Nurlan Sandybayev

Background/Objectives: Sepsis is characterized by systemic immune dysregulation and organ dysfunction, but transcriptomic profiles from different biofluids may provide partially overlapping and distinct molecular readouts of the host response. We characterized transcriptomic profiles of whole blood and urinary cellular fractions in sepsis, with particular emphasis on a urinary transcriptional gradient associated with continuous serum creatinine and on whether this association was mirrored in matched blood. Methods: Targeted RNA sequencing was performed on whole blood from 35 patients with sepsis and 10 healthy controls and on urinary cellular fractions from 21 patients with sepsis and 7 controls using the Ion AmpliSeq Transcriptome Human Gene Expression workflow. Differential expression was assessed with DESeq2, with sequencing-adjusted sensitivity models where appropriate. Sensitivity analyses addressed the highest creatinine value, sex and age, and matched blood–urine creatinine-associated effects. Results: Whole-blood analysis identified 2659 differentially expressed genes (DEGs), including a robust core of 1796 genes characterized by neutrophil–myeloid activation and adaptive-immune suppression. The exploratory urine case–control comparison identified 1552 DEGs but was substantially confounded by sequencing chip. Continuous serum creatinine analysis identified 4064 chip-adjusted urinary DEGs, including a robust core of 3774 genes enriched for inflammatory, interferon, hypoxic, autophagic, lysosomal, vesicular, metabolic, and mitochondrial programs. Exclusion of the highest creatinine sample retained 3192/4064 strict DEGs with the same direction and 2926/3774 robust-core genes. In the same 21 patients, adjusted creatinine-associated effects were weakly concordant between blood and urine at the gene level (Pearson r = 0.192; Spearman ρ = 0.199), with five overlapping strict DEGs and no robust-core overlap. Hallmark concordance was greater but moderate (Pearson r = 0.293; Spearman ρ = 0.464), with 14 shared robust pathways. Conclusions: Transcriptomic profiles of whole blood and urinary cellular fractions showed distinct but partially overlapping host-response patterns in sepsis. The serum creatinine-associated urinary transcriptional axis was robust across sensitivity analyses and was only weakly mirrored at the gene level in matched blood, despite partial pathway-level convergence. These findings should be interpreted as serum creatinine-associated transcriptional patterns rather than as evidence of kidney-specific injury or validated diagnostic or prognostic signatures. Independent longitudinal cohorts and orthogonal molecular validation are required.

Delays in pathogen and antimicrobial resistance (AMR) profiling adversely affect patient outcomes. Next-generation sequencing (NGS) may complement conventional microbiology (CM), yet real-world value of NGS in pneumonia diagnosis remains unclear. We quantified concordance between a commercial NGS panel and CM for pathogen detection and genotypic AMR prediction in 48 pneumonia inpatients with culture-confirmed infections. Archived sputum was analysed using the Ion AmpliSeq Pan-Bacterial targeted panel with 16S rRNA profiling. CM comprised culture, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) identification and disc-diffusion antibiotic susceptibility testing. NGS recovered 27/50 pathogens detected by CM (54.0%, 95% CI 40.4–67.0), with more organisms per sample than CM (mean 2.42 versus 1.04), including uncultured taxa, indicating broader detection. AMR sensitivity of NGS was low (41.2%, 105/255; 95% CI 35.3–47.3; ranging from 1.1% for fluoroquinolones to 100% for cephamycins/lincosamides/tetracyclines) and remained low (37.6–69.8%) across alternative read and abundance cut-offs. Overall, the commercial NGS panel expanded pathogen detection beyond culture but showed only moderate concordance with CM and limited sensitivity for AMR phenotypes; it is therefore best regarded as an adjunct to CM and phenotypic susceptibility testing in pneumonia, not a replacement.

