Characterization of extensively drug-resistant Mycobacterium tuberculosis isolates circulating in Siberia

Abstract

BackgroundThe spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis compromises effective control of tuberculosis (TB) in Siberia. Early identification of drug-resistant isolates is, therefore, crucial for effective treatment of this disease. The aim of this study was to conduct drug susceptibility testing and identify mutations in drug resistance genes in clinical isolates of M. tuberculosis from some TB patients presenting for treatment in Siberia.MethodsThirty randomly selected clinical isolates of M. tuberculosis were obtained from the Novosibirsk Research Institute of Tuberculosis, Russia. Isolates were screened for drug resistance and characterized by variable number of tandem repeats (VNTR)-typing using 15 standard and four additional loci. Deligotyping on multiple large sequences was performed using 10 loci.ResultsTwenty-nine of the isolates were assigned XDR status. Twenty-eight isolates belonged to the M. tuberculosis Beijing family, from which 11 isolates were considered the M11 type (39%), two the M2 type (7%), and one the M33 type (3%). Seventeen isolates (60.7%) from this family exhibited unique genetic patterns. The remaining two isolates belonged to the Latino-American Mediterranean family. Gene sequences (rpoB, katG, rrs, rpsL, tlyA, gidB, gyrA, gyrB) were analyzed to identify mutations that confer resistance to rifampicin, isoniazid, amikacin, kanamycin, capreomycin, and ofloxacin. The most common mutations among the XDR isolates were S531L in RpoB, S315T in KatG, various codon 94 mutations in gyrA, A90V in GyrA, K43R in RpsL, and 1401 A → G in rrs; these confer resistance to rifampicin, isoniazid, ofloxacin, streptomycin and kanamycin/capreomycin, respectively. There was high congruence between the two typing methods (VNTR typing and deligotyping) and RD105, RD149, RD152, RD181, and RD207 regions of difference were absent from the 28 Beijing family isolates.ConclusionsDeligotyping can be used for rapid and reliable screening of M. tuberculosis isolates, followed by more in-depth genotyping. Identification of Beijing family isolates with extensive drug resistance confirms that such strains have epidemiological importance in Siberia. Rapid detection of mutations that lead to drug resistance should facilitate selection of effective drug therapies, and the development of early prevention strategies to combat this infection.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2334-14-478) contains supplementary material, which is available to authorized users.

Multi- and Extensively Drug Resistant Mycobacterium tuberculosis in South Africa: a Molecular Analysis of Historical Isolates

“…These results are in line with other studies in South Africa and other countries that reported the same trends (12). Mutation Ser531Leu, which is common in XDR-TB isolates (13), was also identified in two of the three XDR-TB isolates included in this study. Another mutation described as associated with XDR-TB and pre-XDR-TB (mutation 526), was seen in 24 MDR-TB isolates in our study, but not in the XDR-TB or pre-XDR-TB isolates.…”

Characterization of Mutations Conferring Resistance to Rifampin in Mycobacterium tuberculosis Clinical Strains

“…This type of mutation is particularly expected in strains with MDR and extensively drug-resistant (XDR) phenotypes, in which the accumulation of resistance-associated mutations would normally be detrimental to the survival of the bacilli. One observation confirming this is the exceptionally high proportion of the rpoB Ser450Leu mutation among XDR strains (39)(40)(41).…”

“…For all strains resistant to RMP (growth at a critical concentration of 40 mg/liter), the MICs of RMP were determined. This was done in duplicate, in L-J medium containing incremental concentrations of the drug (40,100,200,400, and 800 mg/liter). The MIC was defined as the lowest concentration of RMP that inhibited more than 99% of the bacterial growth compared to a drug-free control.…”

Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster

“…Among the 57 proteins that were not detectable in the proteomes of Beijing B0/W148 strains but present in the proteome of H37Rv, 33 carried genetic mutations compared to the H37Rv genome. Among these, six genes (Rv0072 (part of RD105), Rv1576c and Rv1586c (part of RD149), Rv1762c (part of RD152), Rv2263 (part of RD181) and Rv2818c (part of RD207)) mapped to chromosome regions showing differences between the two groups of strains 20 . The absence of two proteins from the Beijing B0/W148 group can be explained by an insertion (Rv0888: 987586 insGG) and a deletion (Rv1997: 2241032 delG) in the coding regions of their respective genes, which both lead to sequence changes causing protein coding frameshifts.…”