School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
School of Life Sciences, Westlake University, Hangzhou, Zhejiang, PR China.
Int J Syst Evol Microbiol. 2024 Feb;74(2). doi: 10.1099/ijsem.0.006264.
Infectious diseases threaten endangered species, particularly in small isolated populations. Seabird populations on the remote Amsterdam Island in the Indian Ocean have been in decline for the past three decades, with avian cholera caused by proposed as the primary driver. However, species have also been sporadically detected from albatrosses on Amsterdam Island and may be contributing to some of the observed mortality. In this study, we genomically characterized 16 species isolates obtained from three Indian yellow-nosed albatross () chick carcasses in 2019. Histological analyses suggest that they died of bacterial septicaemia. Two isolates were sequenced using both Illumina short-read and MinION long-read approaches, which - following hybrid assembly - resulted in closed circular genomes. Mapping of Illumina reads from the remaining isolates to one of these new reference genomes revealed that all 16 isolates were closely related, with a maximum of 13 nucleotide differences distinguishing any pair of isolates. The nucleotide diversity of isolates obtained from the same or different carcasses was similar, suggesting all three chicks were likely infected from a common source. These genomes were compared with a global collection of genomes from and other species from the same genus. The isolates from albatrosses were phylogenetically distinct, sharing a most recent common ancestor with . Based on phylogenomic analysis and standard thresholds for average nucleotide identity and digital DNA-DNA hybridization, these isolates represent a novel species, for which we propose the name sp. nov. The type strain is A18Y020d (=CIP 112216=DSM 115297). The implications of this bacterium for albatross conservation will require further study.
传染病威胁着濒危物种，尤其是在小而孤立的种群中。过去三十年来，印度洋偏远的阿姆斯特丹岛上的海鸟数量一直在减少，由 引起的禽霍乱被认为是主要驱动因素。然而， 种也偶尔在阿姆斯特丹岛上的信天翁身上检测到，可能导致了部分观察到的死亡率。在这项研究中，我们从 2019 年三只印度洋黄鼻信天翁雏鸟的尸体中获得了 16 个 种分离株，并对其进行了基因组特征分析。组织学分析表明，它们死于细菌性败血症。使用 Illumina 短读和 MinION 长读两种方法对其中两个分离株进行了测序，经过混合组装后，得到了闭合的环状基因组。将剩余分离株的 Illumina 读数映射到其中一个新的参考基因组上，结果表明这 16 个分离株密切相关，任何两个分离株之间最多有 13 个核苷酸差异。从同一或不同尸体中获得的分离株的核苷酸多样性相似，这表明这三只雏鸟可能来自同一传染源。将这些基因组与来自 和同一属的其他物种的全球基因组集合进行了比较。从信天翁中分离出的菌株在系统发育上是不同的，与 共享最近的共同祖先。基于系统基因组分析和平均核苷酸同一性和数字 DNA-DNA 杂交的标准阈值，这些分离株代表了一个新的 种，我们提议将其命名为 sp. nov.。模式株为 A18Y020d（=CIP 112216=DSM 115297）。这种细菌对信天翁保护的影响需要进一步研究。
