In vitro Synergistic Activities of Fosfomycin in Combination with Other Antimicrobial Agents Against Carbapenem-Resistant Escherichia coli Harboring bla_NDM-1 on the IncN2 Plasmid and a Study of the Genomic Characteristics of These Pathogens

Figures & data

Table 1 Minimum Inhibitory Concentration (MIC) Values of 11 Antibiotics and 1 β-Lactamase Inhibitor Against bla_NDM-1-Harboring CREC Isolates

Isolate Code	MIC Value (µg/mL)
	FOS	IPM	MEM	DOR	CIP	LVX	TIG	STFX	CT	GN	AMK	SUL
CREC003	0.25 (S)	32 (R)	64 (R)	16 (R)	128 (R)	32 (R)	0.5 (S)	8 (R)	4 (R)	32 (R)	2 (S)	128
CREC004	0.5 (S)	16 (R)	32 (R)	32 (R)	64 (R)	32 (R)	0.5 (S)	4 (I)	4 (R)	16 (R)	2 (S)	128
CREC038	256 (R)	32 (R)	64 (R)	32 (R)	128 (R)	32 (R)	1 (S)	8 (R)	4 (R)	1 (S)	2 (S)	128

Abbreviations: FOS, fosfomycin; IPM, imipenem; MEM, meropenem; CIP, ciprofloxacin; DOR, doripenem; LVX, levofloxacin; SUL, sulbactam; TIG, tigecycline; STFX, sitafloxacin; CT, colistin; GN, gentamicin; AMP, amikacin; R, resistance; I, intermediate resistance; S, susceptible.

Table 2 The Synergistic Effects of Fosfomycin in Combination with Other Antimicrobial Agents Against bla_NDM-1-Harboring CREC Isolates

Combination	No. of Isolates
	Synergy	Indifference	Antagonistic
Fosfomycin + Imipenem	0	3	0
Fosfomycin + Meropenem	0	3	0
Fosfomycin + Doripenem	0	3	0
Fosfomycin + Gentamicin	1	2	0
Fosfomycin + Amikacin	1	2	0
Fosfomycin + Ciprofloxacin	1	2	0
Fosfomycin + Levofloxacin	0	3	0
Fosfomycin + Sitafloxacin	1	2	0
Fosfomycin + Sulbactam	0	2	1
Fosfomycin + Colistin	1	2	0
Fosfomycin + Tigecycline	1	2	0

Figure 1 Distribution of antimicrobial resistance (AMR) genes in bla_NDM-1-harboring CREC isolates.

Figure 2 Distribution of mobile genetic elements (MGEs) in bla_NDM-1-harboring CREC isolates.

Figure 3 Distribution of virulence-associated genes in bla_NDM-1-harboring CREC isolates.

Table 3 CRISPR-Cas System in bla_NDM-1-Harboring CREC Isolates

Isolate Code	Source of Isolation	Sequence Type (ST)	CRISPR Region			Cas Region
			CRISPR Position	No. of Direct Repeat (DR)	No. of Spacer	Cas Position	cas Locus	Cas Type
CREC003	Rectum	448	Position 1	2	1	Position 1	cas6_csy3_csy2_csy1_cas3-cas2_cas1	Cas type-IF
			Position 2	19	18	Position 2	cas2_cas1_cas6_cas5_cas7_cse2_cse1_cas3	Cas type-IE
			Position 3	14	13
			Position 4	2	1
			Position 5	12	11
			Position 6	10	9
			Position 7	2	1
CREC004	Rectum	448	Position 1	14	13	Position 1	cas1_cas3-cas2_csy1_csy2_csy3_cas6	Cas type-IF
			Position 2	19	18	Position 2	cas2_cas1_cas6_cas5_cas7_cse2_cse1_cas3	Cas type-IE
			Position 3	2	1
			Position 4	12	11
			Position 5	10	9
			Position 6	2	1
			Position 7	2	1
CREC038	Rectum	131	Position 1	2	1	-	-	-
			Position 2	2	1
			Position 3	5	4
			Position 4	7	6
			Position 5	8	7

Figure 4 Presence of bacteriophage genomes in bla_NDM-1-harboring CREC isolates.

Figure 5 Presence of bacteriocin-encoding genes in bla_NDM-1-harboring CREC isolates.

Figure 6 Structure of IncN2 plasmid in bla_NDM-1-harboring CREC isolates.

Figure 7 Genomic diversity among bla_NDM-1-harboring CREC isolates compared to previously published genomes.

Notes: (A) A pie chart of the pan-genome, (B) a pan-genome frequency plot, and (C) a presence and absence matrix against a phylogenetic tree.