Yeter Düzenli Kar, İmran Sağlık, Gökalp Rüstem Aksoy
et al.
IntroductionRespiratory tract infections (RTI) are a leading cause of hospitalization in children and remain a significant contributor to morbidity. Our study aimed to examine the epidemiology of RTI in children with hemato-oncologic disease during and after the coronavirus 2019 (COVID-19) pandemic.MethodsThis retrospective study evaluated nasopharyngeal swab samples that were tested using multiplex PCR from 185 children hospitalized with respiratory symptoms between January 2020 and March 2025.ResultsA total of 313 RTI agents were identified in 185 children with hemato-oncologic disorders across 271 infectious episodes. The median age was 6 years. The infection rates for upper respiratory tract infections (URTI) and lower respiratory tract infections (LRTI) were 45% and 55%, respectively. A statistically significant difference was found between patients with URTI and LRTI in terms of CRP, tachypnea, dyspnea, duration of fever, duration of hospital stay due to infection, need for intensive care unit, and oxygen requirements (p < 0.05). The most common pathogens causing RTI were rhinovirus/enterovirus and influenza A/B, and their frequencies increased significantly in the post-pandemic period. Co-infections were significantly more common in the LRTI group during the post-pandemic period. Nine out of 185 children (5%) died.ConclusionChildren with hematologic-oncologic disease are at risk for RTI. The most common agent was found to be rhinovirus/enterovirus. RTI outbreaks were observed especially as a result of the reductions in non-pharmacological measures implemented during the pandemic. In our study, the largest RTI outbreak was seen between November 2023 and May 2024 following the end of the COVID-19 pandemic.
In April 2025, a human seasonal reassortant influenza A(H1N2) virus with a 7:1 genetic constellation was detected in Sweden in a patient seeking primary care for influenza-like illness. The neuraminidase gene of this virus was from A(H3N2) and the remaining genes from A(H1N1)pdm09. The patient recovered. No additional cases have been detected through routine surveillance. This is so far the only identified A(H1N2) reassortant among three seasonal A(H1N1)pdm09 and A(H3N2) reassortants reported in GISAID from Europe during the 2024/25 season.
Farida Handayani, Endah Tri Widanarti, Citra W. Kusuma
et al.
ABSTRACT Leptospirosis is an endemic zoonotic disease with protean clinical manifestations caused by pathogenic spirochetes of the Leptospira genus. The microscopic agglutination test (MAT) is the gold standard for leptospirosis diagnosis and can only be conducted in a reference laboratory. Therefore, alternative tests, such as the IgM anti-Leptospira rapid diagnostic test (RDT), are preferred for general use. In this study, we aimed to compare the accuracy of four products of anti-Leptospira IgM detection RDTs, which are available in Indonesia, against the gold standard of Leptospira MAT. This study was a diagnostic validation test using bioarchived serum from 364 human serum samples tested by MAT from August to September 2020 in Demak, Central Java, Indonesia. The four products were (i) Fokus Leptospira, (ii) Answer Leptospira, (iii) SD Bioline Leptospira IgG/IgM, and (iv) Uji Leptospira IgM, sequentially renamed RDT-1 to RDT-4. Interobserver agreements were analyzed using the kappa value. The diagnostic performance of the four RDTs were compared against MAT results as the gold standard. We also evaluated the combination of two RDTs’ performance, which were RDT (1 + 2), RDT (1 + 3), RDT (1 + 4), RDT (2 + 4), and RDT (3 + 4). We found that the kappa coefficients of RDT-1, RDT-2, and RDT-4 were greater than 80%, while RDT-3 had a moderate kappa value of 69.1%. RDT-1, RDT-2, and RDT-4 had moderate to good sensitivities of 78.2%, 74.3%, and 83.6%, respectively, while RDT-3 had the lowest sensitivity at 30.9%. RDT-3 demonstrated the highest specificity. RDT-2 showed the highest predictive value at 75.9%, while RDT-4 showed the highest negative predictive value at 96.9%. In addition, the combination of two RTDs provided better diagnostic performances. The four RDTs performed varied in their ability to diagnose leptospirosis, but only RDT-4 showed a sensitivity of more than 80%. We recommend caution in diagnosing only one RDT result. Testing by other RDTs and confirmation by MAT are strongly recommended.IMPORTANCEThe performance of the anti-Leptospira IgM antibody rapid diagnostic tests (RDTs) has yet to be evaluated. In this study, we compare the accuracy of these four RDTs available in Indonesia against the gold standard of Leptospira microscopic agglutination test (MAT). Utilizing the best performance of RDT in the point of care with limited facilities will be effective since MAT is complicated, laborious, and time-consuming if done at public health centers. The MAT requires maintaining the culture of each live Leptospira strain circulating in the region and needs trained personnel.
