出身背景
鲍曼不动杆菌是医院感染的重要原因，尤其是在重症监护室。它有耐受各种环境和多种抗生素的倾向。我们的研究旨在表征来自医院环境和临床分离株的鲍曼不动杆菌的比较基因组。
方法
临床和环境分离的鲍曼不动杆菌是从一所大学医院收集的。进行抗生素敏感性测试，鉴定抗生素耐药性基因（ARGs），并进行重复元素回文PCR（rep PCR）分型。从来自同一病房的环境和临床样本中分离出8个具有代表性的鲍曼不动杆菌，使用Illumina平台进行全基因组测序（WGS）。
后果
从312个医院环境样本中共获得106个鲍曼不动杆菌分离株。从AMBU袋（77.9%）、床栏（66.7%）和吸管（66.7%。blaOXA-23 blaNDM和blaOXA-58分别存在于80.2%、78.3%和0.9%的所有分离株中。从同一病房的患者标本中采集了61株鲍曼不动杆菌分离株。在所有鲍曼不动杆菌临床分离株中，MDRAB和XDRAB分别占82%和55.7%。鉴定出的显性ARGs最多的是blaOXA-23（80.3%），其次是blaNDM（55.7%）。使用rep-PCR将所有分离株的遗传多样性分为33种基因型。八个鲍曼不动杆菌的基因组大小在3.78–4.01Mb之间。我们发现八个菌株中有六个是blaNDM-5-羧化鲍曼不动杆菌。观察到位于blaNDM-5上游的移动遗传元件（MGE），如整合素1（intl1）。核心基因组和泛基因组的系统发育关系以及单核苷酸多态性（SNP）计数矩阵揭示了从同一病房获得的鲍曼不动杆菌环境菌株和临床菌株的遗传相似性。
结论
本研究证实，在医院环境中定植的鲍曼不动杆菌是医院感染的主要来源，并为控制鲍曼不动杆菌感染提供了重要信息。
Background
Acinetobacter baumannii (A. baumannii) is an important cause of nosocomial infection, especially in intensive care units (ICUs). It has the propensity to tolerate various environments and multiple classes of antibiotics. Our study aimed to characterize the comparative genomes of A. baumannii from hospital environments and clinical isolates.

Methods
Clinical and environmental A. baumannii isolates were collected from a university hospital. Antibiotic susceptibility testing was performed, antibiotic resistance genes (ARGs) were characterized, and repetitive element palindromic-PCR (rep-PCR) typing was performed. Eight representative A. baumannii isolated from environmental and clinical samples from the same wards were selected for whole-genome sequencing (WGS) using the Illumina platform.

Results
A total of 106 A. baumannii isolates were obtained from 312 hospital environmental samples. A high percentage of samples with A. baumannii colonization were detected from AMBU bags (77.9%), followed by bedrails (66.7%) and suction tubes (66.7%). We found that 93.4% of the environmental isolates were multidrug-resistant A. baumannii (MDRAB), and 44.7% were extremely drug-resistant A. baumannii (XDRAB). blaOXA-23 blaNDM, and blaOXA-58 were present in 80.2%, 78.3%, and 0.9% of all isolates, respectively. Sixty-one A. baumannii isolates were collected from patient specimens in the same ward. Among all A. baumannii clinical isolates, MDRAB and XDRAB accounted for 82% and 55.7%, respectively. The most dominant ARGs identified was blaOXA-23 (80.3%), followed by blaNDM (55.7%). The genetic diversity of all isolates using rep-PCR could be divided into 33 genotypes. The genome size of eight A. baumannii ranged from 3.78–4.01 Mb. We found six of eight strains to be blaNDM-5-harboring A. baumannii. Mobile genetic elements (MGEs), such as integron1 (intl1), located upstream of blaNDM-5 were observed. The phylogenomic relationship of the core and pan genomes as well as the single nucleotide polymorphism (SNP) count matrix revealed the genetic similarity of A. baumannii environmental and clinical strains obtained from the same ward.

Conclusion
This study confirmed that A. baumannii colonized in hospital environments were the main reservoir of nosocomial infection and provides critical information to guide the control of A. baumannii infection.

https://peerj.com/articles/14831/