摘要
目标
本研究的目的是对从中国养猪场分离的耐多药奇异变形杆菌ChSC1905菌株的全基因组序列进行表征。
方法
通过Illumina NovaSeq和Oxford Nanopore平台对基因组进行测序，并通过Canu v.1.5进行组装。通过ResFinder对获得性抗微生物耐药性基因（ARGs）进行鉴定。进行了共轭实验，以确定整合和共轭元素的运动。
后果
菌株ChSC1905表现出MDR表型。菌株ChSC1905的基因组长度为4 038 038 bp，GC含量为39.1%，包含3645个编码序列和110个RNA基因。共鉴定出23个获得性ARGs，其中21个ARGs位于SXT/R391整合偶联元件（ICE）上，包括临床上重要的抗性基因blaCTX-M-65、cfr、fosA3和aac（6′）-Ib-cr。BLAST分析表明，这个新的SXT/R391家族ICE（ICEPmiChnChSC1905，143689bp）参与了由ISVsa3介导的序列反转和由IS26介导的基因重排，并且可以转移到大肠杆菌EC600中。
结论
在本研究中，我们报道了耐多药奇异假单胞菌菌株ChSC1905的基因组序列，该菌株携带了一个新的SXT/R391家族ICE（ICEPmiChnChSC1905），该家族参与了中国的基因重排，这促进了ICE的多样性，应该受到更多的关注。
ABSTRACT
Objectives
The aim of this study was to characterise the whole genome sequence of a multidrug-resistant (MDR) Proteus mirabilis strain ChSC1905 isolated from a swine farm in China.

Methods
The genome was sequenced by Illumina NovaSeq and Oxford Nanopore platforms, and it was assembled via Canu v.1.5. The acquired antimicrobial resistance genes (ARGs) were identified by ResFinder. A conjugation experiment was carried out to determine the mobilisation of integrative and conjugative element.

Results
Strain ChSC1905 exhibited a MDR phenotype. The genome of strain ChSC1905 was 4 038 038 bp in length with a GC content of 39.1%, which contained 3645 coding sequences and 110 RNA genes. A total of 23 acquired ARGs were identified, among which 21 ARGs including the clinically important resistance genes blaCTX-M-65, cfr, fosA3, and aac(6′)-Ib-cr were located on a SXT/R391 integrative and conjugative element (ICE). BLAST analysis showed that this new SXT/R391-family ICE (ICEPmiChnChSC1905 of 143 689 bp) was involved in sequence inversion mediated by ISVsa3 and genetic rearrangement mediated by IS26, and it could be transferred to E. coli EC600.

Conclusion
In this study, we report the genome sequence of MDR P. mirabilis strain ChSC1905 that harboured a novel SXT/R391-family ICE (ICEPmiChnChSC1905) involved in genetic rearrangement in China, which promotes the diversity of ICE and should receive more attention.

https://www.sciencedirect.com/science/article/pii/S2213716522001709