样性，共鉴定出18种已报道的国际高风险克隆株。此外，本研究在5株分离株中检测到exoU与exoS基因共同存在。本研究加深了国内对铜绿假单胞菌分子流行病学与抗菌耐药性的区域研究认知。该研究揭示的克隆型别高度多样性及区域基因组特征，可为公共卫生政策制定提供理论参考，同时有助于指导铜绿假单胞菌耐药性的防控工作。