In the developing gut of infants, Bifidobacteria establish themselves and become one of the predominant microbial populations, playing vital roles in host health by modulating immune responses, inhibiting the growth of pathogenic bacteria, and enhancing nutrient metabolism. While Bifidobacterium strains from Western populations have been extensively studied, those derived from Chinese infants remain underexplored. Given the substantial impact of geography, diet, and host genetics on gut microbiota composition and function, strains from the Chinese population may possess unique probiotic properties with significant scientific and clinical relevance. In this study, we isolated a highly abundant clinical Bifidobacterium breve strain with intrinsically high transformation efficiency from the feces of a healthy Chinese infant. We obtained its complete genome using Oxford Nanopore sequencing. To assess its genetic tractability, we first employed two conventional double-crossover gene knockout strategies. A pyrE mutant was successfully constructed using a shuttle vector, leveraging its 5-fluoroorotic acid (5-FOA) sensitivity as a counterselection marker. To enable efficient, scarless genome editing, we developed a novel dual-plasmid system that markedly improved the selection of single-crossover events. This approach enabled robust and flexible genetic manipulation of a clinically derived B. breve strain that was previously recalcitrant to standard knockout techniques. Our work not only provides a powerful platform for dissecting the probiotic mechanisms of B. breve, but also serves as a valuable reference for the development of genetic tools applicable to other clinically relevant strains.
Our laboratory had isolated a strain of non-Saccharomyces yeast with significant application potential from high-temperature Daqu, Lachancea thermotolerans Y-07. This study aimed to explore the interaction of L. thermotolerans Y-07 with Aspergillus oryzae M-08 and Saccharomyces cerevisiae BS-19 when used for mixed culture fermentation of Baijiu under gradient temperature conditions and to evaluate its impact on Baijiu quality. To this end, changes in biomass, sensory quality, organic acids and volatile flavor compounds were examined during the fermentation process. The results demonstrated that L. thermotolerans Y-07 produced β-phenylethanol, reduced the higher alcohol content, and significantly improved the sensory quality of Baijiu, indicating its positive role in Baijiu brewing. High-temperature conditions not only helped maintain yeast diversity during the fermentation process, but also enhanced aroma richness. The presence of S. cerevisiae BS-19 increased the biomass of L. thermotolerans Y-07 by 21.63%. Under high-temperature conditions, the presence of S. cerevisiae BS-19 facilitated the recovery and proliferation of L. thermotolerans Y-07. This study provides important insights into the mechanism of action of L. thermotolerans in Baijiu brewing and the influence of temperature on microbial interactions during the fermentation process.
