Molecular epidemiology of M. tuberculosis in Ethiopia: A systematic review and meta-analysis

Daniel Mekonnen; Awoke Derbie; Asmamaw Chanie; Abebe Shumet; Fantahun Biadglegne; Yonas Kassahun; Kidist Bobosha; Adane Mihret; Liya Wassie; Abaineh Munshea; Endalkachew Nibret; Solomon Abebe Yimer; Tone Tønjum; Abraham Aseffa

doi:10.1016/j.tube.2019.101858

Molecular epidemiology of M. tuberculosis in Ethiopia: A systematic review and meta-analysis

Tuberculosis (Edinb). 2019 Sep:118:101858. doi: 10.1016/j.tube.2019.101858. Epub 2019 Aug 7.

Authors

Affiliations

¹ Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia; Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia. Electronic address: nigusdaniel@gmail.com.
² Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia; The Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa, Ethiopia. Electronic address: awelove2000@gmail.com.
³ Institute of Land Administration, Bahir Dar University, Bahir Dar, Ethiopia. Electronic address: chanieasmamaw@yahoo.com.
⁴ Felege Hiwot Referral Hospital, Bahir Dar, Ethiopia. Electronic address: abeshumete@gmail.com.
⁵ Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia. Electronic address: fantahun.degeneh@gmail.com.
⁶ Armauer Hansen Research Institute, Addis Ababa, Ethiopia. Electronic address: yonaskass@gmail.com.
⁷ Armauer Hansen Research Institute, Addis Ababa, Ethiopia. Electronic address: kbobosha@gmail.com.
⁸ Armauer Hansen Research Institute, Addis Ababa, Ethiopia; Department of Medical Microbiology, Immunology and Parasitology, College of Medicine and Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia. Electronic address: adane_mihret@yahoo.com.
⁹ Armauer Hansen Research Institute, Addis Ababa, Ethiopia. Electronic address: liya.wassie@ahri.gov.et.
¹⁰ Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia; Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia. Electronic address: abitew2003@yahoo.com.
¹¹ Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia; Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia. Electronic address: endtg2002@yahoo.com.
¹² Department of Microbiology, University of Oslo, PO Box 4950, Nydalen, NO-0424, Oslo, Norway; Coalition for Epidemic Preparedness Innovations, CEPI, P.O. Box 123, Torshov 0412, Oslo, Norway. Electronic address: a.y.solomon@medisin.uio.no.
¹³ Department of Microbiology, University of Oslo, PO Box 4950, Nydalen, NO-0424, Oslo, Norway. Electronic address: tone.tonjum@medisin.uio.no.
¹⁴ Armauer Hansen Research Institute, Addis Ababa, Ethiopia. Electronic address: aseffaa@gmail.com.

Abstract

The molecular epidemiology of Mycobacterium tuberculosis (M. tuberculosis, Mtb) is poorly documented in Ethiopia. The data that exists has not yet been collected in an overview metadata form. Thus, this review summarizes available literature on the genomic diversity, geospatial distribution and transmission patterns of Mtb lineages (L) and sublineages in Ethiopia. Spoligotyping and Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) based articles were identified from MEDLINE via PubMed and Scopus. The last date of article search was done on 12th February 2019. Articles were selected following the PRISMA flow diagram. The proportion of (sub)lineages was summarized at national level and further disaggregated by region. Clustering and recent transmission index (RTI) were determined using metan command and random effect meta-analysis model. The meta-analysis was computed using Stata 14 (Stata Corp. College Station, TX, USA). Among 4371 clinical isolates, 99.5% were Mtb and 0.5% were M. bovis. Proportionally, L4, L3, L1 and L7 made up 62.3%, 21.7%, 7.9% and 3.4% of the total isolates, respectively. Among sublineages, L4.2. ETH/SIT149, L4.10/SIT53, L3. ETH1/SIT25 and L4.6/SIT37 were the leading clustered isolates accounting for 14.4%, 9.7%, 7.2% and 5.5%, respectively. Based on MIRU-VNTR, the rate of clustering was 41% and the secondary case rate from a single source case was estimated at 29%. Clustering and recent transmission index was higher in eastern and southwestern Ethiopia compared with the northwestern part of the country. High level of genetic diversity with a high rate of clustering was noted which collectively mirrored the phenomena of micro-epidemics and super-spreading. The largest set of clustered strains deserves special attention and further characterization using whole genome sequencing (WGS) to better understand the evolution, genomic diversity and transmission dynamics of Mtb.

Keywords: Ethiopia; M. tuberculosis; Molecular epidemiology; Review.

Publication types

Meta-Analysis
Systematic Review

MeSH terms

Bacterial Typing Techniques / methods
Bias
Cluster Analysis
Ethiopia / epidemiology
Genetic Variation
Humans
Minisatellite Repeats / genetics
Mycobacterium tuberculosis / classification
Mycobacterium tuberculosis / genetics*
Phylogeny
Tuberculosis / epidemiology*
Tuberculosis / microbiology*
Tuberculosis / transmission

Grants and funding

D43 TW009127/TW/FIC NIH HHS/United States