Rapid Deletion-Based Subtyping System for the Manila Family of Mycobacterium tuberculosis

Abstract

The Manila family of Mycobacterium tuberculosis is a group of clonal isolates seen throughout the Pacific Basin. Commonly used rapid molecular typing methods often leave large groups of Manila family isolates clustered together. Here we describe a simple deletion-based PCR method that improves the discrimination for Manila family isolates, with or without the use of mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) classification, and that is both rapid and affordable. Twenty-eight Manila family isolates, classified by spoligotyping, were collected from around the Pacific Basin from 1995 to 2003 and were tested for known genomic deletions. Nine of 15 regions of difference tested were identified as potentially discriminatory, with 18 distinct patterns; of these 9, 5 were selected for optimal discrimination using 61 Manila family isolates collected from California in 2009. For this geographically limited sample, the single large cluster was reduced to 14 distinct patterns. When the isolates were tested by spoligotyping and MIRU-VNTR, the addition of deletion analysis increased the number of distinct patterns from 43 to 56. In summary, the two study groups, which together form a single group of 89 isolates by spoligotyping, were segregated into 17 subgroups by our deletion-based subtyping system.

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates

“…A few spoligotyping studies in other island countries, such as in Kiribati 35 and Papua New Guinea 36 , 37 , revealed the rarity of the EAI isolates. The rare EAI isolates, however, usually belonged to EAI2_MNL, which was also reported from Hawaii and Guam 38 . Thus, L1.2.1.1 may associate with Austronesians either due to the founder effect or co-evolution.…”

Clonal Expansion of Both Modern and Ancient Genotypes of Mycobacterium tuberculosis in Southern Taiwan

“…Regions amplified by PCR were sequenced to confirm the reaction. A detailed explanation of this methodology has been described [9] .…”

Genetic Diversity of Mycobacterium tuberculosis Isolates from a Rural Community in the Philippines

“…Classical genotyping techniques such as MIRU-VNTR and spoligotyping also have lower discriminatory power compared to WGS (Phelan et al 2019;Jamieson et al 2014), especially for the Manila strain that has been shown to have very low genetic variability (Douglas et al 2003;Frink et al 2011). It is also possible that the lower discriminatory power of these genotyping tools…”