Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting

Pallerla, Srinivas Reddy; Van Dong, Do; Linh, Le Thi Kieu; Van Son, Trinh; Quyen, Dao Thanh; Hoan, Phan Quoc; Trung, Ngo Tat; The, Nguyen Trong; Rüter, Jule; Boutin, Sébastien; Nurjadi, Dennis; Sy, Bui Tien; Kremsner, Peter G.; Meyer, Christian G.; Song, Le Huu; Velavan, Thirumalaisamy P.

doi:10.1186/s12941-022-00530-6

Annals of Clinical Microbiology and Antimicrobials

Table 3 Comparison of detected bacterial species by Nanopore and conventional culture

From: Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting

ID	Sex	Age	Diagnosis	DNA (ng/µL)	Nanopore	CSF culture	Blood culture (data from routine microbiology)
C1	M	53	Bacterial meningitis	< 1	N	N	N
C2	M	19	Bacterial meningitis, Nephrotic syndrome	< 1	N	N	N
C3	M	54	Bacterial meningitis	51	*S. pneumoniae*	*S. pneumoniae*	N
C4	M	41	Bacterial meningitis	29	S. suis	N	N
C5	M	37	Bacterial meningitis	18	N	N	N
C6	M	21	Bacterial meningitis	47	*S. pneumoniae*	*S. mitis*	N
C7	M	37	Bacterial meningitis	28	N	S. pneumoniae	S. pneumoniae
C8	M	30	Bacterial meningitis/brain trauma	12	S. pneumoniae	N	N
C9	M	44	Bacterial meningitis	10	N	N	N
C10	M	70	Bacterial meningitis	5	*S. suis*	*S. suis*	*S. suis*
C11	M	59	Bacterial meningitis	17	*S. suis*	*S. suis*	N
C12	M	73	Brain abscess after surgery	24	N	P. aeruginosa	S. xylosus
C13	M	51	Bacterial meningitis	39	E. hirae	N	N
C14	M	30	Bacterial meningitis	17	N	S. pneumoniae	S. pneumoniae
C15	M	82	Bacterial meningitis	8	N	N	N
C16	M	60	Bacterial meningitis	12	N	N	N
C17	M	20	Bacterial meningitis	33	*S. pneumoniae*	*S. pneumoniae*	N
C18	M	30	Bacterial meningitis	45	N	N	N
C19^a,b	M	49	Cryptococcus neoformans	4	N	C. neoformans	N
C20	M	72	Bacterial meningitis	25	N	N	N
C21	M	79	Bacterial meningitis	23	N	N	N
C22	M	60	Bacterial meningitis	46	N	N	N
C23	M	60	Bacterial meningitis	7	N. gonorrhoeae	N	N
C24	M	60	Bacterial meningitis	15	N	N	N
C25	M	65	Meningitis	57	*S. suis*	*S. suis*	*S. suis*
C26	M	38	Bacterial meningitis	37	*S. suis*	*S. suis*	*S. suis*
C27^a	M	63	Meningitis after surgical tooth extraction	7	K. pneumoniae	N	N
C28	F	30	Tuberculomeningitis	13	N	N	N
C29	M	41	Bacterial meningitis	22	N	N	N
C30	M	55	Bacterial meningitis	30	*Aeromonas jandaei*	*Aeromonas sobria*	N

BoldItalic indicates concordance, defined as identical results to the species/genus level, between Nanopore sequencing, CSF culture and blood culture
CSF cerebrospinal fluid, M male, F female, N negative
^aPatients deceased
^bFungal infection

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ISSN: 1476-0711

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