P-glycoprotein Research Articles

Genome drafting of nosocomial infection CRE Klebsiella pneumoniae confirming resistance to colistin and eravacycline, carrying blaNDM-1, mcr-1, and blaKPC-2, in neonatology from November to December 2023

BackgroundCarbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical pathogen in healthcare settings, associated with high mortality due to its extensive antibiotic resistance. In this study, we report an outbreak of CRKP in a neonatal intensive care unit (NICU) within a 200-bed tertiary hospital. The main goal of this study was to characterize the phenotypic and genomic profiles of the CRKP isolates involved in the outbreak and to gain insights into their resistance mechanisms and transmission dynamics within the NICU.MethodsThe study was conducted between November and December 2023 in a 5-bed NICU. Monthly surveillance cultures were performed to monitor colonization and infection with multidrug-resistant organisms. CRKP isolates were obtained from blood and nasal swabs of affected neonates. Identification and antimicrobial susceptibility testing were initially conducted using the Vitek®2 system with an N-395 card and further confirmed by 16S rRNA sequencing. Whole-genome sequencing (WGS) and antimicrobial resistance (AMR) profiling were performed to identify resistance genes and virulence factors. For genetic analysis, both Illumina short-read and Nanopore long-read sequencing were used, followed by hybrid assembly for enhanced genome resolution. Plasmid and resistance gene profiles were determined using AMRFinder and PlasmidFinder databases.ResultsA total of three CRKP isolates (designated Kp1, Kp2, and Kp3) were identified. Kp1 and Kp2 belonged to sequence type (ST) ST23 and were genetically near-identical, differing by a single allele, while Kp3 was of a distinct sequence type, ST2096, with 245 allelic differences from Kp1 and Kp2. All isolates were resistant to colistin and carried resistance genes, including mcr-1 and blaNDM-1,blaKPC2 confirming carbapenem resistance. Efflux pump genes and aminoglycoside resistance genes were also detected, providing a multifaceted defence against antibiotics. Plasmid analysis identified several incompatibility groups (IncFI, IncHI, IncFIB, IncX), indicating the potential for horizontal gene transfer of resistance determinants.ConclusionThis study highlights the complexity of CRKP outbreaks in neonatal care, with isolates exhibiting resistance mechanisms that complicate treatment. The plasmid profiles suggest these strains are reservoirs for multidrug-resistant genes, emphasizing the need for strict infection control and ongoing genomic surveillance. For neonatal care, these resistance challenges increase the risk of treatment failures and mortality, underscoring the importance of enhanced infection prevention and novel therapeutic strategies.

Association between ABCB4 variants and intrahepatic cholestasis of pregnancy

The ABCB4 gene encodes multidrug resistance protein 3(MDR3), which is a phosphatidylcholine(PC) transfer enzyme that transfers lecithin from the inner part of the phospholipid bilayer to the extracellular bile. The occurrence of intrahepatic cholestasis of pregnancy(ICP) is closely related to ABCB4 variants, but there is limited research on this topic in southern Anhui, China. We sequenced ABCB4 in pregnant women with ICP and healthy pregnant women to explore the relationship. A total of 30 patients diagnosed with ICP were selected as the study objects and 90 healthy pregnant women were selected as the control group. DNA was extracted from peripheral blood of ICP patients and healthy pregnant women, 27 exons were sequencing by Sanger sequencing. Polymerase chain reaction (PCR) was used to amplify those exons. PolyPhen2, Mutation Taster, Provean, SIFT and Mutpred2 were used to predict protein structure, and Pymol software was used to predict the impact of missense variant c.1954 A > G(p.Arg652Gly) on proteins. Four exonic variants of ABCB4 gene were detected in ICP patients and healthy pregnant women, including synonymous variants c.175 C > T, c.504 C > T,c.711 A > T and missense variant c.1954 A > G(p.Arg652Gly). The incidence of the missense variant c.1954 A > G(p.Arg652Gly) was 6/90 in healthy pregnant womenand 8/30 in ICP patients.In healthy pregnant women with the missense variant c.1954 A > G(p.Arg652Gly), no other exonic variants were found. In ICP patients with missense variant c.1954 A > G(p.Arg652Gly), other exonic variants were found. PolyPhen2, Mutation Taster, Provean, SIFT and Mutpred2 were used to predict that the four exonic variants were benign, while Pymol was used to showed that the missense variant was located in the linker region of MDR3 and had a slight impact on protein function. Among ICP patients with missense variant c.1954 A > G(p.Arg652Gly), patients with three exonic variants(c.504 C > T, c.711 A > T, c.1954 A > G) had higher γ-GT, TBA, ALT and AST than those with two exonic variants. ABCB4 missense variant c.1954 A > G(p.Arg652Gly) requires the combination of other variants(c.175 C > T, c.504 C > T,c.711 A > T) to cause ICP symptoms, and when combined with other variants, it has a superimposed effect.

