Genomic Analysis of Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae in a Chinese Tertiary Hospital

Figures & data

Table 1 Characteristics of Clinical Cases and Isolates

Patients	Years Old	Gender	Isolates	Source	Ward	STs	KL	Virulence Factors	Resistance Genes	Plasmid Replicons	Clinical Outcomes
1	47	Female	FK3004	Sputum	Neurosurgery	ST15	KL24	iucA, rmpA2	KPC-2	IncFIB	Improve, discharge
2	22	Male	FK3006	Sputum	ICU-1	ST15	KL112	iucA, rmpA2	OXA-232	IncFIB, IncHI1B	Improve, be hospitalized
3	72	Male	FK3009	Blood	Emergency ward	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Improve, be hospitalized
4	51	Male	FK3015	Sputum	ICU-2	ST65	KL2	iucA, rmpA2, rmpA, iroB	KPC-3	IncHI1B, IncX5	Delirious, discharge
	51	Male	FK3018	Blood	ICU-2	ST65	KL2	iucA, rmpA2, rmpA, iroB	KPC-3	IncHI1B, IncX5	Delirious, discharge
5	33	Male	FK3016	Blood	ICU-2	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Severe, discharge
6	61	Male	FK3021	Sputum	ICU-1	ST15	KL24	iucA, rmpA2	KPC-2	IncFIB	Cured, discharge
7	60	Male	FK3023	Sputum	Nephrology	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR, IncX3	Improve, discharge
8	65	Female	FK3025	Sputum	Gastrointestinal surgery	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
9	88	Male	FK3033	Sputum	ICU-2	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Delirious, discharge
10	59	Male	FK3035	Pus	Emergency ward	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
11	82	Male	FK3040	Sputum	EICU	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Delirious, discharge
12	62	Male	FK3048	Blood	Hematology	ST65	KL2	iucA, rmpA2, rmpA, iroB	NDM-1	IncHI1B, IncX3	Improve, discharge
13	92	Male	FK3052	Sputum	Gerontology	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncN, IncR	Continue treatment
	92	Male	FK3121	Sputum	Gerontology	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Continue treatment
14	55	Male	FK3053	Stool	ICU-2	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Delirious, discharge
15	50	Male	FK3054	Pleural fluid	ICU-2	ST37	KL25	iucA	KPC-2	IncFIB	Died
16	76	Female	FK3055	Urine	Urinary Surgery	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
	76	Female	FK3056	Blood	Urinary Surgery	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
17	51	Female	FK3057	Stool	Neurosurgery	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Cured, discharge
18	57	Male	FK3058	Sputum	EICU	ST11	KL64	iucA, rmpA2, rmpA	KPC-2, NDM-5	IncFII, IncHI1B, IncR	Delirious, discharge
19	68	Male	FK3061	Urine	ICU-1	ST412	KL57	iucA, rmpA2, rmpA, iroB	KPC-2	-	Severe, discharge
	68	Male	FK3104	Sputum	ICU-1	ST412	KL57	iucA, rmpA2, iroB	KPC-2	-	Severe, discharge
20	70	Male	FK3062	Stool	ICU-2	ST412	KL57	iucA, rmpA2, rmpA, iroB	KPC-2	-	Delirious, discharge
	70	Male	FK3064	Blood	ICU-2	ST412	KL57	iucA, rmpA2, rmpA, iroB	KPC-2	-	Delirious, discharge
21	87	Male	FK3065	Sputum	Gastroenterology	ST11	KL47	iucA	KPC-2	IncFII, IncFIB, IncR	Improve
22	91	Male	FK3101	Sputum	ICU-2	ST37	KL25	iucA	KPC-2	IncFIB	Died
23	59	Male	FK3109	Pipe	ICU-2	ST4080	KL64	iucA, rmpA2	KPC-2	IncFII, IncFIB, IncHI1B, IncR, IncX4	Delirious, discharge
24	65	Male	FK3111	Sputum	Hematology	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncFIB, IncHI1B, IncR	Delirious, discharge
	65	Male	FK3163	Sputum	Hematology	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncFIB, IncHI1B, IncR	Delirious, discharge
25	93	Male	FK3113	Bile	Gerontology	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Continue treatment
26	68	Female	FK3115	Blood	ICU-1	ST412	KL57	iucA, rmpA2, rmpA, iroB	KPC-2	-	Delirious, discharge
27	93	Male	FK3118	Sputum	Gerontology	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Delirious, discharge
28	83	Male	FK3119	Blood	ICU-1	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Delirious, discharge
29	64	Male	FK3122	Sputum	EICU	ST11	KL64	iucA, rmpA2, rmpA	KPC-2, NDM-5	IncFII, IncHI1B, IncR	Delirious, discharge
30	77	Female	FK3124	Sputum	EICU	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Delirious, discharge
31	93	Male	FK3125	Sputum	Gerontology	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Continue treatment
32	51	Male	FK3140	Sputum	ICU-1	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
33	92	Male	FK3154	Sputum	Gerontology	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Continue treatment
	92	Male	FK3159	Secretion	Gerontology	ST11	KL64	iucA, rmpA2, rmpA	KPC-2, OXA-232	IncFII, IncFIB, IncHI1B, IncR	Continue treatment
34	83	Male	FK3155	Sputum	ICU-1	ST11	KL64	iucA	KPC-2	IncFII, IncHI1B, IncR	Delirious, discharge
35	73	Male	FK3157	Sputum	ICU-2	ST412	KL57	iucA, rmpA2, rmpA, iroB	KPC-2	-	Improve, discharge
36	40	Female	FK3160	Stool	Hematology	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
	40	Female	FK3165	Blood	Hematology	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
37	89	Female	FK3161	Sputum	ICU-1	ST15	KL112	iucA, rmpA2	OXA-232	IncFIB, IncHI1B	Delirious, discharge
38	56	Male	FK3164	Sputum	Neurosurgery	ST420	KL20	iucA, rmpA2, rmpA, iroB	KPC-2	IncFIA, IncFIB, IncFII, IncHI1B	Improve, discharge
39	58	Female	FK3166	Sputum	Emergency ward	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
40	73	Male	FK3168	Urine	Cancer Radiochemotherapy Department	ST37	KL25	iucA	KPC-2	IncFIB	Improve, discharge
41	43	Female	FK3169	Sputum	ICU-2	ST15	KL112	iucA, rmpA2	OXA-232	IncFIB, IncHI1B	Uncured
	43	Female	FK3195	Cerebrospinal fluid	ICU-2	ST15	KL112	iucA, rmpA2	OXA-232	IncFIB, IncHI1B	Uncured
42	58	Male	FK3170	Sputum	ICU-1	ST15	KL112	iucA, rmpA2	OXA-232	IncFIB, IncHI1B	Delirious, discharge
43	61	Male	FK3171	Blood	Hematology	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Delirious, discharge
44	54	Male	FK3174	Blood	ICU-2	ST37	KL25	iucA	KPC-2	IncFIB, IncR	Delirious, discharge
45	64	Male	FK3175	Sputum	ICU-2	ST11	KL64	iucA, rmpA2, rmpA	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
46	55	Male	FK3181	Sputum	Nephrology	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
47	68	Male	FK3184	Urine	Endocrinology	ST11	KL47	iucA, rmpA2	NDM-5	IncFII, IncFIB, IncHI1B, IncR, IncX3	Improve, discharge
48	64	Male	FK3186	Sputum	ICU-2	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncHI1B, IncR	Improve, discharge
49	67	Male	FK3187	Sputum	ICU-1	ST11	KL64	iucA	KPC-2	IncFII, IncHI1B, IncR	Delirious, discharge
50	43	Male	FK3188	Pus	EICU	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncFIB, IncHI1B, IncR	Uncured
51	85	Male	FK3191	Sputum	EICU	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncFIB, IncHI1B, IncR	Delirious, discharge
52	63	Male	FK3194	Sputum	Cardiology	ST15	KL24	iucA, rmpA2	KPC-2	IncFIB	Improve
53	63	Male	FK3196	Sputum	Thoracic surgery	ST505	KL64	iucA, rmpA, iroB	OXA-181	IncFIA, IncFIB, IncHI2A, IncHI2, IncX3	Uncured
54	63	Male	FK3198	Sputum	Orthopaedic Sports Medicine	ST11	KL64	iucA, rmpA2	KPC-2	IncFII, IncFIB, IncHI1B, IncR	Cured

