Multi-omics approach for understanding the response of Bacteroides fragilis to carbapenems.

Background: The prevalence of Bacteroides fragilis isolates resistant to first-line beta-lactam drugs is increasing, resulting in reduced treatment efficacy. Investigating the bacterial transcriptome and proteome can uncover links between bacterial genes and resistance mechanisms. In this study, we experimentally assessed in vitro the transcriptional and proteomic profiles of B. fragilis exposed to SICs of meropenem, an effective antimicrobial agent, collected from patients with intra-abdominal diseases at Astana City Hospital, Kazakhstan. Methods: B. fragilis was cultured in brain heart infusion broth and sub-cultured every 48 h for 8 days in media with and without meropenem. Total RNA was extracted from the liquid cultures using a commercial RNeasy mini kit, and strand-specific RNA sequencing (RNA-seq) was performed on the DNBSEQ platform. Raw RNA-seq data were retrieved from BioProject No. PRJNA531645 and uploaded to the NCBI Sequence Read Archive (accession no. SRX22081155). Proteins of B. fragilis were extracted and separated using sodium dodecyl sulphate-polyacrylamide gel electrophoresis, followed by analysis of the eluted peptides using liquid chromatography-tandem mass spectrometry. Cluster analysis utilised the Database for Annotation, Visualisation, and Integrated Discovery. Results: The subinhibitory concentration (SIC) of meropenem was determined to be 0.5 µg/L (minimum inhibitory concentration: 1). Mapping of reads to the reference genome identified 2477 expressed genes in all B. fragilis BFR KZ01 samples. Ten differentially expressed genes (DEGs) were common across comparison groups during and post-antibiotic exposure (wMEM vs. MEM2 and MEM2 vs. rMEM8); however, no substantially enriched Gene Ontology terms were identified. The cluster analysis highlighted a significant enrichment cluster (W-0560 oxidoreductase) of DEGs following antibiotic withdrawal. In total, 859 B. fragilis proteins were identified, with the expressions of three proteins, 3-oxoacyl-[acyl carrier protein] reductase, acetyl-CoA carboxylase biotin carboxylase subunit, and beta-ketoacyl-ACP synthase III, being upregulated in the enriched protein folding category. Notably, chaperone proteins such as FKBP-type peptidyl-prolyl cis-trans isomerases (involved in the cis-trans isomerisation of prolyl peptide bonds) and GroES (a co-chaperone functioning with GroEL) were also identified. Conclusions: Under the influence of low doses of antibiotics defense mechanisms are activated which contribute to the emergence of resistance. These results provide insight into the response of B. fragilis to meropenem exposure, mainly at the SIC, contributing to the understanding bacterial survival strategies under stress conditions.

Genetic variants of ABCB1 and CES1 genes on dabigatran metabolism in the Kazakh population.

Background: Allelic variants of genes encoding enzymes of the esterase system (CES1) and P-glycoprotein (ABCB1) can change the metabolism and pharmacokinetics of dabigatran. Therefore, they act as determining factors in the development of side effects, especially bleeding. We analyzed the genotype-phenotype relationship of ABCB1 (rs1045642, rs4148738, rs2032582, and rs1128503) and CES1 (rs8192935, rs71647871, and rs2244613) polymorphisms in patients with atrial fibrillation who had been treated with dabigatran. Methods: A total of 150 patients were recruited for this study. TaqMan technology was used for SNP genotyping. Results: Patients with the rs2244613 GG genotype had a lower concentration (55.27 ± 34.22 ng/ml) compared to those with the TT genotype (63.33 ± 52.25 ng/ml) (additive model, P = 0.000). Individuals with the rs8192935 AA genotype had a lower concentration (52.72 ± 30.45 ng/ml) compared to those with the GG genotype (79.78 ± 57 ng/ml) (additive model, P = 0.001). The APTT values among the different genotypes of the ABCB1 SNPs, rs4148738 and rs1045642, were significantly different (P = 0.035 and P = 0.024, respectively). Conclusion: Our research demonstrates that the CES1 polymorphisms, rs8192935 and rs2244613, are associated with the pharmacodynamics and pharmacokinetics of dabigatran in the Kazakh subpopulation.

