Genomic analysis of <i>Shigella</i> isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance.

"the short-read sequence data generated in this study have been submitted to enterobase ( https://enterobase warwick ac uk/ ) and to the european nucleotide archive (ena https://www ebi ac uk/ena/ ) under study number prjeb63380.; the plasmid sequences obtained have been deposited in genbank ( https://www ncbi nlm nih gov/genbank/ ) under accession numbers or237793-or237802 (table 2). all the accession numbers of the short-read sequences are listed in data s1 available in the online version of this article.; only four isolates (7 4 %) were identified as s dysenteriae and they belonged to s dysenteriae 12 (3 7 % 2/54) s dysenteriae 2 (1 85 % 1/54) and s dysenteriae 3 (1 85 % 1/54) (data s1).; the s sonnei isolates belonged to lineage 3 particularly to subclade 3 6 1 (80 % 20/25) known as 'cipr parent' (data s1) [ ].; three of the six s flexneri group 1-5 x y isolates belonged to phylogroup (pg) 3 the other three belonging to pg1a (data s1) [ ].; we found that 87 % (47/54) of isolates displayed resistance to three or more antimicrobial drug classes; these isolates were considered to be multidrug-resistant (mdr) ( table 1 data s1).; we identified 19 antimicrobial drug resistance profiles in total the most frequent of which combined resistance to streptomycin sulfonamides trimethoprim tetracycline and nalidixic acid (37 % 20/54) ( table 1 data s1).; moreover 46 3 % (25/54) of the isolates carried more than one aminoglycoside resistance gene ( table 1 fig 1 data s1).; the combined presence of the qnrs1 gene and the gyra mutation in cl-056 led to resistance to ciprofloxacin ( table 1 fig 1 data s1).; the bla oxa-1 gene was carried by six isolates (three s flexneri and three s dysenteriae ) along with at least the tet(b) aada1 and cata1 genes ( table 1 fig 1 data s1).; the bla ctx-m-15 gene was the most common present in 10 of the 15 isolates the bla ctx-m-3 gene being found in the remaining five isolates ( table 1 fig 1 data s1).; two different inc-type plasmids were associated with the esbl genes: inci1 (found in 11/15 isolates resistant to 3gcs) associated with bla ctx-m-15 or bla ctx-m-3 and incfib (found in the remaining four isolates) associated with bla ctx-m-15 ( fig 1 data s1).; there was a high degree of identity between these isolates and all displayed >96 5 % coverage of the incfib plasmid confirming the presence of very similar plasmids in each of these isolates ( fig 2 table s1 data s1).; this plasmid was carried by s boydii isolates belonging to three different serotypes and by one s flexneri 6 isolate ( figs1 and 2 data s1).; this plasmid was carried by s sonnei and s flexneri (serotypes2a and 6) isolated from two different hospitals between 2011 and 2016 ( figs1 and 3 data s1).; it was predominantly found in s sonnei isolates but was also carried by one s flexneri serotype 1c isolate ( figs1 and 4 data s1)."

"Conflicts of interest The authors declare that they have no conflicts of interest."

"Funding information This study was funded by Institut Pasteur and the Fondation Le Roch-Les Mousquetaires. The funders had no role in study design, data collection and analysis, the decision to publish, or preparation of the manuscript."