Phylogenetic Diversity and Microsphere Array-Based Genotyping of Human Pathogenic Fusaria, Including Isolates from the Multistate Contact Lens-Associated U.S. Keratitis Outbreaks of 2005 and 2006

Kerry O'Donnell; Brice A. J. Sarver; Mary Brandt; Douglas C. Chang; Judith Noble-Wang; Benjamin J. Park; Deanna A. Sutton; Lynette Benjamin; Mark Lindsley; Arvind Padhye; David M. Geiser; Todd J. Ward

doi:10.1128/JCM.00533-07

DOI: 10.1128/JCM.00533-07

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FIG. 1.
One of 186 MPTs inferred from analysis of the design panel RPB2 data set, rooted with the outgroup sequence of Lecanicillium lecanii (consistency index = 0.52, retention index = 0.93). Numbers above nodes represent the frequency (%) with which they were recovered from 1,000 bootstrap pseudoreplicates of the data. The six medically important species complexes are indicated by bold internodes. Six unnamed species within the FSSC are indicated by numbers. Isolate numbers that are shaded represent the three most common haplotypes: FOSC 3-a, FSSC 1-a, and FSSC 2-d. Arrowheads identify each of the 18 allele-specific probes used in the identification of species complexes and species in the design (Table 2) and experimental panels (Table 3).

TABLE 1.

Summary of CDC keratitis investigation isolates^a

Complex	Species^b	Haplotype^c	No. of isolates (%)^d
Complex	Species^b	Haplotype^c	Corneal	Environmental	Combined
FSSC			54 (59.3)	64 (64)	118 (61.8)
	FSSC-1	1-a	13 (18)	24 (27)	37 (45)
		1-b	3	2	5
		1-c	2 (4)	2 (3)	4 (7)
		1-?	1	0	1
	FSSC-2	2-a	2 (4)	0	2 (4)
		2-b	2	0	2
		2-d	9 (13)	11 (14)	21 (27)
		2-f	0	2 (4)	2 (4)
		2-g	0	1	1
		2-h	1	0	1
		2-i	0	1	1
		2-j	1	0	1
	FSSC-3	3-a	0	2 (4)	2 (4)
		3-b	2	0	2
		3-c	1	0	1
	FSSC-4	4-a	1	0	1
		4-b	1	0	1
	FSSC-5	5-a	0	1	1
		5-b	0	1	1
		5-c	1	0	1
		5-d	0	1 (3)	1 (3)
	FSSC-6	6-a	0	1	1
	FSSC-7	7-a	0	1	1
	FSSC-8	8-a	1	0	1
	FSSC-9	9-a	0	1	1
FOSC			27 (29.7)	29 (29)	56 (29.3)
	FOSC-3	3-a	10 (15)	16 (19)	26 (34)
		3-b	0	1	1
		3-c	1	0	1
		3-d	0	1	1
		3-e	1 (2)	2	3 (4)
		3-f	1	0	1
		3-g	2 (4)	1	3 (5)
	FOSC-4	4-a	1	0	1
		4-b	2 (3)	1	3 (4)
		4-c	0	1 (4)	1 (4)
GFSC			6 (6.6)	6 (6)	12 (6.3)
	F. fujikuroi		0	1	1
	F. proliferatum		1 (2)	1	2 (3)
	F. sacchari		0	1	1
	F. thapsinum		1	0	1
	F. verticillioides		1	1	2
	F. sp. cf. verticillioides		1 (2)	2	3 (4)
FIESC			2 (2.2)	2 (2%)	4 (2.1)
	F. sp. cf. incarnatum-1	1-a	0	1	1
	F. sp. cf. incarnatum-2	2-a	1	0	1
	F. sp. cf. incarnatum-3	3-a	1	0	1
	F. sp. cf. incarnatum-4	4-a	0	1	1
FDSC			1 (1.1)	0	1 (0.5)
	F. sp. cf. dimerum	1-a	1	0	1
Total			67 (91)	81 (100)	148 (191)

↵ a See Table S1 in the supplemental material for the histories of all 191 isolates.
↵ b Species names can only be applied with confidence to five species with in the GFSC (30, 32). The remaining 17 unnamed species are distributed among the following species complexes: 9 with in the FSSC (1 to 9), 2 with in the FOSC (3 and 4), F. sp. cf. verticillioides with in the GFSC, 4 with in the FIESC (F. sp. cf. incarnatum 1 to 4), and F. sp. cf. dimerum with in the FDSC.
↵ c Haplotypes were determined by multilocus DNA sequence-based genotyping as described in Materials and Methods.
↵ d The number of isolates in parentheses for each species studied by MLST includes putative clones (see Table S1 in the supplemental material for details). The frequency (%) of isolates recovered from cornea and the patient's environment for each species complex includes putative clones.

TABLE 2.

