Bioinformatics describes novel Loci for high resolution discrimination of leptospira isolates.
Bioinformatics describes novel Loci for high resolution discrimination of leptospira isolates.
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DOI：
10.1371/journal.pone.0015335
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发表时间：
2010-10-15
期刊：
影响因子：
3.7
通讯作者：
Nascimento AL
中科院分区：
文献类型：
--
作者：
Cerqueira GM;McBride AJ;Hartskeerl RA;Ahmed N;Dellagostin OA;Eslabão MR;Nascimento AL
钩端螺旋体病是世界上最广泛的人畜共患病之一，有超过260种致病血清型，迫切需要一个分子分类系统。钩端螺旋体多位点序列分型方法的建立。正在解决这个问题。本研究的目的是确定基因座的潜力，以提高钩端螺旋体菌株歧视的测序为基础的方法。我们使用生物信息学来评估预先存在的基因座，这些基因座有可能增加对爆发菌株的区分。通过使用单个或串联序列的系统发育分析来评估先前存放的序列数据。我们确定并评估了ligB，secY，rpoB和lipL 41位点的适用性，单独和组合，区分38个致病性钩端螺旋体菌株，并根据它们所属的物种进行聚类。基因座间的同源性为82.0- 92.0%，种间同源性为97.7- 98.5%。使用ligB-secY-rpoB-lipL 41超基因座，可以区分34/38株，其属于六种致病性钩端螺旋体。此外，该序列与来自先前MLST方案的16种序列类型的超位点连接，该方案用于研究钩体克隆与泰国人钩体病爆发的关联。它们的使用增强了现有方案的辨别力。lipL 41和rpoB基因座使分离率从81.0%提高到100%，但增强的方案仍然局限于L. interrogans和L. kirschneri种。作为我们研究的第一个目的，ligB-secY-rpoB-lipL 41超级基因座在评价的菌株中表现出令人满意的区分水平。第二，将rpoB和lipL 41基因座纳入MLST方案为区分L. interrogans和L. kirschneri，并可能在未来的流行病学研究有用。
Leptospirosis is one of the most widespread zoonoses in the world and with over 260 pathogenic serovars there is an urgent need for a molecular system of classification. The development of multilocus sequence typing (MLST) schemes for Leptospira spp. is addressing this issue. The aim of this study was to identify loci with potential to enhance Leptospira strain discrimination by sequencing-based methods. We used bioinformatics to evaluate pre-existing loci with the potential to increase the discrimination of outbreak strains. Previously deposited sequence data were evaluated by phylogenetic analyses using either single or concatenated sequences. We identified and evaluated the applicability of the ligB, secY, rpoB and lipL41 loci, individually and in combination, to discriminate between 38 pathogenic Leptospira strains and to cluster them according to the species they belonged to. Pairwise identity among the loci ranged from 82.0–92.0%, while interspecies identity was 97.7–98.5%. Using the ligB-secY-rpoB-lipL41 superlocus it was possible to discriminate 34/38 strains, which belong to six pathogenic Leptospira species. In addition, the sequences were concatenated with the superloci from 16 sequence types from a previous MLST scheme employed to study the association of a leptospiral clone with an outbreak of human leptospirosis in Thailand. Their use enhanced the discriminative power of the existing scheme. The lipL41 and rpoB loci raised the resolution from 81.0–100%, but the enhanced scheme still remains limited to the L. interrogans and L. kirschneri species. As the first aim of our study, the ligB-secY-rpoB-lipL41 superlocus demonstrated a satisfactory level of discrimination among the strains evaluated. Second, the inclusion of the rpoB and lipL41 loci to a MLST scheme provided high resolution for discrimination of strains within L. interrogans and L. kirschneri and might be useful in future epidemiological studies.
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影响因子：
11.8
作者：
Gouvela, Edilane L.;Metcalfe, John;Ko, Albert I.
通讯作者：
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影响因子：
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作者：
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DOI：
10.1099/ijs.0.63783-0
发表时间：
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通讯作者：
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作者：
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通讯作者：
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作者：
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