High-resolution melting (HRM)-based detection of polymorphisms in the malic enzyme and glucose-6-phosphate isomerase genes for Leishmania infantum genotyping

Buffi, Gloria; Ceccarelli, Marcello; Diotallevi, Aurora; Abruzzese, Michelalberto; Bruno, Federica; Castelli, Germano; Vitale, Fabrizio; Andreoni, Francesca; Bencardino, Daniela; Magnani, Mauro; Galluzzi, Luca

doi:10.1186/s13071-023-05878-y

Table 5 Summary of genotyping results of strains and clinical samples/isolates analyzed in this study

From: High-resolution melting (HRM)-based detection of polymorphisms in the malic enzyme and glucose-6-phosphate isomerase genes for Leishmania infantum genotyping

Sample no.	Sample ID	Type of sample (zymodeme)	ME sequence	qPCR-ME65	GPI sequence	qPCR-GPI88	Genotype
1	MCAN/ES/98/LLM-724	Reference strain (MON-1)	390T¹	n.a.	1831G¹	n.a.	1
2	MHOM/PT/2000/IMT260	Reference strain (MON-1)	390T¹	n.a.	1831G¹	n.a.	1
3	MHOM/ES/1986/BCN16	Reference strain (MON-1)	390T¹	n.a.	1831G¹	n.a.	1
4	MHOM/FR/1997/LSL29	Reference strain (MON-1)	390T¹	n.a.	1831G¹	n.a.	1
5	MHOM/ES/1993/PM1	Reference strain (MON-1)	390T¹	n.a.	1831G¹	n.a.	1
6	MHOM/FR/1995/LPN114	Reference strain (MON-1)	390T¹	n.a.	1831G¹	n.a.	1
7	MHOM/FR/1996/LEM3249	Reference strain (MON-29)	390G¹	n.a.	1831G¹	n.a.	2
8	MHOM/ES/1991/LEM2298	Reference strain (MON-183)	390G¹	n.a.	1831G¹	n.a.	2
9	MHOM/ES/1988/LLM175	Reference strain (MON-198)	390G¹	n.a.	1831G¹	n.a.	2
10	MHOM/IT/1994/ISS1036	Reference strain (MON-228)	390G¹	n.a.	1831G¹	n.a.	2
11	MHOM/ES/1992/LLM373	Reference strain (MON-199)	390G¹	n.a.	1831R¹	n.a.	5
12	MHOM/MT/1985/BUCK	Reference strain (MON-78)	390G¹	n.a.	1831A¹	n.a.	3
13	MHOM/FR/78/LEM75	Reference strain (MON-1)	390T²	390T	1831G²	1831G	1
14	MHOM/TN/80/IPT1	Reference strain (MON-1)	390G²	390G	1831A²	1831A	3
15	MHOM/DZ/82/LIPA59	Reference strain (MON-24)	390G¹	390G	1831A³	1831A	3
16	MHOM/ES/81/BCN1	Reference strain (MON-29)	390G¹	390G	1831G³	1831G	2
17	MHOM/IT/86/ISS218	Reference strain (MON-72)	390T¹	390T	1831G³	1831G	1
18	MHOM/IT/93/ISS822	Reference strain (MON-201)	390T¹	390T	1831R³	1831R	4
19	MHOM/IT/08/31U	Reference strain (MON-1)	390T²	390T	1831G²	1831G	1
20	MHOM/IT/08/49U	Reference strain (MON-1)	390T¹	390T	n.a.	1831G	1
21	Pan-30	Clinical isolate	390T²	390T	1831A²	1831A	6
22	Pan-42	Clinical isolate	390T²	390T	1831G²	1831G	1
23	Pan-64	Clinical isolate	390T²	390T	1831A²	1831A	6
24	10816	Clinical isolate (MON-1)	390T¹	390T	n.a.	1831G	1
25	V2921	Clinical isolate (MON-1)	n.a.	390G	1831R³	1831R	5
26	791	Clinical isolate (MON-1)	390T¹	390T	n.a	1831G	1
27	MHOM/IT/2019/cur-1	Clinical isolate	390G²	390G	1831R²	1831R	5
28	Elr-sci	Clinical isolate	390T²	390T	1831G²	1831G	1
29	Bra-aii	Clinical isolate	390G²	390G	1831A²	1831A	3
30	Plo-roi	Clinical sample	n.a.	390T	n.a.	1831G	1
31	Aro-sai	Clinical sample	390T³	390T	1831G³	1831G	1
32	Els-mai^a	Clinical sample	n.a.	390T	1831A³	1831A	6
33	Els-mai^b	Clinical sample	n.a.	390T	1831G³	1831G	1
34	Toy-gai	Clinical sample	n.a.	390T	n.a.	1831G	1
35	Koa-cro	Clinical sample	n.a.	390T	n.a.	1831G	1
36	Zeo-sci	Clinical sample	n.a.	390T	1831G³	1831G	1
37	Gia-spi	Clinical sample	390T¹	390T	1831G³	1831G	1
38	Grg-rao	Clinical sample	390T¹	390T	n.a.	1831G	1
