characterization of type i-f crispr-cas system in laribacter hongkongensis isolates from animals, the environment and diarrhea patients.
Characterization of type I-F CRISPR-Cas system in Laribacter hongkongensis isolates from animals, the environment and diarrhea patients.
机构信息
Department of Nosocomial Infection Administration, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
Office, Luohu district Center for Disease Control and Prevention, Shenzhen 518000, China.
出版信息
Int J Food Microbiol. 2021 May 16;346:109153. doi: 10.1016/j.ijfoodmicro.2021.109153. Epub 2021 Mar 11.
Laribacter hongkongensis is a foodborne organism that is associated with gastroenteritis and diarrhea in humans. Here we describe the structural characteristics and potential function of CRISPR systems to obtain insight into the genotypic diversity of L. hongkongensis. Specifically, we analyzed the genomic content of six L. hongkongensis genomes and identified two CRISPR loci (CRISPR1 and CRISPR2) belonging to the I-F subtype of CRISPR systems. CRISPR1 was flanked on one side by cas genes and a 170 bp-long putative leader sequence, while CRISPR2 arrays located further and processed by the same cas genes. Then a combination of PCR and sequencing was used to determine the prevalence and distribution of the two CRISPR arrays in 112 L. hongkongensis strains isolated from patients, animals, and water reservoirs. In total, the CRISPR1-Cas system of complete subtype I-F was detected in 91.5% (108/118) of the isolates, whereas CRISPR2 locus existed in 72.0% (85/118). Ten strains only possessed part of the cas genes of subtype I-F and four of them with CRISPR2 array. The two loci contained highly conserved and identical direct repeat sequences which were stable in their RNA secondary structure. Additionally, 2564 total spacers including 980 unique spacers arranged in 59 alleles were identified. Homology analysis showed only 1.8% (18/980) of the spacers matched with plasmid or phage. CRISPR polymorphism present in human isolates and frog isolates was more closely related and more extensive than that of fish isolates based on spacer polymorphism. The elucidation of the structural characteristics of the CRISPR-Cas system may be helpful for further studying the specific mechanism of adaptive immunity and other biological functions mediated by CRISPR in L. hongkongensis. The conservation of CRISPR loci and hypervariable repeat-spacer arrays imply the potential for molecular typing of L. hongkongensis.
香港阿克曼菌是一种食源性病原体，与人类的胃肠炎和腹泻有关。在这里，我们描述了 CRISPR 系统的结构特征和潜在功能，以深入了解香港阿克曼菌的基因型多样性。具体来说，我们分析了 6 株香港阿克曼菌基因组的基因组内容，并鉴定了 2 个属于 CRISPR 系统 I-F 亚类的 CRISPR 基因座（CRISPR1 和 CRISPR2）。CRISPR1 的一侧被 cas 基因和一个 170bp 长的假定前导序列侧翼包围，而 CRISPR2 阵列则位于更远的位置，并由相同的 cas 基因加工。然后，我们采用 PCR 和测序相结合的方法，在从患者、动物和水库中分离出的 112 株香港阿克曼菌中，确定了这两个 CRISPR 基因座的流行率和分布情况。在 118 株分离株中，91.5%（108/118）检测到完整的 I-F 型 CRISPR1-Cas 系统，而 CRISPR2 基因座存在于 72.0%（85/118）的分离株中。有 10 株仅具有 I-F 型部分 cas 基因，其中 4 株带有 CRISPR2 基因座。这两个基因座包含高度保守且相同的直接重复序列，在 RNA 二级结构中稳定存在。此外，鉴定出 2564 个间隔序列，包括 980 个独特的间隔序列，排列在 59 个等位基因中。同源性分析显示，只有 1.8%（18/980）的间隔序列与质粒或噬菌体匹配。基于间隔序列多态性，人类分离株和青蛙分离株中的 CRISPR 多态性与鱼类分离株相比更为密切相关且更为广泛。阐明 CRISPR-Cas 系统的结构特征可能有助于进一步研究香港阿克曼菌中适应性免疫的特定机制和其他由 CRISPR 介导的生物学功能。CRISPR 基因座和高变重复-间隔序列阵列的保守性表明，香港阿克曼菌的分子分型具有潜力。
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