Clinical metagenomic sequencing for rapid diagnosis of pneumonia and meningitis caused by Chlamydia psittaci

Table 1 Patients’ demographic and clinical characteristics

Patient No.	1	2	3	4	5
Sex	M	M	M	F	M
Age (yr)	75	73	44	66	5
Symptoms	Fever, cough	Fever	Fever, cough	Fever, cough	Fever, dizziness, vomiting, convulsions
Chronic disease	Hypertension, diabetes, coronary heart disease, lacunar infarction, prostatic hyperplasia, amoebic dysentery	Hepatitis B	No history	No history	No history
Exposure history	Birds	Chickens	Birds	Psittacine birds	Birds
Fever	39.7℃	40.9℃	40.1℃	40.0℃	39.9℃
Leucocytes	8.46 × 109/L	2.98 × 109/L	14.51 × 109/L	2.93 × 109/L	24.01 × 109/L
Neutrophils	83.20%	83.20%	85.20%	49.90%	88.20%
Platelet count	106.00 × 109/L	106.00 × 109/L	191.00 × 109/L	286.00 × 109/L	301.00 × 109/L
Procalcitonin	1.65 ng/mL	0.49 ng/mL	0.01 ng/mL	0.19 ng/mL	4.28 ng/mL
C-reactive protein	241.70 mg/L	169.00 mg/L	225.40 mg/L	96.30 mg/L	6.30 mg/L
Aspartate aminotransferase	53.5 U/L	Normal	Normal	65.1 U/L	Normal
Glutamate aminotransferase	Normal	Normal	124.2 U/L	172.3 U/L	Normal
Urea nitrogen	14.5 mmol/L	Normal	Normal	Normal	Normal
Creatinine	353.0 μmol/L	Normal	Normal	Normal	Normal
Mycoplasma pneumoniae IgG titer	1:40	Negative	1:40	Negative	1:160
CSF culture	N/A	N/A	N/A	N/A	Streptococcus pneumoniae
Diagnosis	Psittacosis pneumonia	Psittacosis pneumonia	Psittacosis pneumonia	Psittacosis pneumonia	Purulent meningitis, Psittacosis meningitis
Antibiotics	Piperacillin, tazobactam, etimicin, moxifloxacin	Ganciclovir, tigecycline	Piperacillin, tazobactam, moxifloxacin, tigecycline	Piperacillin, tazobactam, moxifloxacin	Ceftazidime, vancomycin, ceftriaxone sodium, azithromycin, rifampicin
Hospitalization (d)	13	11	11	10	23

CSF: Cerebrospinal fluid; N/A: Not applicable.

Table 2 Pathogenic microorganisms detected using metagenomic next generation sequencing

Patient No.	Total reads	Chlamydia psittaci		Other microbes detected
		Reads	Genome coverage rate	Reads	Genome coverage rate
1	22128603	231	1.45%	-	-
2	33738995	305	1.81%	207	0.11% (Chlamydia albicans)
3	50359059	2	0.01%	-	-
4	41903841	6	0.02%	-	-
5	18745727	2137	7.76%	388	0.73% (Streptococcus pneumonia)

Genome coverage rate was defined as matched reads length per genome length.