Background/Objectives: Staphylococcus aureus, particularly methicillin-resistant strains, is a leading cause of severe pneumonia. Understanding local molecular epidemiology, including virulence gene profiles and antimicrobial resistance (AMR) mechanisms, is crucial for effective infection control. This pilot study aimed to characterize S. aureus isolates from pneumonia patients in Karaganda, Kazakhstan. Methods: We collected 48 respiratory samples from patients with pneumonia across three medical institutions. Bacterial identification was performed using MALDI-TOF MS. Antimicrobial susceptibility testing (AST) was carried out using European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Whole-genome sequencing of S. aureus isolates was conducted on an Ion Torrent S5 platform. Genomic analysis included multilocus sequence typing (MLST), identification of virulence and AMR genes, and phylogenetic reconstruction. Results: S. aureus was identified in 14.6% (n = 7) of pneumonia cases included in this study. All isolates (100%, n = 7) were phenotypically resistant to benzylpenicillin. The mecA gene was detected in 57.1% of isolates (n = 4), while phenotypic resistance to methicillin was observed in 28.6% (n = 2) of the isolates. Resistance to azithromycin (57.1%, n = 4) and levofloxacin (42.9%, n = 3) was observed among the isolates. Two isolates (28.6%) were multidrug-resistant (MDR). Genomic analysis revealed the prevalence of the ST22 clone (57.1%, n = 4) in the studied cohort. Other sequence types were ST97, ST8, and ST45 (14.3% each). Phylogenetic analysis showed clustering consistent with MLST profiles. All isolates carried a conserved core virulence arsenal, including hemolysin (hla, hlg), biofilm-forming genes (icaADBC), immune evasion genes (sak, scn), and iron acquisition genes (isd). The Panton–Valentine leukocidin (PVL) genes were detected in three isolates. AMR gene analysis revealed the ubiquitous presence of mepA and tetracycline efflux pump genes, along with regulatory genes (arlRS, mepR, mgrA). The blaZ and ermA genes were not detected despite high phenotypic resistance to penicillin and macrolides. Conclusions: This study reports the identification of the virulent and resistant ST22 S. aureus clone in pneumonia cases in Karaganda, Kazakhstan. The discordance between phenotypic and genotypic AMR profiles underscores the necessity for integrated diagnostic approaches.

Background and Aims: Pneumonia is an inflammatory condition of the lower respiratory tract, commonly caused by infection and associated with substantial morbidity and healthcare utilization. The burden of pneumonia on healthcare is exacerbated by limited data on pathogenic causes and associated antimicrobial resistance (AMR). Here, we conducted a literature review and synthesized data on the microbial causes and AMR in hospitalized pneumonia patients from Kazakhstan. Methods: We searched PubMed, Medline, Embase, Web of Science, the Cochrane Central Register of Controlled Trials, eLIBRARY, and CyberLeninka for observational studies of hospitalized pneumonia patients reporting microbiologically confirmed pathogen and antimicrobial resistance data from Kazakhstan. Exclusion criteria were unclear pneumonia definitions or absence of pathogen‐specific AMR data. We assessed study quality using the Joanna Briggs Institute checklist and extracted data on microbial prevalence and resistance rates by pathogen‐antibiotic combinations. We synthesized microbial etiology and AMR patterns and performed random‐effects meta‐analysis of prevalence data. Results: Nine studies represented 1534 isolates from 1474 inpatients (2008–2022). The most prevalent pathogens were Streptococcus pneumoniae (17.8%), Streptococcus spp. (17.3%), Haemophilus influenzae (12.6%), and Klebsiella pneumoniae (10.7%). Hospital‐acquired pathogens comprised 48% of isolates. Acinetobacter baumannii had the highest resistance, exceeding 70% across major antibiotic classes. Escherichia coli had high resistance to β‐lactams (> 66%) and fluoroquinolones (63%). Pseudomonas aeruginosa had 60% fluoroquinolone and 27% carbapenem resistance. Fluoroquinolone resistance was widespread across multiple pathogens. K. pneumoniae had relatively lower resistance rates. Pathogen distribution varied by clinical setting and patient population. Conclusion: Data on the etiologic causes and AMR in pneumonia are sparse in Kazakhstan and methodologically heterogeneous. Hospital‐acquired pneumonia pathogens were highly prevalent and associated with high AMR rates. These findings underscore the need for improved pathogen surveillance and antimicrobial stewardship in Kazakhstan to address the high burden of antibiotic‐resistant and hospital‐acquired pneumonia.