Associations of Brain Arteriovenous Malformation-Related Factors with Epileptic Seizure Presentations.

BACKGROUND: Arteriovenous malformations (AVMs) are abnormal tangles of arteries and veins that connect directly without an intervening capillary bed. Epileptic seizures are the second most common symptom in patients with brain AVMs, occurring in 30 to 50% of cases. However, the exact mechanism of epileptic seizure development in AVMs remains unclear. In this study, we aimed to investigate the factors associated with epileptic seizures in patients with brain arteriovenous malformation (AVMs) in Kazakhstan. METHODS: A case-control study was conducted, which included 163 patients diagnosed with brain AVMs. Demographic and clinical data were collected and analyzed, and multivariate logistic regression was built to assess the factors associated with seizures in brain AVMs. RESULTS: from this rupture of vessels OR = 0.36 95% CI (0.14-0.91, a medium-to-high Spetzler-Martin score (III-V) OR = 6.16 (2.14-17.69) and OR = 3.05 (1.08-8.68), respectively), location in brain cortex (frontal lobe OR = 6.16 (2.04-18.54), parietal lobe OR = 9.37 (3.26-26.91), temporal lobe OR = 4.57 (1.56-13.36), occipital lobe OR = 0.27 (0.08-0.91), and the presence of hemiparesis OR = 0.12 (0.02-0.66) in adverse outcomes were statistically significantly associated with the presence of epileptic seizures in brain arteriovenous malformations patients. CONCLUSIONS: To conclude, this contributed to model factors associated with brain arteriovenous malformations that are linked to epileptic seizures.

Association of ADIPOQ Gene Polymorphisms with Type 2 Diabetes and Obesity Risk in the Kazakh Population: A Case-Control and Population-Based Study.

Type 2 diabetes mellitus (T2DM) is a socially significant disease with increasing prevalence worldwide. It is characterized by heterogeneous metabolic disorders and is associated with various risk factors, including BMI, abnormal lipid levels, hypertension, smoking, dietary preferences, physical inactivity, sedentary lifestyle, family history of diabetes, prediabetes or gestational diabetes, inflammation, intrauterine environment, age, sex, ethnicity, and socioeconomic status. Assessing the genetic risk of developing T2DM in specific populations remains relevant. The ADIPOQ gene, encoding adiponectin, is directly related to the risk of developing T2DM, obesity, and cardiovascular diseases. Our study demonstrated significant associations of ADIPOQ gene polymorphisms with the risk of developing T2DM and obesity, as well as with fasting glucose levels and BMI, in the Kazakh population. Specifically, rs266729 was significantly associated with T2DM and obesity in the Kazakh population, while other studied polymorphisms (rs1501299, rs2241766, and rs17846866) did not show a significant association. These findings suggest that ADIPOQ gene polymorphisms may influence T2DM risk factors and highlight the importance of genetic factors in T2DM development. However, further research in larger cohorts is needed to confirm these associations.

Whole-genome sequence and annotation of Salmonella enterica subsp. enterica strain QazSL-4.

Here, we present the whole-genome sequence of Salmonella enterica subsp. enterica strain QazSL-4 isolated from a chicken fillet in 2018, Almaty, Kazakhstan. The genome obtained using Illumina MiSeq technology consists of 49 contigs with a total length of 4,711,816 bp with a GC content of 52.1%.

Long-Term Outcomes of Endovascular Embolization in a Vein of Galen Aneurysmal Malformation: A Single-Center Experience.

