Insight into genetic diversity of Mycobacterium tuberculosis in Kandy, Sri Lanka reveals predominance of the Euro-American lineage. (October 2019)

• Record Type: Journal Article
• Authors: Mendis, Charitha; Thevanesam, Vasanthi; Kumara, Athula; Wickramasinghe, Susiji; Madegedara, Dushantha; Gamage, Chandika; Gordon, Stephen V.; Suzuki, Yasuhiko; Ratnatunga, Champa; Nakajima, Chie
• Is Part Of: International journal of infectious diseases. Volume 87(2019)
• Page Start: 84
• Page End: 91
• Publication Date: 2019-10
• Subjects: Mycobacterium tuberculosis -- Spoligotype -- MIRU-VNTR -- Lineage 4 (Euro-American lineage) -- Sri Lanka; Communicable diseases -- Periodicals; Communicable Diseases -- Periodicals; Communicable diseases; Periodicals; Electronic journals; 616.9
• DOI: 10.1016/j.ijid.2019.07.001
• Languages: English
• ISSNs: 1201-9712

Abstract

Highlights: The predominant Mycobacterium tuberculosis lineage circulating in Kandy, Sri Lanka was found to be lineage 4, the Euro-American lineage. SIT1 (Beijing, lineage 2) was the most prevalent spoligotype international type (SIT) found. Two out of 19 Beijing/SIT1 isolates from new tuberculosis patients had the pre-multidrug resistance katG G944C mutation (Ser315Thr). Locally evolved lineage 4/ SIT3234 showed clonal expansion and has the potential to be a growing threat to public health. Abstract: Objective: Sri Lanka is a country where the molecular epidemiology of Mycobacterium tuberculosis (MTB) is poorly explored. Therefore, this study was performed to identify circulating lineages/sub-lineages of MTB and their transmission patterns. Methods: DNA was extracted from 89 isolates of MTB collected during 2012 and 2013 from new pulmonary tuberculosis patients in Kandy, Sri Lanka and analyzed by spoligotyping, large sequence polymorphism (LSP), mycobacterial interspersed repetitive unit–variable number tandem repeat (MIRU-VNTR) typing, and drug resistance-associated gene sequencing. Results: The predominant lineage was lineage 4 (Euro-American, 45.9%), followed by lineage 1 (Indo-Oceanic, 29.4%), lineage 2 (East-Asian, 23.5%), and lineage 3 (Central-Asian, 1.2%). Among 26 spoligotype patterns, eight were undesignated or new types and seven of these belonged to lineage 4. Undesignated lineage 4/SIT124 ( n = 2/8) and SIT3234 ( n = 8/8) clustered together based on 24-locus MIRU-VNTR typing. The dominant sub-lineage was Beijing/SIT1 ( n = 19), with the isoniazid resistance katG G944C mutation (Ser315Thr) detected in two of them. Conclusions: The population structure of MTB in Kandy, Sri Lanka was different from that in the South Asian region. The clonal expansion of locally evolved lineage 4/SIT3234 and detection of the pre-multidrug resistant Beijing isolates from new tuberculosis patients is alarming and will require continuous monitoring.