Abstract
To characterize the molecular structure of IncR plasmid-related sequences, comparative genomic analysis was conducted using 261 IncR plasmid backbone-related sequences. Among the sequences, 257 were IncR plasmids including the multidrug-resistance IncR plasmid pR50-74 from Klebsiella pneumoniae strain R50 of this work, and the other four were from bacterial chromosomes. The IncR plasmids were derived from different bacterial genera or species, mainly Klebsiella pneumoniae (70.82%, 182/257), Escherichia coli (11.28%, 29/257), Enterobacter cloacae (7.00%, 18/257), and Citrobacter freundii (3.50%, 9/257). The bacterial chromosomes carrying IncR plasmid backbone sequences were derived from Proteus mirabilis AOUC-001 and Klebsiella pneumoniae KPN1344, among others. The IncR backbone sequence of P. mirabilis AOUC-001 chromosome shows the highest identity with that of pR50-74. Complex class 1 integrons carrying various copies of ISCR1-sdr-qnrB6-△qacE/sul1 (ISCR1-linked qnrB6 unit) were identified in IncR plasmids. In addition to two consecutive copies of qnrB6-qacE-sul1, the other resistance genes encoded on pR50-74 are all related to mobile genetic elements, such as IS1006, IS26, and the class 1 integron. This study provides a clear understanding of the mobility and plasticity of the IncR plasmid backbone sequence and emphasizes the important role of ISCR in the recruitment of multicopy resistance genes.
Highlights
IncR was first characterized as a new plasmid incompatibility group in 2009 [1]
Integrons and insertion sequence common region (ISCR) elements were originally named common regions (CRs), which represent a family of mobile genetic elements (MGEs) that are similar to the insertion sequence (IS) element [6]
The resistance genes are mainly related to the antibiotics of florfenicol, tetracycline, quinolone, aminoglycoside, rifampicin, trimethoprim, streptomycin, and sulfonamides (Table 1), in accordance with the results of antimicrobial susceptibility testing of the bacterium (Table 2)
Summary
IncR was first characterized as a new plasmid incompatibility group in 2009 [1]. The first sequenced IncR single-replicon plasmid was pEFER, though IncR often coexists with other replicons such as IncC, IncN, IncHI, and IncFII [2]. There are an increasing number of reports about IncR plasmids carrying various resistance genes, such as blaKPC-2, blaDHA-1, blaNDM-1, blaVIM-1, qnrS1, or armA, in clinical Enterobacterales, especially in Klebsiella pneumoniae strains from different geographical regions [3,4,5]. The pool of resistance genes carried by IncR replicon plasmids may spread to transferable plasmids through transposition or plasmid recombination events, contributing to the high plasticity of multiple-replicon plasmids [2]. As complex class 1 integrons are powerful gene-capturing tools that can mobilize extremely large sections of DNA encoding a variety of resistance genes related to chloramphenicol, trimethoprim, quinolone, and βlactam antibiotics [7], these elements play important roles in the recruitment and spread of resistance genes
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