Clinical, laboratory profile and molecular characterization of Orientia tsutsugamushi among fatal scrub typhus patients from Karnataka, India

Figures & data

Figure 1. Study flow chart. DAMA; discharge against Medical advice.

Table 1. Clinical manifestations and organ involvement of the scrub typhus cohort (N = 261).

Variables	Succumbed (N = 9) n% Median (IQR)	Recovered (N = 252) n% Median (IQR)	P-value
Fever	7 (77)	247 (98)	0.020
Chills and Rigours	3 (33)	101 (40.1)	1.00
Headache	0 (0)	81 (32.1)	0.061
Myalgia	3 (33)	71 (28.2)	0.716
Vomiting	2 (22)	71 (28.2)	1.00
Abdominal pain	4 (44)	68 (27)	0.266
Cough	2 (22)	63 (25)	1.00
Breathlessness	4 (44)	47 (18.7)	0.076
Eschar	2 (22)	33 (13.1)	0.345
Altered sensorium	2 (22)	21 (8.3)	0.183
Jaundice	3 (33)	18 (7.1)	0.028
Diarrhoea	0 (0)	9 (3.6)	1.00
Seizure	0 (0)	5 (2)	1.00
Duration of illness (days)	4 (4, 6.5)	7 (5, 10)	0.016
Severity and Organ involvement
Severity	9 (100)	147 (58.3)	0.012
Cardiovascular	7 (77)	26 (10.3)	<0.001
Respiratory	9 (100)	60 (23.8)	<0.001
Central nervous system	1 (11)	13 (5.2)	0.396
Hematology	1 (11)	17 (6.7)	0.480
Renal	6 (66)	31 (12.3)	<0.001
Hepatic	8 (88)	95 (37.7)	0.003

Figure 2. Phylogenetic tree of Orientia tsutsugamushi 56 kDa TSA gene. Highlighted with green triangles are sequences of the survivors and highlighted in red are sequences of the succumbed.

Table 2. Clinical characteristics and complications in patients succumbed to scrub typhus (N = 9).

Variables	Case 1 68yrs/ Male, Retired person from Udupi Dist.	Case 2 60yrs/ Female, Housewife from Chitradurga Dist.	Case 3 68yrs/ Male, Farmer from Chitradurga Dist.	Case 4 60yrs/ Female, Farmer from Udupi Dist.	Case 5 26yrs/ Male, Unskilled worker from Davangere Dist.	Case 6 65yrs/ Female, Housewife from Haveri Dist.	Case 7 40yrs/ Female, Housewife from Haveri Dist.	Case 8 70yrs/ Male, Retired person from Udupi Dist.	Case 9 65yrs/ Male, Farmer from Chikmaglur Dist.
Days of illness	4	6	7	1	4	4	5	4	15
Comorbidity	Type 2 DM, H/o PTB	Type 2 DM	Nil	Nil	Nil	COPD	Glaucoma	Nil	CKD, DM, HTN, H/o TB Lymphadenitis
Complications	MODS, Bilateral pneumonia, Severe ARDS, Sepsis, Refractory septic shock	AKI-non oliguric, Severe sepsis with refractory shock	MDR E.Coli sepsis, Duodenal perforation, Postoperative delirium, Paroxysmal atrial fibrillation	MODS (AKI-stage 3, Right-sided pneumonia -ventilator acquired) Candida tropicalis, ARDS, Hyperkalemia, Sepsis with septic shock,	MODS (AKI, myocarditis, hepatitis), Sepsis with septic shock	MODS (ARDS, Type 2 Respiratory failure, AKI, DIC), Upper GI bleed, Sepsis with septic shock	MODS (AKI, Acute hepatitis, Acute pancreatitis), Sepsis with septic shock	MODS (AKI, ARDS), Klebsiella pneumoniae, Sepsis with shock.	Septic shock, Left lower lobe pneumonia (PDR Acinetobacter baumanii), Septic encephalopathy
Co-positive	–	–	–	–	–	Leptospira IgM	–	Leptospira IgM	Leptospira IgM
Treatment	Doxycycline, Meropenem, Teicoplanin, Oseltamivir	Doxycycline, Azithromycin, Ceftriaxone	Doxycycline, Ceftriaxone, Piperacillin tazobactam, Meropenem, Colistin, Tigecycline	Azithromycin, Ceftriaxone, Piperacillin tazobactam	Azithromycin, Piperacillin tazobactam	Doxycycline, Azithromycin, Piperacillin tazobactam	Doxycycline, Ceftriaxone, Penicillin	Azithromycin, Ceftriaxone, Meropenem, Tigecycline, Polymixin B	Azithromycin, Doxycycline, Meropenem, Tigecycline, Polymixin B
Steroid Therapy, Dose and Duration	Hydrocortisone 100 mg IV stat/ 50 mg every 6 h 2 days	Methylprednisolone 40 mg IV BD 2 days	--	Methylprednisolone/ Hydrocortisone 40 mg IV BD/ 100 mg IV STAT 3 days/ 1 dose	Methylprednisolone 40 mg IV BD 2 days	Hydrocortisone 100 mg IV 1 dose	Hydrocortisone/ Methylprednisolone 100 mg IV stat/ 40 mg IV BD 1 dose/ 1 dose	--	--
Death (No. of days after admission)	3	5	20*	9	2	3*	2	10	11*

AKI: Acute kidney injury; ARDS: Acute respiratory distress syndrome; CKD: Chronic kidney disease; COPD: Chronic obstructive pulmonary disease; DIC: Disseminated intravascular coagulation; DM: Diabetes mellitus; GI: Gastro-intestinal; HTN: Hypertension; MODS: Multi organ dysfunction syndrome; MDR: Multi-drug resistant; PDR: Pan drug resistant; PTB: Pulmonary tuberculosis; TB: Tuberculosis.

