Comparative analysis of Vibrio cholerae isolates from Ghana reveals variations in genome architecture and adaptation of outbreak and environmental strains.
Comparative analysis of Vibrio cholerae isolates from Ghana reveals variations in genome architecture and adaptation of outbreak and environmental strains.
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DOI：
10.3389/fmicb.2022.998182
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发表时间：
2022
影响因子：
5.2
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中科院分区：
文献类型：
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霍乱的反复流行表明霍乱弧菌在不同的应激条件下对生态转移和持久性具有强大的适应机制。跟踪病理生物学性状的演变需要对来自流行地区的分离株进行比较基因组研究。在这里，我们研究了霍乱弧菌临床分离株和环境分离株之间的遗传分化，强调了与基因衰变、基因组可塑性以及获得毒力和适应性状相关的基因组差异。与进化上不同的环境菌株相比，临床分离株具有较高的同源基因频率和较少的基因变异，显示出高度的系统发育亲缘性。环境分离株的分化与包含可移动遗传元件的区域的广泛基因组重排有关，导致许多断点、重定位和插入，以及基因组岛中毒力决定因素acf、zot、tcp和ctx的丧失。此外，4个分离株具有针对弧菌噬菌体和质粒特异性间隔的CRISPR-Cas系统。CRISPR-Cas系统的基因组同源性和同源性分析表明是水平获取的。其他噬菌体和质粒防御系统（如Zorya、DdmABC、DdmDE和i型限制性修饰系统）在分离株中的分布存在显著差异，表明环境分离株更倾向于质粒或噬菌体传播特性。我们的研究结果表明，霍乱弧菌菌株经历了广泛的基因组重排和基因获取，反映了它们在生态转变和致病性中的适应性。
Recurrent epidemics of cholera denote robust adaptive mechanisms of Vibrio cholerae for ecological shifting and persistence despite variable stress conditions. Tracking the evolution of pathobiological traits requires comparative genomic studies of isolates from endemic areas. Here, we investigated the genetic differentiation among V. cholerae clinical and environmental isolates by highlighting the genomic divergence associated with gene decay, genome plasticity, and the acquisition of virulence and adaptive traits. The clinical isolates showed high phylogenetic relatedness due to a higher frequency of shared orthologs and fewer gene variants in contrast to the evolutionarily divergent environmental strains. Divergence of the environmental isolates is linked to extensive genomic rearrangements in regions containing mobile genetic elements resulting in numerous breakpoints, relocations, and insertions coupled with the loss of virulence determinants acf, zot, tcp, and ctx in the genomic islands. Also, four isolates possessed the CRISPR-Cas systems with spacers specific for Vibrio phages and plasmids. Genome synteny and homology analysis of the CRISPR-Cas systems suggest horizontal acquisition. The marked differences in the distribution of other phage and plasmid defense systems such as Zorya, DdmABC, DdmDE, and type-I Restriction Modification systems among the isolates indicated a higher propensity for plasmid or phage disseminated traits in the environmental isolates. Our results reveal that V. cholerae strains undergo extensive genomic rearrangements coupled with gene acquisition, reflecting their adaptation during ecological shifts and pathogenicity.