Multi-locus sequence analysis reveals great genetic diversity among Mycoplasma capricolum subsp. capripneumoniae strains in Asia

Akhtar, Arooba; Boissière, Anne; Hao, Huafang; Saeed, Muhammad; Dupuy, Virginie; Exbrayat, Antoni; Khan, Farhan Anwar; Chu, Yuefeng; Manso-Silván, Lucía

doi:10.1186/s13567-022-01107-z

Veterinary Research

Table 1 List of Mccp strains and genomes analysed in this study and corresponding MLSA types.

From: Multi-locus sequence analysis reveals great genetic diversity among Mycoplasma capricolum subsp. capripneumoniae strains in Asia

Strain	Supplier	Reference	Year	^#Geographic origin	Host	GenBank	MLSA	Group
97095-Tigray	NVI-E	[26]	1988	Ethiopia, Tigray	Capra hircus	ND	1-010	A
9277-PF1	VRA	[26]	< 1992	Sudan, NA	Capra hircus	ND	1-010	ND
99108-P1*	SVS	[26]	1999	Eritrea, Adi Keshi/Kenya, Tigray	Capra hircus	ND	1-010	A
04012 ^§	AWWP	[20]	2004	Qatar, Al Shahaniya	Capra aegagrus	CP040917	1-010	A
13092	EAD	[7]	2013	UAE, Abu Dhabi	Gazella marica	ND	1-011	A
14001	EAD	[7]	2014	UAE, Abu Dhabi	Oryx leucoryx	ND	1-011	A
16034	EAD	[6]	2016	UAE, Al-Ain	Oryx dammah	ND	1-011	A
M74/93	NVI-S	[19]	1993	Uganda, Karamoja	Ovis aries	ND	1-020	ND
M79/93*	NVI-S	[19]	1993	Uganda, Karamoja	Capra hircus	ND	1-020	A
149F09-SNC1	VLA	[21]	2009	Mauritius, West	Capra hircus	ND	1-030	ND
ILRI 181	ILRI	[22]	2012	Kenya, Laikipia	Capra hircus	LN515399	1-030	A
14020	TVLA	[6]	2013	Tanzania, Manyara, Kiteto	Capra hircus	ND	1-040	A
8789	LRVZF	[27]	1987	Chad, Karal, Dandi	Capra hircus	ND	2-010	B
94156^§	LRVZF	[26]	1994	Chad, N'Djamena	Capra hircus	CP041708	2-010	B
05021^§	VRA	[4]	2004	Sudan, Darfour, Nyala	Capra hircus	CP041700	2-010	B
95043^§	LABOCEL	[26]	1995	Niger, Goure	Capra hircus	CP041705	2-020	B
M1601	LVRI	[28, 29]	2007	China, Gansu	Capra hircus	CP017125	3-010	D
44F04	PVCRI	[30]	2004	Turkey, Thrace	Capra hircus	ND	3-020	C
09018	CIRAD	[31]	2009	Tajikistan, Rogun	Capra hircus	ND	3-020	ND
12002^§	MoA-T	[5]	2011	Tajikistan, NA	Capra hircus	CP041702	3-020	C
C550/1^§	CVRL	[26]	1991	UAE, Dubai	Capra hircus	CP041703	3-030	C
Gabes	CIRAD	[32]	1980	Tunisia, Gabes	Capra hircus	ND	4-010	E
Gabes/102p	CIRAD	[4]	1980	Tunisia, Gabes	Capra hircus	ND	4-010	E
LKD	CIRAD	[32]	1980	Tunisia, Kebili Douz	Capra hircus	ND	4-010	E
9081-487P	MAF-O	[26]	1990	Oman, NA	Capra hircus	ND	4-010	E
07033-033C1^§	FU	[33]	2007	Turkey, Elazig	Capra hircus	CP041712	4-010	E
7/2^§	MRI	[34]	1988	Oman, NA / Turkey, NA	Capra hircus	CP041701	4-020	E
97097-Erer^§	NVI-E	[26]	1997	Ethiopia, Erer	Capra hircus	CP041706	5-010	F
AMRC-C758^§	AU	[35]	1981	Sudan, NA	Capra hircus	CP041711	5-020	F
Yatta B^§	NVI- S	[26]	< 1997	Kenya, Yatta	Capra hircus	CP041707	5-020	F
F38^§	CIRAD	[12, 22]	1976	Kenya, NA	Capra hircus	LN515398	5-030	F
94029-C5^§	AVS	[26]	1994	Oman, NA	Capra hircus	CP041709	5-040	F
91039-C3^§	NVI-E	[36]	1991	Ethiopia, Awash	Capra hircus	CP041710	5-050	F
9231-Abomsa^§	CIRAD	[36, 37]	1982	Ethiopia, Gojjam	Capra hircus	LM995445	5-060	F
92138-CLP1	NVI-E	[26]	1992	Ethiopia, Bishoftu	Capra hircus	ND	5-060	F
1303-SF	LVRI	NA	2013	China, Tibet, Nagqu	Ovis aries	ND	6-010	ND
SD3	HVRI	[38]	2006	China, Shandong	Capra hircus	ND	6-020	ND
87001	HVRI	[25, 39]	1958	China, Shandong	Capra hircus	CP006959	6-030	G
1209LFT	LVRI	NA	2012	China, Tibet, Nagqu	Pantholops hodgsonii	ND	6-040	ND
*1411LFT1*	LVRI	NA	2014	China, Tibet, Nagqu	Pantholops hodgsonii	CP101367	6-040	ND
*zly1402F*	LVRI	NA	2014	China, Tibet, Nagqu	Pantholops hodgsonii	ND	6-040	ND
zly1309F	LVRI	[40]	2013	China, Tibet, Nagqu	Pantholops hodgsonii	CP019061	6-050	H
Gilgit	UoA-P	[10]	2019	Pakistan, Baltistan, Gilgit	Capra hircus	ND	7-010	ND

