Byrne Alexander, Bissonnette Nathalie, Ollier Séverine, Tahlan Kapil
Department of Biology, Memorial University of Newfoundland , St. John's, Newfoundland and Labrador, Canada.
Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada , Sherbrooke, Quebec, Canada.
Microbiol Spectr. 2023 Aug 16;11(5):e0171623. doi: 10.1128/spectrum.01716-23.
subsp. (MAP) causes Johne's Disease (JD) in ruminants, which is responsible for significant economic loss to the global dairy industry. Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with genetically distinct strains of a pathogen, whereas within-host changes in an infecting strain leading to genetically distinguishable progeny is called microevolution. The two processes can influence host-pathogen dynamics, disease progression and outcomes, but not much is known about their prevalence and impact on JD. Therefore, we obtained up to 10 MAP isolates each from 14 high-shedding animals and subjected them to whole-genome sequencing. Twelve of the 14 animals examined showed evidence for the presence of MSIs and microevolution, while the genotypes of MAP isolates from the remaining two animals could be attributed solely to microevolution. All MAP isolates that were otherwise isogenic had differences in short sequence repeats (SSRs), of which SSR1 and SSR2 were the most diverse and homoplastic. Variations in SSR1 and SSR2, which are located in and , respectively, affect the genetic reading frame, leading to protein products with altered sequences and computed structures. The ORF1 gene product is predicted to be a MAP surface protein with possible roles in host immune modulation, but nothing could be inferred regarding the function of ORF2. Both genes are conserved in complex members, but SSR1-based modulation of reading frames seems to only occur in MAP, which could have potential implications on the infectivity of this pathogen. IMPORTANCE Johne's disease (JD) is a major problem in dairy animals, and concerns have been raised regarding the association of subsp. (MAP) with Crohn's disease in humans. MAP is an extremely slow-growing bacterium with low genome evolutionary rates. Certain short sequence repeats (SSR1 and SSR2) in the MAP chromosome are highly variable and evolve at a faster rate than the rest of the chromosome. In the current study, multiple MAP isolates with genetic variations such as single-nucleotide polymorphisms, and more noticeably, diverse SSRs, could simultaneously infect animals. Variations in SSR1 and SSR2 affect the products of the respective genes containing them. Since multiple MAP isolates can infect the same animal and the possibility that the pathogen undergoes further changes within the host due to unstable SSRs, this could provide a compensative mechanism for an otherwise slow-evolving pathogen to increase phenotypic diversity for overcoming host responses.
亚种（MAP）可导致反刍动物患副结核（JD），给全球乳制品行业造成重大经济损失。混合菌株感染（MSI）是指易感宿主同时感染同一病原体的不同基因菌株，而感染菌株在宿主体内发生变化导致产生基因上可区分的后代则称为微观进化。这两个过程会影响宿主与病原体的动态关系、疾病进展和结果，但人们对它们在副结核中的流行情况及其影响了解甚少。因此，我们从14头高排菌动物中各获取了多达10株MAP分离株，并对其进行全基因组测序。在接受检测的14头动物中，有12头显示出存在混合菌株感染和微观进化的证据，而其余两头动物的MAP分离株基因型则仅可归因于微观进化。所有其他方面同基因的MAP分离株在短序列重复（SSR）方面存在差异，其中SSR1和SSR2最为多样且具有同塑性。分别位于[具体位置1]和[具体位置2]的SSR1和SSR2的变异会影响基因阅读框，导致蛋白质产物的序列和计算结构发生改变。ORF1基因产物预计是一种MAP表面蛋白，可能在宿主免疫调节中发挥作用，但关于ORF2的功能无法得出任何推断。这两个基因在[具体名称]复合体成员中是保守的，但基于SSR1对[具体基因]阅读框的调节似乎仅发生在MAP中，这可能对该病原体的传染性有潜在影响。重要性副结核（JD）是奶牛养殖业中的一个主要问题，人们对亚种（MAP）与人类克罗恩病之间的关联也有所关注。MAP是一种生长极其缓慢的细菌，基因组进化速率较低。MAP染色体中的某些短序列重复（SSR1和SSR2）高度可变，且进化速度比染色体的其他部分更快。在当前研究中，多个具有单核苷酸多态性等基因变异、更显著的是具有多样SSR的MAP分离株可同时感染动物。SSR1和SSR2的变异会影响包含它们的各自基因的产物。由于多个MAP分离株可感染同一动物，且由于不稳定的SSR病原体在宿主体内可能会进一步发生变化，这可能为原本进化缓慢的病原体提供一种补偿机制，以增加表型多样性来克服宿主反应。
