Co-Infection Pneumonia with Mycobacterium abscessus and Pneumocystis jiroveci in a Patient without HIV Infection Diagnosed by Metagenomic Next-Generation Sequencing

Figures & data

Table 1 The Pathogen and Sequence Reads Detected by mNGS in BALF and Blood Samples

Sample	Pathogen	Sequence Reads
BALF	M. abscessus	1315
BALF	P. jirovecii	44
BALF	CMV	649
Blood	M. abscessus	0
Blood	P. jirovecii	368
Blood	CMV	44

Abbreviations: M. abscessus, Mycobacterium abscessus; P. jirovecii, Pneumocystis jiroveci; CMV, Cytomegalovirus.

Figure 1 Chest CT performed on admission (A1, A2), on day 9 (B1, B2), on day 17 (C1, C2), on day 26 (D1, D2), and five months after discharge (E1, E2).

Figure 2 A, B, C detected from BALF, D and E detected from Blood. (A) The sequence reads for CMV allowed assembly of a CMV reference genome (NC_006273.2); (B) The P. jirovecii sequence reads assembled to a P. jirovecii reference genome (NW_017264779.1); (C) The sequence M. abscessus reads mapped to M. abscessus reference genome (NC_010397.1). (D) The sequence reads for CMV allowed assembly of a CMV reference genome (NC_006273.2); (E) The P. jirovecii sequence reads assembled to a P. jirovecii reference genome (NW_017264779.1).

Table 2 The Important Laboratory Results on Admission and After Treatment

Laboratory Parameters	On Admission	After Treatment	Normal Range
WBC count	9.38	3.97	3.5–9.5×10E9/L
Platelet count	291	89	100–350×10E9/L
LYMP	0.65	1.01	1.1–3.2×10E9/L
Hemoglobin	126	100	130–175g/L
ALT	40	18	3–35IU/L
AST	37	15	13–35IU/L
BUN	5.6	4.27	2.4–8.2mmol/L
Creatinine	68	88	31.8–116umol/L
hsCRP	43.2	4.8	0–10mg/L
PCT	0.025	0.022	0–0.05ng/mL
HIV	Negative	NA	Negative
Syphilis	Negative	NA	Negative
Hepatitis B and C	Negative	NA	Negative
Syphilis	Negative	NA	Negative
BDG	<3.836	NA	0–10 pg/mL
ANCA	Negative	NA	Negative
ENA	Negative	NA	Negative
Anti-dsDNA	Negative	NA	Negative
ANA	Negative	NA	Negative
TSH	0.7793	NA	0.35–4.94uIU/mL
DNA copies of CMV	9E2	<500	<500 copies/mL
CD4+T cells/lymphocyte	17%	NA	27%-51%
NK cells/lymphocyte	2%	NA	7%-40%
Acid-fast bacilli smear	Negative	NA	Negative
Culture of sputum	Negative	NA	Negative
GeneXpert MTB/RIF assay	Negative	NA	Negative
Sputum immunofluorescence staining for Pneumocystis organisms	Negative	NA	Negative

Abbreviations: WBC, white blood cell; LYMP, absolute value of lymphocyte; AST, aspartate aminotransferase; ALT, alanine aminotransferase; BUN, blood urea nitrogen; hsCRP, hypersensitive C-reactive protein; PCT, procalcitonin; BDG, 1,3-beta-D-glucan; ANA, antinuclear antibody; anti-dsDNA, anti-double stranded DNA antibody; ANCA, antineutrophil cytoplasmic antibody; ENA, extractable nuclear antigen; TSH, thyroid stimulating hormone; N/A, not available.

Figure 3 The details of antibiotic and main process of disease.

Figure 4 The cycle threshold (Ct) value for mtLSU of BALF and blood detected by PneumoGenius^® real-time PCR were 32.5 and 36.31, respectively.

Abbreviations: PC, positive control; NC, negative control; Ct, cycle threshold.