Design panel of fusaria analyzed by allele-specific genotyping and RPB2 sequencing

NRRL no.	Equivalent no.^a	Yr	Isolate source	Origin	Identified by Luminex/RPB2^b	ID^c (complex/species probe)^d
3211	Sandoz 484	1966		Switzerland	FIESC	10.7 (IEC-f)
5537	ATCC 28805		Fescue hay	Missouri	FIESC	4.6 (IEC-f)
13335	FRC R-2138				FIESC	11.5 (IEC-f)
13379	FRC R-5198				FIESC	14.6 (IEC-f)
13448	CBS 749.97	1997	Sorgum root	New South Wales, Australia	GFSC/F. nygamai	4.1 (GFC-c)
13566	IMI 375349		Rice	Taiwan	F. fujikuroi	3.9 (GFC-c), 13.7 (F-c)
13604	CBS 748.97	1997	Millet	Namibia	GFSC/F. napiforme	2.9 (GFC-c)
13614	CBS 258.54	1954	Rice (NRRL 13614)	Vietnam	F. proliferatum	4.8 (GFC-c), 16.6 (P-a)
13713	FRC T-428		Millet	South Africa	FCSC	10.7 (CC-c)
20423	ATCC 42771		Lizard skin	India	FIESC	19.7 (IEC-f)
20425	CBS 131.73	1973	Banana	Bahamas	FIESC	11.8 (IEC-f)
22172	CBS 734.97	1997	Corn	Germany	F. verticillioides	3.1 (GFC-c), 9.4 (V-a)
25229	IMI 240460		Mycetoma	Italy	F. thapsinum	5.4 (GFC-c), 11.4 (T-e)
25483	CBS 217.78	1978	Millet	Namibia	FCSC	14.8 (CC-c)
25489	CBS 144.44	1944			FIESC	5.9 (IEC-f)
26360	FRC O-755		Cornea	Tennessee	FOSC	3.7 (OC-a)
26421	CBS 140.95	1995	Systemic infIection	Egypt	GFSC/F. nygamai	7.1 (GFC-c)
28023	CBS 537.81		Coccidae	Galapogos Islands	Lecanicillium lecanii	N/A
28505	FRC R-8670		Soil debris	South Africa	FCSC	8.7 (CC-c)
28682	96-6008			Germany	F. verticillioides	4.4 (GFC-c), 14.6 (V-a)
31005	BBA 62211			Iran	FIESC	8.4 (IEC-f)
31010	BBA 64316		Artemisia vulgaris	Germany	FIESC	16.8 (IEC-f)
31011	BBA 69079		Thuja	Germany	FIESC	10.9 (IEC-f)
31160	MDA #3		Lung	Texas	FIESC	3.9 (IEC-f)
31167	MDA #10		Sputum, leukemia	Texas	FIESC	11.9 (IEC-f)
32173	MDA F2		Arm tissue, leukemic	Delaware	F. sp. cf. dimerum	11.0 (DC-d), 5.6 (D-c)
32174	MDA F8		Skin, leukemic	Florida	F. proliferatum	4.1 (GFC-c), 16.2 (P-a)
32175	MDA F10		Sputum	Texas	FIESC	10.7 (IEC-f)
32179	MDA F18		Sputum, leukemic	Texas	F. thapsinum	4.6 (GFC-c), 11.3 (T-e)
32434	CBS 623.92	1992	Foot lesion	Germany	FSSC	6.8 (SC-d)
32521	FRC T-852		Cancer patient		FCSC	10.9 (CC-c)
32868	FRC R-8880		Blood	Ohio	FIESC	11.0 (IEC-f)
34032	UTHSC 98-2172	1998	Mandibular absess	Texas	FIESC	6.1 (IEC-f)
36064	FRC O-1747				FOSC	6.2 (OC-a)
36168	CBS 110148		Gymnocalycium damsii	Germany	FDSC	35.1 (DC-d)
36511	CBS 572.94	1994	Pigeon pea	India	GFSC/F. nygamai	6.1 (GFC-c)
36536	CBS 673.94	1994			GFSC/F. napiforme	4.5 (GFC-c)