Prognostic impact of clinical and genetic factors on delayed elimination of methotrexate in children with acute lymphoblastic leukemia

Background. Methotrexate (MTX) in high doses (1000–5000 mg/m2), occupies one of the leading places in modern programs of therapy of acute lymphoblastic leukemia (ALL) in children. Achievement of high long-term survival rates in children with ALL has become possible thanks to this drug. However, no less important problem is the toxicity of the treatment and prediction of its efficacy and safety, in this regard, the role of pharmacogenetic studies in the identification of polymorphisms in candidate genes affecting the pharmacokinetics of MTX is increasing.Objective. To determine predictors of delayed elimination of methotrexate using pharmacokinetic biomarkers in children with acute lymphoblastic leukemia.Materials and methods. We prospectively analyzed the database of pediatric patients with ALL within the framework of an observational (cohort) singlecenter study. The study included 124 children diagnosed with ALL who received therapy according to the ALL-IC BFM 2009 protocol including high-dosed MTX. Real-time PCR method was used to study polymorphisms of ABCB1 and SLCO1B1 genes. The study material was peripheral blood. Statistical analysis ofpharmacogenetic biomarkers influence on toxicity and efficacy of therapy was performed using SPSS Statistics 26.0 program (USA). To form mathematical prognostic models, we used the method of logistic function construction using binary logistic regression with step-by-step selection of factors and, if necessary, additional construction of ROC-curves with subsequent ROC-analysis. Differences were considered significant at p < 0.05; at p ≥ 0.05, differences were considered unlikely and statistically insignificant.Results. Based on the results of the conducted complex analysis of efficacy and safety of high-dosed MTX therapy, a reliable (p < 0.001) prognostic model with high sensitivity, specificity and efficacy (>70 %, respectively) was developed, demonstrating the interrelationships of clinical and genetic factors influencing the delay of MTX elimination in children with ALL, which confirms the necessity of implementing pharmacogenetic testing in real clinical practice.Conclusion. Determination of polymorphisms of genes providing transport and metabolism of cytostatics should be used in practical work of oncohematological clinics for individualization of therapy and ensuring its safety.

Pharmacogenetic markers and macrolide safety in influenza patients: insights from a prospective study.

Macrolides are widely used antibiotics, but adverse drug reactions (ADRs), particularly in genetically predisposed individuals, can compromise their safety. This study examines the impact of pharmacogenetic markers on macrolide safety in participants with bacterial complications of influenza. To evaluate how polymorphisms in genes encoding transporter proteins (ABCB1) and enzymes (CYP3A4, CYP3A5) influence ADR risk during macrolide therapy. A prospective study included 100 participants with lower respiratory tract bacterial complications of influenza treated with azithromycin or erythromycin for five days. Genotyping targeted ABCB1 (3435C>T), CYP3A4 (C>T intron 6), and CYP3A5 (6986A>G) polymorphisms. ADRs were monitored daily and correlated with genetic markers. The ABCB1 (3435C>T) polymorphism was associated with higher rates of abdominal pain and diarrhea in CT and TT genotypes (OR = 2.12, p = 0.043). The CYP3A4 (C>T intron 6) polymorphism increased ADR risk in erythromycin-treated participants (OR = 24.0, p = 0.0339). No significant effects were observed for CYP3A5 (6986A>G). Genetic polymorphisms in ABCB1 and CYP3A4 genes predict macrolide-related ADRs. Pharmacogenetic screening could improve macrolide safety, particularly for genetically susceptible individuals.

Linifanib alone and in combination with metronomic chemotherapy is active on cutaneous T-cell lymphoma cells by targeting the AKT/mTOR signaling pathway.

