First Insights into the Phylogenetic Diversity of Mycobacterium tuberculosis in Nepal

Abstract

BackgroundTuberculosis (TB) is a major public health problem in Nepal. Strain variation in Mycobacterium tuberculosis may influence the outcome of TB infection and disease. To date, the phylogenetic diversity of M. tuberculosis in Nepal is unknown.Methods and FindingsWe analyzed 261 M. tuberculosis isolates recovered from pulmonary TB patients recruited between August 2009 and August 2010 in Nepal. M. tuberculosis lineages were determined by single nucleotide polymorphisms (SNP) typing and spoligotyping. Drug resistance was determined by sequencing the hot spot regions of the relevant target genes. Overall, 164 (62.8%) TB patients were new, and 97 (37.2%) were previously treated. Any drug resistance was detected in 50 (19.2%) isolates, and 16 (6.1%) were multidrug-resistant. The most frequent M. tuberculosis lineage was Lineage 3 (CAS/Delhi) with 106 isolates (40.6%), followed by Lineage 2 (East-Asian lineage, includes Beijing genotype) with 84 isolates (32.2%), Lineage 4 (Euro-American lineage) with 41 (15.7%) isolates, and Lineage 1 (Indo-Oceanic lineage) with 30 isolates (11.5%). Based on spoligotyping, we found 45 different spoligotyping patterns that were previously described. The Beijing (83 isolates, 31.8%) and CAS spoligotype (52, 19.9%) were the dominant spoligotypes. A total of 36 (13.8%) isolates could not be assigned to any known spoligotyping pattern. Lineage 2 was associated with female sex (adjusted odds ratio [aOR] 2.58, 95% confidence interval [95% CI] 1.42–4.67, p = 0.002), and any drug resistance (aOR 2.79; 95% CI 1.43–5.45; p = 0.002). We found no evidence for an association of Lineage 2 with age or BCG vaccination status.ConclusionsWe found a large genetic diversity of M. tuberculosis in Nepal with representation of all four major lineages. Lineages 3 and 2 were dominating. Lineage 2 was associated with clinical characteristics. This study fills an important gap on the map of the M. tuberculosis genetic diversity in the Asian region.

Molecular characterization of Mycobacterium tuberculosis isolates from elephants of Nepal

“…Both of the human isolates had spoligotype SIT138 categorized as EAI5, 22 which is the most frequently observed EAI type in this country. 25 This SNP seems to have occurred on a specific lineage of the clade, since other EAI5-SIT138 isolates obtained in Nepal did not have the SNP (Figure 3). …”

“…22,25 This lineage is predominantly observed in Indo-Oceanic areas like south India or the Philippines; 31,32 however, its prevalence in Nepal is relatively low. In the recent report, 25 the prevalence of Indo-Oceanic lineage was 11.5% in Nepal and our observation results were also very similar (unpublished data).…”

“…22,25 This lineage is predominantly observed in Indo-Oceanic areas like south India or the Philippines; 31,32 however, its prevalence in Nepal is relatively low. In the recent report, 25 the prevalence of Indo-Oceanic lineage was 11.5% in Nepal and our observation results were also very similar (unpublished data). Spoligotypes of 2 elephant isolates were different from known EAI patterns; however, those patterns are producible from EAI by massive spacer deletions by an IS6110 insertion or a homologous recombination, which is occasionally observed in this region consisted of repetitive sequences.…”

Insertion Element IS6110 based characterisation of Nepalese tuberculosis strains into different genetic lineages

“…A key factor is the geographical location of Nepal, interlocked between China and India, two countries, which together account for approximately a third of annual global new cases (11% and 24%, respectively) [1]. A recent study of 261 Nepalese isolates found any drug resistance (any drug resistance has been defined as resistance to isoniazid, rifampicin, streptomycin, ethambutol, fluoroquinolones, and/or aminoglycosides) in 12.8%% of Mtb strains that were new untreated cases, with the most frequent lineages reported as CAS/Delhi (40.6%), East Asian (including Beijing) (32.2%), Euro-American (15.7%) and Indo-oceanic (11.5%) [13]. To gain further insight into the characteristics and diversity of Mtb in Nepal, our study aimed to categorise isolates for the first time using IS6110 FAFLP PCR and to assign them to different genetic lineages.…”

MixedMycobacterium tuberculosisLineage Infection in 2 Elephants, Nepal

“…The elephant B isolate belonged to the Indo-Oceanic lineage (East African–Indian 5 spoligo-international type 1365) (Table). The prevalence of the Indo-Oceanic lineage among human TB patients in Nepal is only 11.5% ( 8 ). The drug resistance–associated region sequences rpoB , katG , inhA promoter region, and gyrA were all wild types in both isolates.…”