Out of 43 strains listed 39 were used for diversity analysis, with additional strains/passages originating from the same or consecutive outbreaks (framed) used for stability analysis. New strains not included in 2011 [4] are underlined and those not previously genotyped are double underlined. MLSA data from 36 strains was obtained by locus amplification and sequencing, of which 5 (in bold) directly from non-viable samples. Strains for which MLSA data were exclusively extracted from genomic data are italicised. Corresponding whole genome sequence typing groups according to [5] and [6] are provided when available.
AU Aarhus University, Denmark, AVS Agriculture and Veterinary Services, Oman, AWWP Al Wabra Wildlife Preservation, Qatar, CIRAD Centre de coopération international en recherche agronomique pour le développement, France, CVRL Central Veterinary Research Laboratory, UAE, EAD Environment Agency, Abu Dhabi, UAE, FU Firat University, Turkey, HVRI Harbin Veterinary Research Institute, China, ILRI International Livestock Research Institute, Kenya, LABOCEL Laboratoire Central de l’Elevage de Niamey, Niger, LRVZF Laboratoire de Recherches Vétérinaires et Zootechniques de Farcha, Chad, LVRI Lanzhou Veterinary Research Institute, China, MAF-O Ministry of Agriculture and Fisheries, Oman, MRI Moredun Research Institute, UK, MoA-T Ministry of Agriculture, Tajikistan, NA Non-Available, ND Not Determined, NVI-E National Veterinary Institute, Ethiopia, NVI-S National Veterinary Institute, Sweden, PVCRI Pendik Veterinary Control and Research Institute, Turkey, SVS Senhit Veterinary Service, Eritrea, TVLA Tanzania Vet Lab Agency, UAE United Arab Emirates, UoA-P University of Agriculture, Pakistan, VLA Veterinary Laboratory Agency, Weybridge, UK,VRA Veterinary Research Administration, Sudan.
^#place of isolation/previous location of the animals.
^*could not be differentiated by large-scale genotyping [5].
^§MLSA data obtained both by PCR and sequencing and by extraction from genomic data.

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