Cutaneous T-cell lymphomas (CTCLs) are a rare and heterogeneous subset of skin-localized, non-Hodgkin lymphomas. Our aim was to evaluate the in vitro antitumor activity of the multi-kinase inhibitor linifanib, either alone or in combination with metronomic vinorelbine (mVNR) or etoposide (mETO), on CTCL cells. In vitro proliferation assay and Luminex analysis showed that long-term, daily exposure of linifanib significantly inhibited the proliferation of the human CTCL cell line HH, in a concentration-dependent manner (IC50 = 48.4 ± 20.4nM) and the phosphorylation of AKT/mTOR signaling pathway. The concomitant exposure of linifanib plus mVNR or mETO resulted in a strong synergism, with combination index values < 1. Linifanib significantly increased the VNR and ETO intracellular concentrations in HH cells, evaluated by UPLC-HRMS technology, and strongly reduced the ABCB1 and ABCG2 gene expression in HH. In conclusion, we reported a striking antitumor activity of daily, long-term linifanib and a clear synergistic effect when administered in combination with mCHEMO on CTCL cells, as a promising base for future clinical approaches in T-cell lymphomas.

Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits

BackgroundThe widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.ResultsOur results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10 mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5 mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.ConclusionThe results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion.4ZqjNsN9dRS1iWJDwru5hLVideo

Effect of Fecal Microbiota Transplant on Antibiotic Resistance Genes Among Patients with Chronic Pouchitis.

Pouchitis is common among patients with ulcerative colitis (UC) who have had colectomy with ileal pouch-anal anastomosis. Antibiotics are first-line therapy for pouch inflammation, increasing the potential for gut colonization with multi-drug resistant organisms (MDRO). Fecal microbial transplant (FMT) is being studied in the treatment of pouchitis and in the eradication of MDRO. Prior work using aerobic antibiotic culture disks suggests that some patients with chronic pouchitis may regain fluoroquinolone sensitivity after FMT. However, gut MDRO include anaerobic, fastidious organisms that are difficult to culture using traditional methods. We aimed to assess whether FMT reduced the abundance of antibiotic resistance genes (ARG) or affected resistome diversity, evenness, or richness in patients with chronic pouchitis. We collected clinical characteristics regarding infections and antibiotic exposures for 18 patients who had previously been enrolled in an observational study investigating FMT as a treatment for pouchitis. Twenty-six pre- and post-FMT stool samples were analyzed using FLASH (Finding Low Abundance Sequences by Hybridization), a CRISPR/Cas9-based shotgun metagenomic sequence enrichment technique that detects acquired and chromosomal bacterial ARGs. Wilcoxon rank sum tests were used to assess differences in clinical characteristics, ARG counts, resistome diversity and ARG richness, pre- and post-FMT. All 13 of the patients with sufficient stool samples for analysis had recently received antibiotics for pouchitis prior to a single endoscopic FMT. Fecal microbiomes of all patients had evidence of multi-drug resistance genes and ESBL resistance genes at baseline; 62% encoded fluoroquinolone resistance genes. A numerical decrease in overall ARG counts was noted post-FMT, but no statistically significant differences were noted (P = 0.19). Richness and diversity were not significantly altered. Three patients developed infections during the 5-year follow-up period, none of which were associated with MDRO. Antibiotic resistance genes are prevalent among antibiotic-exposed patients with chronic pouchitis. FMT led to a numerical decrease, but no statistically significant change in ARG, nor were there significant changes in the diversity, richness, or evenness of ARGs. Further investigations to improve FMT engraftment and to optimize FMT delivery in patients with inflammatory pouch disorders are warranted.

Expression of ABCB1, ABCC1, and LRP in Mesenchymal Stem Cells from Human Amniotic Fluid and Bone Marrow in Culture-Effects of In Vitro Osteogenic and Adipogenic Differentiation.