43373	CDC 2006743215	2006	Contact lens	Malaysia	FSSC 2	2.6 (SC-d), 4.5 (S-2)
43374	CDC 2006743216	2006	Cornea	Nigeria	FSSC 2	12.1 (SC-d), 18.4 (S-2)
43375	CDC 2006011016	2006	Cornea	New Jersey	FSSC 1	8.5 (SC-d), 4.2 (S-1)
43431	CDC 2006011126	2006	Cornea	Connecticut	FOSC	5.7 (OC-a)
43433	CDC 2006011214	2006	Cornea	Ohio	FSSC 2	20.2 (SC-d), 29.7 (S-2)
43441	CDC 2006743414	2006	Cornea	Pennsylvania	FSSC 3	10.6 (SC-d), 11.9 (S-34)
43442	CDC 2006743415	2006	Cornea	Pennsylvania	FOSC	5.0 (OC-a)
43445	CDC 2006743419	2006	Cornea	Connecticut	FSSC 2	15.1 (SC-d), 22.0 (S-2)
43454	CDC 2006743427	2006	Cornea	Massachusetts	FOSC	6.0 (OC-a)
43455	CDC 2006743230	2006	Cornea	Vermont	FOSC	5.1 (OC-a)
43458	CDC 2006743233	2006	Cornea	Singapore	FSSC 2	14.3 (SC-d), 23.0 (S-2)
43464	CDC 2006743239	2006	Cornea	Singapore	FSSC 2	13.8 (SC-d), 21.8 (S-2)
43466	CDC 2006743429	2006	Contact lens case	Ohio	FOSC	4.9 (OC-a)
43468	CDC 2006743431	2006	Cornea	Iowa	FSSC	4.8 (SC-d)
43470	CDC 2006743433	2006	Cornea	Illinois	F. fujikuroi	2.7 (GFC-c), 10.5 (F-c)
43474	CDC 2006743441	2006	Cornea	Illinois	FSSC	8.7 (SC-d)
43489	CDC 2006743456	2006	Cornea	Maryland	FSSC	7.4 (SC-d)
43490	CDC 2006743457	2006	Cornea	Michigan	FSSC 2	6.4 (SC-d), 8.7 (S-2)
43503	CDC 2006743471	2006	Contact lens case	Connecticut	FSSC 4	11.3 (SC-d), 11.6 (S-4)
43504	CDC 2006743483	2006	Cornea	Pennsylvania	FOSC	5.8 (OC-a)
43514	CDC 2006743560	2006	Cornea	Florida	FSSC 2	11.9 (SC-d), 15.9 (S-2)
43521	CDC 2006743567	2006	Cornea	Florida	FOSC	6.3 (OC-a)
43527	CDC 2006743573	2006	Cornea	Florida	FSSC	3.8 (SC-d)
43528	CDC 2006743574	2006	Cornea	Florida	FSSC 2	7.1 (SC-d), 12.1 (S-2)
43529	CDC 2006743575	2006	Cornea	Florida	FSSC 4	7.4 (SC-d), 7.4 (S-4)
43532	CDC 2006743578	2006	Cornea	Florida	FSSC 2	15.6 (SC-d), 20.8 (S-2)
43533	CDC 2006743579	2006	Cornea	Florida	FSSC 1	5.9 (SC-d), 3.4 (S-1)
43536	CDC 2006743582	2006	Cornea	Florida	FSSC 3	6.4 (SC-d), 8.1 (S-34)
43537	CDC 2006743583	2006	Cornea	Florida	FSSC 3	9.7 (SC-d), 11.5 (S-34)
43539	CDC 2006743490	2006	Cornea	Missouri	FOSC	6.9 (OC-a)
43540	CDC 2006743491	2006	Cornea	Kansas	FSSC 1	6.1 (SC-d), 2.8 (S-1)
43655	CDC 2006743515	2006	Contact lens case fluid	Ohio	FOSC	5.9 (OC-a)
43656	CDC 2006743516	2006	Contact lens	Minnesota	F. verticillioides	2.8 (GFC-c), 11.4 (V-a)
43665	CDC 2006743525	2006	Contact lens	North Carolina	F. proliferatum	3.4 (GFC-c), 12.7 (P-a)
43668	CDC 2006743529	2006	Cornea	New Jersey	FOSC	6.1 (OC-a)
43726	CDC 2006743692	2006	Cornea	Ohio	FDSC	53.2 (DC-d)

