Evaluation of ESX Sequence Variations within Mycobacterium tuberculosis Clinical and Laboratory Isolates

Author(s): Melisha Sukkhu and Yeshnee Naidoo

The ESX family of genes (esxA-W) in Mycobacterium tuberculosis (Mtb) encodes 23 effector molecules influencing immunogenicity and pathogenicity. This study was aimed at identifying and evaluating variations in ESX sequence profiles in clinical and laboratory isolates, using amplicon sequencing, and examining how diversity might influence immune responses. Using spoligotyping and a strain specific test, the genotypes for all isolates were confirmed. Following amplicon sequencing, all 23 ESX genes were evaluated for variations between the Beijing, KwaZulu-Natal (KZN) and other genetic isolate groupings as well as within isolates. 23 ESX genes from 55 clinical isolates (20 Beijing, 25 KZN and 10 other) and 3 Laboratory strains (H37Rv, H37Ra and BCG) were sequenced. 482 single nucleotide polymorphisms (SNPs) were identified in 12 ESX genes relative to H37Rv. Majority of the identified 363 nsSNPs occured in Beijing isolates. No mutations were observed in esxA, B, C, E, G, H, J, R, S and T. Six unique nsSNPs were identified in the Beijing isolates: esxI (Q20L), esxO (E52G), 2 in esxP (T3S; N83D), esxU (P63S) and esxW (T2A). Three unique nsSNPs were identified in the KZN isolates: esxK (A58T), esxL (R33S) with the esxL polymorphism resulting from a dinucleotide change. These results identify new mutations in the ESX family, some of which were not detected by genome sequencing.


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