Identification of a novel genomic resistance island PmGRI1-STP3 and an SXT/R391 integrative conjugative element in Proteus mirabilis of swine origin in China

Abstract

ObjectivesThis study aimed to determine the genetic environment of antimicrobial resistance genes in Proteus mirabilis strain STP3 isolated from a diarrhoeic pig on a swine farm in Sichuan Province, China. MethodsStrain STP3 was subjected to antimicrobial susceptibility testing. Illumina MiSeq (200× coverage) and Nanopore PromethION (100× coverage) platforms were used for genome sequencing. A conjugation experiment was performed to determine the transferability and stability of antimicrobial resistance genes in this strain. ResultsThe assembled circular genome of P. mirabilis STP3 was 4 115 975 bp with a GC content of 39.58%; no plasmid sequence was detected. A novel genomic resistance island (PmGRI1-STP3) and an SXT/R391 integrative conjugative element (ICE) variant (ICEPmiChnSTP3) were characterised in P. mirabilis STP3. PmGRI1-STP3 of 52.7 kb was located at the 3′ end of tRNA-Sec and shared the greatest identity with PmGRI1-C55 (54% coverage, 99.99% identity). PmGRI1-STP3 carried 16 resistance genes, including the clinically important extended-spectrum β-lactamase (ESBL) gene blaCTX-M-3. ICEPmiChnSTP3 was inserted into the prfC gene. It carried 18 resistance genes, including the rRNA methyltransferase gene cfr and the fluoroquinolone resistance gene aac(6′)-Ib-cr. A class 2 integron (dfrA1–sat2–aadA1) was also identified on transposon Tn7. Mobilisation experiments indicated that ICEPmiChnSTP3 was conjugally mobilised to Escherichia coli. However, PmGRI1-STP3 appeared to lose its mobilisation ability. ConclusionThe identification of two genomic islands (GIs) in this study suggested that genetic elements might be key mediators for resistance gene acquisition in P. mirabilis and that IS26-mediated rearrangements promote the diversity of GIs.