↵ a ATCC, American Type Culture Collection, Manassas, VA; BBA, Biologische Bundesanstalt für Land- und Forstwirtschaft, Institute für Mikrobiologie, Berlin, Germany; CBS, Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands; CDC, Centers for Disease Control and Prevention, Atlanta, GA; FRC, Fusarium Research Center, The Pennsylvania State University, State College, PA; IMI, CABI Biosciences, Egham, Surrey, England; MDA, M. D. Anderson Cancer Center, Houston, TX; UTHSC, University of Texas Health Sciences Center, San Antonio, TX.
↵ b Isolates belonging to FSSC groups 1 to 4 are indicated (5, 44).
↵ c ID, index of discrimination determined as minimum target fluorescent intensity/maximum nontarget fluorescence intensity.
↵ d See Table 4 for a complete listing of the probes. Note that the probes listed here lack the F for Fusarium prefix.

TABLE 3.

Experimental panel of fusaria analyzed by allele-specific genotyping and RPB2 sequencing

NRRL no.	Equivalent no.^a	Yr	Isolate source	Origin	Identified by Luminex/RPB2^b	ID^c (complex/species probe^d)
13459	CBS 961.87	1984	Plant debris	South Africa	F. proliferatum/F. concolor	0 (GFC-c, GFCO-c), 6.7 (PF-b)
28000	CDC B-4536	1987	Blood, leukemic	Georgia	FSSC 3/FSSC	23.5 (SC-d), 17.0 (S-34)
28001	CDC B-4572	1987	Skin, leukemic	Colorado	FSSC 3/FSSC	33.1 (SC-d), 47.1 (S-34)
28002	CDC B-4581	1987	Skin, leukemic	Georgia	FSSC 3/FSSC	29.6 (SC-d), 19.6 (S-34)
28003	CDC B-4680	1988	Toenail	Washington, DC	F. fujikuroi	4.4 (GFC-a), 14.6 (F-c)
28005	CDC B-4687	1988	Hospital venilation system	Illinois	F. proliferatum	8.9 (GFC-c), 17.0 (P-a)
28006	CDC B-4688	1988	Hospital venilation system	Illinois	F. thapsinum	3.3 (GFC-c), 6.2 (T-e)
28007	CDC B-4689	1988	Hospital venilation system	Illinois	F. thapsinum	3.5 (GFC-c), 8.9 (T-e)
28008	CDC B-4701	1988	Hospital venilation system	Illinois	FSSC 1/FSSC	5.9 (SC-d), 7.2 (S-1)
28009	CDC B-5543	1994	Viterous fluid	Texas	FSSC 1/FSSC	25.2 (SC-d), 6.5 (S-1)
28010	CDC B-5546	1995	Viterous fluid	Texas	FSSC 1/FSSC	36.4 (SC-d), 7.1 (S-1)
28011	CDC B-5548	1994	Viterous fluid	Texas	FSSC 1/FSSC	29.3 (SC-d), 7.0 (S-1)
28014	CDC B-5754	1997	Leg wound, diabetic	California	FSSC 2	9.8 (SC-d), 13.5 (S-2)
28016	CDC B-5779	1997	Bronchial wash, leukemic	Ohio	FSSC	7.1 (SC-d)
28017	CDC B-5780	1997	Catheter, lekemic	Ohio	FSSC	19.1 (SC-d)
28018	CDC B-5781	1997	Catheter, lekemic	Ohio	FSSC	8.2 (SC-d)
28019	CDC B-5782	1997	Skin lesion, leukemic	Ohio	FSSC	17.5 (SC-d)
28029	CDC B-3335	1980	Corneal transplant	California	FIESC	9.6 (IEC-f)
28030	CDC B-3723	1983	Skin lesion, leukemic	Thailand	FSSC	4.6 (SC-d)
28031	CDC B-3882	1984	Toe nail	South Carolina	FOSC	7.1 (OC-a)
28033	CDC B-4422	1987	Leukemic	Italy	FSSC 1	14.5 (SC-d), 5.9 (S-1)
28035	CDC B-4809	1989	Lymph node	Arkansas	F. proliferatum	3.5 (GFC-c), 8.4 (P-a)
37068	CBS 110192		Soil	Australia	FDSC	5.4 (DC-d)
37071	CBS 110320		Toenail	Chile	F. sp. cf. dimerum	15.9 (DC-d), 7.4 (D-c)
43544	CDC 2006743496	2006	Cornea	Ohio	FSSC 1	13.9 (SC-d), 7.4 (S-1)
43545	CDC 2006743497	2006	Cornea	Ohio	F. proliferatum	4.0 (GFC-c), 15.2 (P-a)
43547	CDC 2006743499	2006	Contact lens	Minnesota	F. verticillioides	2.6 (GFC-c), 11.9 (V-a)