Background/Objectives: Klebsiella pneumoniae is a major Gram-negative pathogen associated with community-acquired pneumonia (CAP) and a critical contributor to antimicrobial resistance (AMR). Culture-based diagnostics remain the clinical standard but may underestimate microbial diversity and resistance gene profiles. This pilot study compared pathogen detection and antimicrobial resistance gene (ARG) repertoires in matched K. pneumoniae pure cultures and primary sputum samples using targeted next-generation sequencing (tNGS). Methods: We analyzed 153 sputum samples from patients with CAP. Among 48 culture-positive cases, 22 (14% overall; 54% culture-positive) yielded K. pneumoniae. MALDI-TOF MS, phenotypic drug susceptibility testing, and tNGS were conducted on both culture isolates and matched sputum specimens. Microbial composition, ARG diversity, and method concordance were evaluated, with focused analysis of discordant and fatal cases. Results: K. pneumoniae was detected in 14.4% of all CAP cases and accounted for 54.2% of culture-positive samples. Identification rates differed across methods: 35% by MALDI-TOF MS, 45% by culture tNGS, and 29% by sputum tNGS. Sputum tNGS revealed substantially higher microbial diversity than cultures (3.04 vs. 1.42 species per sample) and detected more than sixfold unique ARGs (38 vs. 7), including clinically relevant determinants that were absent from culture isolates. Concordance was high between MALDI-TOF MS and culture tNGS (κ = 0.712), but low between sputum and culture tNGS (κ = 0.279). Among twelve K. pneumoniae isolates included in AMR analysis, all showed resistance to β-lactams, and two-thirds exhibited MDR/XDR phenotypes. Genotypic screening identified seven ARGs, but major ESBL and carbapenemase genes were not detected, suggesting the presence of alternative resistance mechanisms. Overall, sputum tNGS provided additional etiological and resistome information not captured by cultivation and complemented classical diagnostics in CAP involving K. pneumoniae. Conclusions: Culture-based diagnostics and tNGS provide complementary insights into the detection and resistance profiling of K. pneumoniae in CAP, with sputum tNGS revealing broader microbial and resistome information than pure cultures, while classical methods remain essential for species confirmation and phenotypic AST. An integrated diagnostic approach combining both methodologies may improve pathogen detection, guide antimicrobial therapy, and enhance AMR surveillance in K. pneumoniae-associated CAP.

Low pathogenic H9N2 avian influenza viruses have become widespread in wild birds and poultry worldwide, raising concerns about their potential to spark pandemics or their role in enhancing the virulence and infectivity of H5Nx viruses through genetic reassortment. Therefore, influenza monitoring studies, including those of H9N2 viruses, are crucial for understanding, evaluating, and mitigating the risks associated with avian infections, and have broader implications for global public health. Although H9N2 viruses are not considered enzootic in Kazakhstan, they have been repeatedly detected in wild waterfowls and domestic poultry. In this study, all eight gene segments of influenza A/H9N2 viruses isolated in various regions of Kazakhstan between 2014 and 2020 were sequenced and analyzed. Molecular characterization revealed the presence of genetic markers associated with mammalian infectivity and disease potential. Furthermore, their predicted receptor binding site sequences indicate their potential capacity to attach to human-type receptors. These findings highlight the importance of continued surveillance and molecular investigation to better understand the evolution and zoonotic potential of H9N2 viruses in Kazakhstan.

This study presents the results of analyzing the sputum microbiome of 46 patients diagnosed with pneumonia using targeted NGS sequencing of the 16S rRNA gene. As a result of the study, 114 species of bacteria belonging to 47 genera and 29 families were identified. Based on the obtained data, potential pathogens associated with the development of pneumonia were identified, and a quantitative analysis of their prevalence among patients was conducted. At the species level, Streptococcus pneumoniae was detected in 26 samples (56.5%). Acinetobacter baumannii was found in 10 samples (21.7%). Klebsiella pneumoniae was detected in 9 samples (19.5%), and Pseudomonas aeruginosa was found in 17.4% of samples. Other species that may be involved in the development of pneumonia included Escherichia coli, Haemophilus influenzae, and Staphylococcus aureus in 15.2%, 10.87%, and 8.7% of samples, respectively. Additionally, Neisseria meningitidis was detected in 5 samples (10.8%), and Stenotrophomonas maltophilia was found in two samples. The obtained results can contribute to a deeper understanding of microbiome communities associated with pneumonia and enrich knowledge about the microbiome of the upper respiratory tract. These data may be useful for developing new strategies for the diagnosis and treatment of pneumonia, as well as for optimizing preventive measures.