BACKGROUND: A vein of Galen aneurysmal malformation (VGAM) is a rare congenital cerebral vascular condition with a high mortality rate if left untreated. This study describes the long-term outcomes of patients with VGAM, who were treated with endovascular embolization. METHODS: This retrospective analysis focused on VGAM patients who underwent one or more endovascular embolization sessions between January 2008 and December 2022. The study included newborns and children under 18 years. Data encompassed clinical and demographic characteristics, types of endovascular embolization, treatment complications, mortality rates, and long-term outcomes. RESULTS: Out of 22 VGAM cases, the majority were boys (86.36%), and the average age of the participants was 38 months, ranging from 25 days to 17 years. Endovascular embolization using liquid embolizing agents was the most common intervention (50%), and around 73% of patients underwent multiple sessions. Some patients underwent ventriculoperitoneal shunting (VPS) due to persistent hydrocephalus. In long-term outcomes, four patients (18.2%) showed developmental delays, and 16 patients (72.7%) had a positive outcome. CONCLUSIONS: Combining endovascular therapy with a comprehensive management strategy significantly reduces mortality rates and improves the possibility of normal neurological development in patients.

Effect of Plant Preservative MixtureTM on Endophytic Bacteria Eradication from In Vitro-Grown Apple Shoots.

Endophytic contaminants are a common problem for the in vitro propagation of woody plants and have significant economic repercussions for the conservation of plant genetic resources and commercial micropropagation. In this study, first, the microbial contamination that appeared around the base of in vitro-grown apple shoots was identified as Bacillus megaterium. Then, plant preservative mixture (PPMTM) was used as a bactericidal agent in plant tissue culture. Its efficacy for eradicating endophytic B. megaterium in in vitro cultures of apple was tested. In vitro-contaminated shoots were grown in tissue culture medium supplemented with 0.2% v/v PPMTM for 12 weeks and then transferred to medium without any PPMTM and cultured for 24 weeks. This study showed that PPMTM is an effective agent for controlling the growth of B. megaterium. Our results highlight the species-specific response of apple shoots to PPMTM. PPMTM was effective in controlling endogenous microbial contaminations from apple varieties 'Golden Delicious', 'Landsberger Renette', 'Suislepper', and 'Aport krovavo-krasnyi'; meanwhile, in 'KG 7' and 'Gold Rush', all the plants grown in the absence of PPMTM were still bacterially contaminated, even though they were pre-treated for 12 weeks in PPMTM-supplemented medium. These results therefore suggest the essentiality of further testing of extended incubation of PPMTM in these cultivars that had outbreaks of bacterial contamination.

Associations of Reported Genetic Risk Loci with Sporadic Brain Arteriovenous Malformations: Meta-analysis.

An arteriovenous malformation (AVM) is an abnormal nidus of blood vessels that is characterized by a direct connection between arteries and veins without intervening in the capillary network. The exact underlying cause of sporadic AVMs is unknown, but many studies have reported genetic associations between genes that contribute to angiogenesis, vasculogenesis, and inflammation. Eleven studies retrieved from Medline Complete, PubMed, and Google Scholar up to February 2022 were included. Heterogeneity was assessed using I2 and Q-tests. Publication bias was also assessed for the shortlisted CDKN2B-AS1 rs1333040 (T > C), ACVRL1 rs2071219 (A > G), and rs11169953 (C > T) polymorphisms. The rs1333040 polymorphism showed a lower association with sporadic brain AVM for T versus C in an allelic model (OR = 0.59, 95% confidence interval [CI] = 0.41-0.84). In the recessive model, rs2071219 for AA + AG vs. GG was OR = 0.62, 95% CI = 0.43-0.9. In the recessive model, rs11169953 CC + CT vs. TT was OR = 0.56, 95% CI = 0.33-0.95. In summary, the results of this study support the association between CDKN2B-AS1 and ACVRL1 polymorphisms and sporadic brain arteriovenous malformations. This study summarized the existing information and showed the need for more replication studies on the genetic basis of sporadic AVM. In the future, more genome-wide studies should be conducted to validate and fill existing gaps in knowledge about the mechanisms of sporadic AVM development.

Whole-Exome Sequencing Reveals Pathogenic SIRT1 Variant in Brain Arteriovenous Malformation: A Case Report.

