English abstract
Background and aim: Tuberculosis (TB) is one of the top 10 leading cause of death
worldwide, and is the leading cause of death, from an infectious disease, other than
COVID-19, ranking above HIV/AIDS. In Oman, the national TB control program has
successfully implemented strategies that led to 85% reduction in all forms of TB,
between 1981 and 2005. However, the past decade has witnessed a stagnating trend in TB
cases. At the same time, spoligotyping analysis revealed similar Mycobacterium
tuberculosis lineages, and a large proportion of shared strains, among nationals and
expatriates. The present study has therefore, using a more discriminatory genetic marker,
24-locus MIRU-VNTR, examined the genetic structure of M. tuberculosis in different
regions in Oman, and assessed transmission dynamics among Omanis and expatriates.
Methods: A total of 192 M. tuberculosis isolates, collected from Omani patients (n= 89)
and expatriates (n= 103), from 8 provinces (Muscat (n= 59), Batinah (n= 50), Dhofar (n=
28), Dakhliya (n= 12), Dhahira (n= 11), Sharqiyah (n= 10), Wousta (n= 4) and Buraimi
(n= 1), between 2014 and 2018. The M. tuberculosis isolates were subjected to 24-
MIRU-VNTR genotyping using established protocol. The generated MLGs data was used
to estimate standard population genetic indices (expected heterozygosity (h) and FST) to
assess the extent of diversity and genetic structure of M. tuberculosis.
Results: High extent of allelic diversity of the examined MIRUs was observed among M.
tuberculosis obtained from both Omanis (h = 0.632) and expatriates (h= 0.626), which
remained stable in space and over the study period (2014-2018). However, M.
tuberculosis in Dhofar also exhibited a relatively lower allelic diversity (h= 0.559)
compared to other provinces (average h= 0.621). High extent of genetic relatedness (lack
of differentiation) was seen among M. tuberculosis infecting Omanis and expatriates
(FST= 0.001) as well as drug resistant and susceptible strains (FST= 0.010). Similarly,
there was a lack of differentiation of M. tuberculosis in different provinces (FST= -0.0001
to 0.0544) and over the study years (FST= -0.0002 to 0.0068). However, a moderate
differentiation existed between M. tuberculosis in Dhofar and geographically distant
provinces; Batinah (FST= 0.0544), Muscat (FST= 0.0271) and Sharqiyah (FST= 0.0225).
Pairwise analysis of matching multi-locus haplotypes revealed a higher probability for
pairs of M. tuberculosis isolates to originate from the same province, when sharing a
large number of identical alleles. However, each of the examined 192 M. tuberculosis
isolates displayed a unique MIRU-VNTR profile, demonstrating a high extent of
diversity and indicating absence of transmission.
Conclusion: The stability of high allelic diversity and absence of spatiotemporal genetic
differentiation of M. tuberculosis are indicative of a large population size of the
pathogen. Though, no evidence of transmission was detected, between and among the
Omanis and expatriates. Therefore, LTBI screening and targeted preventative therapy of
high-risk groups can lead to consistent reduction in TB incidence and M. tuberculosis
population size, to achieve the elimination targets of 2035. The moderate differentiation
of M. tuberculosis in Dhofar warrants further analysis to test whether the pathogen is
genetically sub-structured and thus require tailored controlled efforts.
