AUTHOR=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 

TITLE=Avian strains of emerging pathogen Escherichia fergusonii are phylogenetically diverse and harbor the greatest AMR dissemination potential among different sources: Comparative genomic evidence

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1080677

DOI=10.3389/fmicb.2022.1080677

ISSN=1664-302X

ABSTRACT=<sec><title>Introduction</title><p><italic>Escherichia fergusonii</italic> 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 <italic>E. fergusonii</italic>.</p></sec><sec><title>Methods</title><p>Six <italic>E. fergusonii</italic> 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 <italic>E. fergusonii</italic> genomes, while including 125 other <italic>E. fergusonii</italic> genomes available from NCBI database.</p></sec><sec><title>Results and discussion</title><p>Avian and porcine strains of <italic>E. fergusonii</italic> were found to carry significantly higher number of antimicrobial resistance genes (<italic>p</italic> &lt; 0.05) and mobile genetic elements (plasmids, transposons and integrons) (<italic>p</italic> &lt; 0.05), while the pathogenic potential of bovine strains was significantly higher compared to other strains (<italic>p</italic> &lt; 0.05). Pan-genome development trends indicated open pan-genome for all strains (0 &lt; γ &lt; 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 <italic>E. fergusonii</italic> clustered closely with those from Chinese and a singleton Australian isolate. Overall, being the first pangenomic study on <italic>E. fergusonii</italic>, our analysis provided important cues on genomic features of the emerging pathogen <italic>E. fergusonii</italic> while highlighting the potential role of avian strains in dissemination of AMR.</p></sec>