High Diversity ofMycobacterium tuberculosisGenotypes in South Africa and Preponderance of Mixed Infections among ST53 Isolates

Abstract

The reemergence of tuberculosis (TB) has become a major health problem worldwide, especially in Asia and Africa. Failure to combat this disease due to nonadherence or inappropriate drug regimens has selected for the emergence of multiple-drug-resistant (MDR) TB. The development of new molecular genotyping techniques has revealed the presence of mixed Mycobacterium tuberculosis infections, which may accelerate the emergence of drug-resistant strains. There are some studies describing the local distribution of circulating strains in South Africa, but to date, reports describing the frequency and distribution of M. tuberculosis genotypes, and specifically MDR genotypes, across the different provinces are limited. Thus, 252 isolates (of which 109 were MDR) from eight of the nine provinces of South Africa were analyzed by spoligotyping. Spoligotyping showed 10 different lineages, and ST53 (11.1%) and ST1 (10.3%) were the most frequent genotypes. Of the 75 different spoligopatterns observed, 20 (7.9%) were previously unreported. Analysis of the mycobacterial interspersed repetitive units of variable-number tandem repeats of the ST53 and ST1 isolates revealed that ϳ54% of the ST53 isolates were of mixed M. tuberculosis subpopulations. Drug resistance (defined as resistance to at least isoniazid and/or rifampin) could only be linked to a history of previous anti-TB treatment (adjusted odds ratio, 4.0; 95% confidence interval, 2.27 to 7.10; P ‫؍‬ <0.0001). This study describes a high diversity of circulating genotypes in South Africa in addition to a high frequency of mixed M. tuberculosis subpopulations among the ST53 isolates. MDR TB in South Africa could not be attributed to the spread of any single lineage.Tuberculosis (TB) is a major cause of illness and death worldwide but especially in Asia and Africa (42). Twenty-two countries designated high TB burden countries account for 80% of all new cases worldwide (42). As of 2008, South Africa was ranked fourth among these, with an incidence rate of 940 cases per 100,000 persons (42) (up from 536 in 2005 [41]). Due to nonadherence to drug regimens or the use of inappropriate drug regimens, the TB epidemic has been largely exacerbated by the emergence of multidrug-resistant (MDR) TB (7).Traditionally, it has been assumed that TB is caused by an infection with a single strain and that recurrences are the result of reactivation of the strain causing the first episode (6, 24, 39). However, it has recently been shown that patients, both human immunodeficiency virus (HIV) positive and HIV negative, in high-incidence settings may have more than one strain in the same sputum sample (24, 39) and that mixed infections may cause complications in the treatment of the disease if a patient is infected with both a sensitive and a resistant Mycobacterium tuberculosis isolate (39). Extensively drug-resistant (XDR) TB strains (defined as resistant to isoniazid [INH] and rifampin [RIF], in addition to any fluoroquinolones and at least one injectable anti-TB drug) (5) were first reported in...

Evaluation of Two Molecular Assays for Rapid Detection of Mycobacterium tuberculosis Resistance to Fluoroquinolones in High-Tuberculosis and -Multidrug-Resistance Settings

“…All of these strains were isolated from retreatment patients and could therefore be explained by a mixed infection with sensitive and resistant strains. Mixed infections are seen in areas with high rates of TB and MDRTB (11,41). However, double alleles were identified by VNTR typing in one of three mixed strains only.…”

Molecular Detection of Mixed Infections of Mycobacterium tuberculosis Strains in Sputum Samples from Patients in Karonga District, Malawi

“…However, it is possible that, had we the means to investigate all samples in this study by also using MIRU-VNTR typing, we may have identified more mixed infections. Of the 3 most commonly used techniques for genotyping M. tuberculosis isolates (IS6110-RFLP, spoligotyping, and MIRU-VNTR typing), it is MIRU-VNTR typing that has the greatest capacity to detect the presence of multiple strains, as has been previously demonstrated (11,(22)(23)(24).…”

“…This belief was first challenged when phage typing identified the presence of more than one M. tuberculosis strain in isolates obtained from a single patient (2,17). With the development of DNA fingerprinting (28) and other PCR-based genotyping methods (15,27) to differentiate M. tuberculosis strains, the presence of multiple strains within a single patient has been demonstrated during routine genotyping studies (5,19,20,24,33). The results from these and further studies designed to specifically examine mixed infections (1,10,20,22,23,29,32) have shown that they occur in different geographical settings among both HIV-negative and HIV-positive tuberculosis (TB) patients.…”

Systematic Survey of Clonal Complexity in Tuberculosis at a Populational Level and Detailed Characterization of the Isolates Involved

“…However, some of these studies examine anecdotal cases (2) and others analyze this phenomenon only in specific M. tuberculosis lineages (35) or specific phenotypes (34). Those which follow population-based designs to determine the proportion of clonally complex TB cases are performed mainly in epidemiological contexts with a markedly high incidence of TB (8,10,29,30,35) and/or where the possibility of overexposure is more likely (28).…”

“…Several clonally complex phenomena have been observed, including mixed infections with more than one strain (29,30,35), simultaneous presence of clonal variants (microevolution phenomena) (1, 2), or even different distributions of strains/clonal variants infecting independent anatomical sites in the same patient (6,15).…”