Genomic characterization of multidrug-resistant <i>Escherichia albertii</i> of fish origin-first isolation and insights into a potential food safety threat

<h4>Introduction</h4><i>Escherichia albertii</i> is an emerging food-borne pathogen with zoonotic potential which is often under-reported due to misidentifications.<h4>Materials and methods</h4>The current study identified <i>E. albertii</i> from retail fish sold in market which was confirmed by phenotypic (colorless colonies on Xylose-Rhamnose-Melibiose MacConkey Agar), genotypic (dual target uniplex PCR-based detection) and genomic methods (CheckM analysis). In this paper we report the phenotypic characters of the isolate and genomic features such as resistome, virulome and mobilome followed by <i>in silico</i> O and H antigen based typing and comparative phylogenomics using various tools (RAST, RGI v6.0.0, ABRicate v1.0.1, PathogenFinder v1.1, PlasmidFinder v2.0, BacAnt v3.3.1, Phigaro v2.4.0, MAFFT v7.490, FigTree v1.4.4).<h4>Results and discussion</h4>Multidrug resistance was identified with reduced susceptibility to gentamicin, azithromycin, ceftazidime and cefotaxime with a Multiple Antibiotic Resistance (MAR) index of 0.33. Clinically important virulence genes such as <i>eae, cdt, east1</i> formed a part of the virulome and the probability of being pathogenic to humans was found to be 0.883. The genome was found to harbor mobile genetic elements such as plasmids [IncFIA, IncFIB(pB171), IncFII(pSE11)], transposons (Tn<i>3411</i>, Tn<i>6292</i>) and prophages (Siphoviridae, Myoviridae, Podoviridae). Various typing methods such as biotyping, multilocus sequence typing and <i>in silico</i> O and H antigen typing classified the isolate into biotype 3, multi locus sequence type 4596, O-genotype 4 and H-genotype 1. Phylogenomically, the isolate was placed close to isolate from neighboring country of China. Identification of virulent multidrug-resistant <i>E. albertii</i> from new food source such as fishes increases the risk for fish eating population and necessitates the requirement of further elucidation and development of appropriate control strategies.