43583	UTHSC 06-989	2006	Cornea	Ohio	FSSC 1	13.3 (SC-d), 5.8 (S-1)
43584	UTHSC 06-743	2006	Catheter tip	Florida	FSSC 3	6.2 (SC-d), 6.9 (S-34)
43585	UTHSC 06-295	2006	Tissue	Utah	FSSC 2	3.2 (SC-d), 5.8 (S-2)
43586	UTHSC 05-3538	2005	Cornea	Texas	FSSC 2	11.1 (SC-d), 18.8 (S-2)
43588	UTHSC 05-3530	2005	Corneal transplant	Illinois	FSSC 1	17.1 (SC-d), 16.4 (S-1)
43589	UTHSC 05-3333	2005	Blood	Ohio	FSSC 1	13.2 (SC-d), 5.2 (S-1)
43590	UTHSC 05-2824	2005	Blood	Maine	FSSC 1	14.1 (SC-d), 7.8 (S-1)
43591	UTHSC 05-2680	2005	Cornea	Florida	FSSC 1	15.7 (SC-d), 7.1 (S-1)
43592	UTHSC 06-689	2006	Cornea	Massachusetts	FOSC	5.7 (OC-a)
43593	UTHSC 05-3159	2005	Nail	South Carolina	FOSC	6.7 (OC-a)
43594	UTHSC 05-1643	2005	Cornea	Massachusetts	FOSC	5.7 (OC-a)
43595	UTHSC 05-721	2005	Blood	California	FOSC	4.0 (OC-a)
43596	UTHSC 04-1934	2004	Lung	Arkansas	FOSC	5.7 (OC-a)
43597	UTHSC 04-584	2004	Bronchial wash	Utah	FOSC	4.5 (OC-a)
43598	UTHSC 03-753	2003	Foot tissue	Florida	FOSC	5.4 (OC-a)
43599	UTHSC 06-1103	2006	Toe	Florida	F. verticillioides	17.2 (GFC-c), 4.7 (V-a)
43600	UTHSC 05-3141	2005	Cornea	Massachusetts	F. verticillioides	6.1 (GFC-c), 25.1 (V-a)
43601	UTHSC 05-1039	2005	Skin	Maryland	F. verticillioides	5.0 (GFC-c), 29.0 (V-a)
43602	UTHSC 05-850	2005	Sputum	Wisconsin	F. verticillioides	7.1 (GFC-c), 26.3 (V-a)
43603	UTHSC 05-431	2005	Skin	Ohio	F. verticillioides	6.5 (GFC-c), 22.5 (V-a)
43604	UTHSC 05-430	2005	Nasal sinus	Ohio	F. verticillioides	5.6 (GFC-c), 26.3 (V-a)
43605	UTHSC 04-700	2004	Skin	Massachusetts	F. verticillioides	6.6 (GFC-c), 25.0 (V-a)
43606	UTHSC 04-695	2004	Trachea	Lousiana	F. verticillioides	5.9 (GFC-c), 25.3 (V-a)
43608	UTHSC 03-2552	2003	Peritoneal fluid	Minnesota	F. verticillioides	4.5 (GFC-c), 15.4 (V-a)
43609	UTHSC 06-952	2006	Palate	Florida	F. proliferatum	5.6 (GFC-c), 19.2 (P-a)
43610	UTHSC 06-836	2006	Skin	Iowa	F. fujikuroi	15.9 (GFC-c), 17.0 (F-c)
43611	UTHSC 06-492	2006	Lacrimal duct	Texas	F. proliferatum	2.7 (GFC-c), 9.4 (P-a)
43612	UTHSC 06-432	2006	Nail	Florida	F. fujikuroi	4.5 (GFC-c), 15.1 (F-c)
43613	UTHSC 06-197	2006	Cornea	Utah	F. proliferatum	5.3 (GFC-c), 19.8 (P-a)
43614	UTHSC 04-1974	2004	Nose	Texas	F. proliferatum	6.0 (GFC-c), 22.9 (P-a)
43615	UTHSC 04-1772	2004	Ethmoid sinus	Ohio	F. proliferatum	6.9 (GFC-c), 23.7 (P-a)
43616	UTHSC 03-3232	2003	Tissue	Utah	F. proliferatum	6.0 (GFC-c), 21.8 (P-a)
43617	UTHSC 03-60	2003	Blood	Colorado	F. proliferatum	7.2 (GFC-c), 25.0 (P-a)
43618	UTHSC 02-1631	2002	Blood	Texas	F. proliferatum	3.8 (GFC-c), 13.0 (P-a)
43619	UTHSC 05-2847	2005	Index finger	Texas	FIESC	12.7 (IEC-f)
43622	UTHSC 03-2501	2003	Lung	Texas	FIESC	8.5 (IEC-f)
43623	UTHSC 03-59	2003	Maxillary sinus	Colorado	FIESC	18.7 (IEC-f)
43624	UTHSC 02-2060	2002	Sputum	Texas	FIESC	11.8 (IEC-f)
43625	UTHSC 02-1698	2002	Maxillary sinus	Texas	FIESC	12.8 (IEC-f)
43627	UTHSC 05-3559	2005	Bronchial wash	Texas	FCSC	15.5 (CC-c)
43628	UTHSC 05-3396	2005	Finger wound	Florida	FCSC	16.1 (CC-c)
43629	UTHSC 05-3200	2005	Blood	Utah	FCSC	14.7 (CC-c)
43630	UTHSC 05-2743	2005	Sputum	Texas	FCSC	5.0 (CC-c)
43631	UTHSC 05-2441	2005	Leg biopsy	Texas	FCSC	18.7 (CC-c)
