Srinivas Kandhan, Ghatak Sandeep, Pyngrope Daniel Aibor, Angappan Madesh, Milton Arockiasamy Arun Prince, Das Samir, Lyngdoh Vanita, Lamare John Pynhun, Prasad Mosuri Chendu Bharat, Sen Arnab
Division of Veterinary Public Health, ICAR - Indian Veterinary Research Institute, Bareilly, India.
Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India.
Front Microbiol. 2023 Jan 20;13:1080677. doi: 10.3389/fmicb.2022.1080677. eCollection 2022.
is regarded as an emerging pathogen with zoonotic potential. In the current study, we undertook source-wise comparative genomic analyses (resistome, virulome, mobilome and pangenome) to understand the antimicrobial resistance, virulence, mobile genetic elements and phylogenetic diversity of .
Six strains (5 multidrug resistant strains and 1 biofilm former) were isolated from poultry (duck faeces and retail chicken samples). Following confirmation by phenotypic and molecular methods, the isolates were further characterized and their genomes were sequenced. Comparative resisto-virulo-mobilome analyses and pangenomics were performed for genomes, while including 125 other genomes available from NCBI database.
Avian and porcine strains of were found to carry significantly higher number of antimicrobial resistance genes ( < 0.05) and mobile genetic elements (plasmids, transposons and integrons) ( < 0.05), while the pathogenic potential of bovine strains was significantly higher compared to other strains ( < 0.05). Pan-genome development trends indicated open pan-genome for all strains (0 < γ < 1). Genomic diversity of avian strains was found to be greater than that from other sources. Phylogenetic analysis revealed close clustering among isolates of similar isolation source and geographical location. Indian isolates of clustered closely with those from Chinese and a singleton Australian isolate. Overall, being the first pangenomic study on , our analysis provided important cues on genomic features of the emerging pathogen while highlighting the potential role of avian strains in dissemination of AMR.
被视为一种具有人畜共患病潜力的新兴病原体。在本研究中，我们进行了基于来源的比较基因组分析（抗性组、毒力组、可移动基因组和泛基因组），以了解该病原体的抗菌抗性、毒力、可移动遗传元件和系统发育多样性。
从家禽（鸭粪和零售鸡肉样本）中分离出6株该病原体菌株（5株多重耐药菌株和1株生物被膜形成菌）。经表型和分子方法确认后，对分离株进行进一步鉴定并对其基因组进行测序。对该病原体的基因组进行了比较抗性 - 毒力 - 可移动基因组分析和泛基因组学研究，同时纳入了NCBI数据库中可获得的其他125个该病原体基因组。
发现该病原体的禽类和猪类菌株携带的抗菌抗性基因数量（P < 0.05）和可移动遗传元件（质粒、转座子和整合子）数量（P < 0.05）显著更高，而牛类菌株的致病潜力与其他菌株相比显著更高（P < 0.05）。泛基因组发展趋势表明所有菌株的泛基因组都是开放的（0 < γ < 1）。发现禽类菌株的基因组多样性大于其他来源的菌株。系统发育分析显示，相似分离来源和地理位置的分离株紧密聚类。该病原体的印度分离株与来自中国的分离株以及一株单独的澳大利亚分离株紧密聚类。总体而言，作为对该病原体的首次泛基因组研究，我们的分析提供了关于这种新兴病原体基因组特征的重要线索，同时突出了禽类菌株在抗菌药物抗性传播中的潜在作用。
