Comprehensive Surveillance and Sampling Reveal Carbapenem-Resistant Organism Spreading in Tertiary Hospitals in China

Figures & data

Table 1 Characteristics of Patients in ICU-1

Patient Number	Isolate ID	Gender	Age	Underlying Disease	Admission Date	Sample Date	Species	Rectal Swab Screen	Sample Specimen Source	Outcome	Date of Discharge or Death	Cause of Death
Pt1	ab5	Male	43	Central nervous system infection	2018/12/25	2019/1/3	CRAB	Not done	Sputum	Improved	2019/3/28	/
	kp5					2019/3/3	CRKP		Sputum
	kp11					2019/3/4	CRKP		CSF
Pt2	ab11	Female	51	Myasthenia gravis; Severe pneumonia	2019/1/9	2019/1/27	CRAB	Not done	Blood	Died	2019/2/6	Infection
Pt3	ab9	Male	46	Severe pneumonia; eczema scroti	2019/1/23	2019/2/15	CRAB	Not done	BALF	Improved	2019/3/1	/
	kp7					2019/2/26	CRKP		Sputum
Pt4	ab12	Male	64	Pulmonary aspergillosis	2019/2/12	2019/2/19	CRAB	Not done	BALF	Improved	2019/3/11	/
Pt5	Kp10	Male	68	Liver failure; Hepatorenal syndrome	2019/2/12	2019/3/22	CRKP	Not done	Fiber bronchoscopy aspirates	Died	2019/3/31	Liver failure, Hepatorenal syndrome, Severe pneumonia
	kp9					2019/3/29	CRKP		Pus
Pt6	ab10	Male	34	Brain abscesses; ventriculitis	2019/2/15	2019/2/15	CRAB	02/19 ESBL positive	CSF	died	2019/2/27	Central nervous system infection
	kp8					2019/2/20	CRKP		CSF
Pt7	kp6	Male	66	Central nervous system infection (Encephalitis)	2019/2/25	2019/2/27	CRAB	02/26 negative	Sputum	Improved	2019/3/20	/
	ab6					2019/3/4	CRKP		Sputum
	ab13					2019/3/4	CRAB		Sputum
Pt8	ab2	Male	43	Severe pneumonia (adenovirus infection)	2019/2/28	2019/3/11	CRAB	03/05 negative	Blood	Died	2019/3/15	Septic shock
	ab3					2019/3/12	CRAB		Sputum
Pt9	kp1	Male	78	Severe pneumonia	2019/2/28	2019/3/15	CRKP	02/28 ESBL positive	Sputum	Died	2019/4/1	Severe pneumonia, CRKP infection
	kp2					2019/3/19	CRKP		Blood
Pt10	ab4	Male	73	Disseminated nocardiosis	2019/3/11	2019/3/12	CRAB	03/11 ESBL positive	Sputum	Improved	2019/4/24	/
	kp4					2019/3/16	CRKP		Sputum
	kp12					2019/4/20	CRKP		Blood
Pt11	ab1	Female	71	Severe pneumonia	2019/3/12	2019/3/12	CRAB	Not done	Sputum	Improved	2019/4/6	/
Pt12	ab8	Male	59	Viral meningoencephalitis	2019/3/20	2019/3/24	CRAB	03/21 ESBL positive	Sputum	Improved	2019/4/4	/
Pt13	ab14	Male	75	Severe pneumonia	2019/3/22	2019/3/28	CRAB	0327 Negative	Sputum	Improved	2019/4/2	/

Figure 1 The timeline of patients in ICU-1 and ICU-2. (A) Timeline of 13 patients enrolled in ICU-1. The corresponding strain numbers were showed near patient’s number. Black and red box showed sample data of CRKP and CRAB, respectively. The room stay of Room 1, 2, 3, 4 in ICU-1 was represented by different stripes. Red star meant the death date of patient. (B) Timeline of 11 patients enrolled in ICU-2. The corresponding strain numbers were showed near patient’s number. Black and red box showed sample data of CRKP and CRAB, respectively. The room stay of Room 1, 2, 3, 4 and 5 in ICU-2 was represented by different stripes. Red star meant the death date of patient.

Table 2 Characteristics of Patients in ICU-2

Number	Isolate ID	Gender	Age	Underlying Disease	Admission Date	Sample Date	Rectal Screen	Species	Sample Specimen Source	Outcome	Date of Discharge or Death	Cause of Death
Pt A	W873	Male	65	Central nervous system infection	2019/10/28	2019/10/28	2019/11/11 positive	CRKP	Rectal Swab	Improved	2019/12/17	/
Pt B	W909	Male	45	Cerebral hemorrhage	2019/11/1	2019/11/6	2019/10/28 negative	CRKP	Sputum	Improved	2019/11/21	/
Pt C	W902	Female	21	Intracranial tumor	2019/10/14	2019/11/4	Not done	CRKP	Sputum	Improved	2019/11/18	/
Pt D	W916	Female	24	Moyamoya disease	2019/10/17	2019/11/6	Not done	CRKP	Sputum	Improved	2019/11/21	/
Pt E	W920	Male	65	Cerebral infarction	2019/9/25	2019/11/7	2019/10/28 negative	CRKP	Sputum	Death	2019/11/19	Cerebral infarction
	W938					2019/11/11		CRKP	Rectal Swab
Pt F	W942	Male	19	Autoimmune encephalitis	2019/10/22	2019/11/11	Not done	CRKP	Sputum	Improved	2019/12/25	/
Pt G	W945	Male	42	Intracranial tumor	2019/10/21	2019/11/12	not done	CRKP	Sputum	Improved	2019/12/25	/
Pt H	W948	Male	50	Central nervous system infection	2019/11/5	2019/11/12	2019/11/5	CRKP	CSF	Improved	2019/12/23	/
Pt I	W901	Female	29	Cerebral infarction	2019/10/22	2019/11/7	Not done	CRKP	CSF	Improved	2019/11/29	/
Pt J	W937	Male	42	Intracranial tumor	2019/10/21	2019/11/11	2019/11/11 positive	CRKP	Rectal Swab	Improved	2019/11/15
	W932					2019/11/11		CRKP	Sputum
Pt K	W 963	Female	49	Intracranial tumor	2019/11/1	2019/11/14	Not done	CRKP	Sputum	Improved	2019/12/17	/

Figure 2 Phylogenetic tree of CRKP isolates in ICU-1 and ICU-2. (A) The genetic structure of total 30 CRKP isolates. The yellow and green range represented two clades in ICU-1 while purple range indicated strains in ICU-2. (B) The detailed phylogenetic tree of CRKPs in ICU-1. The upper branch indicated Clade 1, and the lower branch was classified Clade 2. (C) The detailed phylogenetic tree of CRKPs in ICU-2. Samples with grey dots showed strains isolated from environment. Sequence type were showed as stripes. Blue and red binary data meant antibiotic resistance genes (including resistance genes against aminoglycoside, beta-lactams, carbapenem, fluoroquinolone, and macrolide) and virulence genes (rmpA, rmpA2, and iuc1), respectively.

Figure 3 Phylogenetic tree of CRAB isolates in ICU-1. Samples with grey dots showed strains isolated from environment. Sequence type were showed as stripes. Blue binary data meant antibiotic resistance genes (including resistance genes against aminoglycoside, beta-lactams, macrolide, tetracycline, and genes of OXA-23, sul and Sull).