BACKGROUND Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization. RESULTS We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 indels, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation analyses indicate that genes of the VapBC family, a toxin-antitoxin system, and genes related to cell wall remodeling are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations were only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamate, respectively) gene families. We also detected large deletions in ancient and modern M. pinnipedii strains, including a few occurring only in modern strains, indicating a process of genome reduction occurring over the past one thousand years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 deletions may have occurred independently, twice, over the evolutionary course of the MTBC. CONCLUSION The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. Mycobacterium pinnipedii proteomes of the studied isolates showed a high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.

中文翻译：

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Pinnipedii菌株的基因组测序：南美海狮（Otaria flavescens）的遗传特征和超感染证据。

背景技术作为结核分枝杆菌复合体（MTBC）的成员的pinnipedii分枝杆菌能够感染几种宿主物种，包括人类。最近，从秘鲁的哥伦布时期以前的木乃伊中回收了这种生物的古代DNA，引发了人们对欧洲殖民之前美洲结核病的起源和发生频率的争论。结果我们从该南美bacterial的不同器官中获得的两个Pinnipedii分离株（MP1和MP2）的基因组测序开始，对该细菌物种进行了首次比较基因组研究。我们的结果表明，MP1和MP2相差113个SNP（单核苷酸多态性）和46个indel，构成了海狮中混合菌株感染的首次报道。SNP注释分析表明VapBC家族的基因 毒素-抗毒素系统，与细胞壁重塑相关的基因处于进化压力之下，这些菌株中的蛋白质序列发生了变化。OrpinMCL分析与七个现代的M. pinnipedii分离株表明，这些菌株具有高度相似的蛋白质组。基因变异仅与假设的蛋白质和PE / PPE（分别为脯氨酸-谷氨酸和脯氨酸-脯氨酸-谷氨酸）基因家族相关。我们还检测到了古代和现代的Pinnipedii菌株中的大量缺失，包括仅在现代菌株中出现的一些缺失，这表明过去一千年来发生了基因组减少的过程。我们的系统生物学分析表明，存在两个与地理位置相关的M.pinnipedii现代集群，可能还有寄主物种，以及一个与古代M.关联的基础节点。pinnipedii菌株。先前描述的MiD3和MiD4缺失可能在MTBC的进化过程中独立发生了两次。结论在这种海狮中存在过度感染（即混合菌株感染）表明，pinnipedii分枝杆菌在该种群中是高度流行的。尽管与结核分枝杆菌相比处于基因组衰退状态，但研究菌株的pinnipedii分枝杆菌蛋白质组却显示出高度的保守性。这一发现表明，需要对更多的基因组进行测序和分析，以增加在菌株中发现存在变异基因的机会，或者在细菌形成之前发生了Pinnipedii的M.基因组重塑。结论在这种海狮中存在过度感染（即混合菌株感染）表明，pinnipedii分枝杆菌在该种群中是高度流行的。尽管与结核分枝杆菌相比处于基因组衰退状态，但研究菌株的pinnipedii分枝杆菌蛋白质组却显示出高度的保守性。这一发现表明，需要对更多的基因组进行测序和分析，以增加在菌株中发现存在变异基因的机会，或者在细菌形成之前发生了Pinnipedii的M.基因组重塑。结论在这种海狮中存在过度感染（即混合菌株感染）表明，pinnipedii分枝杆菌在该种群中是高度流行的。尽管与结核分枝杆菌相比处于基因组衰退状态，但研究菌株的pinnipedii分枝杆菌蛋白质组却显示出高度的保守性。这一发现表明，需要对更多的基因组进行测序和分析，以增加在菌株中发现存在变异基因的机会，或者在细菌形成之前发生了Pinnipedii的M.基因组重塑。