43632	UTHSC 05-1260	2005	Cornea	Florida	FCSC	10.0 (CC-c)
43633	UTHSC 03-3472	2003	Maxillary sinus	Tennessee	FCSC	9.6 (CC-c)
43634	UTHSC 02-1276	2002	Horse cornea	Alabama	FCSC	22.2 (CC-c)
43635	UTHSC 06-638	2006	Horse	Nebraska	FIESC	12.9 (IEC-b)
43636	UTHSC 06-170	2006	Dog	Texas	FIESC	13.3 (IEC-f)
43637	UTHSC 05-1729	2005	Dog, cutaneous	Pennsylvania	FIESC	20.1 (IEC-f)
43638	UTHSC R-3500	2004	Manatee	Florida	FIESC	9.0 (IEC-b)
43639	UTHSC 04-135	2004	Manatee	Florida	FIESC	13.2 (IEC-b)
43640	UTHSC 04-123	2004	Dog, nasal	Texas	FIESC	15.6 (IEC-f)
43641	UTHSC 06-1377	2006	Horse eye	Missouri	Unknown/Fusarium sp.	2.9 (5f2-ab), 3.6 (7cf-ab)
43673	CDC 2006743501	2006	Contact lens case fluid	New Jersey	FSSC 2	11.2 (SC-d), 16.0 (S-2)
43674	CDC 2006743553	2006	Contact lens case	Kentucky	FOSC	3.7 (OC-a)
43675	CDC 2006743554	2006	Cornea	Kentucky	FSSC 1	14.4 (SC-d), 7.6 (S-1)
43676	CDC 2006743585	2006	Cornea	Illinois	FSSC 1	14.2 (SC-d), 7.9 (S-1)
43677	CDC 2006743586	2006	Contact lens case	Illinois	FSSC 1	3.9 (SC-d), 7.4 (S-1)
43678	CDC 2006743587	2006	Contact lens case	California	FOSC	4.0 (OC-a)
43679	CDC 2006743588	2006	Contact lens	California	FOSC	3.4 (OC-a)
43680	CDC 2006743589	2006	Contact lens case fluid	Texas	FIESC	10.9 (IEC-b)
43681	CDC 2006743591	2006	Cornea	South Dakota	FSSC	6.7 (SC-d)
43682	CDC 2006743592	2006	Cornea	Maine	F. verticillioides	2.6 (GFC-c), 11.5 (V-a)
43683	CDC 2006743593	2006	Cornea	California	FSSC 1	14.6 (SC-d), 8.4 (S-1)
43684	CDC 2006743594	2006	Cornea	California	FSSC 1	14.2 (SC-d), 8.3 (S-1)
43685	CDC 2006743595	2006	Cornea	California	FSSC 1	15.0 (SC-d), 5.9 (S-1)
43686	CDC 2006743597	2006	Contact lens case	California	FOSC	4.6 (OC-a)
43687	CDC 2006743599	2006	Contact lens solution cap	Kentucky	FOSC	4.8 (OC-a)
43690	CDC 2006743602	2006	Contact lens	Puerto Rico	FSSC 2	8.1 (SC-d), 13.5 (S-2)
43691	CDC 2006743603	2006	Contact lens	Puerto Rico	FSSC 2	6.4 (SC-d), 11.0 (S-2)
43692	CDC 2006743604	2006	Cornea	Washington	FOSC	3.3 (OC-a)
43693	CDC 2006743606	2006	Contact lens	Texas	F. thapsinum	4.5 (GFC-c), 12.0 (T-e)
43694	CDC 2006743607	2006	Cornea	Texas	FIESC	13.9 (IEC-f)
43695	CDC 2006743608	2006	Contact lens solution	Texas	FSSC 1	15.2 (SC-d), 10.0 (S-1)
43696	CDC 2006743609	2006	Cornea	Texas	FOSC	3.3 (OC-a)
43697	CDC 2006743611	2006	Cornea	Pennsylvania	F. verticillioides	2.9 (GFC-c), 12.8 (V-a)
43698	CDC 2006743612	2006	Cornea	Pennsylvania	FOSC	3.7 (OC-a)
43699	CDC 2006743615	2006	Contact lens case	Minnesota	FSSC 1	9.8 (SC-d), 6.0 (S-1)
43700	CDC 2006743616	2006	Cornea	Minnesota	FSSC 1	14.0 (SC-d), 8.0 (S-1)
43701	CDC 2006743617	2006	Cornea	Minnesota	FSSC 1	14.9 (SC-d), 8.0 (S-1)
43702	CDC 2006743618	2006	Contact lens case fluid	Ohio	FSSC 2	7.7 (SC-d), 13.7 (S-2)
43703	CDC 2006743619	2006	Contact lens case	South Dakota	FSSC	7.0 (SC-d)
43704	CDC 2006743620	2006	Contact lens	South Dakota	FSSC	5.9 (SC-d)
43705	CDC 2006743622	2006	Contact lens case fluid	Puerto Rico	FSSC 2	8.4 (SC-d), 13.3 (S-2)
43706	CDC 2006743623	2006	Cornea	Ohio	FOSC	3.9 (OC-a)
43707	CDC 2006743596	2006	Cornea	California	FOSC	4.2 (OC-a)
43708	CDC 2006743598	2006	Contact lens solution	California	FOSC	6.5 (OC-a)
