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Incompatibility group C (IncC) plasmids have received attention due to their broad host range and because they harbor key antibiotic resistance genes. Because these resistance genes can spread from food-producing animals to human, the proliferation of these plasmids represents a public health risk. In this study, a total of 20 IncC plasmids were collected from food-producing animals in China, and characterized by Oxford Nanopore Technologies (ONT) long-read sequencing. Based on four key differences of the IncC backbone, 4 IncC plasmids were classified as type 1, 15 were classified as type 1/2 hybrid, and one was classified as type 2. The 15 type 1/2 hybrids were further divided into 13 type 1/2a and 2 type 1/2b, based on sequence differences arising from different homologous recombination events between type 1 and type 2 IncC backbones. Genome comparison of accessory resistance modules showed that different IncC plasmids exhibited various phenotypes via loss and gain of diverse modules, mainly within the blaCMY-carrying region, and two antibiotic resistance islands designated ARI-A and ARI-B. Interestingly, in addition to insertion and deletion events, IS26 or IS1294-mediated large sequence inversions were found in the IncC genome of the 4 type1/2a plasmids, suggesting that insertion sequence (IS)-mediated rearrangements also promote the diversity of the IncC genome. This study provides insight into the structural diversification and multidrug resistance of IncC plasmids identified from food-producing animals in China.

ObjectivesTo characterize the MDR genomic islands (GIs) in Proteus mirabilis isolates.MethodsTwo P. mirabilis strains (C55 and C74) of chicken origin were subjected to WGS (HiSeq and PacBio) and the MDR GIs were determined.ResultsP. mirabilis strains C55 and C74 are clonal strains and harbour different Proteus genomic island 2 (PGI2) variants (PGI2-C55 and PGI2-C74). The MDR region of PGI2-C55 is composed of two class 1 integrons, separated by a region containing seven copies of IS26 and eight resistance genes, including blaCTX-M-3 and fosA3. The region in PGI2-C74 is a complete In4-type class 1 integron, harbouring five gene cassettes (dfrA16, blaCARB-2, aadA2, cmlA1 and aadA1). In addition, C55 and C74 carry an SXT/R391 integrative and conjugative element (ICEPmiJpn1), harbouring blaCMY-2, and a novel 50.46 kb genomic resistance island named PmGRI1-C55. PmGRI1-C55 harbours a tyrosine-type recombinase/integrase that might be responsible for the integration of PmGRI1-C55 at the 3′ end of tRNA-Sec. It carries an MDR region derived from Tn2670 that harbours a Tn21 region and carries six resistance genes (catA1, blaTEM-1b, aphA1a, sul2, strA and strB). Blast analysis showed diverse PmGRI1 variants in P. mirabilis and Escherichia coli strains.ConclusionsThe finding of the two new PGI2 variants highlights that the homologous recombination between shared components of class 1 integrons and transposition by IS26 promote the diversity of MDR regions in PGI2. PmGRI1 is a new GI that carries various resistance genes identified in P. mirabilis and E. coli.

Objectives The aim of this study was to characterise the whole genome sequence of linezolid-intermediate Enterococcus hirae strain CQP3-9 isolated from a large-scale swine farm in Sichuan Province, China, in August 2018. Methods An Illumina MiSeq platform (400-bp paired-end reads with 230-fold average coverage) and PacBio RS II sequencing instrument (100-fold average read depth) were used for genome sequencing. The chromosome and two plasmids were assembled using the software SMRT portal v.3.2.0. Acquired antimicrobial resistance genes were identified using ResFinder 3.1. Results The genome of E. hirae strain CQP3-9 consists of one 2 695 881-bp chromosome, one 125 915-bp plasmid (pCQP3-9_1) and one 33 132-bp plasmid (pCQP3-9_2). The genome of CQP3-9 contains 2458 coding sequences and 89 RNA genes. The poxtA gene is the only linezolid resistance gene in CQP3-9, located on plasmid pCQP3-9_2 that co-harbours erm(B) (macrolide resistance), fexB (chloramphenicol and florfenicol resistance), and tet(M) and tet(L) (tetracycline resistance). Conclusion Here we report for the first time the phenicol–oxazolidinone–tetracycline resistance gene poxtA in E. hirae, located on a plasmid that co-harbours erm(B), fexB, tet(L) and tet(M). The genome sequence of E. hirae CQP3-9 provides valuable information for the dissemination of poxtA among enterococci.