IntroductionThis study adopted the intercropping pattern opepper (Capsicum annuum L.) and Chinese chives (Allium tuberosum), combined with high-throughput sequencing and microbial network analysis, to systematically reveal the mechanisms of intercropping on the structural regulation and functional synergy of the crop rhizosphere microbiome and root-stem endophyte communities.MethodsThree treatments were set up: blank control, solo cultivation, and intercropping.Combined with high-throughput sequencing and network analysis, the reorganization patterns of rhizosphere and endophyte communities were systematically analyzed.ResultsIntercropping induced differential responses of microbial communities in the two crops: it significantly increased the bacterial α-diversity in Chinese chives leaves, and the Shannon index of pepper roots also showed an upward trend, while the microbial diversity in pepper rhizosphere soil was inhibited. In contrast, among roots, the “pepper intercropped with Chinese chives” group had the highest total number of OTUs and the largest number of unique OTUs. Microbial communities exhibited cross-host transfer characteristics: the migration rate of microbial communities from pepper roots to Chinese chives rhizosphere reached 46.57%, and 69.54% of the microbial communities in Chinese chives roots originated from pepper roots. Specifically, Aureimonas and Sphingomonadaceae were significantly enriched in pepper leaves, the relative abundance of Pantoea in Chinese chives leaves increased by 11.5 times, and the abundance of Flavobacterium in pepper rhizosphere increased by 94%. Microbial co-occurrence network analysis confirmed the optimization of functional synergy: the proportion of positive interactions in pepper leaves increased to 90.45%, and the negative interactions of Bradyrhizobium decreased by 97%, the proportion of positive interactions of functional bacteria in Chinese chives rhizosphere reached 88.96%, and Bacillus enhanced positive connections while maintaining an abundance of 10.23%–20.87%, the number of positive interactions of Streptomyces in pepper rhizosphere doubled. Network stability showed spatial variation: the robustness of stem microbial networks was significantly improved, while the vulnerability of rhizosphere microbial networks increased.DiscussionThis study provides microbial theoretical support for the intercropping system to optimize nitrogen utilization by driving pepper to enrich the growth-promoting bacteria Sphingomonadaceae, and to enhance disease resistance by promoting Chinese chives to recruit the biocontrol bacteria Bacillus, thereby forming a microecological regulation mechanism with functional complementarity.
Water is essential for life. An adequate, safe, and accessible water supply must be available to all. Hence, this research aimed to isolate and characterize bacteria from borehole water samples located at the Presco campus, Ebonyi State University, Abakaliki, and test the antibiotic susceptibility patterns of the bacteria isolated. Twelve (12) water samples were collected from six (6) locations in duplicates and analyzed using standard microbiological methods. Serial dilutions were performed on the samples and dilutions of 103 were plated using the pour plate method. After the incubation periods, colonies were counted and expressed in CFU/mL, biochemical tests were carried out and the antibiotics susceptibility profiles of the bacteria isolated were evaluated. From the results, the total microbial counts ranged from 1.0 x 10^4 to 5.9 x 10^4 CFU/mL, indicating high contamination of the water samples. The morphology and biochemical tests revealed the presence of Shigella species 5 (45.4%) and Salmonella species 6 (54.6%). Shigella species were highly resistant to both Trimethoprim-Sulphamethoxazole and Amoxicillin (80%) and to Tetracycline (100%) but were susceptible to Ceftriaxone (100%) and Ciprofloxacin (80%). On the other hand, Salmonella species showed a resistant pattern of 83.3% to Tetracycline, Ciprofloxacin, and Ceftriaxone but were susceptible to Levofloxacin (100%) and Cefepime (83.3%). This result is of public health importance as these organisms can threaten individuals utilizing these boreholes as the source of drinking water.
Linda Batsa Debrah, Charles Gyasi, Monica Ahiadorme
et al.
Abstract Background Onchocerciasis causes chronic systemic inflammation. Several studies have used markers such as haemato-biochemical indices to predict the occurrence of systemic inflammation. This study assessed the variability and predictability of haemato-biochemical indices and blood composite ratios (BCRs) in microfilariae positive (MF+) and microfilariae negative (MF-) subgroups of onchocercomata participants. Methods One hundred and five (105) MF + and 34 MF- participants were retrospectively recruited into the study. Screening for the presence of O. volvulus microfilariae was done from skin snips taken from the left and right iliac crests of participants using established and approved protocols. Haematological and biochemical indices were measured using standard laboratory automated analyzers. Blood composite ratios (BCRs) were calculated as ratios of the absolute parameters involved. Results A significantly increased total WBC, absolute eosinophil, eosinophil percent and absolute basophil were observed in the MF + participants compared to MF- participants. Reduced gamma-glutamyl transferase (GGT) with increased estimated glomerular filtration rate (eGFR) was significantly associated with MF + participants compared to MF- participants. BCRs were significantly higher for eosinophil-to-neutrophil ratio (ENR), eosinophil-to-monocyte ratio (EMR), eosinophil-to-basophil ratio (EBR) and eosinophil-to-lymphocyte ratio (ELR) in MF + participants compared to MF- participants. After multivariate adjustment, onchocercomata participants with increased eosinophil counts (aOR = 13.86, 95% CI [2.07–92.90], p = 0.007), ENR x10 (aOR = 1.42, 95% CI [1.05–1.93], p = 0.025), EMR (aOR = 2.64, 95% CI [1.25–5.60], p = 0.011), EBR (aOR = 1.07, 95% CI [1.01–1.10], p = 0.020) and ELR x10 (aOR = 1.69, 95% CI [1.14–2.51], p = 0.009) were more likely to have microfilaridermia. Conclusions Elevated eosinophil counts with higher ENR, EMR, EBR and ELR levels are significantly associated with microfilaridermia in onchocercomata participants. Combining BCRs with eosinophil count significantly led to an improvement in the conventional model for predicting microfilaridermia.
