Metagenomic Next-Generation Sequencing in Diagnosis of a Case of Pneumocystis jirovecii Pneumonia in a Kidney Transplant Recipient and Literature Review

Figures & data

Figure 1 Chest images. (A) Chest X-ray showing bilateral patchy, cloudy opacities in the lower lungs with some adjacent pleural thickening and adhesion before treatment. (B and C) Chest HRCT showing diffused stripes as well as reticular and ground-glass opacities with honeycomb structures, primarily in the lower lungs before treatment. (D and E) Chest HRCT scan showing a faint patchy opacity in the lateral segment (white arrow).

Table 1 Main Laboratory Test Results Before and After Treatment

Laboratory Parameters	Normal Range	Pre-Treatment*	Post-Treatment*^a
White blood cell count/L	3.50–9.50 x 10^9	12.65 x 10^9	6.55 x 10^9
Hemoglobin, g/L	115.0–150.0	165.0	149.0
Platelet count/L	101–320 x 10 ^9	248 x 10^9	151 x 10^9
Neutrophil %	40.0–75.0	86.7	54.7
Lymphocyte %	20.0–50.0	7.4	18.3
Alanine aminotransferase, U/L	7.0–40.0	14.0	96.0
Aspartate aminotransferase, U/L	13.0–35.0	9.0	30.0
NT-proBNP, ng/L	0–97	214	n/a
Serum albumin, g/L	40.0–55.0	43.0	67.0
Lactate dehydrogenase, U/L	120–250	301	361
Creatinine, umol/L	41.0–73.0	189	169
Urea nitrogen, mmol/L	2.60–7.50	13.3	17.8
Calcium, mmol/L	2.11–2.52	2.40	2.34
C-reactive protein, mg/L	<10	48.10	n/a
Procalcitonin, ng/mL	0.00–0.05	0.09	n/a
1,3-beta-D-glucan, pg/mL	<60	<10.0	n/a
Galactomannan	<0.5	<0.5	n/a
Total T lymphocyte count/μL	810–2860	739	n/a
CD4+ T cell count/μL	420–1440	256	n/a
CD8+ T cell count/μL	238–1250	456	n/a
CD4+/CD8+ ratio	0.80–2.74	0.56	n/a

Notes: *Abnormal values are indicated in bold face. ^aOn the 16th day of hospitalization.

Abbreviations: n/a, not available; NT-proBNP, N-terminal pro b-type natriuretic peptide.

Table 2 Reports of PCP Cases Detected by Metagenomics Next-Generation Sequencing (mNGS)

Reference No.	Authors	Year	No. of PCP Cases	Common Underlying Diseases	Sample Types	NGS Platform	No. of Reads for P. jirovecii, Media (Range)	Most Common Co-Infecting Pathogens
[^Citation14]	Wang et al	2019	13	Cancers, anemia	BALF and lung biopsy	Torrent Proton	122 (6–303,572)	CMV, Aspergillus
[^Citation15]	Irinyi et al	2019	3	n/a	BALF, sputum	Nanopore MinION	9 (2–14)	Candida, Lecanora, Diplodia
[^Citation16]	Camargo et al	2020	1	Leukemia	Blood	Illumina NextSeq 500	263	None
[^Citation17]	Li et al	2020	9	Immuno-deficiency	BALF	BGISEQ-50	246 (5–4857)	None
[^Citation18]	Zhang et al	2019	13	Cancers, pemphigus, anemia,	BALF, sputum, blood and lung biopsy	n/a	34 (5–787)	HHV, HSV1, Candida albicans,

Abbreviations: n/a, not available; BALF, bronchoalveolar lavage fluid; HHV, human herpes virus; HSV1, human simple virus 1; CMV, cytomegalovirus.

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