Sequence Analysis of IncA/C and IncI1 Plasmids Isolated from Multidrug-Resistant Salmonella Newport Using Single-Molecule Real-Time Sequencing

Abstract

Multidrug-resistant (MDR) plasmids play an important role in disseminating antimicrobial resistance genes. To elucidate the antimicrobial resistance gene compositions in A/C incompatibility complex (IncA/C) plasmids carried by animal-derived MDR Salmonella Newport, and to investigate the spread mechanism of IncA/C plasmids, this study characterizes the complete nucleotide sequences of IncA/C plasmids by comparative analysis. Complete nucleotide sequencing of plasmids and chromosomes of six MDR Salmonella Newport strains was performed using PacBio RSII. Open reading frames were assigned using prokaryotic genome annotation pipeline (PGAP). To understand genomic diversity and evolutionary relationships among Salmonella Newport IncA/C plasmids, we included three complete IncA/C plasmid sequences with similar backbones from Salmonella Newport and Escherichia coli: pSN254, pAM04528, and peH4H, and additional 200 draft chromosomes. With the exception of canine isolate CVM22462, which contained an additional IncI1 plasmid, each of the six MDR Salmonella Newport strains contained only the IncA/C plasmid. These IncA/C plasmids (including references) ranged in size from 80.1 (pCVM21538) to 176.5 kb (pSN254) and carried various resistance genes. Resistance genes floR, tetA, tetR, strA, strB, sul, and mer were identified in all IncA/C plasmids. Additionally, bla and sugE were present in all IncA/C plasmids, excepting pCVM21538. Plasmid pCVM22462 was capable of being transferred by conjugation. The IncI1 plasmid pCVM22462b in CVM22462 carried bla and sugE. Our data showed that MDR Salmonella Newport strains carrying similar IncA/C plasmids clustered together in the phylogenetic tree using chromosome sequences and the IncA/C plasmids from animal-derived Salmonella Newport contained diverse resistance genes. In the current study, we analyzed genomic diversities and phylogenetic relationships among MDR Salmonella Newport using complete plasmids and chromosome sequences and provided possible spread mechanism of IncA/C plasmids in Salmonella Newport Lineage II.

Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals

“…Conversely, I1 was the most prevalent replicon type (aside from ColE), accounting for 29% of the total plasmids identified, but only contained 13% of the total AR genes. These findings are consistent with previous studies that isolated A/C and I1 plasmids (Cao et al, 2018). A/C plasmids containing up to 13 AR genes have been identified in isolates from animals in other studies (Hoffmann et al, 2017).…”

Transferable Plasmids of Salmonella enterica Associated With Antibiotic Resistance Genes

“…The most common AR genes carried by IncA/C are str AB (aminoglycosides), sul 2 (sulfonamides), tet AR (tetracycline), bla CMY-2 (β-lactams), and flo R (chloramphenicols). Other genes for resistance to aminoglycosides, tetracyclines, trimethoprim, chloramphenicols, and cephalosporins have also been identified ( Welch et al, 2007 ; Hoffmann et al, 2017 ; Cao et al, 2018 ). In Salmonella isolated in the United States, IncA/C plasmids have been found in several different serotypes and animal commodities, especially cattle ( Lindsey et al, 2009 ; Folster et al, 2017 ; Mollenkopf et al, 2017 ).…”

“…Notably, IncA/C plasmids have been found in many Salmonella Newport isolates ( Table 2 ; Cao et al, 2015 ). Salmonella Newport has been isolated from cattle containing IncC plasmids with AR genes for at least five classes of antibiotics ( Cao et al, 2018 ). Isolates in a 2017 study of human and dairy cattle associated Salmonella of serotypes Dublin, Newport, and Typhimurium showed that all Dublin and Newport isolates tested contained sul 2, str A, str B, tet A, and bla CMY-2 .…”

Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation

“…Identifying the 20 plasmid types in the nearly-clonal clinical clade was surprising given that our literature review only found 11 plasmid types that had been previously observed in Salmonella Newport [15][16][17][18][19][20][21]. This indicates a much greater diversity of plasmids in Salmonella Newport than currently reported and warrants further investigation.…”

“…Plasmids are small (generally between 1 and 200 kbp) intracellular genetic elements that can semi-independently replicate and are thought to be the most impactful source of rapid horizontal transfer in microbial communities [13,14]. Multiple plasmids, representing various incompatibility types (Inc), have been observed in Salmonella Newport (i.e., IncA/C, IncR, IncI1, IncN, IncH, IncF, ColE1, IncP); however, plasmids are likely under-identified given that most were found while looking for genes conferring antimicrobial resistance [15][16][17][18][19][20][21].…”