Multiple-locus variable-number tandem-repeat analysis of Streptococcus pneumoniae and comparison with multiple loci sequence typing

Table 2 Genetic diversity of the 331 isolates of S. pneumoniae

Marker name	DI*	95% CI †	Marker set by author
Marker name	DI*	95% CI †	This paper	Koeck 2008 [[19]]	Pichon 2010 [[26]]	Elberse 2011 [[25]]
			(A)		(B)	(C)
ms15_507bp_45bp_7U	0.607	[0.588-0.626]				+
ms17_167bp_45bp_3U	0.852	[0.847-0.857]	+	+	+
ms19_663pb_60pb_10U	0.674	[0.658-0.691]	+	+	+
ms25_426bp_45bp_4U	0.788	[0.779-0.797]	+	+	+	+
ms26_492bp_51bp_6U	0.714	[0.703-0.726]
ms27_326bp_45bp_3U	0.561	[0.543-0.579]	+
ms31_594bp_45bp_9U	0.695	[0.683-0.708]
ms32_280pb_45bp_2U	0.598	[0.585-0.611]				+
ms33_407bp_45bp_2U	0.737	[0.725-0.748]	+	+		+
ms34_239bp_45bp_1U	0.682	[0.670-0.695]			+
ms35_349bp_49bp_4U	0.572	[0.557-0.587]
ms36_274pb_45pb_2U	0.793	[0.786-0.801]			+
ms37_501bp_45bp_7U	0.855	[0.851-0.859]	+	+	+	+
ms38_309bp_45bp_2U	0.557	[0.535-0.578]				+
ms39_275bp_45bp_2U	0.812	[0.804-0.819]	+		+
ms40_376bp_45bp_3U	0.789	[0.782-0.797]		+		+
ms41_166pb_14pb_2U	0.567	[0.548-0.586]		+
All markers	0.989	[0.987-0.991]
Congruence (%)			47.2	59	65.1	43.8

The marker name contains all the numbers necessary to characterize the marker in reference to a given sequenced genome (reference strain, R6). For example, in “ms15_507bp_45bp_7U”, - ms means minisatellite, - 507 bp is the size of the amplification product of this marker; - 45 bp is the size of the repeat unit, - 7 is the number of repeats. Markers used by authors are noticed by a cross (+), authors seven Markers set are noticed as following: (A) this paper, (B) Pichon’s and (C) Elberse’s. The MLST/MLVA congruence in percent by author is indicated at the bottom of the table.
* DI: diversity index. † CI: confidence interval.

ISSN: 1471-2180