Complete genome sequence and antimicrobial resistance analysis of ESBL-producing Shigella sonnei carrying small cryptic plasmids isolated in northern Italy

Abstract

Herein, we sequenced and assembled the genome of an S. sonnei isolate carrying several small plasmids using a hybrid approach combining Oxford Nanopore technologies (ONT) and Illumina platforms. Whole genome sequencing was conducted using the Illumina iSeq 100 and the Oxford Nanopore MinION systems, and the resulting reads were used for hybrid genome assembly with Unicycler. Coding sequences were annotated with RASTtk, while genes involved in antimicrobial resistance and virulence were identified with AMRFinderPlus. Plasmid nucleotide sequences were aligned to the NCBI nr database using BLAST, and replicons were identified using PlasmidFinder. The genome consisted of a chromosome of 4.801.657 base pairs, three major plasmids (212.849 bp, 86.884 bp and 83.425 bp) and 12 small cryptic plasmids (ranging from 8.390 bp to 1.822 bp). BLAST analysis revealed that all plasmids were highly similar to previously deposited sequences. Genome annotation predicted 5.522 coding regions, including 19 antimicrobial resistance genes, four of which located in small plasmids, and 17 virulence genes, with four of these located in a large virulence plasmid. The presence of antimicrobial resistance genes on small cryptic plasmids may represent an overlooked mechanism for the propagation of these genes among bacterial populations. Our work provides new data on these elements which may inform the development of new strategies to control the spread of ESBL-producing bacterial strains.