Salmonella enterica Serovar Typhimurium Isolates from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type.
Salmonella enterica Serovar Typhimurium Isolates from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type.
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DOI：
10.1128/aem.01979-21
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发表时间：
2022-03-22
影响因子：
4.4
通讯作者：
Dudley EG
中科院分区：
文献类型：
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作者：
Fu Y;M'ikanatha NM;Lorch JM;Blehert DS;Berlowski-Zier B;Whitehouse CA;Li S;Deng X;Smith JC;Shariat NW;Nawrocki EM;Dudley EG
肠炎沙门氏菌血清型鼠伤寒沙门氏菌通常被认为是宿主多面手；然而，某些分离株与特定宿主相关，并表现出宿主适应的遗传特征。在这里，我们对1978年至2019年期间从美国30个州收集的野生鸟类中分离出的131株鼠伤寒沙门氏菌进行了测序。我们发现，从包括雀鸟、水鸟（Aequornithes）和larids（海鸥和燕鸥）在内的广泛寄主群体中分离的鼠伤寒沙门氏菌代表了三个不同的谱系，并且某些鼠伤寒沙门氏菌CRISPR类型在单个谱系中呈现。我们还发现，野生鸟类分离株形成的谱系与大多数来自家养动物的分离株不同，这些谱系的基因组通过机器学习分类器大大提高了鼠伤寒杆菌基因组对野生鸟类的来源归属。此外，还检测了鼠伤寒沙门氏菌与雀形目、水鸟和larids的毒力基因特征。雀形虫分离株往往缺乏鼠伤寒沙门氏菌特异性毒力质粒。雀鸟、水鸟和larid谱系的分离物与人类临床分离物具有密切的遗传相关性，包括2021年美国爆发的与雀鸟有关的分离物。这些观察结果表明，来自美国野生鸟类的鼠伤寒沙门氏菌可能具有宿主适应性，本研究中检查的具有代表性的基因组数据集可以改进源预测并促进暴发调查。鼠伤寒沙门氏菌在宿主内的进化可能导致病原体适应特定宿主。在这里，我们报告不同的禽鼠伤寒沙门氏菌谱系具有不同的毒力基因特征的出现。这些发现强调了野生鸟类作为鼠伤寒沙门氏菌储存库的重要性，并有助于我们了解野生鸟类鼠伤寒沙门氏菌的遗传多样性。我们的研究表明，鼠伤寒沙门氏菌可能在美国的野生鸟类中经历了适应性进化。具有代表性的野生鸟类鼠伤寒沙门氏菌基因组，以及在这些鸟类分离物中鉴定出的毒力基因特征，对鼠伤寒沙门氏菌来源归属和流行病学监测具有重要价值。
Salmonella enterica serovar Typhimurium is typically considered a host generalist; however, certain isolates are associated with specific hosts and show genetic features of host adaptation. Here, we sequenced 131 S. Typhimurium isolates from wild birds collected in 30 U.S. states during 1978–2019. We found that isolates from broad taxonomic host groups including passerine birds, water birds (Aequornithes), and larids (gulls and terns) represented three distinct lineages and certain S. Typhimurium CRISPR types presented in individual lineages. We also showed that lineages formed by wild bird isolates differed from most isolates originating from domestic animal sources, and that genomes from these lineages substantially improved source attribution of Typhimurium genomes to wild birds by a machine learning classifier. Furthermore, virulence gene signatures that differentiated S. Typhimurium from passerines, water birds, and larids were detected. Passerine isolates tended to lack S. Typhimurium-specific virulence plasmids. Isolates from the passerine, water bird, and larid lineages had close genetic relatedness with human clinical isolates, including those from a 2021 U.S. outbreak linked to passerine birds. These observations indicate that S. Typhimurium from wild birds in the United States are likely host-adapted, and the representative genomic data set examined in this study can improve source prediction and facilitate outbreak investigation. IMPORTANCE Within-host evolution of S. Typhimurium may lead to pathovars adapted to specific hosts. Here, we report the emergence of disparate avian S. Typhimurium lineages with distinct virulence gene signatures. The findings highlight the importance of wild birds as a reservoir for S. Typhimurium and contribute to our understanding of the genetic diversity of S. Typhimurium from wild birds. Our study indicates that S. Typhimurium may have undergone adaptive evolution within wild birds in the United States. The representative S. Typhimurium genomes from wild birds, together with the virulence gene signatures identified in these bird isolates, are valuable for S. Typhimurium source attribution and epidemiological surveillance.