Background/Objectives: Acinetobacter baumannii is an increasingly significant nosocomial pathogen causing severe infections globally. The emergence of multidrug-resistant A. baumannii strains has raised concerns about the efficacy of current treatment options. This study aimed to investigate the molecular epidemiology and antimicrobial resistance patterns of A. baumannii isolates from Kazakhstan. Methods: We collected nine A. baumannii isolates in 2022–2023 in Karaganda, Kazakhstan, which were then subjected to whole-genome sequencing (WGS) using the IonTorrent platform for genome characterization. Multilocus sequence typing (MLST) was used to classify the isolates into distinct clonal complexes. In addition, antibiotic susceptibility testing was conducted using the standard methods for a range of antibiotics commonly used against A. baumannii. Results: Our results revealed a high degree of genomic diversity among isolates from Kazakhstan, with multiple distinct classes identified: ST78 (n = 4, 44.4%), ST15 (n = 2, 22.2%), ST2 (n = 2, 22.2%), and ST193 (n = 1, 11%). MLST analysis showed that ST78^Pas/1104^Oxf (harboring blaOXA-72 and blaOXA-90 genes) were prevalent among the multidrug-resistant isolates. Based on the results of MLST, KL, and OCL, the analyzed isolates were assigned to specific international clones: IC2—ST2(Pas)-KL2/168-OCL1, IC4—ST15(Pas)-KL9-OCL7, and IC6—ST78(Pas)-KL49-OCL1. Notably, these isolates exhibited resistance to multiple antibiotics including meropenem, imipenem, gentamicin, amikacin, and ciprofloxacin. Conclusions: This study highlighted the complex molecular epidemiology of A. baumannii in Kazakhstan over a two-year period, underscoring the need for targeted surveillance strategies to monitor antimicrobial resistance patterns. The emergence and dissemination of multidrug-resistant strains within this timeframe emphasizes the importance of whole-genome sequencing as a diagnostic tool and underscores the challenges posed by these infections.

Diagnosis of acute respiratory infections (ARIs) is challenging due to the broad diversity of potential microbial causes. We used metagenomic next-generation sequencing (mNGS) to analyze the nasopharyngeal virome of ARI patients, who had undergone testing with a clinical multiplex PCR panel (Amplisens ARVI-screen-FRT). We collected nasopharyngeal swabs from 49 outpatient adults, 32 of whom had ARI symptoms and were PCR-positive, and 4 asymptomatic controls in Kazakhstan during Spring 2021. We assessed the biodiversity of the mNGS-derived virome and concordance with PCR results. PCR identified common ARI viruses in 65% of the symptomatic cases. mNGS revealed viral taxa consisting of human, non-human eukaryotic and bacteriophage groups, comprising 15, 11 and 28 genera, respectively. Notable ARI-associated human viruses included rhinovirus (16.3%), betaherpesvirus 7 (14.3%) and Epstein-Barr virus (8.16%). The primary phage hosts were Streptococcus spp. (32.7%), Pseudomonas aeruginosa (24.5%) and Burkholderia spp. (20.4%). In total, 47% of ARIs were linked solely to bacterial pathogens, a third to viral-bacterial co-infections, and less than 10% to only viral infections by mNGS. PCR showed low concordance with mNGS, except for rhinovirus. These results underscore the importance of broad diagnostic methods and question the effectiveness of commonly used PCR panels in ARI diagnosis.

Clonal rootstocks of apple trees are one of the main components of intensive horticulture, and they play an important role in regulating tree growth, yield, fruit quality, and resistance to biotic and abiotic stresses. In the two-year monitoring survey reported here, eleven rootstocks mainly used for cultivar grafting in Kazakhstan were assessed for fire blight resistance, taking genetic background into consideration. The loci FB_F7 on LG7 and FB_MR5 and RLP1 on LG3 were analyzed on the basis of SCAR and SNP markers. The rootstocks ‘Geneva 41’, ‘62-396’, and ‘Geneva16’, bearing resistant alleles for five markers (AH0JFXM, AH21B92, AH4AAGA, AH5I8MI, and AH6R6SQ), four markers (AH0JFXM, AH21B92, AH4AAGA, and AH5I8MI), and one (AH4AAGA) SNP marker, respectively, were not infected during the monitoring period despite weather conditions in 2022 being favorable for the development and spread of Erwinia amylovora. No connection was identified between the presence of a resistant allele for the AE10-375 marker and fire blight resistance responses. This is the first study to evaluate the fire blight resistance of foreign and local rootstocks grown in the Kazakhstan southern region.