Arteriovenous malformations of the brain (bAVMs) are plexuses of pathological arteries and veins that lack a normal capillary system between them. Intracranial hemorrhage (hemorrhagic stroke) is the most frequent clinical manifestation of AVM, leading to lethal outcomes that are especially high among children and young people. Recently, high-throughput genome sequencing methods have made a notable contribution to the research progress in this subject. In particular, whole-exome sequencing (WES) methods allow the identification of novel mutations. However, the genetic mechanism causing AVM is still unclear. Therefore, the aim of this study was to investigate the potential genetic mechanism underlying AVM. We analyzed the WES data of blood and tissue samples of a 30-year-old Central Asian male diagnosed with AVM. We identified 54 polymorphisms in 43 genes. After in-silica overrepresentation enrichment analysis of the polymorphisms, the SIRT1 gene variant (g.67884831C>T) indicated a possible molecular mechanism of bAVM. Further studies are required to evaluate the functional impact of SIRT1 g.67884831C>T, which may warrant further replication and biological investigations related to sporadic bAVM.

Activated leukocyte cell adhesion molecule/cluster of differentiation 166 rs10933819 (G>A) variant is associated with familial intracranial aneurysms.

Rupture of intracranial aneurysms (IAs) is the most common cause of subarachnoid hemorrhage (SAH). Currently, there is sufficient evidence to indicate that inflammatory responses contribute to aneurysm rupture. Moreover, the familial occurrence of SAH suggests that genetic factors may be involved in disease susceptibility. In the present study, a clinically proven case of IA in a patient who is a heterozygous mutation carrier of the activated leukocyte cell adhesion molecule (ALCAM)/cluster of differentiation 166 (CD166) gene, is reported. Genomic DNA was extracted from two siblings diagnosed with SAH and other available family members. A variant prioritization strategy that focused on functional prediction, frequency, predicted pathogenicity, and segregation within the family was employed. Sanger sequencing was also performed on the unaffected relatives to assess the segregation of variants within the phenotype. The verified mutations were sequenced in 145 ethnicity-matched healthy individuals. Based on whole exome sequencing data obtained from three individuals, two of whom were diagnosed with IAs, the single-nucleotide variant rs10933819 was prioritized in the family. Only one variant, rs10933819 (G>A), in ALCAM co-segregated with the phenotype, and this mutation was absent in ethnicity-matched healthy individuals. Collectively, ALCAM c1382 G>A p.Gly229Val was identified, for the first time, as a pathogenic mutation in this IA pedigree.

Effect of Targeted Embolization on Seizure Outcomes in Patients with Brain Arteriovenous Malformations.

BACKGROUND: Seizures are one of the most debilitating manifestations of brain arteriovenous malformations (AVMs). This study aimed to evaluate the effect of curative embolization on brain AVM patients presenting with seizures. METHODS: The records of patients who underwent embolization for brain AVM from January 2012 to December 2020 were evaluated and patients presenting with seizures were interviewed. Patient responses were evaluated according to the International League Against Epilepsy (ILAE) and Engel classifications. Statistical analyses of factors associated with seizure outcomes and complications were performed using ANOVA and Fischer's exact tests. RESULTS: The mean age of the participants was 35.2 ± 10.7 years. More than 80% of the patients received no or suboptimal dosages of antiepileptic drugs (AEDs) prior to embolization. Positive seizure dynamics were observed in 50% of the patients post-procedure. A correlation was found between length of seizures in anamnesis and outcomes of both Engel and ILAE score, where shorter length was associated with better outcomes. Post-embolization hemorrhage was associated with initial presentation with hemorrhage. CONCLUSIONS: The embolization of brain AVMs had a positive effect on seizure presentation and a relatively low prevalence of complications. However, the results of the study are obscured by inadequate AED treatment received by the patients, which prompts prospective studies on the topic with careful patient selection.

Development and Evaluation of Alternative Methods to Identify the Three Most Common Serotypes of Salmonella enterica Causing Clinical Infections in Kazakhstan.

