Genetic diversity and molecular epidemiology of multidrug-resistant Mycobacterium tuberculosis in Minas Gerais State, Brazil

Abstract

BackgroundWe aimed to characterize the genetic diversity of drug-resistant Mycobacterium tuberculosis (MTb) clinical isolates and investigate the molecular epidemiology of multidrug-resistant (MDR) tuberculosis from Minas Gerais State, Brazil.MethodsOne hundred and four MTb clinical isolates were assessed by IS6110-RFLP, 24-locus mycobacterial interspersed repetitive units variable-number tandem repeats (MIRU-VNTR), TB-SPRINT (simultaneous spoligotyping and rifampicin-isoniazid drug-resistance mutation analysis) and 3R-SNP-typing (analysis of single-nucleotide polymorphisms in the genes involved in replication, recombination and repair functions).ResultsFifty-seven different IS6110-RFLP patterns were found, among which 50 had unique patterns and 17 were grouped into seven clusters. The discriminatory index (Hunter and Gaston, HGDI) for RFLP was 0.9937. Ninety-nine different MIRU-VNTR patterns were found, 95 of which had unique patterns and nine isolates were grouped into four clusters. The major allelic diversity index in the MIRU-VNTR loci ranged from 0.6568 to 0.7789. The global HGDI for MIRU-VNTR was 0.9991. Thirty-two different spoligotyping profiles were found: 16 unique patterns (n = 16) and 16 clustered profiles (n = 88). The HGDI for spoligotyping was 0.9009. The spoligotyped clinical isolates were phylogenetically classified into Latin-American Mediterranean (66.34 %), T (14.42 %), Haarlem (5.76 %), X (1.92 %), S (1.92 %) and U (unknown profile; 8.65 %). Among the U isolates, 77.8 % were classified further by 3R-SNP-typing as 44.5 % Haarlem and 33.3 % LAM, while the 22.2 % remaining were not classified. Among the 104 clinical isolates, 86 were identified by TB-SPRINT as MDR, 12 were resistant to rifampicin only, one was resistant to isoniazid only, three were susceptible to both drugs, and two were not successfully amplified by PCR. A total of 42, 28 and eight isolates had mutations in rpoB positions 531, 526 and 516, respectively. Correlating the cluster analysis with the patient data did not suggest recent transmission of MDR-TB.ConclusionsAlthough our results do not suggest strong transmission of MDR-TB in Minas Gerais (using a classical 100 % MDR-TB identical isolates cluster definition), use of a smoother cluster definition (>85 % similarity) does not allow us to fully eliminate this possibility; hence, around 20–30 % of the isolates we analyzed might be MDR-TB transmission cases.

Burden of transmitted multidrug resistance in epidemics of tuberculosis: a transmission modelling analysis

“… 31 Worldwide spread of MDR strains of the Beijing lineage has also been observed, and even when sampling is global and avoids bias from local outbreaks, clustering has been observed among 42% to 100% of MDR isolates within any single Beijing clonal complex. 18 Other molecular epidemiologic studies have yielded much lower estimates of MDR clustering, 16 , 17 but genotypic clustering is an imperfect and lower-bound estimate of MDR transmission (especially when sampling coverage is incomplete and study duration is short). This principle is evidenced by the finding that even MDR-TB cases with no history of previous TB treatment – and thus no opportunity to acquire MDR in any way other than through transmission – did not belong to any identified cluster in many studies.…”

“…For example, when individuals are infected with drug-resistant strains and subsequently develop MDR-TB disease in an area where drug susceptibility testing is not routinely performed for new cases, these patients will be initially notified as drug-susceptible, and only after failing initial treatment might they be notified as (previously treated) MDR-TB. Molecular epidemiologic studies have variably found that from <25% 16 , 17 to >80% 18 of MDR-TB clinical isolates are genetically clustered, but incomplete sampling biases these numbers as an estimate of transmitted disease. 19 To understand how current notification data regarding the prevalence of MDR-TB would translate into the estimated proportion of MDR-TB that arises from prior TB treatment versus from MDR transmission, a mechanistic understanding of MDR-TB transmission in the context of TB notification practices is required.…”

Characterization of Mycobacterium tuberculosis isolates from Hebei, China: genotypes and drug susceptibility phenotypes

“…where N is the total number of strains in the typing method, s is the total number of different patterns discriminated by that method, and n j is the number of strains belonging to the j th pattern. The HGDI value was calculated using the discriminatory power calculator available at http://www.hpa-bioinfotools.org.uk/cgi-bin/DICI/DICI.pl [ 18 ]. The clustering rate was defined as (n c −c)/N, where n c is the total number of clustered strains, c is the number of clusters and N is the total number of strains.…”

A Genomic Signature for Genotyping Mycobacterium tuberculosis

“…In this study, we proposed a new set of 10 SNPs using a total of 249 MTB genomes selected first by the inclusion/ exclusion (IE) criteria using spoligotyping and phylogenies, followed by the selection of the nonsynonymous SNPs present in the most conserved COG (cluster of orthologous groups) of each genotype (Beijing, CAS, EAI, Haarlem, LAM, X, Ural, T, AFRI1 and AFRI2) of MTB. The addition of spoligotyping provides higher informative results on the phylogeographic distribution of MTB׳s genotypic diversity [ 22 ].…”