Abstract
BackgroundTo understand the population dynamics and propose more effective preventive strategies, defining the population structure of the circulating Mycobacterium tuberculosis strains is important.MethodsA total of 177 M. tuberculosis complex isolates from pulmonary tuberculosis (TB) cases in southwest Ethiopia were genotyped by spoligotyping. Of the strains included in this study, 126 were pan‐susceptible strains while the remaining 51 isolates were resistant to one or more first‐line anti‐TB drugs. The genotyping results were compared to the international spoligotyping (SITVIT) database of the Pasteur Institute of Guadeloupe and the newly revised publicly available international multi‐marker database (SITVITWEB/SPOLDB4). An online tool Run TB‐Lineage was also used to predict the major lineages using a conformal Bayesian network analysis.ResultsThe spoligotyping of the 177 isolates resulted in 69 different spoligotype patterns of which 127 (71.8%) were clustered into 19 spoligoclusters (with clustering rate of 61.02%). Each cluster contains 2–29 isolates. Of the isolates with corresponding SIT in SITVIT/SDB4, the predominant strains identified were SIT 37 of the T3 subfamily with 29 isolates followed by SIT 53 of the T1 subfamily with 20 isolates. SIT 777 of the H4 subfamily and SIT 25 of the CAS1_DELHI subfamily each consisting of six isolates were identified. Eighty spoligotype patterns were orphan as they were not recorded in the SITVIT2/SPDB4 database. Further classification of the isolates on the basis of major lineages showed that 82.5% and 14.1% of the isolates belonged to Euro‐American and East African Indian lineages, respectively, while 2.8% of the isolates belonged to Mycobacterium africanum and 0.6% to Indo‐Oceanic.ConclusionThe ill‐defined T and H clades were predominant around Jimma. The substantial number of orphans recorded in the study area warrants for additional studies with genotyping methods with better resolution and covering whole areas of southwest Ethiopia.
Highlights
To understand the population dynamics and propose more effective preventive strategies, defining the population structure of the circulating Mycobacterium tuberculosis strains is important
TA B L E 2 Description of 24 shared types (SITs; n = 97 isolates) which have already been registered in the SITVIT2 or SpolDB4 database and corresponding spoligotyping defined lineages/sub‐lineages isolated from the Jimma Zone, southwest Ethiopia
The population structure of M. tuberculosis iso‐ lates was investigated in adults around Jimma, southwest Ethiopia
Summary
Tuberculosis (TB) remains a public health challenge globally in spite of the availability of vaccine and drugs for treatment. The country is one of the high burden countries for the multidrug‐resis‐ tant tuberculosis (MDR‐TB) and HIV (World Health Organization, 2017). According to WHO 2011 report, drug‐resistant TB was 1.6% among new cases and 12% among retreatment cases (World Health Organization, 2011). In 2017 report of the WHO, the rate increased to 2.7% for new cases and 14% for retreatment cases (World Health Organization, 2017). The objective of this study was to investigate the population structure of the mycobacterial isolates collected during November 2010 to June 2012 from Jimma area. One hundred and sev‐ enty‐seven (177) isolates confirmed as M. tuberculosis using para nitro benzoic acid inhibition test, and RD9 typing was further analyzed by spoligotyping according to the standardized proto‐ col (Kamerbeek et al, 1997) and following manufacturer’s in‐ structions (reagents from Ocimum Biosolution, custom Master Mix from ABgene). The 43‐digit binary code was converted to 15‐digit octal code (base 8, having the digits 0–7)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have