An optimized method for bacterial strain differentiation, based on combination of Repeated Sequences and Whole Genome Alignment Differential Analysis (RS&WGADA), is presented in this report. In this analysis, 51 Acinetobacter baumannii multidrug-resistance strains from one hospital environment and patients from 14 hospital wards were classified on the basis of polymorphisms of repeated sequences located in CRISPR region, variation in the gene encoding the EmrA-homologue of E. coli, and antibiotic resistance patterns, in combination with three newly identified polymorphic regions in the genomes of A. baumannii clinical isolates. Differential analysis of two similarity matrices between different genotypes and resistance patterns allowed to distinguish three significant correlations (p < 0.05) between 172 bp DNA insertion combined with resistance to chloramphenicol and gentamycin. Interestingly, 45 and 55 bp DNA insertions within the CRISPR region were identified, and combined during analyses with resistance/susceptibility to trimethoprim/sulfamethoxazole. Moreover, 184 or 1374 bp DNA length polymorphisms in the genomic region located upstream of the GTP cyclohydrolase I gene, associated mainly with imipenem susceptibility, was identified. In addition, considerable nucleotide polymorphism of the gene encoding the gamma/tau subunit of DNA polymerase III, an enzyme crucial for bacterial DNA replication, was discovered. The differentiation analysis performed using the above described approach allowed us to monitor the distribution of A. baumannii isolates in different wards of the hospital in the time frame of several years, indicating that the optimized method may be useful in hospital epidemiological studies, particularly in identification of the source of primary infections.

本报告介绍了基于重复序列和全基因组比对差异分析 (RS&WGADA) 组合的细菌菌株分化优化方法。在这项分析中，根据位于 CRISPR 区域的重复序列的多态性、编码大肠杆菌EmrA 同源物的基因变异，对来自一个医院环境和来自 14 个医院病房的 51 株鲍曼不动杆菌多重耐药菌株进行分类，和抗生素耐药模式，结合鲍曼不动杆菌基因组中三个新发现的多态性区域临床分离株。不同基因型和抗性模式之间的两个相似性矩阵的差异分析允许区分三个显着相关性（p < 0.05) 172 bp DNA 插入与对氯霉素和庆大霉素的抗性相结合。有趣的是，鉴定了 CRISPR 区域内的 45 和 55 bp DNA 插入，并在分析过程中结合了对甲氧苄啶/磺胺甲恶唑的耐药性/敏感性。此外，确定了位于 GTP 环化水解酶 I 基因上游的基因组区域中 184 或 1374 bp 的 DNA 长度多态性，主要与亚胺培南敏感性相关。此外，还发现了编码 DNA 聚合酶 III（一种对细菌 DNA 复制至关重要的酶）的 gamma/tau 亚基的基因的相当多的核苷酸多态性。使用上述方法进行的分化分析使我们能够监测鲍曼不动杆菌的分布在几年的时间范围内在医院不同病房分离出分离物，表明优化的方法可能对医院流行病学研究有用，特别是在确定原发感染源方面。