摘要
      本研究对60个中国Morganella分离株进行了基因组测序，并对其中12个进行了全测序。然后，收集了166个全球测序的Morganella分离株，包括上述60个，进行基于平均核苷酸同一性的基因组分类和基于核心单核苷酸多态性的系统发育分析。建立了基于基因组序列的Morganella物种分类方案，相应地，将两个常规Morganellas物种重新定义为两个复合体，并分别进一步分为四个和两个基因物种。至少有88个获得性抗微生物耐药性基因（ARGs）在这166个分离株中传播，并且主要在来自医院的分离株中流行。IS26/IS15DI、IS10和IS1R以及Tn3-、Tn21-和Tn7亚家族单位转座子经常出现在这166个分离株中。此外，对来自完全测序的12个分离株的18个Morganella染色体附属遗传元件（AGEs）以及来自GenBank的5个原型AGEs进行了详细的序列比较。这23个AGEs被分为8个不同的组，属于复合/单位转座子、转座子原噬菌体、整合和可移动元件以及整合和偶联元件，它们携带至少52个ARG，涉及对15类抗菌药物的耐药性。这23个AGEs中有11个获得了大型附属模块，这些模块表现出复杂的镶嵌结构，并包含许多抗微生物耐药性基因座和相关的ARGs。将含有ARG的AGEs整合到Morganella染色体中，将有助于ARG在Morganlla中的积累和传播，并增强Morganella在复杂多样的抗菌选择压力下的适应和存活。
ABSTRACT
In this study, draft-genome sequencing was conducted for 60 Chinese Morganella isolates, and furthermore, 12 of them were fully sequenced. Then, a total of 166 global sequenced Morganella isolates, including the above 60, were collected to perform average nucleotide identity-based genomic classification and core single nucleotide polymorphism-based phylogenomic analysis. A genome sequence-based species classification scheme for Morganella was established, and accordingly, the two conventional Morganella species were redefined as two complexes and further divided into four and two genospecies, respectively. At least 88 acquired antimicrobial resistance genes (ARGs) were disseminated in these 166 isolates and were prevalent mostly in the isolates from hospital settings. IS26/IS15DI, IS10 and IS1R, and Tn3-, Tn21-, and Tn7-subfamily unit transposons were frequently presented in these 166 isolates. Furthermore, a detailed sequence comparison was applied to 18 Morganella chromosomal accessory genetic elements (AGEs) from the fully sequenced 12 isolates, together with 5 prototype AGEs from GenBank. These 23 AGEs were divided into eight different groups belonging to composite/unit transposons, transposable prophages, integrative and mobilizable elements, and integrative and conjugative elements, and they harbored at least 52 ARGs involved in resistance to 15 categories of antimicrobials. Eleven of these 23 AGEs acquired large accessory modules, which exhibited complex mosaic structures and contained many antimicrobial resistance loci and associated ARGs. Integration of ARG-containing AGEs into Morganella chromosomes would contribute to the accumulation and dissemination of ARGs in Morganella and enhance the adaption and survival of Morganella under complex and diverse antimicrobial selection pressures.

https://journals.asm.org/doi/full/10.1128/spectrum.02650-21