Genetic diversity of Mycobacterium tuberculosis complex strains isolated from patients with pulmonary tuberculosis in Anambra State, Nigeria

ABSTRACT

In this study, we analyzed Mycobacterium tuberculosis complex [MTC] genetic diversity in Anambra State, Nigeria based on spoligotyping followed by 5-loci exact tandem repeats [ETRs]. Spoligotyping of 180 MTC strains isolated in 2009-2011 from pulmonary tuberculosis [TB] patients led to a total of 31 distinct patterns. A comparison with the SITVIT2 international database showed that all the 31 patterns could be classified as Shared-types [SITs] in this database; briefly, 26/31 SITs [n = 174 isolates] matched a preexisting shared-type in the database, whereas 5/31 SITs [n = 6 isolates] were newly created due to 2 or more strains belonging to an identical new pattern within this study [S1T3396] or after a match with an orphan in the database [S1T3397, S1T3398, S1T3399 and S1T3400]. A total of 18/31 SITs containing 167 or 92.8% isolates were clustered within this study [2-89 isolates per cluster] while 13/31 SITs contained unique strains. Using VNTR typing, a total of 36 distinct patterns were identified; 27 patterns [n = 157 isolates] matched a pattern already reported in the SITVIT2 database. Combination of both the methods generated 47 combined patterns for the 180 strains 17 belonged to clustered isolates [n = 127 isolates or 70.5%] while 30 corresponded to as many unique strains [note 23 strains could not be typed using 5-loci ETRs]. No correlation was found between the spoligotyping pattern and the HIV status of the patient or drug sensitivity of the strain. This study showed that the LAM10-CAM prototype SIT61 accounted for highest number of isolates [n = 89] in Anambra State, showing its relative contribution to the TB burden in the study