Department of Microbiology, All India Institute of Medical Sciences,New Delhi, India.
Sitaram Bharatiya Institute of Science and Research, New Delhi, India.
Infect Genet Evol. 2020 Jul;81:104230. doi: 10.1016/j.meegid.2020.104230. Epub 2020 Feb 6.
IS6110 restriction fragment length polymorphism (RFLP) analysis is widely used for molecular epidemiological studies of tuberculosis. Role of spoligotyping and Fluorescent Amplified Fragment Length Polymorphism (FAFLP) was studied in low-copy number IS6110 strains of Mycobacterium tuberculosis complex (Mtbc).
The study isolates included 70 strains of Mtbc collected from different regions of India. IS6110 restriction fragment, spoligotyping and FAFLP were performed for genotypic analysis.
A single copy of IS6110 was found in 30% of isolates with 90.5% of them harboring characteristic 1.5-Kb IS6110 restriction fragment.IS6110RFLP identified 51 different types, FAFLP 41 types, and spoligotyping 31 types. Combination of all three techniques identified 67 different types.IS6110 RFLP analysis was found sensitive for genotyping isolates with more than one copy of IS6110 (Hunter Gaston Discriminatory Index (HGDI-1) while, neither spoligotyping (HGI-0.89) nor FAFLP (HGDI-0.92) or their combinations were as good. The discriminatory power of spoligotyping (HGDI- 0.89) in isolates with a single copy of IS6110 was higher than IS6110-RFLP.Clustering was reduced to 67% using spoligotyping and to 38% with FAFLP.
Combination of FAFLP and Spoligotyping may prove to be valuable in studying the epidemiology of M. tuberculosis strains harboring few copies of IS6110 element.
IS6110 限制片段长度多态性（RFLP）分析广泛用于结核分枝杆菌的分子流行病学研究。本研究探讨了低拷贝数结核分枝杆菌复合群（Mtbc）中 spoligotyping 和荧光扩增片段长度多态性（FAFLP）的作用。
本研究共分离了 70 株来自印度不同地区的 Mtbc 菌株。对这些菌株进行了 IS6110 限制片段、 spoligotyping 和 FAFLP 分析，以进行基因型分析。
30%的菌株中存在单个拷贝的 IS6110，其中 90.5%的菌株携带特征性的 1.5-Kb IS6110 限制片段。IS6110RFLP 鉴定了 51 种不同的类型，FAFLP 鉴定了 41 种， spoligotyping 鉴定了 31 种。三种技术的组合鉴定了 67 种不同的类型。IS6110 RFLP 分析对具有多个拷贝的 IS6110（Hunter Gaston 区分指数（HGDI-1））的菌株进行基因分型较为敏感，而 spoligotyping（HGI-0.89）和 FAFLP（HGDI-0.92）或它们的组合则不然。在具有单个拷贝的 IS6110 的菌株中， spoligotyping（HGDI-0.89）的区分能力高于 IS6110-RFLP。 spoligotyping 将聚类减少到 67%，FAFLP 将聚类减少到 38%。
FAFLP 和 spoligotyping 的组合可能对研究携带少量 IS6110 元件的结核分枝杆菌菌株的流行病学具有重要价值。