In this study, we aimed to compare the performance of conventional PCR and real-time PCR assays as screening methods for identification of three frequent, clinically significant Salmonella serovars in Kazakhstan. We determined the diagnostic efficacy of three molecular methods for detection of S. enterica subsp. enterica and typing S. Typhimurium, S. Enteritidis, and S. Virchow. A total of 137 clinical samples and 883 food samples were obtained in Almaty in 2018-2019. All tests showed high analytical specificity for detecting S. enterica and its corresponding serovariants (100%). The sensitivity of real-time PCR for each of the tested targets was 1-10 microbial cells and in conventional PCR 10-100 microbial cells. The trials with conventional PCR and real-time PCR had a diagnostic efficacy (DE) of 100% and 99.71%, respectively. The DE of real-time PCR and conventional PCR for detecting S. Enteritidis and S. Typhimurium was 99.90%, while the DE of conventional PCR and real-time PCR for detecting S. Virchow was 99.31% and 99.80%, respectively. The RAPD-PCR analysis of the genomic DNA of Salmonella enterica showed the genetic kinship of S. Enteritidis isolates, and the genetic heterogeneity of S. Typhimurium and S. Virchow isolates. Thus, the developed methods can be considered as alternatives to classical serotyping using antisera.

Determinants of resistance in Bacteroides fragilis strain BFR_KZ01 isolated from a patient with peritonitis in Kazakhstan.

OBJECTIVES: Bacteroides fragilis is one of the most important human anaerobic pathogens often found in various clinical infections. The purpose of this study was to determine the susceptibility of a B. fragilis clinical strain (BFR_KZ01) from Kazakhstan to the most commonly used anti-anaerobic drugs at the local level and to detect genes associated with resistance to these antibiotics. METHODS: Species identification of the bacterial isolate was performed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS) and 16S rRNA gene sequencing. Susceptibility to broad-spectrum antibiotics (metronidazole, meropenem, ciprofloxacin, clindamycin and tetracycline) most commonly used for the treatment of intra-abdominal infections (IAIs) was determined. Mass spectra groups essential for identifying cfiA-positive strains among clinical isolates were studied using ClinProTools 3.0.22 software. An Ion Torrent PGM™ platform was used for whole-genome sequencing (WGS) of the studied isolate. RESULTS: The resulting WGS data of strain BFR_KZ01 was submitted to GenBank. In total, 5300 coding sequences (CDSs) and 69 RNA genes were determined. Analysis of the whole-genome data revealed that the studied strain harbours cfiA, nimB, tetQ and gyrA genes conferring resistance to key drugs used in treatment of the IAIs. MALDI-TOF/MS analysis assigned strain BFR_KZ01 to Group II (cfiA-positive); however, BFR_KZ01 was phenotypically sensitive to meropenem (mean MIC, 1.3 mg/L). CONCLUSION: Determinants of drug resistance in strain BFR_KZ01 were identified. It was revealed that B. fragilis strain BFR_KZ01 from Kazakhstan is multidrug-resistant since it carries nimB, tetQ and gyrA genes conferring resistance to metronidazole, tetracycline and ciprofloxacin.

Analysis of Bacteroides fragilis Clinical Strains Isolated in Kazakhstan.

Our aim was to study the nucleotide sequences of 9 previously undescribed strains of B. fragilis collected from patients with intra-abdominal diseases at city hospitals in Nur-Sultan, Kazakhstan.

The medieval Mongolian roots of Y-chromosomal lineages from South Kazakhstan.