Abbreviations: EICU, emergency intensive care unit; ICU, intensive care unit.

Table 2 Antibiotic Susceptibilities of 63 Carbapenem-Resistant K. pneumoniae

Antibiotics	Sensitivity (%)	Intermediate (%)	Resistance (%)
Aztreonam	1.6	0.00	98.4
Ciprofloxacin	6.3	1.6	92.1
Levofloxacin	6.3	4.8	88.9
Tobramycin	69.8	8.0	22.2
Gentamicin	73.0	3.2	23.8
Amikacin	80.9	3.2	15.9
Cefoxitin	4.8	9.5	85.7
Ceftriaxone	0.00	0.00	100.0
Cefepime	3.2	1.6	95.2
Imipenem	1.6	1.6	96.8
Piperacillin/Tazobactam	0.0	0.00	100.0
Trimethoprim/Sulfamethoxazole	42.9	-	57.1
Amoxicillin/Clavulanic acid	0.00	1.6	98.4

Figure 1 Phylogenetic tree based on core genome alignment of 63 Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae in a tertiary hospital in East China. The different STs and KLs is color-coded and illustrated at the tips. The clusters also differed with several colors. The occurrence of resistance and virulence genes, and plasmid replicons were also color-coded. The tree was rooted in the midpoint. Scale bar represents 0.01 mutations per nucleotide position.