Mesenchymal stem cells (MSCs) are multipotent cells with the potential to differentiate into various lineages. They have also the potential to protect themselves against harmful stimuli to maintain their functional integrity. Drug resistance-related transporters such as ABCB1 (P-glycoprotein; P-gp), ABCC1 (MRP1; multidrug resistance-related Protein 1), and LRP (lung resistance protein) may protect MSCs against toxic substances such as chemotherapeutic agents. This study evaluated ABCB1, ABCC1, and LRP before and after the differentiation of MSCs derived from human amniotic fluid (AF) and bone marrow (BM). P-gp expression in both AFMSCs and BMMSCs was analyzed by immunocytochemistry, and pump function was analyzed by cell viability assay with doxorubicin (DOX) and Rhodamine 123 (Rh 123) dye exclusion. ABCB1, ABCC1, and LRP gene expression was determined by RT-PCR both before and after osteogenic and adipogenic differentiation. The MES-SA/DX5 cell line was used as a model of resistance to DOX and the overexpression of P-gp. Both AFMSCs and BMMSCs displayed a high P-gp expression, although lower than MES-SA/DX5 control cells. It was shown that both, undifferentiated AFMSCs and BMMSCs, have high cell viability in response to DOX, similar to the MES-SA/DX5 lineage. ABCB1 was less expressed in BM than in AFMSCs in undifferentiated samples, while no differences were observed in the expression of ABCC1 and LRP. AFMSCs showed an increase in ABCB1 after osteogenic differentiation, whereas BMMSCs exhibited lower ABCB1 and ABCC1 expression after osteogenic and adipogenic differentiation. The findings suggest that ABCB1, ABCC1, and LRP gene expression in AFMSCs and BMMSCs is influenced by differentiation processes and further support the concept that these transporters modulate MSC differentiation in a cell source-dependent way.

A family with gallstone disease: defining inherited risk in the era of clinical genetic testing.

Gallstones are among the most frequent hepatobiliary conditions. Although in most cases, they remain asymptomatic, they can cause complications and, in such cases, invasive treatments like endoscopic retrograde cholangiography (ERC) or cholecystectomy are required. Here, we present the results of genetic testing of a single family with a high incidence of symptomatic gallstones and cholestatic liver phenotypes. Gallstone disease was detected among seven family members spanning three generations, and DNA samples were available from five of them. Genotyping was performed using TaqMan assays for known, selected genetic risk factors for gallstones and cholestasis, as well as next generation sequencing (NGS) of three genes involved in hepatobiliary transport. In all genotyped patients, we detected at least one copy of the gallstone-predisposing p.D19H variant in the hepatobiliary sterol transporter ABCG5/8, and in three cases, this variant was found in the rare homozygous state. In addition, the patients were all homozygous carriers of two intronic variants (c.2211+16C >T and c.3508-16T>C) and two common polymorphisms (c.504C>T and c.711A>T) in the ABCB4 gene, as well as the ATP8B1 gene variant c.696T>C. All genotyped patients also carried the predisposing variants c.1331C>T and c.3084A>G of the hepatobiliary bile salt export pump ABCB11 in either heterozygous or homozygous form. Hence, we propose that these variants taken together may have contributed to the high frequency of gallstone disease in this family, although functional studies for some variants are still lacking. In this report, we present these findings and discuss the challenges associated with interpreting sequencing data.

Influence of ABCB1 polymorphisms on aripiprazole and dehydroaripiprazole plasma concentrations

Aripiprazole (ARI) is an atypical antipsychotic which is a substrate of P-glycoprotein (P-gp), a transmembrane glycoprotein that plays a crucial role in eliminating potentially harmful compounds from the organism. ARI once-monthly (AOM) is a long-acting injectable form which improves treatment compliance. Genetic polymorphisms in ABCB1 may lead to changes in P-gp function, leading to individual differences in drug disposition. The present study aims to determine how the different variants of the three most prevalent SNPs of the ABCB1 gene affect plasma concentrations of ARI, of its active metabolite dehydroaripiprazole (DHA) and ARI/DHA ratio in patients under AOM treatment. The metabolizing state of the two main aripiprazole metabolizing enzymes (CYP2D6 and CYP3A4) were considered to specifically study the effect of P-gp on plasma concentrations of the parent compound and its active metabolite. The study found a clear relationship between the genotypes found for the different ABCB1 SNPs and the ARI/DHA ratio. Specifically, patients with GG genotype in G2677T have almost twice the ratio compared to TT genotype. Similarly, this increase is also found in C3435T with 1.4-fold and in C1236T with 1.6-fold for the same genotypes. Regarding haplotypes, significant differences were obtained between CC-GG-CC and TT-TT-TT patients, with an 87.9% higher ratio in patients with the CC-GG-CC haplotype. There was a clear trend towards lower ARI concentrations and higher DHA concentrations when the presence of mutated T alleles increases. The ABCB1 gene could be a good partner along with CYP2D6 and CYP3A4 genotyping in conjunction with monitoring ARI plasma concentrations.

Plasmid hybrids as vectors for antibiotic resistance in environmental Escherichia coli.

