title: 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 (SIT3396) or after a match with an orphan in the database (SIT3397, SIT3398, SIT3399 and SIT3400). 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.
authors.affiliation: Nnamdi Azikiwe University Teaching Hospital, Nnewi, Anambra State, Nigeria.
authors.forename: Gertrude N
authors.initials: GN
authors.lastname: Uzoewulu
authors.affiliation: Zankli Medical Centre, Abuja, Nigeria.
authors.forename: Lovett
authors.initials: L
authors.lastname: Lawson
authors.affiliation: University of Benin, Edo State, Nigeria.
authors.forename: Ibeh S
authors.initials: IS
authors.lastname: Nnanna
authors.affiliation: World Health Organization TB Supranational Reference Laboratory, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France. Electronic address: nrastogi@pasteur-guadeloupe.fr.
authors.forename: Nalin
authors.initials: N
authors.lastname: Rastogi
authors.affiliation: University of Hertfordshire, Hatfield, England, UK. Electronic address: m.goyal@herts.ac.uk.
authors.forename: Madhu
authors.initials: M
authors.lastname: Goyal
mesh_terms: D000328:Adult; D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008297:Male; D018598:Minisatellite Repeats; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000302:isolation & purification*; D009549:Nigeria / Q000453:epidemiology; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D014397:Tuberculosis, Pulmonary / Q000453:epidemiology / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial
keywords: Exact tandem repeat; Mycobacterium tuberculosis; Nigeria; Spoligotyping; Tuberculosis; Variable number of tandem repeats