Two tales: Worldwide distribution of Central Asian (CAS) versus ancestral East-African Indian (EAI) lineages of Mycobacterium tuberculosis underlines a remarkable cleavage for phylogeographical, epidemiological and demographical characteristics

Couvin, David; Reynaud, Yann; Rastogi, Nalin

doi:10.1371/journal.pone.0219706

Cited by 28 publications

(35 citation statements)

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“…In a recent study, the global proportion of MDR in CAS population was estimated at 30.63% [57]. In our study, based on the pooled prevalence of MDR genotype, CAS was found (1.21%) as a one of the dominant genotypes.…”

Section: Discussionsupporting

confidence: 47%

Variation in Mycobacterium tuberculosis population structure in Iran: a systemic review and meta-analysis

et al. 2021

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Background Acquiring comprehensive insight into the dynamics of Mycobacterium tuberculosis (Mtb) population structure is an essential step to adopt effective tuberculosis (TB) control strategies and improve therapeutic methods and vaccines. Accordingly, we performed this systematic review and meta-analysis to determine the overall prevalence of Mtb genotypes/ sublineages in Iran. Methods We carried out a comprehensive literature search using the international databases of MEDLINE and Scopus as well as Iranian databases. Articles published until April 2020 were selected based on the PRISMA flow diagram. The overall prevalence of the Mtb genotypes/sublineage in Iran was determined using the random effects or fixed effect model. The metafor R package and MedCalc software were employed for performing this meta-analysis. Results We identified 34 studies for inclusion in this study, containing 8329 clinical samples. Based on the pooled prevalence of the Mtb genotypes, NEW1 (21.94, 95% CI: 16.41–28.05%), CAS (19.21, 95% CI: 14.95–23.86%), EAI (12.95, 95% CI: 7.58–19.47%), and T (12.16, 95% CI: 9.18–15.50%) were characterized as the dominant circulating genotypes in Iran. West African (L 5/6), Cameroon, TUR and H37Rv were identified as genotypes with the lowest prevalence in Iran (< 2%). The highest pooled prevalence rates of multidrug-resistant strains were related to Beijing (2.52, 95% CI) and CAS (1.21, 95% CI). Conclusions This systematic review showed that Mtb populations are genetically diverse in Iran, and further studies are needed to gain a better insight into the national diversity of Mtb populations and their drug resistance pattern.

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Section: Discussionsupporting

confidence: 47%

Variation in Mycobacterium tuberculosis population structure in Iran: a systemic review and meta-analysis

et al. 2021

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“…However, MTBC populations are diverse also within subcontinental regions. For example, the MTBC population in Southern India is dominated by L1, while the most prevalent lineage in the North is L3 ( Couvin et al , 2019 ). To investigate fine-scale processes in greater detail, including local adaptation, large population-based studies will be necessary.…”

Section: Discussionmentioning

confidence: 99%

“…While L2 and L4 strains occur across the world, L1 strains are predominantly found around the rim of the Indian Ocean (East Africa, South Asia, and Southeast Asia). L3 has a distinct geographic range (East Africa, Central Asia, Western Asia, and South Asia) that overlaps partially with L1 ( Couvin et al , 2019 ; Wiens et al , 2018 ). While many MTBC lineages also occur in Northern Europe, North America, Australia and New Zealand, in these low-burden regions, the majority of TB cases are imported through recent migrations, and local transmission is rare ( White et al , 2017 ).…”

Section: Introductionmentioning

confidence: 99%

“…Yet, much of TB research to date has focused on the laboratory strain H37Rv (belonging to L4) and a few other strains belonging to L2 and L4, because of their broad geographic range, and their association with drug resistance. By contrast, L1 and L3 have largely been neglected, and only few studies have investigated the global populations of these two lineages ( Couvin et al , 2019 ; O’Neill et al , 2019 ). This knowledge gap is particularly severe as L1 and L3 are endemic to some of the world regions with the heaviest TB burden.…”

Section: Introductionmentioning

confidence: 99%

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Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

et al. 2021

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Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around the rim of the Indian Ocean, the region that accounts for most of the world’s new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Methods: We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection. Results: We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics . For L1 we identified signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Conclusions: Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.

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“…This finding is in line with previous studies that have been based on classical genotyping methods and reported rates of 40% or higher of the so-called Central Asia spoligotype family in central and eastern Sudan (5,15,35). Moreover, Couvin et al (36) identified Sudan as an L3 hotspot in Africa. In this regard, it is intriguing to speculate whether L3 strains in general or certain subgroups have developed particular pathobiologic properties rendering them more virulent in East Africa host populations.…”

Section: Discussionmentioning

confidence: 99%

Mycobacterium tuberculosisComplex Lineage 3 as Causative Agent of Pulmonary Tuberculosis, Eastern Sudan1

Shuaib¹,

Khalil²,

Wieler³

et al. 2020

Emerg. Infect. Dis.

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T uberculosis (TB) remains a major global health problem; 10 million new cases were reported in 2018 (1). In Sudan, the estimated national TB incidence in 2018 was 71/100,000 persons; a total of 20,638 cases were reported (1). However, the TB burden is by no means homogeneous across the country. For instance, in eastern Sudan, TB notifications reached 275/100,000 persons in 2012 (2,3). Prevalence of multidrug-resistant TB (MDR TB) (i.e., resistant to isoniazid and rifampin) was estimated at 2.9% in new and 13% in retreatment cases; however, studies have reported MDR TB rates of 6%-22% (1,4-10). Ongoing transmission is one of the key challenges for TB control programs, especially in countries with a high TB burden (1,11). In recent years, molecular techniques have been increasingly used to clarify and trace transmission of Mycobacterium tuberculosis complex (MTBC) strains and to direct and guide targeted TB control actions (12,13). However, availability of molecular techniques is limited in many countries in Africa with a high TB burden (11). In Sudan, drug-resistant TB often goes undetected, resulting in inadequate treatment, illness, death, and ongoing transmission (1,14). Local laboratories have limited access to mycobacterial culture and drug susceptibility testing (DST) or DNA-based techniques (14). Therefore, MDR TB rates might be underestimated in eastern Sudan. In addition, mutations that mediate drug resistance have not been investigated. Taken together, these factors indicate that, although TB is a huge health problem in eastern Sudan, precise data on the phylogeny and transmission dynamics of MTBC strains, as well as on resistance patterns, is sparsely available (2,3,7,8,15). Studies using molecular epidemiologic tools are rare and have used classical genotyping techniques, such as

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Two tales: Worldwide distribution of Central Asian (CAS) versus ancestral East-African Indian (EAI) lineages of Mycobacterium tuberculosis underlines a remarkable cleavage for phylogeographical, epidemiological and demographical characteristics

Cited by 28 publications

References 50 publications

Variation in Mycobacterium tuberculosis population structure in Iran: a systemic review and meta-analysis

Variation in Mycobacterium tuberculosis population structure in Iran: a systemic review and meta-analysis

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

Mycobacterium tuberculosisComplex Lineage 3 as Causative Agent of Pulmonary Tuberculosis, Eastern Sudan1

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