Anuntakarun Songtham, Sawaswong Vorthon, Jitvaropas Rungrat, Praianantathavorn Kesmanee, Poomipak Witthaya, Suputtamongkol Yupin, Chirathaworn Chintana, Payungporn Sunchai
Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.
Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand.
Genomics Inform. 2021 Sep;19(3):e31. doi: 10.5808/gi.21037. Epub 2021 Sep 30.
Leptospirosis is a zoonotic disease caused by spirochetes from the genus Leptospira. In Thailand, Leptospira interrogans is a major cause of leptospirosis. Leptospirosis patients present with a wide range of clinical manifestations from asymptomatic, mild infections to severe illness involving organ failure. For better understanding the difference between Leptospira isolates causing mild and severe leptospirosis, illumina sequencing was used to sequence genomic DNA in both serotypes. DNA of Leptospira isolated from two patients, one with mild and another with severe symptoms, were included in this study. The paired-end reads were removed adapters and trimmed with Q30 score using Trimmomatic. Trimmed reads were constructed to contigs and scaffolds using SPAdes. Cross-contamination of scaffolds was evaluated by ContEst16s. Prokka tool for bacterial annotation was used to annotate sequences from both Leptospira isolates. Predicted amino acid sequences from Prokka were searched in EggNOG and David gene ontology database to characterize gene ontology. In addition, Leptospira from mild and severe patients, that passed the criteria e-value < 10e-5 from blastP against virulence factor database, were used to analyze with Venn diagram. From this study, we found 13 and 12 genes that were unique in the isolates from mild and severe patients, respectively. The 12 genes in the severe isolate might be virulence factor genes that affect disease severity. However, these genes should be validated in further study.
钩端螺旋体病是一种由钩端螺旋体属的螺旋体引起的人畜共患病。在泰国，问号钩端螺旋体是钩端螺旋体病的主要病因。钩端螺旋体病患者临床表现多样，从无症状、轻度感染到涉及器官衰竭的严重疾病。为了更好地了解引起轻度和重度钩端螺旋体病的钩端螺旋体分离株之间的差异，使用Illumina测序对两种血清型的基因组DNA进行测序。本研究纳入了从两名患者分离的钩端螺旋体DNA，一名患者症状较轻，另一名患者症状较重。使用Trimmomatic去除双端读数的接头，并以Q30分数进行修剪。使用SPAdes将修剪后的读数构建为重叠群和支架。使用ContEst16s评估支架的交叉污染。使用Prokka细菌注释工具对两种钩端螺旋体分离株的序列进行注释。在EggNOG和David基因本体数据库中搜索Prokka预测的氨基酸序列，以表征基因本体。此外，将来自轻度和重度患者且在针对毒力因子数据库的blastP中符合e值<10e-5标准的钩端螺旋体用于绘制维恩图进行分析。通过本研究，我们分别在轻度和重度患者的分离株中发现了13个和12个独特的基因。重度分离株中的12个基因可能是影响疾病严重程度的毒力因子基因。然而，这些基因应在进一步研究中进行验证。
