Genomic context of a Proteus mirabilis strain carrying both SGI1 and SXT/R391 resistance genomic islands

ObjectiveTo characterize the gene structure and resistance genes of two resistance-related genomic islands (SGI1 and SXT/R391) of a Proteus mirabilis strain (CA151922) isolated from a patient.

MethodsPolymerase chain reaction (PCR) was conducted to detect the specific integrase gene of SGI1 and SXT/R391, respectively. Next-generation sequencing was performed for the strain CA151922. The contigs of SGI1 and SXT/R391 were extracted and assembled from the whole sequenced genomes against each reference. Online predicting and annotating open reading frames (ORFs) were conducted. Each sequence was used in a BLASTn tool to obtain high homology variants in public database. Non-redundant homologous gene set was identified by cd-hit, a cluster of homologous tree was built by using R 3.4.4. Resistance phenotype was detected with micro-broth dilution method.

ResultsProteus mirabilis strain CA151922 carried two resistance-related genomic islands, i.e. SGI1 (SGI1-B) and SXT/R391 (ICEPmiJpn1). Compared with known variants of SGI1-B and ICEPmiJpn1, the sequence identity ranged from 97% to 99% and from 96% to 99%, respectively. Compared with each classic sequence, different resistance gene(s) were found, however, SGI1-B and ICEPmiJpn1 harbored different β-lactamase genes. Strain CA151922 was multi-drug resistant to eighteen antibiotics, only ampicillin and sulfonamides were related to the resistance genes on genomic islands, which suggested that resistance phenotype were not all encoded by genes at genomic island.

ConclusionBoth SGI1 and SXT/R391 resistance-related genomic islands were identified for the first time in a strain of P. mirabilis, which increased the complexity and severity of drug resistance. Surveillance for resistance-related genomic islands in multi-drug resistant strains should be strengthened.