Abstract:
Shigella spp. are Gram-negative rod-shaped bacteria belonging to the family
Enterobacteriaceae and are known to be a major cause of bacillary dysentery
worldwide. In this study, whole-genome sequencing was used for the molecular
characterization of ESBL producing Shigella spp. isolates collected from hospitals in
Lebanon. PCRs were performed to detect β-lactam resistance gene reservoirs and to
identify genes involved in virulence and host adaptation. PCR-based replicon typing
(PBRT) was performed to identify patterns of plasmid distribution. For comparative
analysis, multi-locus sequence typing (MLST), whole-genome based SNP analysis,
Pan-genome analysis and pulsed-field gel electrophoresis (PFGE) were performed to
determine the phylogenic relatedness of the isolates and to trace evolutionary lineages.
Our study revealed that, eight of the isolates were ESBL producers; resistance to β-lactam was mainly manifested by the presence of blaCTX-M-15, blaCTX-M-3, and blaTEM-1B
genes. Inc I1α and IncFII were the prevalent incompatibility groups, with IncI1α being
detected in all the isolates, and IncFII in eight of the isolates. β-lactam resistance
determinants were found mainly on these two plasmids. class 2 integron was the most
common integron detected (nine of the isolates) whereas class 1 was only seen in two
of the isolates. The ten sequenced isolates were distributed on three multi-locus
sequence types (MLST) (ST152, ST145 and ST245) with ST152 being the predominant. Our study focuses on important virulence determinants and effector
proteins used by the bacterium to destroy the host. Individual PCRs were performed
to detect the presence of virA (motility), ial (invasion), ipaH (immune system
modulation), set and sen (enterotoxins). The study provided an overview of the major
plasmid families circulating in multidrug resistant Shigella in Lebanon. The results
obtained revealed the role of integrons and gene cassettes in the dissemination of
antimicrobial resistant determinants in Shigella and gave an insight of the phylogenic
relationships between the undertaken isolates and other worldwide-recovered representatives. This study and through the use of genome-based approaches helped
in better understanding the diversity of Shigella, its pathogenesis and drug resistance
at the molecular level, and the risk factors associated with the mobilization of plasmids
between Shigella spp. and other enteric pathogens
