The predominance of Ethiopian specificMycobacterium tuberculosisfamilies and minimal contribution ofMycobacterium bovisin tuberculous lymphadenitis patients in Southwest Ethiopia

Abstract

Background:Ethiopia has an extremely high rate of extrapulmonary tuberculosis, dominated by tuberculous lymphadenitis (TBLN). However, little is known about Mycobacterium tuberculosiscomplex (MTBc) lineages responsible for TBLN in Southwest Ethiopia. Methods:A total of 304 MTBc isolates from TBLN patients in Southwest Ethiopia were genotyped primarily by spoligotyping. Isolates of selected spoligotypes were further analyzed by 15-loci mycobacterial interspersed repetitive unit–variable number tandem repeat (MIRU-VNTR) (n = 167) and qPCR-based single nucleotide polymorphism (n = 38). Isolates were classified into main phylogenetic lineages and families by using the reference strain collections and identification tools available atMIRU-VNTRplusdata base. Resistance to rifampicin was determined by Xpert MTB/RIF. Results:The majority of isolates (248; 81.6%) belonged to the Euro-American lineage (Lineage 4), with the illdefined T and Haarlem as largest families comprising 116 (38.2%) and 43 (14.1%) isolates respectively. Of the T family, 108 isolates were classified as being part of the newly described Ethiopian families, namely Ethiopia_2 (n = 44), Ethiopia_3 (n = 34) and Ethiopia_H37Rv-like (n = 30). Other sub-lineages included URAL (n = 18), S (n = 17), Uganda I (n = 16), LAM (n = 13), X (n = 5), TUR (n = 5), Uganda II (n = 4) and unknown (n = 19). Lineage 3 (Delhi/CAS) was the second most common lineage comprising 44 (14.5%) isolates. Interestingly, six isolates (2%) were belonged to Lineage 7, unique to Ethiopia. Lineage 1 (East-African Indian) and Lineage 2 (Beijing) were represented by 3 and 1 isolates respectively. M. boviswas identified in only two (0.7%) TBLN cases. The cluster rate was highest for Ethiopia_3 isolates showing clonal similarity with isolates from North Ethiopia. Lineage 3 was significantly associated with rifampicin resistance. Conclusions:In TBLN in Southwest Ethiopia, the recently described Ethiopia specific Lineage 4 families were predominant, followed by Lineage 3 and Lineage 4-Haarlem. The contribution ofM. bovisin TBLN infection is minimal.