Genomic characterization of a large plasmid containing a bla NDM-1 gene carried on Salmonella enterica serovar Indiana C629 isolate from China

Abstract

Background: The bla _NDM-1 gene in Salmonella species is mostly reported in clinical cases, but is rarely isolated from red and white meat in China.

Methods: A Salmonella Indiana (S. Indiana) isolate was cultured from a chicken carcass procured from a slaughterhouse in China. Antimicrobial susceptibility was tested against a panel of agents. Whole-genome sequencing of the isolate was carried out and data was analyzed.

Results: A large plasmid, denoted as plasmid pC629 (210,106 bp), containing a composite cassette, consisting of IS26-bla _NDM-1-ble _MBL -△trpF-tat-cutA-ISCR1-sul1-qacE△1-aadA2-dfrA12-intI1-IS26 was identified. The latter locus was physically linked with bla _OXA-1, bla _CTX-M-65, bla _TEM-1-encoding genes. A mercury resistance operon merACDEPTR was also identified; it was flanked on the proximal side, among IS26 element and the distally located on the bla _NDM-1 gene. Plasmid pC629 also contained 21 other antimicrobial resistance-encoding genes, such as aac(6')-Ib-cr, aac(3)-VI, aadA5, aph(4)-Ia, arr-3, blmS, brp, catB3, dfrA17, floR, fosA, mph(A), mphR, mrx, nimC/nimA, oqxA, oqxB, oqxR, rmtB, sul1, sul2. Two virulence genes were also identified on plasmid pC629.

Conclusion: To the best of our knowledge, this is the first report of bla _NDM-1 gene being identified from a plasmid in a S. Indiana isolate cultured from chicken carcass in China.

Keywords: Carbapenem resistance; Chicken carcass; China; Extensively-drug resistance; Salmonella enterica serovar Indiana; bla NDM-1 gene.

Fig. 1

Representation of plasmid pC629. Antibiotic resistance genes, metal resistance genes, and virulence factor genes were shown in the circle

Fig. 2

Major structural features of plasmid pC629 compared with several plasmids from NCBI. a. Major structural features of plasmid pC629 compared with plasmids pC06114_1, pNDM-CIT, and pCC1409-1 identified in Escherichia coli, Citrobacter freundii, and Klebsiella pneumoniae, respectively. ORFs are shown as arrowheads (blue arrows, IS26, ISCR1, and tnpM; red arrows, antibiotic resistance genes; pink arrows, membrane protein, MP; white arrows, hypothetical proteins, HP; green arrows, integrase related genes –see the key to the right hand side of the panel). b. Major structural features of plasmid pC629 compared with plasmids pS414, pSJ_255, pSTA155, p112298-KPC, pEK499, and pUUH239.2 identified in Salmonella Indiana, Escherichia coli, Salmonella Indiana, Citrobacter freundii, Escherichia coli and Klebsiella pneumoniae, respectively. ORFs are shown with arrowheads (blue arrows, IS26, IS6100 and other transposase related genes; red arrows, antibiotic resistance genes; pink arrows, membrane protein, MP; white arrows, hypothetical proteins, HP; green arrows, integrase related genes –see the key to the right hand side of the panel). c. Major structural features of plasmid pC629 plasmid compared with plasmids pHNSHP45-2, pSJ_255, and p42-2 all identified in Escherichia coli. ORFs are shown with arrows (blue arrows, IS26; red arrows, antibiotic resistance genes –see the key to the right hand side of the panel). d. Major structural features of plasmid pC629 compared with plasmids p397Kp, pCT-KPC, and p1205p1 identified in Klebsiella pneumoniae, Klebsiella pneumoniae, and Shigella flexneri, respectively. ORFs are shown with arrows (blue arrows, IS26; red arrows, antibiotic resistance genes; white arrows, hypothetical proteins, HP –see the key to the right hand side of the panel). e. Major structural features of plasmid pC629 plasmid compared with plasmids pGD0503Z13, pHK0653, and pCN061p6 identified in Escherichia coli, Salmonella species and Escherichia coli, respectively. ORFs are shown with arrows (blue arrows, IS26; red arrows, antibiotic resistance genes; white arrows, hypothetical proteins, HP –see the key to the right hand side of the panel)

Fig. 3

Major structural features of plasmid pC629 compared with plasmids pHSO91147, pBK34397, and pKPHS2 identified in Klebsiella pneumoniae, Escherichia coli and Klebsiella pneumoniae, respectively. ORFs are shown with arrows (blue arrows, transposase; red arrows, metal resistance genes; pink arrows, membrane protein, MP; green arrows, integrase related genes -–see the key to the right hand side of the panel)