BACKGROUND: The majority of the Kazakhs from South Kazakhstan belongs to the 12 clans of the Senior Zhuz. According to traditional genealogy, nine of these clans have a common ancestor and constitute the Uissun tribe. There are three main hypotheses of the clans' origin, namely, origin from early Wusuns, from Niru'un Mongols, or from Darligin Mongols. We genotyped 490 samples of South Kazakhs by 35 Y-chromosomal SNPs (single nucleotide polymorphism) and 17 STRs (short tandem repeat). Additionally, 133 samples from citizen science projects were included into the study. RESULTS: We found that three Uissun clans have unique Y-chromosomal profiles, but the remaining six Uissun clans and one non-Uissun clan share a common paternal gene pool. They share a high frequency (> 40%) of the C2*-ST haplogroup (marked by the SNP F3796), which is associated with the early Niru'un Mongols. Phylogenetic analysis of this haplogroup carried out on 743 individuals from 25 populations of Eurasia has revealed a set of haplotype clusters, three of which contain the Uissun haplotypes. The demographic expansion of these clusters dates back to the 13-fourteenth century, coinciding with the time of the Uissun's ancestor Maiky-biy known from historical sources. In addition, it coincides with the expansion period of the Mongol Empire in the Late Middle Ages. A comparison of the results with published aDNA (ancient deoxyribonucleic acid) data and modern Y haplogroups frequencies suggest an origin of Uissuns from Niru'un Mongols rather than from Wusuns or Darligin Mongols. CONCLUSIONS: The Y-chromosomal variation in South Kazakh clans indicates their common origin in 13th-14th centuries AD, in agreement with the traditional genealogy. Though genetically there were at least three ancestral lineages instead of the traditional single ancestor. The majority of the Y-chromosomal lineages of South Kazakhstan was brought by the migration of the population related to the medieval Niru'un Mongols.

Draft Genome Sequence of a Bacteroides fragilis Strain Isolated from Peritoneal Fluid of a Patient from Kazakhstan.

Here, we report the draft genome sequence of Bacteroides fragilis strain KZ02, isolated from a patient with peritonitis hospitalized in a health facility in Nur-Sultan, Kazakhstan. The genome of the strain contains 4,103 protein-coding genes, including the cepA gene, which causes resistance to beta-lactam antibiotics.

LRRK2 Mutations and Asian Disease-Associated Variants in the First Parkinson's Disease Cohort from Kazakhstan.

BACKGROUND: LRRK2 mutations have emerged as the most prevalent and potentially treatable determinants of Parkinson's disease (PD). Peculiar geographic distribution of these mutations has triggered an interest in genotyping PD cohorts of different ethnic backgrounds for LRRK. OBJECTIVE: Here, we report on the results of LRRK2 screening in the first Central Asian PD cohort. METHODS: 246 PD patients were consecutively recruited by movement disorder specialists from four medical centers in Kazakhstan, and clinicodemographic data and genomic DNA from blood were systematically obtained and shipped to the Institute of Neurology University College London together with DNAs from 200 healthy controls. The cohort was genotyped for five LRRK2 mutations (p.Gly2019Ser, p.Arg1441His, p.Tyr1699Cys, p.Ile2020Thr, and p.Asn1437His) and three East Asian disease-associated variants (p.Gly2385Arg, p.Ala419Val, and p.Arg1628Pro) via Kompetitive allele-specific polymerase chain reaction assay analysis. RESULTS: None of the study subjects carried LRRK2 mutations, whereas the following Asian variants were found with insignificant odds ratios (OR): p.Gly2385Arg (1.2%, minor allele frequency (MAF) 0.007, OR 1.25, p=0.8), p.Ala419Val (3.7%, MAF 0.02, OR 1.5, p=0.8), p.Ala419Val (3.7%, MAF 0.02, OR 1.5. CONCLUSIONS: We showed that East Asian LRRK variants could be found in Central Asian populations but their pathogenicity remains to be elucidated in larger PD cohorts.

Genetic Risk Factors for Intracranial Aneurysm in the Kazakh Population.

An intracranial aneurysm (IA) is a weak or thin area on a blood vessel in the brain that balloons as it fills with blood. Genetic factors can influence the risk of developing an aneurism. The purpose of this study was to explore the relationship between single nucleotide polymorphisms (SNPs) and IA in Kazakh population. The patients were genotyped for 60 single nucleotide polymorphisms. Genotyping was performed on the QuantStudio 12K Flex (Life Technologies). A linear regression analysis found 13 SNPs' significant association with development and rupture of IA: the rs1800956 polymorphism of the ENG gene, rs1756 46 polymorphism of the JDP2 gene, variant rs1800255 of the COL3A1, rs4667622 of the UBR3, rs2374513 of the c12orf75, rs3742321 polymorphism of the StAR, the rs3782356 polymorphism of MLL2 gene, rs3932338 to 214 kilobases downstream of PRDM9, rs7550260 polymorphism of the ARHGEF, rs1504749 polymorphism of the SOX17, the rs173686 polymorphism of CSPG2 gene, rs6460071 located on LIMK1 gene, and the rs4934 polymorphism of SERPINA3. A total of 13 SNPs were identified as potential genetic markers for the development and risk of rupture of aneurysms in the Kazakh population. Similar results were obtained after adjusting for the confounding factors of arterial hypertension and age.

