Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome

Zhong, Juan; Liu, Yanfen; Luo, Na; Wei, Qiu; Su, Qisi; Zou, Jun; Wu, Xiaozhong; Huang, Xianzhen; Jiang, Yuting; Liang, Lijuan; Li, Hongmian; Lin, Jianyan

doi:10.1186/s12941-023-00608-9

Annals of Clinical Microbiology and Antimicrobials

Table 2 Distribution of diagnoses based on culture, Xpert and mNGS confirmation of species identity of isolates

From: Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome

Sample Id	Sample type	Microbial classification	mNGS-positive results	Total reads	Culturing-positive results	Xpert
B2106316_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	*Mycobacterium tuberculosis	600	Mycobacterium spp.	Mycobacterium tuberculosis
		Fungi	Pneumocystis jirovecii	1
		dsDNA virus	Human gammaherpesvirus 4	304
BH211504_AA	Bronchoalveolar lavage fluid	Fungi	Pneumocystis jirovecii	32	Talaromyces marneffei	NA
		Fungi	Penicillium marneffei	12,298
		dsDNA virus	Human cytomegalovirus	7
		dsDNA virus	Human gammaherpesvirus 4	4948
BH211505_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	Rothia slime	14,959	Mycobacterium spp.	NA
		Gram-negative bacteria	Isoeveillonella spp.	11,915
		Gram-negative bacteria	Prevotella niger	55,489
		dsDNA virus	Human gammaherpesvirus 4	4
B2103830_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	Streptococcus parasanguis	1893	Haemophilus influenzae	NA
		Gram-positive bacteria	Streptococcus pneumoniae	705
		Gram-negative bacteria	Haemophilus parainfluenzae	1019
		Gram-negative bacteria	*Haemophilus influenzae	437
		Fungi	Candida albicans	9
		Fungi	Pneumocystis jirovecii	1
		dsDNA virus	Human gammaherpesvirus 4	9
		dsDNA virus	Human cytomegalovirus	4
B2103362_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	Streptococcus pneumoniae	718	Candida albicans	NA
		Gram-positive bacteria	Oral Streptococcus	2178
		Gram-negative bacteria	Klebsiella pneumoniae	84
		Fungi	*Candida albicans	5024
		dsDNA virus	Human gammaherpesvirus 4	6
B2102995_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	Tropheryma whipplei	13,336	Talaromyces marneffei	NA
		Gram-positive bacteria	Streptococcus pneumoniae	917
		Fungi	Penicillium marneffei	35
		dsDNA virus	Human gammaherpesvirus 4	55
B2102820_AA	Bronchoalveolar lavage fluid	Gram-negative bacteria	Enterobacter cloacae	849	Escherichia coli and Mycobacterium spp.	NA
		Gram-negative bacteria	Pseudomonas aeruginosa	1119
		Gram-negative bacteria	*Escherichia coli	23,469
		Gram-negative bacteria	Klebsiella pneumoniae	134,747
		dsDNA virus	Human gammaherpesvirus 4	11,103
		dsDNA virus	Human cytomegalovirus	160
B2102821_AA	Bronchoalveolar lavage fluid	Gram-negative bacteria	*Klebsiella pneumoniae	64,903	Klebsiella pneumoniae	NA
		Fungi	Candida albicans	3
		dsDNA virus	Human gammaherpesvirus 4	98
B2102822_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	Streptococcus pneumoniae	1451	Mycobacterium spp.	NA
		Gram-positive bacteria	Streptococcus parasanguis	2830
		Gram-positive bacteria	*Mycobacterium avium	4
		dsDNA virus	Human cytomegalovirus	16
B2102519_AA	Bronchoalveolar lavage fluid	Fungi	Pneumocystis jirovecii	129	Aspergillus spp.	NA
		dsDNA virus	Human cytomegalovirus	168
		dsDNA virus	Human gammaherpesvirus 4	21
