Dynamics of Mycobacterium tuberculosis Lineages in Oman, 2009 to 2018

Abstract

Study aim. Effective Tuberculosis (TB) control measures in Oman have reduced the annual incidence of tuberculosis cases by 92% between 1981 and 2016. However, the current incidence remains above the program control target of <1 TB case per 100,000 population. This has been partly attributed to a high influx of migrants from countries with high TB burdens. The present study aimed to elucidate Mycobacterium tuberculosis infection dynamics among nationals and foreigners over a period of 10 years. Methods. The study examined TB cases reported between 2009 and 2018 and examined the spatial heterogeneity of TB cases and the distribution of M. tuberculosis genotypes defined by spoligotypes and MIRU-VNTR among Omanis and foreigners. Results. A total of 484 spoligoprofiles were detected among the examined isolates (n = 1295). These include 943 (72.8%) clustered and 352 (27.2%) unique isolates. Diverse M. tuberculosis lineages exist in all provinces in Oman, with most lineages shared between Omanis and foreigners. The most frequent spoligotypes were found to belong to EAI (318, 30.9%), CAS (310, 30.1%), T (154, 14.9%), and Beijing (88, 8.5%) lineages. However, the frequencies of these lineages differed between Omanis and foreigners. Of the clustered strains, 192 MTB isolates were further analysed via MIRU-VNTR. Each isolate exhibited a unique MIRU-VNTR profile, indicative of absence of ongoing transmission. Conclusion. TB incidence exhibits spatial heterogeneity across Oman, with high levels of diversity of M. tuberculosis lineages among Omanis and foreigners and sub-lineages shared between the two groups. However, MIRU-VNTR analysis ruled out ongoing transmission.

Drug resistant Mycobacterium tuberculosis in Oman: resistance-conferring mutations and lineage diversity

“…Lineage 2 strains, which includes the Beijing lineage, are most often isolated in Southeast Asia, India and East Africa ( Couvin, Reynaud & Rastogi, 2019 ; Panwalkar, Chauhan & Desikan, 2017 ). Therefore, the high prevalence of the Beijing lineage in Oman (15.1%), can probably be attributed to the large influx of imported TB cases from Southeast Asia, India and East Africa ( Al Abri et al, 2020a ; Al Abri et al, 2020b ), in line with the high frequency of shared spoligotype-defined lineages between Omanis and expatriates ( Table 3 ) ( Al-Mahrouqi et al, 2022 ). Thus, the diversity of drug resistant M. tuberculosis strains in Oman can, in part, be attributed to regular influx of novel drug resistant lineages via expatriates.…”

“…Spacer oligonucleotide typing (spoligotyping) was successfully completed on 1,295 isolates (629 Omanis and 666 expatriates), as described elsewhere ( Al-Mahrouqi et al, 2022 ; Kamerbeek et al, 1997 ). Briefly, the direct repeat (DR) region of M. tuberculosis was amplified using a pair of PCR primers.…”

First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Kuwait and evaluation of REBA MTB-MDR assay for rapid detection of MDR-TB

“…The Beijing genotype originated from China, Korea and Japan and spread through industrialization and urbanization in the twentieth century [ 50 ]. It has been reported globally including India, Philippines and Bangladesh whose nationals are major ethnic groups among expatriates in Kuwait and other adjoining Gulf Cooperation Council (GCC) countries [ 13 , 36 , 50 , 51 ]. Similar results have also been reported from Saudi Arabia and Oman which also have large expatriate population originating from these countries [ 13 , 51 – 53 ].…”

“…It has been reported globally including India, Philippines and Bangladesh whose nationals are major ethnic groups among expatriates in Kuwait and other adjoining Gulf Cooperation Council (GCC) countries [ 13 , 36 , 50 , 51 ]. Similar results have also been reported from Saudi Arabia and Oman which also have large expatriate population originating from these countries [ 13 , 51 – 53 ]. On the contrary, these lineages (except CAS1_Delhi) are underrepresented in other adjoining countries such as Iraq and Iran which do not have large expatriate population from these countries [ 3 , 36 ].…”

“…Spoligotyping is a relatively simple typing method which detects polymorphisms at direct repeat (DR) locus belonging to the clustered regularly interspaced short palindromic repeats (CRISPRs) family of repetitive DNA [9,10]. Although spoligotypes are usually less discriminatory for M. tuberculosis strains in high TB burden countries experiencing active disease transmission, they are highly discriminatory for low TB incidence settings, particularly for countries with large and diverse expatriate population [11][12][13]. Additional fingerprinting data are obtained by mycobacterial interspersed repetitive units (MIRUs)-variable number tandem repeat (VNTR) typing or other methods such as restriction fragment length polymorphism (RFLP) or whole genome sequencing (WGS) [10,[14][15][16].…”