Table 4 The 20 Staphylococcus aureus clinical isolates and their characterization by several properties.

ID pt	ID	SAM	Date	Str	Ph	QUIN	B	ER	CLI	LIN	RCLI	CF	CPA	GEN
1	1S	ESP	10/11/2006	MRSA	SCV	R	S	Nt	R	S	N	Cp		J
2	2S	ESP	11/22/2007	MRSA	SCV	R	S	Nt	R	S	N	Ca	X	N
3	3S	ESP	1/15/2009	MRSA	SCV	S	S	Nt	S	S	N		X	E
4	4S	AT	2/20/2009	MRSA	—	S	S	Nt	S	S	P			A
5	5S	ESP	11/13/2009	MRSA	—	R	S	Nt	R	S	N	Sp		C
6	6S	AT	1/10/2011	MRSA	—	R	S	Nt	R	S	P			K
7	7S	ESP	4/4/2011	MRSA	—	R	S	Nt	R	S	N	Ca	X	D
8	8S	AT	7/22/2013	MRSA	—	R	S	Nt	S	S	N			I
9	9S	ESP	1/15/2014	MRSA	—	S	S	Nt	R	S	P	Ca	X	C
10	10S	AT	1/29/2015	MRSA	—	S	S	Nt	R	S	N	Ca/Cd/Pb		G
11	11S	AT	6/15/2017	MSSA	—	S	S	R	R	S	P			C
12	12S	AT	6/15/2017	MSSA	—	S	S	R	R	S	P			U
13	13S	AT	5/23/2017	MSSA	—	I	S	I	I	S	N	Sa		B
14	14S	AT	5/25/2017	MSSA	—	S	S	S	S	S	N			C
15	15S	AT	5/24/2017	MSSA	—	S	S	R	S	S	N		X	C
16	16S	AT	5/26/2017	MSSA	—	S	S	R	R	S	N			H
17	17S	AT	5/25/2017	MSSA	—	S	S	R	R	S	N	Af		M
18	18S	ESP	5/24/2017	MSSA	—	S	S	R	R	S	P	Ca	X	C
19	19S	ESP	6/15/2017	MSSA	—	S	S	R	R	S	P		X	L
20	20S	ESP	5/19/2017	MSSA	—	R	S	R	R	S	P		X	F

ID pt: patient identification; ID: strain code; SAM:Sample; Date: Date of collection; Str:Strain; Ph: phenotype; QUIN: quinolones; B: Trimethoprim/Sulfamethoxazole; ER: Erythromycin; CLI: Clindamycin; LIN: linezolid; RCLI: Inducible Clindamycin resistance; CF: Fungal Co-infection; CPA: P. aeruginosa co-infection; GEN: pts genotype; Esp: sputum; AT: hypopharyngeal suction; MRSA: Methicillin Resistant S. aureus; MSSA: Methicillin Sensitive S. aureus; SCV: Small colony variant; R: Resistant;S: Susceptible; I: Intermediate; N: Negative; Nt: non-tested; Af: Aspergillus fumigatus; Ca: Candida albicans; Cp: Candida parapsilosis; Sp: Scedosporium prolificans; Cd: Candida dubliniensis; Pb: Pseudoallescheria boydii; Sa: Scedosporium apiospermum. X: denotes positive for this feature; -: denotes common phenotype. See Table 6 showing the correlation between letter code, CFTR gene mutation of the patient and bacterial strain isolated from the same patient.

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