Draft Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Sputum of Kazakh Patients

Kairov, Ulykbek; Kozhamkulov, Ulan; Molkenov, Askhat; Rakhimova, Saule; Askapuli, Ayken; Zhabagin, Maxat; Akhmetova, A.; Yerezhepov, Dauren; Abilova, Zhannur; Abilmazhinova, Aliya; Bismilda, Venera; Chingisova, L. T.; Zhumadilov, Zhaxybay; Akilzhanova, Ainur

doi:10.1128/genomea.00466-15

Cited by 8 publications

(6 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous studies in Kazakhstan were reported about the mutations associated with drug resistance in genes of M. tuberculosis . For example, some research work conducted in Kazakhstan was carried out investigating the mutations in genes of M. tuberculosis responsible for drug resistance to various anti-TB drugs, especially for rifampicin and isoniazid [ 17 , 18 , 19 ], molecular genotyping of M. tuberculosis [ 20 , 21 , 22 , 23 ], and whole-genome sequencing [ 24 , 25 , 26 , 27 ]. Hillemann et al [ 17 ] in their study evaluated the possible associations of specific mutations leading to resistance to rifampicin and isoniazid with isolates of the Beijing genotype and isolates of other M. tuberculosis genotypes (non-Beijing strains) from Kazakhstan in the early 2000s.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…Only some publications relate to preliminary data and reported several genome sequences of DR (including one XDR and several MDR) clinical isolates of M. tuberculosis isolated in Kazakhstan performed by using a next-generation sequencing platform [ 24 , 25 , 26 , 27 , 28 , 29 ]. Drafts of complete genome sequences of two Kazakhstani isolates [ 24 ] and one isolate with extensive drug resistance [ 26 , 27 ] were published by our group. Drug resistance mutations in the genome were reported as a part of the study of the mechanisms of Reversion of Antibiotic Resistance in MDR Mycobacterium tuberculosis induced by a Nanomolecular Iodine-Containing Complex FS-1 [ 25 ].…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Whole-Genome Sequence-Based Characterization of Pre-XDR M. tuberculosis Clinical Isolates Collected in Kazakhstan

et al. 2023

Self Cite

View full text Add to dashboard Cite

Background: Kazakhstan has a high burden of multidrug-resistant tuberculosis in the Central Asian region. This study aimed to perform genomic characterization of Mycobacterium tuberculosis strains obtained from Kazakhstani patients with pre-extensively drug-resistant tuberculosis diagnosed in Kazakhstan. Methods: Whole-genome sequencing was performed on 10 pre-extensively drug-resistant M. tuberculosis strains from different regions of Kazakhstan. All strains had high-confidence resistance mutations according to the resistance grading system previously established by the World Health Organization. The genome analysis was performed using TB-Profiler, Mykrobe, CASTB, and ResFinder. Results: Valuable information for understanding the genetic diversity of tuberculosis in Kazakhstan can also be obtained from whole-genome sequencing. The results from the Phenotypic Drug Susceptibility Testing (DST) of bacterial strains were found to be consistent with the drug resistance information obtained from genomic data that characterized all isolates as pre-XDR. This information can help in developing targeted prevention and control strategies based on the local epidemiology of tuberculosis. Furthermore, the data obtained from whole-genome sequencing can help in tracing the transmission pathways of tuberculosis and facilitating early detection of outbreaks. Conclusions: The results from whole-genome sequencing of tuberculosis clinical samples in Kazakhstan provide important insights into the drug resistance patterns and genetic diversity of tuberculosis in the country. These results can contribute to the improvement of tuberculosis control and management programs in Kazakhstan.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Whole-Genome Sequence-Based Characterization of Pre-XDR M. tuberculosis Clinical Isolates Collected in Kazakhstan

et al. 2023

Self Cite

View full text Add to dashboard Cite

show abstract

“…Several studies on biological diversity and identification of mutations in specific genomic regions encoding drug resistance were performed in Kazakhstan ( Kozhamkulov et al, 2011 ; Ibrayeva et al, 2014 ; Akhmetova et al, 2015 ; Skiba et al, 2015 ). Only a few publications related to whole-genome sequencing of clinical isolates performed by next-generation sequencing platforms have briefly reported draft genome sequences of Mtb strains circulating in Kazakhstan ( Ilin et al, 2015 ; Kairov et al, 2015 ; Daniyarov et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Genomic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Strains From Patients in Kazakhstan

