Detection of Two Copies of a bla_NDM-1-Encoding Plasmid in Escherichia coli Isolates from a Pediatric Patient with Diarrhea

Figures & data

Table 1 Antimicrobial Susceptibility Testing of E. coli Strain TCM3e1 Isolates and Associated Transconjugants

Antibiotics	MIC (mg/mL)/Antimicrobial Susceptibility
	TCM3e1	J53-pTCM3e1	J53
Ampicillin	≥256/R	>16/R	= 4/S
Cefazolin	>16/R	>16/R	≤4/S
Ceftazidime	≥256/R	>16/R	≤1/S
Cefotaxime	≥256/R	>32/R	≤1/S
Cefepime	≥96/R	>16/R	≤2/S
Imipenem	8/R	8/R	≤1/S
Meropenem	8/R	8/R	≤1/S
Piperacillin	>64/R	>64/R	≤4/S
Amoxicillin-clavulanate	16/R	>16/8/R	≤4/2/S
Ampicillin/sulbactam	>16/8/R	>16/8/R	≤4/2/S
Piperacillin-tazobactam	>64/4/R	>64/4/R	≤4/4/S
Trimethoprim-sulfamethoxazole	>2/38R	>2/38R	≤0.5/9.5/S
Tetracycline	≥256/R	≤2/S	≤2/S

Note: These data are derived from the 2019 CLSI guidelines.

Abbreviations: S, sensitive; R, resistant; I, intermediately resistant.

Table 2 Genome and Plasmids of E. coli Strain TCM3e1

Genomic Structure	Size	GC Content	CDS No.	Accession No.	Resistance Genes Present	Replicon Type
TCM3e1 chromosome	4,994,807 bp	50.51%	5030	CP066806	blaCMY-62, arnA, PmrB, PmrC, PmrF, fyuA, kdpE, APH (3”)-Ib, sul2, APH (6)-Id, PmrE, blaTEM-1, blaCTX-M-105	IncQ
pTCM3e1-1	131,861 bp	47.21%	182	CP066807	blaTEM-1	IncFIB
pTCM3e1-2	191,962 bp	51.72%	254	CP066808	blaNDM-1, bleo, sul1, aadA17, dfrA12, blaCTX-M-61	IncC

Figure 1 Genetic structure of plasmid pNDM-TCM3e1. This circular graph was created to illustrate the backbone and the location of the genetic load region of pNDM-TCM3e1. Genes are denoted by yellow rectangles. The GC skew is depicted as the inner circle in black and the GC content as the outer circle in green and purple. The blue region represents conjugation.

Table 3 Match in GenBank of the E. coli Strain TCM3e1 Plasmid

	GenBank_ID	Length (bp)	Covery (%)	Identity (%)	Species Origin
Plasmid pTCM3e1-1	NZ_CP015160.1	212,180	54.28	98.97	Escherichia coli
	NZ_LT985252.1	179,021	66.97	98.59	Escherichia coli
	NZ_CP031295.1	245,305	47.05	98.83	Escherichia coli
	NZ_CP024238.1	274,465	47.02	96.59	Escherichia coli
	NZ_AP018785.1	169,561	52.37	98.93	Escherichia coli
Plasmid pTCM3e1-2	NZ_LR697099.1	273,158	87.47	99.22	Klebsiella pneumoniae
	NZ_CP028197.1	444,417	65.98	99.99	Salmonella enterica subsp.
	NZ_CP023274.1	191,769	80.16	99.22	Proteus mirabilis
	NZ_LT904892.1	192,619	73.77	100	Salmonella enterica subsp.
	NZ_CP008824.1	319,976	69.67	99.99	Enterobacter cloacae

Figure 2 Alignment of sequences surrounding the region of bla_NDM-1. Genes are denoted by arrowheads and colored based on gene function classification. Red letters are for bla_NDM-1. Resistant genes are indicated with red arrowheads. IS elements are indicated in blue. White arrows indicate integron IntI1. The tandem repeat fragment surrounding the bla_NDM-1 gene is highlighted with a light grey frame.

Abbreviations: bla_NDM-1, New Delhi metallo-β-lactamase gene; bleo, bleomycin resistance gene; sul1, sulfonamide resistance gene; aadA17, aminoglycoside 3-N-acetyltransferase ANT-(3”); dfrA1, dihydrofolate reductase; IS, insertion sequence; intl1, integron gene.