关键词: AMR Escherichia fergusonii avian comparative genomics emerging mobilome pangenomics phylogeny

来  源:   DOI:10.3389/fmicb.2022.1080677   PDF(Pubmed)

Abstract:
UNASSIGNED: Escherichia fergusonii 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 E. fergusonii.
UNASSIGNED: Six E. fergusonii 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 E. fergusonii genomes, while including 125 other E. fergusonii genomes available from NCBI database.
UNASSIGNED: Avian and porcine strains of E. fergusonii were found to carry significantly higher number of antimicrobial resistance genes (p < 0.05) and mobile genetic elements (plasmids, transposons and integrons) (p < 0.05), while the pathogenic potential of bovine strains was significantly higher compared to other strains (p < 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 E. fergusonii clustered closely with those from Chinese and a singleton Australian isolate. Overall, being the first pangenomic study on E. fergusonii, our analysis provided important cues on genomic features of the emerging pathogen E. fergusonii while highlighting the potential role of avian strains in dissemination of AMR.
摘要:
UASSIGNED:埃希氏菌被认为是一种具有人畜共患潜力的新兴病原体。在目前的研究中,我们进行了来源比较基因组分析(抗性组,病毒组,动员体和pangenome)以了解抗菌素耐药性,毒力,费氏弧菌的可移动遗传元件和系统发育多样性。
UNASSIGNED:从家禽(鸭粪便和零售鸡样品)中分离出6株E.Fergusonii菌株(5株多重耐药菌株和1株生物膜形成剂)。通过表型和分子方法确认后,对分离株进行了进一步鉴定,并对其基因组进行了测序.对E.Fergusonii基因组进行了比较性的病毒动员体分析和pangenomics,同时包括来自NCBI数据库的125个其他E.Fergusonii基因组。
UNASSIGNED:研究发现,禽和猪的E.fergusonii菌株携带明显更多的抗微生物抗性基因(p<0.05)和可移动的遗传元件(质粒,转座子和整合子)(p<0.05),而牛菌株的致病潜力明显高于其他菌株(p<0.05)。全基因组发展趋势表明所有菌株的全基因组开放(0<γ<1)。发现禽类菌株的基因组多样性大于其他来源的基因组多样性。系统发育分析显示,具有相似隔离源和地理位置的分离株之间存在紧密的聚类。E.fergusonii的印度分离株与来自中国人和单胎澳大利亚的分离株紧密聚集。总的来说,是第一个关于弗格森的全基因组研究,我们的分析为新出现的病原体E.Fergusonii的基因组特征提供了重要线索,同时突出了禽类菌株在AMR传播中的潜在作用.
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