This study investigated the potential role of phages in the dissemination of antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) in Escherichia coli (E. coli). A comprehensive in silico analysis of 18,410 phage sequences retrieved from the National Center for Biotechnology Information database (NCBI) revealed distinct carriage patterns for ARGs and VFGs between lytic, temperate, and chronic phage types. Notably, 57 temperate phages carried ARGs, particularly associated with multidrug and aminoglycoside resistance. Temperate phages (8.97%, 635/7081) and chronic phages (8.09%, 14/173) exhibited a significantly higher prevalence of VFGs (Chi-Square, p≤0.05), particularly associated with exotoxin-related genes, compared to lytic phages (0.05%, 6/11,156). This underscores the role phages play as reservoirs and potential vectors for the dissemination of ARGs and VFGs in bacteria. Our environmental E. coli isolates (n=60) were found to carry 179 intact prophages containing polymyxin, macrolide, tetracycline, and multidrug resistance genes as well as various VFGs. This study documents the presence of phage-plasmids (P-Ps) in environmental E. coli isolates, offering new insights into horizontal gene transfer (HGT) mechanisms. Notably, the blaCTX-M-15 gene, associated with beta-lactam resistance, was identified in two P-Ps, suggesting a potentially novel route for the dissemination of beta-lactam resistance. The diverse replicon types observed in P-Ps suggest a broader integration capacity compared to traditional plasmids, potentially enabling the blaCTX-M-15 gene dissemination across diverse bacterial species. This study provides valuable insights into the multifaceted role of phages in shaping the antimicrobial resistance landscape. Further research is necessary to fully understand the intricate mechanisms underlying phage-mediated ARG and VFG dissemination.

Effect of microplastics concentration and size on pollutants removal and antibiotic resistance genes (ARGs) generation in constructed wetlands: a metagenomics insight

The accrual of microplastics (MPs) and antibiotics poses synergistic threats to the environment. This study systemically examined the effect of environmental-level (μg/L) MPs (90–110 μm) and nanoplastics (NPs, 700nm) on constructed wetlands (CWs) treating oxytetracycline-contaminated wastewater via metagenomics analysis. Polystyrene (PS) MPs notably hindered the removal of nitrogen, phosphorus, and oxytetracycline, particularly at high level (1000μg/L), with removal rates of 73.34%, 59.59%, and 99.34%, respectively. Among them, the removal of NH4+-N decreased the most in comparison to CK, at 15.26%. Antibiotic resistance genes (ARGs) copies/16S rRNA ranged from 0.26 to 0.42 in CWs, exceeding that found in rivers by a factor of 1.5 to 2.5 times. The relative abundance of multidrug resistance genes (mdtB, acrB, mexF, mdtC, and mexT) and tetracycline resistance genes (txtA, tetG, and tetP) exhibited a pronounced increase under MPs exposure, ranging from 0.06 to 0.14 and 0.01 to 0.08 copies/16S rRNA, respectively. Redundancy and network analyses emphasized robust associations among contaminant reduction, ARG abundance, and microbial community. Partial least squares path modeling indicated MPs exerted a more profound influence on pollutant removal (coefficient = 0.8194), microbial community (coefficient = 0.3358) and ARGs dissemination (coefficient = 0.6566) compared to NPs. MPs concentrations significantly affects pollutants removal and ARGs proliferation, and MPs with larger sizes amplified ARG dissemination. This research highlights the influence of MPs on CW-mediated wastewater treatment and ARGs accumulation, offering valuable insights for developing ecological wastewater treatment strategies tailored to multi-pollutant scenarios. These insights are fundamental in developing sustainable solutions to the adverse impacts of MPs on ecosystems.

RETRACTION: Kaempferol Increases Apoptosis in Human Acute Promyelocytic Leukemia Cells and Inhibits Multidrug Resistance Genes.

M. Moradzadeh, A. Tabarraei, H. R. Sadeghnia, A. Ghorbani, A. Mohamadkhani, S. Erfanian, and A. Sahebkar, "Kaempferol Increases Apoptosis in Human Acute Promyelocytic Leukemia Cells and Inhibits Multidrug Resistance Genes," Journal of Cellular Biochemistry 119, no. 2 (2018): 2288-2297, https://doi.org/10.1002/jcb.26391. The above article, published online on October 20, 2017 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Christian Behl; and Wiley Periodicals LLC. The retraction has been agreed upon following an investigation into concerns raised by a third party, which revealed inappropriate image panel duplications between this article (Figure 5A,B) and other articles published by an overlapping group of authors, in which the images represent different experimental conditions. The explanation provided by the authors could not address these concerns. Thus, the editors have lost confidence in the presented data and consider the conclusions of this manuscript substantially compromised. A. Sahebkar disagrees with the retraction, the other co-authors remained unresponsive.

Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes.

The deep-sea ecosystem, a less-contaminated reservoir of antibiotic resistance genes (ARGs), has evolved antibiotic resistance for microbes to survive and utilize scarce resources. Research on the diversity and distribution of these genes in deep-sea environments is limited. Our metagenomics study employed short-read-based (SRB) and assembled-contig-based (ACB) methods to identify ARGs in deep-sea waters and sediments and assess their potential pathogenicity. SRB prediction was found to be more effective for studying the abundance and diversity of these genes, while combining both methods better illustrated the relationship of ARGs with the hosts. Deep-sea waters (DSW) and trenches had the highest diversity of ARGs, including β-lactams, multidrug resistance genes, and rifamycins. Mobile genetic elements, such as IncQ and RP4 plasmids, were also identified. The ratio of nonsynonymous to synonymous substitutions (pN/pS) values of these genes suggest different evolutionary strategies in response to deep-sea conditions and possible human impacts. These resistome profiles provide valuable insights into their natural origins as well as the ecological and evolutionary implications of antibiotic resistance in deep-sea ecosystems. The exploration of the global distribution of ARGs in diverse deep-sea environments is a novel approach that will assist in understanding their potential reservoirs and evolutionary mechanisms. Therefore, employing a comprehensive approach to studying ARGs is particularly necessary. Unique microbial life in deep-sea ecosystems, especially in deep-sea cold seeps sediments (DSCSS), deep-sea waters (DSW), and trench waters (TW), could be a valuable source of new antibiotics and resistance discovery.

ASSOCIATION ANALYSIS OF MULTIDRUG RESISTANCE GENE ABCB1 IN BREAST CANCER PATIENTS OF PUNJAB

Aims: This study aims to determine the frequency distribution of genetic polymorphisms of ABCB1 (rs1128503 and rs1045642) gene in breast cancer patients and the healthy controls and the association of these genotypes, if any, with susceptibility to breast cancer. Methods: The present case control study was conducted on the population of Punjab (North India). The cases included 300 breast cancer confirmed patients and the control group included (n=300) healthy female volunteers from general public after taking clearance from Institutional Ethical Committee (IEC) of Punjabi University, Patiala. Genomic DNA was isolated from whole blood collected in EDTA coated tubes by employing the standard inorganic (Salting Out) extraction method (Miller et al, 1988). PCR-RFLP technique was used for the amplification of the target region of the gene by using a single pair of primers. Genotyping of the PCR products and digested fragments obtained after RFLP was done by agarose gel electrophoresis. For PCR products, 1% gel was made and for the restriction digestion products, 3.5% gel was made. After separation, the bands representing products/ fragments were visualized under UV light for genotyping. Results:The frequency distribution of CC, CT, and TT genotypes of rs1045642 (C3435T) among breast cancer patients were 34%, 46.67% and 19.33% and among controls were 38.67%, 45.67% and 15.67% respectively. The frequencies of genotypes CC, CT and TT of rs1128503 (C1236T) among cases were 28%, 45.67% and 26.33% and among controls were 28.33%, 42% and 29.67%, respectively. The frequency of the wild allele (C) and mutant allele (T) of rs1045642 among cases was 57.33% and 42.67% and among controls, 61.5% and 38.5% respectively. The frequencies of the wild allele (CC) and mutant allele (T) of rs1128503 among cases were 50.83% and 49.17% and among controls were 49.33% and 50.67%, respectively.For association analysis, the contingent chi square test did not show any statistically significant differences between cases and controls for rs1045642 and rs1128503 gene polymorphisms neither at genotypic level and nor at allelic level. Conclusion: We found no evidence that reveals any statistically significant association of C3435T and C1236T polymorphisms with susceptibility to breast cancer in Punjab, India.