et al. 2021

Self Cite

View full text Add to dashboard Cite

Tuberculosis (TB) is an infectious disease that remains an essential public health problem in many countries. Despite decreasing numbers of new cases worldwide, the incidence of antibiotic-resistant forms (multidrug resistant and extensively drug-resistant) of TB is increasing. Next-generation sequencing technologies provide a high-throughput approach to identify known and novel potential genetic variants that are associated with drug resistance in Mycobacterium tuberculosis (Mtb). There are limited reports and data related to whole-genome characteristics of drug-resistant Mtb strains circulating in Kazakhstan. Here, we report whole-genome sequencing and analysis results of eight multidrug-resistant strains collected from TB patients in Kazakhstan. Genotyping and validation of all strains by MIRU-VNTR and spoligotyping methodologies revealed that these strains belong to the Beijing family. The spectrum of specific and potentially novel genomic variants (single-nucleotide polymorphisms, insertions, and deletions) related to drug resistance was identified and annotated. ResFinder, CARD, and CASTB antibiotic resistance databases were used for the characterization of genetic variants in genes associated with drug resistance. Our results provide reference data and genomic profiles of multidrug-resistant isolates for further comparative studies and investigations of genetic patterns in drug-resistant Mtb strains.

show abstract

“…It is extremely important to examine susceptible and resistant strains with different mutations in genes encoding drug metabolism among M.tuberculosis isolates. Previous investigations of M.tuberculosis isolates circulated in Kazakhstan have been performed using Sanger sequencing, spoligotyping, MIRU-VNTR typing and NGS approaches [2] , [3] , [4] . Here, we report the whole genome sequence and analysis of XDR-TB strain, performed by next-generation sequencing platform.…”

Section: Data Descriptionmentioning

confidence: 99%

Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan

et al. 2020

Self Cite

View full text Add to dashboard Cite

Drug-resistant tuberculosis (TB) is a major public health problem. Clinical Mycobacterium tuberculosis (MTB) isolate with Extensively drug-resistant tuberculosis (MTB-XDR) profile was subjected to whole-genome sequencing using a next-generation sequencing platform (NGS) Roche 454 GS FLX+ followed by bioinformatics sequence analysis. Quality of read was checked by FastQC, paired-end reads were trimmed using Trimmomatic. De novo genome assembly was conducted using Velvet v.1.2.10. The assembled genome of XDR-TB-1599 strain was functionally annotated using the PATRIC platform. Analysis of de novo assembled genome was performed using ResFinder, CARD, CASTB and TB-Profiler tools. MIRU_VNTR genotyping on 12 loci and spoligotyping have been performed for XDR-TB-1599 isolate. M. tuberculosis XDR-TB-1599 strain yielded an average read depth of 21-fold with overall 4 199 325 bp. The assembled genome contains 5528 protein-coding genes, including key drug resistance and virulence-associated genes and GC content of 65.4%. We identified that all proteins encoded by this strain contain conserved domains associated with the first-line anti-tuberculosis drugs such as rifampicin, isoniazid, streptomycin and ethionamide. TB-Profiler had higher average concordance results with phenotypic DST (drug susceptibility testing) in comparison with ResFinder, CARD, CASTB profiling to first-line (75% vs 50%) and second-line (25% vs 0%) of anti-TB drugs, correspondingly. To our knowledge, this is the first report of a highly annotated and characterized whole-genome sequence and de novo assembled XDR-TB M.tuberculosis strain isolated from a sputum of new TB case-patient from Kazakhstan performed on Roche 454 GS FLX+ platform. This report highlights an important role of whole-genome sequencing technology and analysis as an advanced approach for drug-resistance investigations of circulated TB isolates.

show abstract

Draft Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Sputum of Kazakh Patients

Abstract: Here, we report the draft genome sequences of two clinical isolates of Mycobacterium tuberculosis (MTB-476 and MTB-489) isolated from sputum of Kazakh patients.

Cited by 8 publications

References 9 publications

Whole-Genome Sequence-Based Characterization of Pre-XDR M. tuberculosis Clinical Isolates Collected in Kazakhstan

Whole-Genome Sequence-Based Characterization of Pre-XDR M. tuberculosis Clinical Isolates Collected in Kazakhstan

Genomic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Strains From Patients in Kazakhstan

Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan

Contact Info

Product

Resources

About