Genomic transmission clusters and circulating lineages of Mycobacterium tuberculosis among refugees residing in refugee camps in Ethiopia

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Meaza, A., Riviere, E., Bonsa, Z., Rennie, V., Gebremicael, G., de Diego-Fuertes, M., Meehan, C.J. ORCID: 0000-0003-0724-8343, Medhin, G., Abebe, G., Ameni, G., Van Rie, A. and Gumi, B., 2023. Genomic transmission clusters and circulating lineages of Mycobacterium tuberculosis among refugees residing in refugee camps in Ethiopia. Infection, Genetics and Evolution, 116: 105530. ISSN 1567-1348

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Official URL: https://doi.org/10.1016/j.meegid.2023.105530

Abstract

Background: Understanding the transmission dynamics of Mycobacterium tuberculosis (Mtb) could benefit the design of tuberculosis (TB) prevention and control strategies for refugee populations. Whole Genome Sequencing (WGS) has not yet been used to document the Mtb transmission dynamics among refugees in Ethiopia. We applied WGS to accurately identify transmission clusters and Mtb lineages among TB cases in refugee camps in Ethiopia.

Method and design: We conducted a cross-sectional study of 610 refugees in refugee camps in Ethiopia presenting with symptoms of TB. WGS data of 67 isolates was analyzed using the Maximum Accessible Genome for Mtb Analysis (MAGMA) pipeline; iTol and FigTree were used to visualize phylogenetic trees, lineages, and the presence of transmission clusters.

Results: Mtb culture-positive refugees originated from South Sudan (52/67, 77.6%), Somalia (9/67, 13.4%). Eritrea (4/67, 6%), and Sudan (2/67, 3%). The majority (52, 77.6%) of the isolates belonged to Mtb lineage (L) 3, and one L9 was identified from a Somalian refugee. The vast majority (82%) of the isolates were pan-susceptible Mtb, and none were multi-drug-resistant (MDR)-TB. Based on the 5-single nucleotide polymorphisms cutoff, we identified eight potential transmission clusters containing 23.9% of the isolates. Contact investigation confirmed epidemiological links with either family or social interaction within the refugee camps or with neighboring refugee camps.

Conclusion: Four lineages (L1, L3, L4, and L9) were identified, with the majority of strains being L3, reflecting the Mtb L3 dominance in South Sudan, where the majority of refugees originated from. Recent transmission among refugees was relatively low (24%), likely due to the short study period. The improved understanding of the Mtb transmission dynamics using WGS in refugee camps could assist in designing effective TB control programs for refugees.

Item Type:

Journal article

Publication Title:

Infection, Genetics and Evolution

Creators:

Meaza, A., Riviere, E., Bonsa, Z., Rennie, V., Gebremicael, G., de Diego-Fuertes, M., Meehan, C.J., Medhin, G., Abebe, G., Ameni, G., Van Rie, A. and Gumi, B.

Publisher:

Elsevier BV

Date:

December 2023

Volume:

116

ISSN:

1567-1348

Identifiers: