Origin and Global Expansion of Mycobacterium tuberculosis Complex Lineage 3

Shuaib, Yassir Adam; Utpatel, Christian; Köhl, Thomas; Barilar, Ivan; Diricks, Margo; Ashraf, Noman; Wieler, Lothar H.; Kerubo, Glennah; Mesfin, Eyob Abera; Diallo, Awa Ba; Al‐Hajoj, Sahal; Ndung’u, P. T.; Fitzgibbon, Margaret; Vaziri, Farzam; Sintchenko, Vitali; Martínez, Elena; Viegas, Sofía; Zhou, Yang; Azmy, Aya; Al-Amry, Khaled; Godreuil, Sylvain; Varma-Basil, Mandira; Narang, Asmita; Ali, Solomon; Beckert, Patrick; Dreyer, Viola; Kabwe, Mwila; Bates, Matthew; Höelscher, Michael; Rachow, Andrea; Gori, Andrea; Tekwu, Emmanuel Mouafo; Sidze, Larissa Kamgue; Jean-Paul, Assam A.; Beng, Véronique Penlap; Ntoumi, Francine; Frank, Matthias; Diallo, Astou Coly Niassy; Mboup, Souleymane; Tessema, Belay; Beyene, Dereje; Khan, Sadiq Noor; Diel, Roland; Supply, Philip; Maurer, Florian P.; Hoffmann, Harald; Niemann, Stefan; Merker, Matthias

doi:10.3390/genes13060990

Cited by 18 publications

(17 citation statements)

References 47 publications

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“…Among the other lineages identified, the East African Indian L3 is known to have significant prevalence along the eastern coast of Africa, South India, and Southeast Asia [13]. The Beijing/East Asian lineage L2 has been recognised as a major driver behind the spread of MDR tuberculosis in the Eurasia region [14]. Additionally, the Delhi/Central Asia lineage was observed in the Middle East and Central Asia, with a higher occurrence in India [15].…”

Section: Discussionmentioning

confidence: 99%

EmergingMycobacterium bovisin Lebanon: a snapshot based on whole-genome sequencing

El Jouaid,

Sobh,

Araj

et al. 2024

Preprint

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Background. Tuberculosis is a pressing public health issue in Lebanon, a country of approximately five million people, including around 1.5 million refugees from Palestine and Syria. Prior research has revealed uncontrolled animal sources of Mycobacterium bovis, emphasizing the necessity for a comprehensive approach to combat tuberculosis in the region. Methods. 48 clinical Mycobacterium tuberculosis complex isolates were identified through whole genome sequence. Also, 43 animal fecal samples were collected from various farms across Lebanon to investigate the presence of the M. tuberculosis complex using CRISPR-csm4 PCR. Results. Genomic analysis revealed that 39/48 (81.25%) of isolates were M. tuberculosis and 9/48 (18.75%) were M. bovis. M. tuberculosis was distributed over four lineages, Indo-Oceanic L1 (n = 3/39)(7.6%), East-Asian L2 (n = 1/39)(2.5%), East-African Indian L3 (n = 5/39)(12.8%) and Euro-American L4 (n = 30/39)(76.9%). Sub-lineage L4.8 (Euro-American (mainly T), comprising 8/39 of the isolates (20.5%) was predominant, followed by sub-lineages L3 (East-African Indian, n = 5/39 isolates)(12.8%), L4.2.2.2 (Euro-American (Ural), n= 4/39 isolates)(10.2%) and L4.6.5 (Euro American, n=4/39 isolates)(10.2%). Nine M. bovis were classified into two clades, designated as unknown2 (n=2/9; 22.2%) and unknown3 (n=7/9; 77.8%). Interestingly, none of the clades or others were detected in the 48 faecal samples using CRISPR standard PCR and qPCR. Conclusions. This study offers insights into human and bovine tuberculosis in Lebanon, emphasizing M. tuberculosis lineages prevalence and M. bovis distribution into two clades, aiding the fight against tuberculosis, especially bovine tuberculosis, and renewing our understanding of tuberculosis dynamics in Lebanon.

