摘要
目标
奇异变形杆菌是一种重要的机会性革兰氏阴性病原体。本研究报道了耐多药（MDR）奇异假单胞菌PM1162的全基因组序列，并探讨了其抗生素抗性基因（ARGs）及其遗传环境。
方法
奇异假单胞菌PM1162是从中国的一种尿路感染中分离出来的。测定了抗菌药物的敏感性，并进行了全基因组测序（WGS）。ARGs、插入序列（IS）元件和原噬菌体分别使用ResFinder、ISfinder和PHASTER软件进行鉴定。分别使用BLAST和Easyfig进行序列比较和图谱生成。
后果
奇异假单胞菌PM1162在其染色体上携带15个ARGs，包括cat、tet（J）、blaCTX-M-14（三个拷贝）、aph（3′）-Ia、qnrB4、blaDHA-1、qacE、sul1、armA、msr（E）、mph（E），aadA1和dfrA1。我们重点分析了四个相关的MDR区域：（1）与blaCTX-M-14相关的遗传背景；（2） 原噬菌体含有blaDHA-1、qnrB4和aph（3′）-Ia；（3） 与mph（E）、msr（E），armA、sul和qacE相关的遗传环境；和（4）携带dfrA1、sat2和aadA1的II类整合子。
结论
本研究报道了耐多药奇异假单胞菌PM1162的全基因组序列及其ARGs的遗传背景。这种对耐多药奇异假单胞菌PM1162的全面基因组分析为其耐多药机制提供了更深入的理解，并阐明了其ARGs的水平传播，从而为遏制和治疗该细菌提供了基础。
ABSTRACT
Objectives
Proteus mirabilis is an important opportunistic Gram-negative pathogen. This study reports the whole genome sequence of multidrug-resistant (MDR) P. mirabilis PM1162 and explores its antibiotic resistance genes (ARGs) and their genetic environments.

Methods
P. mirabilis PM1162 was isolated from a urinary tract infection in China. Antimicrobial susceptibility was determined, and whole genome sequencing (WGS) was performed. ARGs, insertion sequence (IS) elements, and prophages were identified using ResFinder, ISfinder, and PHASTER software, respectively. Sequence comparisons and map generation were performed using BLAST and Easyfig, respectively.

Results
On its chromosome, P. mirabilis PM1162 harboured 15 ARGs, including cat, tet(J), blaCTX-M-14 (three copies), aph(3′)-Ia, qnrB4, blaDHA-1, qacE, sul1, armA, msr(E), mph(E), aadA1, and dfrA1. We focused our analysis on the four related MDR regions: (1) genetic contexts associated with blaCTX-M-14; (2) the prophage containing blaDHA-1, qnrB4, and aph(3′)-Ia; (3) genetic environments associated with mph(E), msr(E), armA, sul, and qacE; and (4) the class II integron harbouring dfrA1, sat2, and aadA1.

Conclusion
This study reported the whole genome sequence of MDR P. mirabilis PM1162 and the genetic context of its ARGs. This comprehensive genomic analysis of MDR P. mirabilis PM1162 provides a deeper understanding of its MDR mechanism and elucidates the horizontal spread of its ARGs, thus providing a basis for the containment and treatment of the bacteria.

https://www.sciencedirect.com/science/article/pii/S2213716523000358