Choudhury Samara T, Piper Kathryn R, Montoya-Giraldo Manuela, Ikhimiukor Odion O, Dettman Jeremy R, Kassen Rees, Andam Cheryl P
Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA.
Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada.
mSystems. 2025 May 20;10(5):e0030125. doi: 10.1128/msystems.00301-25. Epub 2025 Apr 30.
(class Gammaproteobacteria) is a ubiquitous, ecologically widespread, and metabolically versatile species. It is also an opportunistic pathogen that causes a variety of chronic and acute infections in humans. Its ability to thrive in diverse environments and exhibit a wide range of phenotypes lies in part on its large gene pool, but the processes that govern inter-strain genomic variation remain unclear. Here, we aim to characterize the recombination features and accessory genome structure of using 840 globally distributed genome sequences. The species can be subdivided into five phylogenetic sequence clusters (corresponding to known phylogroups), two of which are most prominent. Notable epidemic clones are found in the two phylogroups: ST17, ST111, ST146, ST274, and ST395 in phylogroup 1, and ST235 and ST253 in phylogroup 2. The two phylogroups differ in the frequency and characteristics of homologous recombination in their core genomes, including the specific genes that most frequently recombine and the impact of recombination on sequence diversity. Each phylogroup's accessory genome is characterized by a unique gene pool, co-occurrence networks of shared genes, and anti-phage defense systems. Different pools of antimicrobial resistance and virulence genes exist in the two phylogroups and display dissimilar patterns of co-occurrence. Altogether, our results indicate that each phylogroup displays distinct histories and patterns of acquiring exogenous DNA, which may contribute in part to their predominance in the global population. Our study has important implications for understanding the genome dynamics, within-species heterogeneity, and clinically relevant traits of .
The consummate opportunist inhabits many nosocomial and non-clinical environments, posing a major health burden worldwide. Our study reveals phylogroup-specific differences in recombination features and co-occurrence networks of accessory genes within the species. This genomic variation partly explains its remarkable ability to exhibit diverse ecological and phenotypic traits, and thus contribute to circumventing clinical and public health intervention strategies to contain it. Our results may help inform efforts to control and prevent diseases, including managing transmission, therapeutic efforts, and pathogen circulation in non-clinical environmental reservoirs.
（γ-变形菌纲）是一种无处不在、在生态上广泛分布且代谢功能多样的物种。它也是一种机会致病菌，可在人类中引起各种慢性和急性感染。它能够在不同环境中茁壮成长并表现出广泛的表型，部分原因在于其庞大的基因库，但控制菌株间基因组变异的过程仍不清楚。在此，我们旨在利用840个全球分布的基因组序列来表征[该物种名称未给出]的重组特征和辅助基因组结构。该物种可细分为五个系统发育序列簇（对应于已知的系统发育组），其中两个最为突出。在这两个系统发育组中发现了显著的流行克隆：系统发育组1中的ST17、ST111、ST146、ST274和ST395，以及系统发育组2中的ST235和ST253。这两个系统发育组在其核心基因组中同源重组的频率和特征方面存在差异，包括最频繁重组的特定基因以及重组对序列多样性的影响。每个系统发育组的辅助基因组都具有独特的基因库、共享基因的共现网络和抗噬菌体防御系统。两个系统发育组中存在不同的抗菌抗性和毒力基因库，并表现出不同的共现模式。总之，我们的结果表明，每个系统发育组都表现出独特的获取外源DNA的历史和模式，这可能部分有助于它们在全球种群中的优势地位。我们的研究对于理解[该物种名称未给出]的基因组动态、种内异质性和临床相关特征具有重要意义。
完美的机会致病菌[该物种名称未给出]存在于许多医院和非临床环境中，在全球范围内构成了重大的健康负担。我们的研究揭示了该物种内重组特征和辅助基因共现网络的系统发育组特异性差异。这种基因组变异部分解释了其展现出多样生态和表型特征的非凡能力，从而有助于规避控制它的临床和公共卫生干预策略。我们的结果可能有助于为控制和预防[该物种名称未给出]疾病的努力提供信息，包括管理传播、治疗措施以及非临床环境储库中的病原体循环。