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Section: Discussionmentioning

confidence: 99%

EmergingMycobacterium bovisin Lebanon: a snapshot based on whole-genome sequencing

El Jouaid,

Sobh,

Araj

et al. 2024

Preprint

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“…While we tested fastlin with one specific set of MTBC barcode SNPs, new lineage classifications and their associated barcode SNPs have recently been proposed ( Coscolla et al 2021 , Netikul et al 2022 , Shuaib et al 2022 , Shitikov and Bespiatykh 2023 ). To accommodate the evolving landscape of MTBC lineage typing, we made the scripts required to build and test custom barcode files available on GitHub.…”

Section: Discussionmentioning

confidence: 99%

fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing

Derelle,

Lees,

Phelan

et al. 2023

Bioinformatics

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Summary Fastlin is a bioinformatics tool designed for rapid MTBC lineage typing. It utilises an ultra-fast alignment-free approach to detect previously identified barcode single nucleotide polymorphisms (SNPs) associated with specific MTBC lineages. In a comprehensive benchmarking against existing tools, fastlin demonstrated high accuracy and significantly faster running times. Availability and Implementation fastlin is freely available at https://github.com/rderelle/fastlin and can easily be installed using Conda. Supplementary information Supplementary data are available at Bioinformatics online.

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“…Then the sensitivity and specificity indices were calculated. External validity was tested by defining our dataset as a train set and an additional source of data as a test set, including the collection of 225 strains with their 24 MIRU-VNTR loci and genotype assignments provided from the MIRU-VNTRplus reference database (see text footnote 1) and a part of data from two previous studies ( Homolka et al, 2008 ; Shuaib et al, 2022 ; Supplementary Table 2 ). Then the sensitivity and specificity indices were also calculated.…”

Section: Methodsmentioning

confidence: 99%

The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation

et al. 2022

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The 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping has been used as an international standard method for Mycobacterium tuberculosis (Mtb) genotyping. However, different optimized VNTR loci sets for improving the discrimination of specific Mtb genotypes have been proposed. In this regard, we investigated the efficacy of accumulation of the percentage differences (APDs) compared with the least absolute shrinkage and selection operator (LASSO) regression strategy to identify a customized genotype-specific VNTR loci set which provides a resolution comparable to 24-loci MIRU-VNTR in divergent Mtb populations. We utilized Spoligotyping and 24-loci MIRU-VNTR typing for genotyping 306 Mtb isolates. The APD and LASSO regression approaches were used to identify a customized VNTR set in our studied isolates. Besides, the Hunter-Gaston discriminatory index (HGDI), sensitivity, and specificity of each selected loci set were calculated based on both strategies. The selected loci based on LASSO regression compared with APD-based loci showed a better discriminatory power for identifying all studied genotypes except for T genotype, which APD-based loci showed promising discriminative power. Our findings suggested the LASSO regression rather than the APD approach is more effective in the determination of possible discriminative VNTR loci set to precise discrimination of our studied Mtb population and may be beneficial to be used in finding reduced number loci sets in other Mtb genotypes or sublineages. Moreover, we proposed customized genotype-specific MIRU-VNTR loci sets based on the LASSO regression and APD approaches for precise Mtb strains identification. As the proposed VNTR sets offered a comparable discriminatory power to the standard 24 MIRU-VNTR loci set could be promising alternatives to the standard genotyping for using in resource-limited settings.

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Origin and Global Expansion of Mycobacterium tuberculosis Complex Lineage 3

Cited by 18 publications

References 47 publications

EmergingMycobacterium bovisin Lebanon: a snapshot based on whole-genome sequencing

EmergingMycobacterium bovisin Lebanon: a snapshot based on whole-genome sequencing

fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing

The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation

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