39	Vea-fri	Clinical sample	390T¹	390T	n.a.	n.d.
40	Jon-doe	Clinical sample	n.a.	390T	1831G³	1831G	1
41	Pan-1	Clinical sample	n.a.	390T	1831A³	1831A	6
42	Pan-2	Clinical sample	n.a.	390T	n.a.	n.d.
43	Pan-4	Clinical sample	n.a.	390T	1831R³	1831R	4
44	Pan-5	Clinical sample	n.a.	390T	1831A³	1831A	6
45	Pan-6	Clinical sample	n.a.	390T	1831A³	1831A	6
46	Pan-9	Clinical sample	n.a.	390T	1831A³	1831A	6
47	Pan-10	Clinical sample	n.a.	390T	n.a.	1831A	6
48	Pan-11	Clinical sample	n.a.	390T	n.a.	n.d.
49	Pan-12	Clinical sample	n.a.	390T	n.a.	1831A	6
50	Pan-13	Clinical sample	n.a.	390T	n.a.	n.d.
51	Pan-14	Clinical sample	n.a.	390T	1831G³	1831G	1
52	Pan-15	Clinical sample	n.a.	390T	n.a.	n.d.
53	Pan-16	Clinical sample	n.a.	390T	n.a.	1831A	6
54	Pan-21	Clinical sample	n.a.	390T	1831G³	1831G	1
55	Pan-22	Clinical sample	n.a.	390T	1831G³	1831G	1
56	Pan-24	Clinical sample	n.a.	390T	n.a.	n.d.
57	Pan-25	Clinical sample	n.a.	n.d.	n.a.	n.d.
58	Pan-26	Clinical sample	390T³	390T	1831A³	1831A	6
59	Pan-27	Clinical sample	n.a.	390T	1831A³	1831A	6
60	Pan-28	Clinical sample	n.a.	390T	1831A³	1831A	6
61	Psalb	Clinical sample	390T¹	390T	1831G³	1831G	1
62	Dae-dio	Clinical sample	390G³	390G	1831R³	1831R	5
63	Mao-pai	Clinical sample	n.a.	390G	1831R³	1831R	5
64	Gae-bea	Clinical sample	390G³	390G	1831R³	1831R	5
65	Kua-asn	Clinical sample	n.a.	390G	n.a.	1831A	3
66	1038U	Clinical sample	n.a.	390T	n.a.	1831G	1
67	1522U	Clinical sample	n.a.	390T	n.a.	1831G	1
68	1536U	Clinical sample	n.a.	390T	n.a.	1831G	1
69	1538U	Clinical sample	n.a.	390T	n.a.	1831G	1
70	1578U	Clinical sample	n.a.	390G	n.a.	1831G	2
71	1758U	Clinical sample	390G³	390G	n.a.	1831R	5
72	1759U	Clinical sample	390G³	390G	1831A³	1831A	3
73	1761U	Clinical sample	390G³	390G	1831A³	1831A	3
74	1810U	Clinical sample	n.a.	390G	n.a.	n.d.
75	2000U	Clinical sample	n.a.	n.d.	n.a.	n.d.
76	2068U	Clinical sample	390T³	390T	1831G³	1831G	1
77	2073U	Clinical sample	390K³	390K	1831R³	1831R	7
78	2579U	Clinical sample	390T³	390T	1831A³	1831A	6
79	2596U	Clinical sample	390T³	390T	1831G³	1831G	1
80	2602U	Clinical sample	390G³	390G	1831A³	1831A	3
81	2604U	Clinical sample	390K³	390K	1831R³	1831R	7
82	2618U	Clinical sample	390T³	390T	1831G³	1831G	1
83	2619U	Clinical sample	390T³	390T	1831G³	1831G	1
84	2626U	Clinical sample	390T³	390T	1831G³	1831G	1
85	2629U	Clinical sample	390G³	390G	1831A³	1831A	3
86	2632U	Clinical sample	n.a.	n.d.	n.a.	n.d.
87	2647U	Clinical sample	390G³	390G	1831A³	1831A	3
88	2652U	Clinical sample	390T³	390T	1831G³	1831G	1
89	2660U	Clinical sample	390G³	390G	1831A³	1831A	3
90	2668U	Clinical sample	n.a.	390T	n.a.	n.d.
91	2669U	Clinical sample	390T³	390T	1831G³	1831G	1
92	2746U	Clinical sample	390G³	390G	1831R³	1831R	5
93	2897U	Clinical sample	390G³	390G	1831A³	1831A	3

GPI Glucose-6-phosphate isomerase, ME malic enzyme, n.a. not available; n.d. not detected, qPCR quantitative real-time PCR
Els-mai^a was a left conjunctival swab; Els-mai^b was a right conjunctival swab
¹Sequences published in Ceccarelli et al. [10]
²Sequences obtained by MLST
³Sanger sequences obtained by ABI PRISM 310 Genetic Analyzer

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ISSN: 1756-3305

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