* Patient 3, 6 and 9 were discharged from hospital in critical condition against medical advice. Based on the information received during telephonic follow up, patient 3, 6 and 9 expired 4 days, 2 days and 1 day after discharge respectively.

Table 3. Laboratory findings of the patients succumbed due to scrub typhus (N = 9).

Laboratory Parameters	Reference Range	Case 1	Case 2	Case 3	Case 4	Case 5	Case 6	Case 7	Case 8	Case 9
Haemoglobin (g/dL)	12–17	11.6	10.0	13.2	10.9	11.2	10.5	9.4	11.3	7.2
Total White Blood Cells count (cells/ µL)	4000–10000	10200	9800	5200	14100	15000	11300	7000	20600	28100
Platelets count (cells/ µL)	150000–400000	121000	4000	82000	44000	38000	55000	30000	27000	103000
Total Bilirubin (mg/dL)	Males- 1.4 Female- 0.9	2.91	8.96	2.40	7.58	11.41	2.61	3.86	32.2	1.84
Direct Bilirubin (mg/dL)	0-0.3	2.40	8.07	1.78	6.77	10.27	1.59	3.09	17	1.23
AST (IU/L)	Males- up to 40 Females up to 32	88	426	186	211	143	117	191	81	43
ALT (IU/L)	Males- up to 41 Females up to 33	67	147	118	164	44	58	83.2	60.8	42.7
ALP (U/L)	Males- 40-130 Females- 35-105	131	327	522	699	161	238	209	156	445
Total Protein (g/dL)	6.4–8.3	5.4	4.4	5.3	5.9	4.3	5.7	5.97	4.76	5.9
Serum Albumin (g/dL)	3.5–5.2	3	2	2.6	2.8	1.9	2.4	2.7	2.97	2.55
Creatinine (mg/dL)	Males- 0.7–1.2 Females- 0.5–0.9	2.08	2.94	2.86	1.07	6.01	1.6	1.94	8.2	4.88
C-Reactive Protein (mg/L)	0–5	282.64	305.34	191.67	196.61	–	200.42	–	91.47	–
Procalcitonin (mcg/L)	<0.5	–	7.835	1.128	1.023	–	2.834	1.76	–	45.91
Scrub typhus IgM ELISA OD Value	≥1.0	2.116	3.942	3.496	3.9	3.9	2.91	3.18	2.34	2.86
Nested PCR (56 kDa)	483 bp	Positive	Positive	Positive	Positive	Positive	Positive	Positive	Positive	Positive
Orientia tsutsugamushi Genotype	–	Karp-like	JG-v	JG-v	JG-v	Karp-like	Karp-like	JG-v	JG	–

ELISA: Enzyme-linked Immunosorbent assay; IgM: Immunoglobulin M; JG-v: Japanese Gilliam – variant; JG: Japanese Gilliam; PCR: Polymerase chain reaction.

Table 4. Laboratory parameters of the scrub typhus cohort (N = 261).

Variable	Succumbed (N = 9) n (%) or mean (±SD) or median (IQR)	Recovered (N = 252) n (%) or mean (±SD) or median (IQR)	p-value
Haemoglobin (g/dL)	10.58 ± 1.66	11.91 ± 1.98	0.049
WBC (cells/µL)	11300 (7500, 17800)	8400 (6200, 11400)	0.966
Platelet count (cells/µL)	44,000 (28,500, 92,500)	1,06,000 (59,250, 1,64,250)	0.021
Total bilirubin (mg/dL)	3.86 (2.5, 10.18)	1.27 (0.61, 3.31)	<0.001
Direct bilirubin (mg/dL)	3.09 (1.68, 9.17)	0.71 (0.25, 2.5)	<0.001
Aspartate aminotransferase (IU/L)	143 (84.5, 201)	108.5 (62.25, 165.5)	0.695
Alanine aminotransferase (IU/L)	67 (51, 132.5)	80 (52, 129.9)	0.613
Alkaline phosphatase (U/L)	238 (158.5, 483.5)	174 (108.5, 287.75)	0.082
Serum Creatinine (mg/dL)	2.86 (1.77, 5.44)	0.92 (0.72, 1.29)	<0.001
Total Protein (g/dL)	5.4 (4.58, 5.9)	6.3 (5.6, 6.7)	0.001
Serum Albumin (g/dL)	2.6 (2.2, 2.8)	3 (2.5, 3.4)	0.031

Data availability

All the sequences obtained were deposited to NCBI GenBank with accession numbers OP617281-OP617329, OQ320014 – OQ320038, OQ428197, and OR526472 - OR526477.