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

Juan He; Changwei Lei; Cui Li; Xuechun Wang; Pengfei Cui; Hongning Wang

doi:10.1016/j.jgar.2021.02.018

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

J Glob Antimicrob Resist. 2021 Jun:25:77-81. doi: 10.1016/j.jgar.2021.02.018. Epub 2021 Mar 2.

Authors

Juan He¹, Changwei Lei¹, Cui Li¹, Xuechun Wang¹, Pengfei Cui¹, Hongning Wang²

Affiliations

¹ Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China.
² Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China. Electronic address: whongning@163.com.

PMID: 33667705
DOI: 10.1016/j.jgar.2021.02.018

Abstract

Objectives: This 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.

Methods: Strain 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.

Results: The 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 bla_CTX-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.

Conclusion: The 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.

Keywords: IS26; Integrative and conjugative element; Integrative mobilisable element; Multidrug resistance; Proteus mirabilis; cfr.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
China
Conjugation, Genetic
Genomic Islands*
Genomics
Proteus mirabilis* / genetics
Swine