TB-EFI, a novel 18-Plex microbead-based method for prediction of second-line drugs and ethambutol resistance in Mycobacterium tuberculosis complex.

Several diagnostic tests are being developed to detect drug resistance in tuberculosis. In line with previous developments detecting rifampicin and isoniazid resistance using microbead-based systems (spoligoriftyping and TB-SPRINT), we present here an assay called TB-EFI detecting mutations involved in resistance to ethambutol, fluoroquinolones and the three classical injectable drugs (kanamycin, amikacin and capreomycin) in Mycobacterium tuberculosis. The proposed test includes both wild-type and mutant probes for each targeted locus. Basic analysis can be performed manually. An upgraded interpretation is made available in Excel 2016®. Using a reference set of 61 DNA extracts, we show that TB-EFI provides perfect concordance with pyrosequencing. Concordance between genotypic resistance and phenotypic DST was relatively good (72 to 98% concordance), with lower efficiency for fluoroquinolones and ethambutol due to some untargeted mutations. When compared to phenotypical resistance, performances were similar to those obtained with Hain MTBDRsl assay, possibly thanks to the use of automatized processing of data although some mutations involved in fluoroquinolone resistance could not be included. When applied on three uncharacterized sets, phenotype could be predicted for 51% to 98% depending on the setting and the drug investigated, detecting one extensively drug-resistant isolate in each of a Pakistan and a Brazilian set of 91 samples, and 9 XDR among 43 multi-resistant Kazakhstan samples. By allowing high-throughput detection of second-line drugs resistance and of resistance to ethambutol that is often combined to second-line treatments, TB-EFI is a cost-effective assay for large-scale worldwide surveillance of resistant tuberculosis and XDR-TB control.

Genetic risk factors for restenosis after percutaneous coronary intervention in Kazakh population.

BACKGROUND: After coronary stenting, the risk of developing restenosis is from 20 to 35 %. The aim of the present study is to investigate the association of genetic variation in candidate genes in patients diagnosed with restenosis in the Kazakh population. METHODS: Four hundred fifty-nine patients were recruited to the study; 91 patients were also diagnosed with diabetes and were excluded from the sampling. DNA was extracted with the salting-out method. The patients were genotyped for 53 single-nucleotide polymorphisms. Genotyping was performed on the QuantStudio 12K Flex (Life Technologies). Differences in distribution of BMI score among different genotype groups were compared by analysis of variance (ANOVA). Also, statistical analysis was performed using R and PLINK v.1.07. Haplotype frequencies and LD measures were estimated by using the software Haploview 4.2. RESULTS: A logistic regression analysis found a significant difference in restenosis rates for different genotypes. FGB (rs1800790) is significantly associated with restenosis after stenting (OR = 2.924, P = 2.3E-06, additive model) in the Kazakh population. CD14 (rs2569190) showed a significant association in the additive (OR = 0.08033, P = 2.11E-09) and dominant models (OR = 0.05359, P = 4.15E-11). NOS3 (rs1799983) was also highly associated with development of restenosis after stenting in additive (OR = 20.05, P = 2.74 E-12) and recessive models (OR = 22.24, P = 6.811E-10). CONCLUSIONS: Our results indicate that FGB (rs1800790), CD14 (rs2569190), and NOS3 (rs1799983) SNPs could be genetic markers for development of restenosis in Kazakh population. Adjustment for potential confounder factor BMI gave almost the same results.