Phenotypic and Genotypic Characterization of Carbapenem-Resistant Enterobacteriaceae Recovered from a Single Hospital in China, 2013 to 2017

Figures & data

Table 1 Comparison of Clinical Characteristics of Patients Harboring CRE and CSE Isolates

Clinical Variable	Level	CRE (n = 39)	CSE (n = 94)	P value
Patient age (years), Mean ±SD		52.1±23.5	51.8±25.8	0.682
Sex	Male	28 (71.8%)	68(72.3%)	0.788
	Female	11 (28.2%)	26(27.66%)
Length of hospital stay		90.8±157.6	36.6±56.7	0.047
Underlying disease		19(51.4%)	51(54.2%)	0.811
Use of invasive devices	Catheter use	30 (76.9%)	38(40.4%)	0.001
	Ventilator use	26 (66.7%)	11(11.7%)	0.000
	Tracheotomy	12 (32.4%)	12(12.8%)	0.009
	Intravascular catheter use	22 (56.4%)	24(25.5%)	0.000
	Surgery	15(40.5%)	34(36.2%)	0.645
Exposure to antibiotics more than 7 days before detection of CRE		27 (73.0%)	26(27.7%)	0.000
Transferred departments during hospitalization		12 (30.8%)	13(13.83%)	0.075
Outcome	Died in hospital	7 (17.9%)	42(44.7%)	0.064
	Survived to discharge	32 (82.1%)	52(55.3%)	0.064

Note: P value in bold shows that the variables are statistically significant.

Figure 1 Timelines of 52 CRE isolates containing carbapenemases from different wards during 2013 to 2017.

Figure 2 Core genome phylogenetic tree for all CRE isolates according to ARG and plasmid type. (A), E. coli (B), K. pneumoniae and (C), E. cloacae. Colors illustrated lineages, years, source, wards, ST types and carbapenemases, respectively. Red-filled squares indicate possession of the indicated ARG and blue-filled squares indicated plasmid Inc type.

Table 2 Results of Multivariate Analysis of CRE Patients

Risk Factor	Odds Ratio	95% Confidence Interval	P value
Length of hospital stay	0.997	0.990–1.004	0.424
Catheter use	1.497	0.481–4.657	0.486
Ventilator use	14.689	3.393–63.596	0.000
Tracheotomy	0.133	0.25–0.715	0.019
Intravascular catheter use	1.274	0.374–4.343	0.699
Exposure to antibiotics more than 7 days before detection of CRE	2.281	0.686–7.583	0.179

Note: P value in bold shows that the variables are statistically significant.

Table 3 Antimicrobial Susceptibility of Patient CRE Isolates

Antibiotics	Interpretation			Resistance Rate (%)
	S	I	R
Ampicillin	0	0	52	100.0
Cefotaxime	0	0	52	100.0
Ceftriaxone	2	0	50	96.2
Meropenem	1	0	51	98.1
Tigecycline	51	0	1	1.9
Colistin	45	- ^b	7	13.5
Gentamicin	12	2	38	76.9
Amikacin	30	3	19	42.3
Fosfomycin	16	8	28	69.2
Ciprofloxacin	4	2	46	92.3
Florfenicol	8	-	44	84.6
Sulfamethoxazole/ Trimethoprim	0	-	52	100.0

Abbreviations: S, susceptible; I, susceptible, increased exposure; R, resistant. ^b-, negative.

Figure 3 Core SNP differences between isolates grouped by ST. Isolates listed close to each other were identical at the core genome level. Black lines, the number of SNPs differences between isolates. Color of font and background represent the wards and time that the isolate was collected, respectively.

Figure 4 Genetic environments of Carbapenem resistance genes. (A) bla_NDM (B), bla_IMP and (C) bla_KPC. Arrows, direction of transcription and genes are grouped by colour. Regions of ≥99.0% nucleotide sequence identity are shaded grey. Δ, truncated gene.