. 2019 Jun 13;2:19. Originally published 2018 Apr 18. [Version 2] doi: 10.12688/gatesopenres.12811.2

Table 1. Collection, storage, processing and analysis of clinical samples.

Specimen	Collection container	Storage temperature	Assay	Processing	Laboratory
Blood	Blood culture bottle	+4°C	Blood culture and AST	Real time	CH, LMSE
	Tempus	+4°C/-20°C	Transcriptomics	Batch	NCH
	EDTA tube	+4°C	WBC	Real time	EB, CH
	EDTA tube	+4°C/-80°C	Triplex PCR	Batch	LRM, LMSE
Urine	Sterile container (or sterile adhesive bags for babies)	+4°C	Antibiotic activity *	Batch	LRM, LMSE
Urine	Sterile container (or sterile adhesive bags for babies)	+4°C	Binax	Real time	CH, LMSE
Nasopharyngeal swab	Viral transport medium	+4°C/-80°C	Triplex PCR	Batch	LRM, LMSE
		+4°C/-80°C	Micro-array (BioFire) *	Real time
		+4°C/-80°C	S. pneumo CAPS-PCR	Batch
Nasopharyngeal swab	STGG medium	+4°C	Bacterial culture *	Real time	CH, LMSE
Nasopharyngeal swab	STGG medium	+4°C/-80°C	CAPS-PCR	Batch	LRM, LMSE
Sputum (adults only)	Sterile container	+4°C	Bacterial culture	Real time	CH, LMSE
		+4°C/-80°C	Triplex PCR	Batch	LRM, LMSE
		+4°C/-80°C	Micro-array (BioFire) *	Real time
		+4°C/-80°C	S. pneumo CAPS-PCR	Batch

*: assay also performed in controls; CH: Chtoura hospital; LMSE: Laboratoire Microbiologie Santé et Environnement; LRM: Laboratoire Rodolphe Mérieux; NCH: Nationwide Children’s Hospital; EB: El Bashaer health center.