43709	CDC 2006743600	2006	Contact lens case fluid	Kentucky	FOSC	5.9 (OC-a)
43710	CDC 2006743601	2006	Contact lens	Kentucky	FOSC	5.3 (OC-a)
43711	CDC IFI01-0048	2001	Sinus	Michigan	F. proliferatum	5.3 (GFC-c), 18.6 (P-a)
43713	CDC IFI02-0239	2002	Blood	North Carolina	FOSC	6.7 (OC-a)
43714	CDC IFI03-0214	2003	Sputum	Maryland	F. verticillioides	4.5 (GFC-c), 20.8 (V-a)
43715	CDC IFI04-0065	2004	Skin	Alabama	FSSC 1	5.6 (SC-d), 7.5 (S-1)
43716	CDC IFI04-0194	2004	Blood	-	F. sp. cf. dimerum/FDSC	10.9 (DC-d), 8.7 (D-b), 6.6 (D-c)
43717	CDC IFI03-0179	2003	SubQchest	Michigan	FSSC	9.2 (SC-d)
43724	CDC 2006743696	2006	Cornea	North Carolina	FSSC 1	12.3 (SC-d), 8.0 (S-1)
43725	CDC 2006743697	2006	Contact lens	North Carolina	FSSC 1	10.2 (SC-d), 8.7 (S-1)
43727	CDC 2006743694	2006	Cornea	Florida	FSSC 2	6.7 (SC-d), 12.7 (S-2)
43728	CDC 2006743691	2006	Cornea	Florida	FSSC 2	7.8 (SC-d), 13.1 (S-2)
43729	CDC 2006743621	2006	Contact lens case fluid	Puerto Rico	FSSC 2	8.5 (SC-d), 12.0 (S-2)
43730	CDC 2006743605	2006	Contact lens	Mississippi	FIESC	8.9 (IEC-f)
43731	CDC 2006743689	2006	Contact lens case	Iowa	FSSC 1	8.9 (SC-d), 5.7 (S-1)
43732	CDC 2006743695	2006	Contact lens case	Michigan	FOSC	3.0 (OC-a)
43733	CDC 2006743623	2006	Cornea	Ohio	FOSC	3.0 (OC-a)
43734	CDC 2006743625	2006	Cornea	New York	FOSC	2.9 (OC-a)
43735	CDC 2006743626	2006	Cornea	New York	FOSC	3.1 (OC-a)
43736	CDC 2006013784	2006	Cornea	California	FSSC 1	11.8 (SC-d), 7.0 (S-1)
43803	AFR4	2006	Contact lens case	Florida	FSSC 1	12.0 (SC-d), 6.8 (S-1)
43804	AFR9	2006	Contact lens case	Georgia	FOSC	3.4 (OC-a)
43805	AFR12	2006	Contact lens case	Georgia	FSSC 1	10.2 (SC-d), 8.3 (S-1)
43806	AFR81036	1981	Cornea	Georgia	FSSC 4	8.8 (SC-d), 7.6 (S-4)
43807	CDC 2006014156	2006	Contact lens solution	Nevada	FOSC	5.1 (OC-a)
43808	CDC 2006743699	2006	Unknown	Texas	FOSC	6.9 (OC-a)
43809	CDC 2006743700	2006	Cornea	Ohio	FSSC 1	14.1 (SC-d), 11.0 (S-1)
43810	CDC 2006743701	2006	Cornea	Ohio	FOSC	7.2 (OC-a)
43811	CDC 2006743702	2006	Cornea	Ohio	FSSC	11.0 (SC-d)
43812	CDC 2006743705	2006	Contact lens solution	New York	FSSC 1	11.2 (SC-d), 9.9 (S-1)
43813	CDC 2006743707	2006	Contact lens case	New York	FSSC 1	15.9 (SC-d), 11.4 (S-1)
43814	CDC 2006743708	2006	Contact lens	New York	FSSC 2	4.6 (SC-d), 9.9 (S-2)
43815	CDC 2006743711	2006	Contact lens case	New York	FSSC 1	10.0 (SC-d), 7.1 (S-1)
43816	CDC 2006743713	2006	Contact lens case	New York	FSSC 1	8.4 (SC-d), 6.2 (S-1)
43817	CDC 2006743714	2006	Contact lens	New York	FSSC 1	13.5 (SC-d), 10.2 (S-1)
43818	CDC 2006743716	2006	Contact lens case	New York	FSSC 2	11.6 (SC-d), 24.0 (S-2)
43819	CDC 2006743718	2006	Cornea	Illinois	FSSC 1	14.5 (SC-d), 11.0 (S-1)
43873	CDC 2006743709	2006	Contact lens case	New York	FSSC 1	10.1 (SC-d), 9.5 (S-1)
43874	CDC 2006743710	2006	Contact lens case	New York	FSSC 2	8.2 (SC-d), 20.7 (S-2)
43875	CDC 2006743712	2006	Contact lens case	New York	FSSC 1+FSSC 2/FSSC 1	18.8 (SC-d), 17.5 (S-1), 5.1 (S-2)
43876	CDC 2006743715	2006	Contact lens case	New York	FSSC 2	8.8 (SC-d), 16.8 (S-2)
43877	CDC 2006743727	2006	Cornea	Tennessee	FSSC 1	9.9 (SC-d), 9.9 (S-1)

