Whole-genome-based characterization of Escherichia albertii strains isolated from paediatric diarrhoeal cases in Kolkata, India

<i>Escherichia albertii</i> is a Gram-negative facultative anaerobic bacterium that causes diarrhoea in humans. This study shows the isolation of <i>E. albertii</i> from hospitalized paediatric diarrhoeal cases and genome-based characteristics with putative virulence factors and antimicrobial resistance. <i>E. albertii</i> isolates were identified by species-specific PCR, targeting the gene encoding cytolethal distending toxin (<i>Ea-cdt</i>). The genome of <i>E. albertii</i> was sequenced to identify (i) genes encoding virulence factors (ii) antibiotic resistance-encoding genes, including the mobile genetic elements and (iii) core gene-based phylogenetic relationships and pan-genome features. A total of 10 (1.2%) <i>E. albertii</i> isolates were isolated from 854 faecal samples, of which 6 (60%) were found as the sole pathogen and the remaining 4 (40%) were identified along with other pathogens, such as enteroaggregative <i>Escherichia coli</i>, rotavirus and adenovirus. Patients from whom <i>E. albertii</i> was isolated presented cholera-like diarrhoea, i.e. with watery stool (60%) with moderate dehydration (100%), fever (20%) and abdominal pain (20%). The antimicrobial susceptibility testing of <i>E. albertii</i> showed that most of the isolates were susceptible or reduced susceptible to most of the antibiotics except resistance to erythromycin (80%), tetracycline (50%), nalidixic acid (40%), ampicillin (40%), doxycycline (30%) and ceftriaxone (20%). In the whole-genome sequence, <i>E. albertii</i> isolates revealed several virulence-encoding genes, namely the intimin (<i>eae</i>, <i>E. coli</i> attaching and effacing), the cytolethal distending toxin type II subunit A (<i>cdt-IIA</i>), adhesion (<i>paa</i>, porcine attaching- and effacing-associated), non-LEE (locus of enterocyte effacement) encoded effector A (<i>nleA</i>) and antimicrobial resistance genes (ARGs) conferring resistance to tetracycline (<i>tetA</i>, <i>tetR</i>), sulphonamides (<i>sul2</i>), fluoroquinolones (<i>qnrS</i>) and beta-lactamases (<i>bla</i> _CTX-M, <i>bl</i>a_TEM). The SNP-based phylogenetic analysis of 647 whole genomes of <i>E. albertii</i> isolates from the National Center for Biotechnology Information databases did not reveal any comparable clustering pattern based on the biological source and place of isolation. The genome of some of the <i>E. albertii</i> was closely related to those of the isolates from China and the United Kingdom. The PFGE patterns revealed that most of the <i>E. albertii</i> isolates were distinct clones. This study reports on the extensive genome analysis of diarrhoea-associated <i>E. albertii</i> harbouring multiple virulence and ARGs.