B2102520_AA	Bronchoalveolar lavage fluid	Gram-negative bacteria	Klebsiella pneumoniae	227	Gram-negative bacteria	NA
		Gram-negative bacteria	Helicobacter pylori	321
		Fungi	Penicillium marneffei	157
		dsDNA virus	Human gammaherpesvirus 4	48,541
B2102121_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	Staphylococcus aureus	122	Gram-negative bacteria, Candida glabrata and Candida krusei	NA
		dsDNA virus	Human gammaherpesvirus 4	6038
		Gram-positive bacteria	Streptococcus pneumoniae	3016
		Gram-positive bacteria	Streptococcus parasanguis	3822
		Gram-negative bacteria	*Klebsiella oxytoca	3375
		Fungi	*Candida glabrata	2452
		Fungi	Pichia kudri azwei	231
		Fungi	Penicillium marneffei	144
		Fungi	Aspergillus fumigatus	12
		dsDNA virus	Human cytomegalovirus	8
B2101782_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	Tropheryma whipplei	11,657	Haemophilus haemophilus	NA
		Gram-positive bacteria	Pseudostreptococcus pneumoniae	9
		Gram-positive bacteria	Streptococcus pneumoniae	8
		Gram-negative bacteria	Haemophilus influenzae	27,396
		Fungi	Aspergillus fumigatus	15
B2101349_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	*Mycobacterium kansasii	39	Mycobacterium spp.	NA
B2101349_AA	Bronchoalveolar lavage fluid	V:DNA	Human gammaherpesvirus 4	153	Mycobacterium spp.	NA
B2100619_AA	Bronchoalveolar lavage fluid	Fungi	Pneumocystis jirovecii	70	Mycobacterium spp.	Mycobacterium tuberculosis
		V:DNA	Human gammaherpesvirus 4	359
		V:DNA	Human cytomegalovirus	10
B2100621_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	*Mycobacterium tuberculosis	29	Mycobacterium spp.	NA
		Fungi	Candida albicans	1316
		V:DNA	Human gammaherpesvirus 4	23
B2100395_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	Enterococcus faecium	262	Aspergillus spp.	NA
		Gram-positive bacteria	Streptococcus pneumoniae	3
		Gram-negative bacteria	Pseudomonas aeruginosa	3
		Fungi	Aspergillus fumigatus	3336
		Fungi	Aspergillus flavus	68
		V:DNA	Human gammaherpesvirus 4	490
		V:DNA	Human cytomegalovirus	7
B2100396_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	Streptococcus pneumoniae	716	Rhodococcus equi	NA
		Gram-positive bacteria	*Rhodococcus equi	10,291
		V:DNA	Human gammaherpesvirus 4	21
B2100107_AA	Bronchoalveolar lavage fluid	Gram-negative bacteria	*Klebsiella pneumoniae	665	Gram-negative bacteria	NA
B2006273_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	*Mycobacterium tuberculosis	18	Mycobacterium spp.	NA
B2006273_AA	Bronchoalveolar lavage fluid	V:DNA	Human gammaherpesvirus 4	18	Mycobacterium spp.	NA
B2006130_AA	Bronchoalveolar lavage fluid	V:DNA	Human cytomegalovirus	4	Mycobacterium spp.	NA
B2006023_AA	Bronchoalveolar lavage fluid	Gram-positive bacteria	Oral Streptococcus	36	Mycobacterium spp.	NA
		Gram-positive bacteria	Nocardia beijing	512
		Gram-positive bacteria	Streptococcus pneumoniae	11
		V:DNA	Human gammaherpesvirus 4	143

Note: Sample Id, microbial classification, mNGS-positive results, the number of unique reads and culturing-positive results were revealed and * means confirmed pathogens with pulmonary pathogenicity when # means potential pathogenic agents

Back to article page

ISSN: 1476-0711

Contact us

Submission enquiries: journalsubmissions@springernature.com