Molecular genetic characteristic of pulmonary tuberculosis associated with ABCB1 gene expression of multidrugresistance protein P-gp

Background: Tuberculous inflammation is mediated by a complex molecular signaling pathway, the analysis of which makes it possible to identify promising biomarkers and targets for the development of new diagnostic, prognostic and pharmacological approaches in order to improve the effectiveness of anti-tuberculosis chemotherapy. Determining the relationship between key inflammatory cytokines, the multidrug-resistant protein P-gp and the activity of specific inflammation in the surgical material of patients with pulmonary tuberculosis may prove to be a novel tool in the development of pathogenetic therapy and personalized medicine. Aims: to characterize molecular and genetic profiles of tuberculomas and identify genes that correlate with the expression of the ABCB1 gene of the P-gp protein in the surgical material of patients with pulmonary tuberculosis. Research objectives: 1) to obtain molecular and genetic characteristics of tuberculosis by real-time PCR and compare it with the activity of tuberculous inflammation; 2) to carry out a correlation analysis between the expression of the ABCB1 gene and key cytokines of the tuberculosis process: IL-6, IL-10, IFN-γ, TGF-β, TNF-α, IL-1β. Materials and methods: A prospective cohort study was conducted on the basis of the FSBI CTRI. The object of the study was the surgical material of 35 patients diagnosed with multiple pulmonary tuberculomas. Histological examination methods were used for the morphological assessment of the surgical material. A real-time quantitative PCR method was used to analyze gene expression. Statistical processing was performed using the GraphPad Prism Version 7.04 software package (GraphPad Software, USA). The data is presented as a median with an interquartile range. The nonparametric Mann-Whitney U-test was used to compare the two groups. All p-values were two-sided and p 0.05 was considered statistically significant. The correlation between the variables was estimated using the Spearman correlation coefficient. The correlation analysis was carried out in the Microsoft Office Excel 2010 software. Results: The study revealed that the highest level of expression of ABCB1 gene of the P-gp protein is observed in tuberculomas with high activity of tuberculous inflammation, and its expression is correlated with the expression of the IL6 gene (p0.001) and the expression of the IL10 gene (p0.01). Tuberculomas of this group are also characterized by higher expression of the TGFB1, TNF and IL1B genes, compared with the group of moderate activity of specific inflammation. Conclusions: The data obtained indicate that in addition to pro-/anti-inflammatory cytokines, the P-gp protein plays an important role in the pathogenesis of tuberculous inflammation, especially with its high activity. Further clarification of the P-gp role in tuberculous inflammation may be an important step for the development of new approaches to treat tuberculosis using methods of HDT and personalized medicine.

Identification and validation of KIF20A for predicting prognosis and treatment outcomes in patients with breast cancer

Breast cancer is a leading cause of cancer-related deaths among women globally. It is imperative to explore novel biomarkers to predict breast cancer treatment response as well as progression. Here, we collected six breast cancer samples and paired normal tissues for high-throughput sequencing. By differential expression analysis, we found 1687 DEGs and identified the top 10 hub genes, including TOP2A, CDK1, BUB1B, KIF11, CCNA2, BUB1, CCNB1, KIF20A, DLGAP5 and CDC20. Univariate and multivariate Cox analyses on the METABRIC database and GSE96058 dataset demonstrated that KIF20A was an independent prognostic predictor for overall survival. KIF20A was positively correlated with cell cycle phases, including the cell cycle process, cycle G2 M phase transition and cell cycle DNA replication initiation. Single-cell analyses revealed that KIF20A was enriched in fibroblasts and endothelial within breast cancer stroma. Meanwhile, multidrug resistance (MDR) genes ABCB1, ABCC1 and ABCG2 were co-expressed with KIF20A in fibroblasts and endothelial cells within the stroma. MTABRIC database confirmed that high expression of KIF20A was positively correlated with treatment efficacy in patients with breast cancer. In conclusion, KIF20A could be served as a predictive biomarker for breast cancer prognosis and treatment outcomes. KIF20A may play a significant role by regulating cell cycle progression and modulating stromal progression in breast cancer. Our findings provided novel molecular insights that can guide personalized treatment strategies in breast cancer.

ATP-Binding Cassette Transporter Genes and microRNAs in Pediatric B-Cell ALL: Expression Insights.

