Table_1_Molecular Epidemiology and Clone Transmission of Carbapenem-Resistant Acinetobacter baumannii in ICU Rooms.xlsx

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major cause of nosocomial infections and hospital outbreaks worldwide, remaining a critical clinical concern. Here we characterized and investigated the phylogenetic relationships of 105 CRAB isolates from an intensive care unit from one hospital in China collected over six years. All strains carried blaOXA-23, blaOXA-66 genes for carbapenem resistance, also had high resistance gene, virulence factor, and insertion sequence burdens. Whole-genome sequencing revealed all strains belonged to ST2, the global clone CC2. The phylogenetic analysis based on the core genome showed all isolates were dominated by a single lineage of three clusters and eight different clones. Two clones were popular during the collection time. Using chi-square test to identify the epidemiologically meaningful groupings, we found the significant difference in community structure only existed in strains from separation time. The haplotype and median-joining network analysis revealed genetic differences appeared among clusters and changes occurred overtime in the dominating cluster. Our results highlighted substantial multidrug-resistant CRAB burden in the hospital ICU environment demonstrating potential clone outbreak in the hospital.

耐碳青霉烯类鲍曼不动杆菌（Carbapenem-resistant Acinetobacter baumannii, CRAB）是全球范围内医院感染与医院暴发的主要致病菌之一，仍是临床亟待关注的关键问题。本研究对中国某医院重症监护室（intensive care unit, ICU）六年内收集的105株CRAB分离株进行了表征分析，并解析其系统发育关系。所有菌株均携带介导碳青霉烯类耐药的blaOXA-23、blaOXA-66基因，同时携带大量耐药基因、毒力因子与插入序列。全基因组测序（Whole-genome sequencing）结果显示，所有菌株均属于全球流行克隆CC2的ST2型别。基于核心基因组的系统发育分析表明，所有分离株均隶属于单一进化谱系，该谱系包含3个聚类群与8个不同克隆型。在本次采样周期内，有2个克隆型呈流行态势。采用卡方检验（chi-square test）识别具有流行病学意义的分组后，我们发现分离株的群体结构仅在不同分离时间的菌株间存在显著差异。单倍型（haplotype）与中介连接网络（median-joining network）分析结果显示，不同聚类群间存在遗传差异，且优势克隆型随时间推移发生了更迭。本研究结果凸显了医院ICU环境中广泛存在的多重耐药CRAB感染负担，证实了该医院存在克隆型暴发的潜在风险。