Table 1 Use of mNGS in detection of putative pathogens in neonates in whom infections attributed as the cause of death

From: Metagenomic sequencing of post-mortem tissue samples for the identification of pathogens associated with neonatal deaths

				RNA libraries		DNA libraries
Case number	Underlying CoD^a	Immediate CoD^a	Direct etiologic agent CoD^a	Lung metagenomic	Blood metagenomic	Lung metagenomic	Blood metagenomic
1	Congenital anomalies	LRTI	A.baum	Failed library prep	A.baum	Negative	Negative
2	Prematurity	Meningitis	A.baum	A.baum, K.pneu	A.baum, Kpneu	Negative	Negative
3	Sepsis	LRTI	A.baum, RSV	A.baum	A.baum	*A.baum*^b	Negative
4	Prematurity	LRTI	A.baum	A.baum, U.urealyticum	A.baum, U.urealyticum	*A.baum*^b, U.urealyticum	*A.baum*^b
5	Prematurity	LRTI	A.baum	A.baum	A.baum	*A.baum*^b	Negative
6	Prematurity	Sepsis	A.baum, S.aur, ureaplasma	A.baum	A.baum, ureaplasma, S.aur	*A.baum*^b	*A,baum*^b
7	Prematurity	Sepsis	E.coli	Negative	E.coli	Negative	Negative
8	Prematurity	Sepsis	S.aur, A.baum	A.baum, S.aur, K.aero	A.baum, K.aero	Negative	Negative
9	Prematurity	Sepsis	S.marc	S.marc	S.marc	Negative	Negative
10	LRTI	Sepsis	A.baum	A.baum, S.heme	A.baum	*A.baum*^b	*A.baum*^b
11	Prematurity	Sepsis	A.baum	A.baum	A.baum	Negative	Negative
12	Prematurity	LRTI	A.baum	A.baum	A.baum	*A.baum*^b, E.coli	Negative
13	Prematurity	LRTI	A.baum	A.baum	A.baum	Not done	Not done
14	Congenital anomalies	Sepsis	A.baum	A.baum	A.baum, S.marc, Human adenovirus	Not done	Not done
15	Prematurity	Sepsis	A.baum, K.pneu	A.baum	S.marc, A.baum	Not done	Not done
16	Prematurity	Sepsis	A.baum, S.aur	Negative	A.baum	Not done	Not done
17	Prematurity	LRTI	A.baum	A.baum	A.baum, S.marc	Not done	Not done
18	Prematurity	Sepsis	K.pneu	CMV, S.aur	K.pneu, CMV	Not done	Not done
19	Prematurity	Sepsis	MRSA	Negative	S.marc, Human alpha-herpesvirus 2	Not done	Not done
20	Prematurity	LRTI	K.pneu	Failed library prep	S.marc	Not done	Not done
21	Prematurity	Sepsis	Unspecified organism	K.pneu	E.coli, K.pneu	K.pneu	Negative
22	Sepsis	Respiratory distress syndrome	Unspecified organism	Negative	Negative	Negative	Negative
23	Prematurity	Sepsis	Unspecified organism	Negative	K.pneu, S.mitis	Negative	Negative
24	Prematurity	Sepsis	Unspecified organism	H.heme	Negative	H.heme	Negative
25	Prematurity	Congenital pneumonia	Unspecified organism	K.oxy	Negative	Negative	Negative
26	Prematurity	Sepsis	Unspecified organism	Negative	A.baum	Negative	Negative
27	Prematurity	Sepsis	Unspecified organism	A.baum	Negative	Not done	Not done
28	Prematurity	Sepsis	Unspecified organism	Negative	S.aur	Not done	Not done
29	Prematurity	Sepsis	Unspecified organism	Negative	Negative	Not done	Not done
30	Prematurity	Sepsis	Unspecified organism	Negative	S.marc	Not done	Not done
31	Prematurity	Sepsis	Unspecified organism	Negative	S.marc	Not done	Not done

LRTI Lower respiratory tract infection, A.baum Acinetobacter baumannii, K.pneu Klebsiella pneumonia, E.coli Escherichia coli, RSV respiratory syncytial virus, CMV cytomegalovirus, S.aur Staphylococcus aureus, K.aero Klebsiella aerogenes, S.Marc Serratia marcescens, S.heme Staphylococcus haemolyticus, MRSA Methicillin-resistant Staphylococcus aureus, haemolyticus, H.heme Haemophilus haemolyticus, S.mitis Streptococcus mitis, P.mira Proteus mirabilis, U.urealyticum Ureaplasma urealyticum
^aAs determined by the Determination of Cause of Death (DeCoDe) panel of experts who reviewed all available medical and laboratory reports, including post-mortem blood and lung tissue culture, NAAT using Fast Track diagnostic assays on lung and blood samples. All antemortem and postmortem results are reported in Supplementary Table 2.
^b Indicate where whole genomes were generated

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Table 1 Use of mNGS in detection of putative pathogens in neonates in whom infections attributed as the cause of death

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