Co-occurrence of 3 different resistance plasmids in a multi-drug resistant Cronobacter sakazakii isolate causing neonatal infections

Figures & data

Table 1. Major features of plasmids analyzed.

	Plasmids
Category	p505108-MDR	R478^@	p505108-NDM	pNDM-HN380^@	p505108-T6SS	pESA3^@
Incomparability group	IncHI2	IncHI2	IncX3	IncX3	IncFIB	IncFIB
Total length (bp)	312,880	274,762	53,793	54,035	139,553	131,196
Total number of ORFs	359	304	61	62	126	117
Mean G+C content, %	47.7	45.5	49.0	49.0	56.4	56.8
Length of the backbone (bp)	207,144	212,499	34,700	34,732	131,195	131,196
Accessory modules	The MDR-1 region^#, the MDR-2 region^#, Tn6362^#, the aphA1a region^#, Tn2^#, the ISCfr9-ISCfr15 region, and 2 separate copies of ΔIS903D	The Tn1696-Tn6322 region^#, The sil-cop region^#, Tn10^#, IS186B, and IS150	The blaNDM-1 region^#, and ISKox3		The aphA1a region^#	None

Note.

^@ reference plasmids included in genomic comparison;

^# accessory modules containing resistance genes as listed in Table 2.

Table 2. Drug resistance genes in sequenced plasmids.

Plasmid	Resistance marker	Resistance phenotype	Nucleotide position	Region located
p505108-MDR	The ter locus	Tellurium resistance	62591..82538	The plasmid backbone
	The ars locus	Arsenic resistance	156203..159087
	dfrA18	Trimethoprim resistance	124249..124818	The MDR-1 region
	strAB	Aminoglycoside resistance	126592.. 128231
	The rcn locus	Nickel/cobalt resistance	142132..143642
	blaSHV-12	β-lactam resistance	239239..240099	The MDR-2 region
	blaDHA-1	β-lactam resistance	247503..248642
	aacC3	Aminoglycoside resistance	265953..266762
	aacA27	Aminoglycoside resistance	268847..269428
	aacA4cr	Quinolone and aminoglycoside resistance	235221..235775
	qnrB4	Quinolone resistance	252763..253410
	tetA(D)	Tetracycline resistance	224408..225592
	catA2	Phenicol resistance	220639..221280
	sul1	Sulphonamide resistance	245087..245926
	sul1	Sulphonamide resistance	262128..262967
	arr7	Rifampicin resistance	265412..265807
	The mer locus	Mercuric resistance	102624..106878	Tn6362
	aphA1a	Aminoglycoside resistance	164776..165591	The aphA1a region
	blaTEM-1B	β-lactam resistance	113444..114304	Tn2
p505108-NDM	blaNDM-1	Carbapenem resistance	17827..18639	The blaNDM-1 region
	blaSHV-12	β-lactam resistance	9324..10184
	bleMBL	Bleomycin resistance	17560..17925
p505108-T6SS	acrAB	Acriflavin resistance	13799..17998	The plasmid backbone
	The ars locus	Arsenic resistance	47576..49740
	scsAB	Copper resistance	70758..73326
	aphA1a	Aminoglycoside resistance	77928..78743	The aphA1a region

Table 3. Antimicrobial drug susceptibility profiles.

		MIC (mg/L) /antimicrobial susceptibility
Category	Antibiotics	505108	505108-NDM-EC600	EC600
Penicillin	Ampicillin	>1024/R	>1024/R	<4/S
Cephalosporin	Ceftazidime	>512/R	>512/R	<4/S
Carbapenem	Meropenem	16/R	8/R	<1/S
Cephamycin	Cefoxitin	512/R	128/R	<8/S
Monobactam	Aztreonam	128/R	128/R	<4/S
Aminoglycoside	Amikacin	1024/R	<8/S	<8/S
Tetracycline	Minocycline	32/R	<1/S	<1/S
Phenicol	Chloramphenicol	512/R	<8/S	<8/S
Folate pathway Inhibitors	Trimethoprim	>32/R	<0.25/S	<0.25/S
	Sulfamethoxazole	608/R	4.75/S	4.75/S
Nitrofuran	Nitrofurantoin	32/S	16/S	8/S
Fluoroquinolone	Ciprofloxacin	<1/S	<1/S	<1/S
Macrolide	Azithromycin	8/S	<4/S	4/S
Fosfomycin	Fosfomycin	<64/S	<64/S	<64/S
Glycylcycline	Tigecycline	<1/S	<1/S	<1/S
Lipopeptide	Colistin	<1/S	<1/S	<1/S

Note. S=sensitive; R=resistant.

Figure 1. The MDR-1 region from p505108-MDR and comparison with related regions. Genes are denoted by arrows. Genes, mobile elements and other features are colored based on function classification. Shading denotes regions of homology (> 95% nucleotide identity). Numbers in brackets indicate the nucleotide positions within the corresponding plasmids.

Figure 2. The MDR-2 region from p505108-MDR and comparison with related regions. Genes are denoted by arrows. Genes, mobile elements and other features are colored based on function classification. Shading denotes regions of homology (> 95% nucleotide identity). Numbers in brackets indicate the nucleotide positions within the corresponding plasmids.

Figure 3. Tn6362 from p505108-MDR and comparison with related regions. Genes are denoted by arrows. Genes, mobile elements and other features are colored based on function classification. Shading denotes regions of homology (> 95% nucleotide identity). Numbers in brackets indicate the nucleotide positions within the corresponding plasmids.

Figure 4. The aphA1a regions from p505108-MDR and p505108-T6SS and comparison with related regions. Genes are denoted by arrows. Genes, mobile elements and other features are colored based on function classification. Shading denotes regions of homology (> 95% nucleotide identity). Numbers in brackets indicate the nucleotide positions within the corresponding plasmids. The arrowheads indicated the location of PCR primers and the expected amplicons. See Figure S6 for the PCR results.