Pneumonia Caused by Chlamydia psittaci and SARS-CoV-2 Coinfection Diagnosed Using Metagenomic Next-Generation Sequencing: A Case Report

Figures & data

Table 1 Laboratory Test Results of the Patient with Chlamydia Psittaci Pneumonia and SARS-CoV-2 Coinfection

Parameter	Normal Range	On Admission	1 Week After Starting MFX
WBC (×10^9/L)	4–10	12	7.58
Neutrophils (×10^9/L)	2–7	10.68	5.07
Lymphocytes (×10^9/L)	0.8–4	0.73	1.57
Eosinophils (×10^9/L)	0.5–5	0	0.43
Monocytes (×10^9/L)	3–10	0.57	0.43
Basophils (×10^9/L)	0–1	0.02	0.06
Neutrophil (%)	50–70	89	66.7
Lymphocyte (%)	20–40	6.1%	20.8
Eosinophil (%)	0.5–5	0%	5.7
Monocyte (%)	3–10	4.7%	6
Basophil (%)	0–1	0.2%	0.8
Hemoglobin (g/L)	113–151	124	129
Platelets (×10^9/L)	101–320	243	363
CRP (mg/L)	0–8	78	6
PCT (ng/mL)	0–5	0.16	0.05
CK (U/L)	26–174	171	103
CK-MB (U/L)	0–24	9.4	5.7
Myoglobin (ng/mL)	0–110	48.7	40.5
BNP (pg/mL)	0–100	196	191
AST (U/L)	13–40	47.5	19.4
ALT (U/L)	7–40	38.3	10.4
LDH (U/L)	0–247	227	233
Creatinine (µmol/L)	45–84	106.4	68.5
K (mmol/L)	3.5–5.5	4.07	3.94
Na (mmol/L)	135–145	137	142
Cl (mmol/L)	95–105	99.9	108.4
Ca (mmol/L)	2.08–2.6	2	2.08
P (mmol/L)	0.96–1.62	0.86	1.01
Fibrinogen (g/L)	2–4	7.88	6.19
D-dimer (mg/L)	0–0.5	2.84	2.84

Abbreviations: ALT, alanine aminotransferase; AST, aspartate aminotransferase; BNP, brain natriuretic peptide; CK, creatine kinase; CK-MB, creatine kinase MB isoenzyme; CRP, C-reactive protein; LDH, lactate dehydrogenase; MFX, moxifloxacin; PCT, procalcitonin; WBC, white blood.

Figure 1 Chest computed tomography. (A–C) Chest computed tomography (CT) on admission showing massive consolidation in the left lower lung field and left-sided pleural effusion. (D–F) Chest CT after 1 week of treatment with moxifloxacin, showing a reduction in the consolidation, lung lesions, and pleural infusion. (G–I) Chest CT after 2 weeks of treatment with moxifloxacin.

Figure 2 Detection depths and coverage of SARS-CoV-2 Omicron XBB.1 and Chlamydia psittaci in different sample types. (A and B) Detection depths and coverage of SARS-CoV-2 Omicron XBB.1 in (A) BALF and (B) nasopharyngeal swab specimens. (C and D) Detection depths and coverage of C. psittaci in (C) BALF and (D) nasopharyngeal swab specimens.

Table 2 C. Psittaci and COVID-19 PCR Primers Used in This Study

Primer Set	Sequence (5’-3’)	F/R	Target
C. psittaci	TGAGAAATACCTAGCAAAGTTCCCA	F	OmpA
C. psittaci	TCTCAATGACAATAGGTTGGGTAGG	R
SARS-CoV-2	GACCCTGTGGGTTTTACACTTAA	F	ORF
SARS-CoV-2	AACGATTGTGCATCAGCTGA	R
SARS-CoV-2	GGGGAACTTCTCCTGCTAGAAT	F	N
SARS-CoV-2	CAGACATTTTGCTCTCAAGCTG	R
RPP30	ACCTTGGCTATTCAGTTGTTGC	F	RPP30
RPP30	TGCTCTCAAAACATTGCAGTGA	R

Abbreviations: F, forward; F/R= forward/reverse; R, reverse; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Table 3 mNGS and Confirmative qPCR Results

Sample type	Number of DNA reads with C. psittaci Sequences	Number of RNA Reads with SARS-CoV-2 Omicron XBB.1 Sequences	Number of Reads with Other Pathogen Sequences	C. psittaci Ct on qPCR	SARS-CoV-2 Ct on qPCR
BALF	874	1,847,027	Human alphaherpesvirus 1 (reads 46)	24.59	38.57
Blood	2	/	Human alphaherpesvirus 1 (reads 1)	/	/
Nasopharyngeal swab	4	224,671	Human alphaherpesvirus 1 (reads 25)	/	31.07

Abbreviations: Ct, cycle threshold; qPCR, quantitative polymerase chain reaction; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Figure 3 The patient’s clinical course and treatment. Body temperature alterations and antibacterial therapy, (i) 4.5 g piperacillin-tazobactam administered as an intravenous bolus every 8 hours on days 1–3 and (ii) 0.4 g of moxifloxacin administered as an intravenous bolus once daily on days 4–11.

Abbreviations: BALF, Bronchoalveolar Lavage Fluid; mNGS, Metagenomic Next-Generation Sequencing; SARS-CoV, Severe Acute Respiratory Syndrome Coronavirus.