Abstract
The emergence of bacterial pathogens in environmental hosts represents a major risk to public health. This study aimed at characterizing seven novel environmental strains of
using a genomic approach which was misidentified by phenotypic methods in a previous batch of 27 species thought to be
.
Whole-genome sequencing was performed using the Illumina platform, and the generated raw reads were
assembled. Comparative genomic, resistome, virulome, mobilome, and phylogeny were then investigated using dierent bioinformatics tools.
Six strains were identified as
subsp
and one as
subsp.
. All isolates were resistant to ampicillin, cephalexin, and amoxicillin-clavulanic acid and harbored the
,
types,
, and
genes. One isolate additionally harbored a gene cassettes consisting of
,
,
'
genes. The aminoglycoside-modifying enzyme gene
was bracketed by two insertion elements. Plasmid analyses showed that IncFIB
was the most prevalent plasmid, circulating in six isolates, while one isolate exhibited seven different plasmids. The isolates have virulence genes responsible for capsule formation, lipopolysaccharide, iron uptake aerobactin (
), salmochelins (
), enterobactin siderophore, adherence, and biofilm formation (
, and
).
Our study highlights the ecology and transmission of
(which have the ability to disseminate to other environmental sources including animals) outside the clinical setting and the contribution of water, vegetables, and table surfaces as potential reservoirs of farm-to-fork transmission of disease via local markets in Khartoum, Sudan.