Whole-genome sequencing analysis of a rare Salmonella diarizonae clinical strain carrying multiple plasmids and novel gene cassettes

Abstract

Human infection caused by an uncommon Salmonella enterica subsp. diarizonae (hereafter S. diarizonae) is rising. However, knowledge concerning S. diarizonae is still limited. This study aimed to investigate the genomic features of S. diarizonae S499 isolated from a child patient with gastroenteritis symptom in China. The antimicrobial susceptibility of S. diarizonae S499 was determined by microdilution broth assay. Whole genome was sequenced using Illumina HiSeq X-10 and PacBio RS II platforms and was de novo assembled using Unicycler and SPAdes. Conjugation experiment was performed by a broth mating method. S. diarizonae S499 was a multi-drug resistant (MDR) isolate and showed resistance to all cephalosporin drugs tested. Six plasmids (pS0499A, pS0499B, pS0499C, pS0499D, pS0499E and pS0499F) were identified. A rare gene cassette IS26-blaCTX-M-55-wbuc-△blaTEM-1-IS26-intI1 was repeatedly inserted into pS0499A three times in one locus and reversely inserted into plasmid pS0499D. That enhanced cephalosporin resistance. To the best of our knowledge, this finding has not been reported previously. Both pS0499A and pS0499B contained multiple resistance genes and could transfer to recipient strain E. coli EC600. This article reported the genome features of S. diarizonae S499, which contained four resistant plasmids including a novel plasmid pS0499A with a novel gene cassette rearrangement. These data could contribute to a better understanding of the antimicrobial resistance mechanisms and transmission dynamics of S. diarizonae.