↵ a AFR, Donald G. Ahearn, Georgia State University, Atlanta, GA; CBS, Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands; CDC, Centers for Disease Control and Prevention, Atlanta, GA; UTHSC, University of Texas Health Sciences Center, San Antonio, TX.
↵ b The four most common species with in the FSSC, designated groups 1 to 4 (5, 44), are indicated.
↵ c ID, index of discrimination determined as minimum target fluorescent intensity/maximum non-target fluorescent intensity.
↵ d See Table 4 for a complete listing of the probes. Note that the probes listed here lack the F for Fusarium prefix.

TABLE 4.

Allele-specific primers used in genotyping assay

Target group	Probe^a	Luminex microsphere^c	Sequence (5′-3′)^b
Target group	Probe^a	Luminex microsphere^c	Luminex probe tag^c	Probe^d
Positive control for PCR amplification (5F2 × 7cR)	5f2-aa	35	CAATTTCATCATTCATTCATTTCA	GGGYCARGCTTGTGGTYTGG
Positive control for PCR amplification (5F2 × 7cR)	5f2-ab	37	CTTTTCATCTTTTCATCTTTCAAT	CARGCTTGTGGTYTGGTC
Positive control for PCR amplification (7cF × llaR)	7cf-aa	55	TATATACACTTCTCAATAACTAAC	ATGGARTTCCTCAARTTCC
Positive control for PCR amplification (7cF × llaR)	7cf-ab	78	CTATCTATCTAACTATCTATATCA	ATGGARTTCCTCAARTTCCGTG
FCSC	CC-c	7	CAATTCATTTACCAATTTACCAAT	TTCAGCAGAGAGGGTTTGACC
FCSC	CC-d	44	TCATTTACCAATCTTTCTTTATAC	ACCGTCGATTCCGTYTCGGAACTC
Fusarium sp. cf. dimerum	D-b	23	TTCAATCATTCAAATCTCAACTTT	TGTTCAGGATGCCAAGCAATTCTG
Fusarium sp. cf. dimerum	D-c	51	TCATTTCAATCAATCATCAACAAT	AAGCAATTCTGTAATTCGGTAGTC
FDSC	DC-a	59	TCATCAATCAATCTTTTTCACTTT	AGGCTTGTGGTYTGGTCAAGAACC
FDSC	DC-d	9	TAATCTTCTATATCAACATCTTAC	GAGTGTCTTCTYAGCAAAGTCTCC
Fusarium fujikuroi	F-b	3	TACACTTTATCAAATCTTACAATC	ACCAAGGGACAACTAGTGTTGACG
Fusarium fujikuroi	F-c	77	CAATTAACTACATACAATACATAC	ACACTCACAGAAGAAGAGAAACGA
Fusarium fujikuroi + F. proliferatum	PF-a	18	TCAAAATCTCAAATACTCAAATCA	GAGGTCATGTACAATGGTCACACG
Fusarium fujikuroi + F. proliferatum	PF-b	30	TTACCTTTATACCTTTCTTTTTAC	GATGTCACAGTCGATTCAGTCTCT
Fusarium sp. cf. incarnatum	I-a	26	TTACTCAAAATCTACACTTTTTCA	TGTGAGATTCATCCCAGTATGATC
Fusarium sp. cf. incarnatum	I-b	10	ATCATACATACATACAAATCTACA	CCTGCCGAGACACCAGAAGGC
FIESC	IEC-b	17	CTTTAATCCTTTATCACTTTATCA	TTCGTCAACGGAAGTTGGGTCGGC
FIESC	IEC-f	5	CAATTCAAATCACAATAATCAATC	AAGCATGGAACATACGACAAGCTC
FOSC	OC-a	69	CTATAAACATATTACATTCACATC	AACTACACTGAGATCTTYGAGAAA
Fusarium proliferatum	P-a	28	CTACAAACAAACAAACATTATCAA	GAAGAGGAGAAACGGGCCAAGGCT
FSSC group 1	S-1	40	CTTTCTACATTATTCACAACATTA	GGTGATGCCACGCCTTTCACCGAC
FSSC group 2	S-2	94	CTTTCTATCTTTCTACTCAATAAT	GGTATCGTGGCYCCCGGTGTGCGC
FSSC groups 3 and 4	S-34	14	CTACTATACATCTTACTATACTTT	CGCTTGCTACTCTGGTTACAACCAA
FSSC group 4	S-4	6	TCAACAATCTTTTACAATCAAATC	ACGCCGCTGCGAAGTACCGAGAAT
FSSC	SC-d	95	TACACTTTAAACTTACTACACTAA	ACAATTGCMCATTTGATTGAATGC
FSSC	SC-f	76	AATCTAACAAACTCATCTAAATAC	ATTGAATGCCTCCTCAGTAAGGTG
Fusarium thapsinum	T-b	29	AATCTTACTACAAATCCTTTCTTT	ATGTGTTATGTCAGTGTCGGCTCC
Fusarium thapsinum	T-e	100	CTATCTTTAAACTACAAATCTAAC	CAAGTCATTCTGACAGTCAACGCG
Fusarium verticillioides	V-a	33	TCAATTACTTCACTTTAATCCTTT	CTTGTTCGTGATATCCGAGACCGC
Fusarium verticillioides	V-d	12	TACACTTTCTTTCTTTCTTTCTTT	CTTGATGAGGATGGTATCGTGGCA
GFSC	GFC-a	65	CTTTTCATCAATAATCTTACCTTT	GTYCACTTCGAAGTATCRCTTGTT
GFSC	GFC-c	85	ATACTACATCATAATCAAACATCA	CRGAAGARGAGAARCGRGCYAAGG
GFSC + FOSC	GFCO-c	80	CTAACTAACAATAATCTAACTAAC	YCGTGARCARAAGAATGATGARGC
GFSC + FOSC	GFCO-d	24	TCAATTACCTTTTCAATACAATAC	GACAGGAGGATATGCCTTTCAGCC

↵ a Minimum fluorescence intensity values for the 12 probes in boldface were not used to calculate the ID, because they did not perform as well as the other probes. The V-d probe frequently gave high background non-target fluorescence values and was therefore excluded from the ID scores.
↵ b M, AC; R, AG; Y, CT.
↵ c Microspheres and tag sequences were assigned at the Luminex website.
↵ d Probe sequences used to identify the various target groups within Fusarium spp.

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Supplemental file 1 - Table S1 (Multilocus DNA sequence typing of CDC cultures obtained from corneal scrapings and the environment)
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