Acute lymphocytic leukemia (ALL), characterized by uncontrolled growth of abnormal lymphocytes, predominantly affects children. Genetic analysis focusing on genes and microRNAs reveals important information about the biology of ALL, enabling accurate diagnosis and treatment. This study examines gene and microRNA expression in B cell ALL to improve early diagnosis and personalized treatment. Bone marrow samples were collected from patients both before and after the induction phase of chemotherapy. Comprehensive diagnostic techniques including flow cytometry, molecular assays, real-time PCR for common translocations, karyotyping, and complete blood count (CBC) analysis were employed. These methods were utilized to determine the type and risk assessment of ALL, identify specific gene and microRNA expressions, and measure blood cell counts. The study comprised 12 patients, all under the age of 18. Post-treatment RT-PCR analysis revealed significant reductions in the expression of the ABCB1 gene, miR-129-5p, and miR-9-5p following the induction phase of chemotherapy. Karyotype analysis indicated that two patients were hypodiploid; unfortunately, both of these patients did not survive. MicroRNAs and ABC genes serve as predictive and prognostic biomarkers in Acute Lymphoblastic Leukemia (ALL) and should be carefully reconsidered. It is more accurate to state that while microRNAs and ABC genes may potentially influence treatment response in ALL, further research is crucial to fully understand their roles in determining treatment outcomes.

Dissemination mechanisms of unique antibiotic resistance genes from flowback water to soil revealed by combined Illumina and Nanopore sequencing.

As a byproduct of shale gas extraction, flowback water (FW) is produced in large quantities globally. Due to the unique interactions between pollutants and microorganisms, FW always harbor multiple antibiotic resistance genes (ARGs) that have been confirmed in our previous findings, potentially serving as a point source for ARGs released into the environment. However, whether ARGs in FW can disseminate or integrate into the environmental resistome remains unclear. In this study, unique ARGs from FW were identified, and the ARG profiles in soil and FW-spiked soil were compared using a combination of Illumina and Nanopore sequencing. The results indicated that the total abundance of the soil resistome increased by 30.8 % in soil contaminated with FW. Of this increase, 11.1 % was attributable to the integration of exogenous ARGs from FW into the soil resistome. Sequence alignment at the gene level further confirmed the successful integration of 20 unique ARG sequences classified as multidrug and vancomycin resistance genes into the soil resistome. These 20 ARG sequences were detected only in the FW. Multiple lines of evidence indicated that horizontal gene transfer dominated ARG dissemination in soil contaminated by FW. This conclusion is supported by the discrepancy between changes in mobile ARGs and host abundance, the upregulation of oxidative stress-related genes (SOD1 and SOD2) and the SOS response (lexA and recA), as well as the upregulation of genes related to quorum sensing (virD4, virB9, and virB3) and naked DNA uptake (pilD, pilT, and pilQ).

Transcriptional responses to in vitro macrocyclic lactone exposure in Toxocara canis larvae using RNA-seq.

Toxocara canis, the causative agent of zoonotic toxocariasis in humans, is a parasitic roundworm of canids with a complex lifecycle. While macrocyclic lactones (MLs) are successful at treating adult T. canis infections when used at FDA-approved doses in dogs, they fail to kill somatic third-stage larvae. In this study, we profiled the transcriptome of third-stage larvae derived from larvated eggs and treated in vitro with 10 μM of the MLs - ivermectin and moxidectin with Illumina sequencing. We analyzed transcriptional changes in comparison with untreated control larvae. In ivermectin-treated larvae, we identified 608 differentially expressed genes (DEGs), of which 453 were upregulated and 155 were downregulated. In moxidectin-treated larvae, we identified 1,413 DEGs, of which 902 were upregulated and 511 were downregulated. Notably, many DEGs were involved in critical biological processes and pathways including transcriptional regulation, energy metabolism, neuronal structure and function, physiological processes such as reproduction, excretory/secretory molecule production, host-parasite response mechanisms, and parasite elimination. We also assessed the expression of known ML targets and transporters, including glutamate-gated chloride channels (GluCls), and ATP-binding cassette (ABC) transporters, subfamily B, with a particular focus on P-glycoproteins (P-gps). We present gene names for previously uncharacterized T. canis GluCl genes using phylogenetic analysis of nematode orthologs to provide uniform gene nomenclature. Our study revealed that the expression of Tca-glc-3 and six ABCB genes, particularly four P-gps, were significantly altered in response to ML treatment. Compared to controls, Tca-glc-3, Tca-Pgp-11.2, and Tca-Pgp-13.2 were downregulated in ivermectin-treated larvae, while Tca-abcb1, Tca-abcb7, Tca-Pgp-11.2, and Tca-Pgp-13.2 were downregulated in moxidectin-treated larvae. Conversely, Tca-abcb9.1 and Tca-Pgp-11.3 were upregulated in moxidectin-treated larvae. These findings suggest that MLs broadly impact transcriptional regulation in T. canis larvae.