Comparison of two multilocus sequence based genotyping schemes for Leptospira species.
Comparison of two multilocus sequence based genotyping schemes for Leptospira species.
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两种基于多位点序列的钩端螺旋体基因分型方案的比较。
DOI：
10.1371/journal.pntd.0001374
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发表时间：
2011-11
影响因子：
3.8
通讯作者：
Peacock SJ
中科院分区：
文献类型：
--
作者：
Ahmed A;Thaipadungpanit J;Boonsilp S;Wuthiekanun V;Nalam K;Spratt BG;Aanensen DM;Smythe LD;Ahmed N;Feil EJ;Hartskeerl RA;Peacock SJ
已经开发了几种基于序列的钩端螺旋体属的基因分型方案。本研究的目的是使用两种最常用的方案对临床和参考分离株进行基因分型，并比较和对比结果。共分离到48株L.问号线虫（n = 40）和L. 通过Thaipadungpanit等人描述的7个位点MLST方案对kirschneri（n =8）进行分型， 以及Ahmed等人描述的6个基因座基因分型方案，（分别称为7 L和6L）。两个湖由于在lipL 32中缺失了三个核苷酸，因此不能使用6L对问号线虫分离株进行分型。其余46株分离株用7 L法分为21个序列型（ST），用6L法分为30个基因型。7 L和6L的总体核苷酸多样性（基于串联序列）分别为3.6%和2.3%。7 L和6L的D值（区分能力）相当，即92.0（95% CI 87.5-96.5）vs. 93.5（95% CI 88.6-98.4）。对每个位点计算的dN/dS比值表明，没有一个位点处于正选择下。基于每个方案的级联序列重构邻居连接树。这两棵树都显示出两个不同的类群，对应于L。interrogans和L. kirschneri，并且两者都鉴定了分别含有10个和7个临床分离株的两个克隆。有六个实例中，6L分裂单个ST的7 L定义成密切相关的集群。我们注意到两个树之间的差异，其中两对菌株之间的遗传相关性更密切相关的7 L比6L。这种遗传分析表明，这两种方案是可比的。我们讨论了它们的实际优点和缺点。两种独立的基于多基因座序列的基因分型方案（在此分别表示为7和6个基因座的方案的7 L和6L）用于钩端螺旋体属，这导致了科学界不确定应该采用哪种方法。本研究的目的是将这两种方案应用于一个致病性钩端螺旋体的单一集合，评估其性能，并描述每个方案的实际优点和缺点。我们使用了各种系统发育的方法来比较输出数据，发现这两个方案给出了非常相似的结果。7 L的优点在于它是基于管家基因的常规多位点测序分型（MLST）方案，并且由可通过计算机访问的数据库支持，通过该数据库，基因型可以由任何研究者容易地分配为已知或新的序列类型，但是目前仅适用于L。interrogans和L. kirschneri。相反，6L可应用于所有致病性钩端螺旋体属，但不是设计上的常规MLST方案，并且不能在线获得。来自271个菌株的6L序列已被发布到公共领域，使用该方案对新序列进行系统发育分析需要下载和离线分析。
Several sequence based genotyping schemes have been developed for Leptospira spp. The objective of this study was to genotype a collection of clinical and reference isolates using the two most commonly used schemes and compare and contrast the results. A total of 48 isolates consisting of L. interrogans (n = 40) and L. kirschneri (n = 8) were typed by the 7 locus MLST scheme described by Thaipadungpanit et al., and the 6 locus genotyping scheme described by Ahmed et al., (termed 7L and 6L, respectively). Two L. interrogans isolates were not typed using 6L because of a deletion of three nucleotides in lipL32. The remaining 46 isolates were resolved into 21 sequence types (STs) by 7L, and 30 genotypes by 6L. Overall nucleotide diversity (based on concatenated sequence) was 3.6% and 2.3% for 7L and 6L, respectively. The D value (discriminatory ability) of 7L and 6L were comparable, i.e. 92.0 (95% CI 87.5–96.5) vs. 93.5 (95% CI 88.6–98.4). The dN/dS ratios calculated for each locus indicated that none were under positive selection. Neighbor joining trees were reconstructed based on the concatenated sequences for each scheme. Both trees showed two distinct groups corresponding to L. interrogans and L. kirschneri, and both identified two clones containing 10 and 7 clinical isolates, respectively. There were six instances in which 6L split single STs as defined by 7L into closely related clusters. We noted two discrepancies between the trees in which the genetic relatedness between two pairs of strains were more closely related by 7L than by 6L. This genetic analysis indicates that the two schemes are comparable. We discuss their practical advantages and disadvantages. Two independent multilocus sequence based genotyping schemes (denoted here as 7L and 6L for schemes with 7 and 6 loci, respectively) are in use for Leptospira spp., which has led to uncertainty as to which should be adopted by the scientific community. The purpose of this study was to apply the two schemes to a single collection of pathogenic Leptospira, evaluate their performance, and describe the practical advantages and disadvantages of each scheme. We used a variety of phylogenetic approaches to compare the output data and found that the two schemes gave very similar results. 7L has the advantage that it is a conventional multi-locus sequencing typing (MLST) scheme based on housekeeping genes and is supported by a publically accessible database by which genotypes can be readily assigned as known or new sequence types by any investigator, but is currently only applicable to L. interrogans and L. kirschneri. Conversely, 6L can be applied to all pathogenic Leptospira spp., but is not a conventional MLST scheme by design and is not available online. 6L sequences from 271 strains have been released into the public domain, and phylogenetic analysis of new sequences using this scheme requires their download and offline analysis.
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影响因子：
3.7
作者：
Cerqueira GM;McBride AJ;Hartskeerl RA;Ahmed N;Dellagostin OA;Eslabão MR;Nascimento AL
通讯作者：
Nascimento AL
实时PCR的开发和验证，用于检测临床材料中致病性钩端螺旋体。
影响因子：
3.7
作者：
Ahmed A;Engelberts MF;Boer KR;Ahmed N;Hartskeerl RA
通讯作者：
Hartskeerl RA
影响因子：
9.4
作者：
HERRMANN, JL;BELLENGER, E;SAINTGIRONS, I
通讯作者：
SAINTGIRONS, I
影响因子：
9.4
作者：
HUNTER, PR;GASTON, MA
通讯作者：
GASTON, MA
影响因子：
9.4
作者：
CORNEY, BG;COLLEY, J;GRAHAM, GC
通讯作者：
GRAHAM, GC