Sareh Farahani, Abbas Akhavanesepahi, Sayed abbas Shojaosadati
et al.
Introduction: Due to the increasing trend of industrial development and also the industrial production, the presence of heavy metals along with industrial wastewater is undeniable. Despite the various ways to remove heavy metals, choosing biological methods can be the best way to control them. Using bacteria in this field can be very useful and inexpensive with less harm.
Materials and Methods: In the present study, various aquatic environments including rivers, ponds, industrial effluents, and activated sludge were sampled. Bacteria were identified based on the growth in iron-specific culture medium in terms of shape and 16S rRNA gene. These bacteria were cultured in specific culture media for iron-oxidizing bacteria, Luria-Bertoni (LB) and PHG II, containing 2 ppm of mercury chloride and cadmium chloride. The samples were then examined for the reduction or non-change of mercury and cadmium concentrations by atomic absorption spectrometry.
Results: The results of the present study showed that the isolated bacteria were rod-shaped and chemoorganotrophic belonging to the genus Bacillus. The average percentages of mercury and cadmium removal by the isolated bacteria were about 95% and 40%, respectively. The highest percentage of the removal of both heavy metals was observed in the effluent sample of iron factory wastewater.
Discussion and Conclusion: Iron oxidizing bacteria were identified as reducing agents of heavy metals in the laboratory environment. These bacteria grew in both LB medium and iron-specific culture medium. The highest percentage of the removal of both heavy metals was observed in the effluent sample of the iron processing plant. Based on the results, it can be said that the bacteria of each environment have adapted to the compounds of that place and are the best option to remove compounds such as heavy metals.
Daria Krefft, Maciej Prusinowski, Paulina Maciszka
et al.
Abstract Background The widespread usage of protein expression systems in Escherichia coli (E. coli) is a workhorse of molecular biology research that has practical applications in biotechnology industry, including the production of pharmaceutical drugs. Various factors can strongly affect the successful construction and stable maintenance of clones and the resulting biosynthesis levels. These include an appropriate selection of recombinant hosts, expression systems, regulation of promoters, the repression level at an uninduced state, growth temperature, codon usage, codon context, mRNA secondary structure, translation kinetics, the presence/absence of chaperons and others. However, optimization of the growth medium’s composition is often overlooked. We systematically evaluate this factor, which can have a dramatic effect on the expression of recombinant proteins, especially those which are toxic to a recombinant host. Results Commonly used animal tissue- and plant-based media were evaluated using a series of clones in pET vector, containing expressed Open Reading Frames (ORFs) with a wide spectrum of toxicity to the recombinant E. coli: (i) gfpuv (nontoxic); (ii) tp84_28—which codes for thermophilic endolysin (moderately toxic); and (iii) tthHB27IRM—which codes for thermophilic restriction endonuclease-methyltransferase (REase-MTase)—RM.TthHB27I (very toxic). The use of plant-derived peptones (soy peptone and malt extract) in a culture medium causes the T7-lac expression system to leak. We show that the presence of raffinose and stachyose (galactoside derivatives) in those peptones causes premature and uncontrolled induction of gene expression, which affects the course of the culture, the stability of clones and biosynthesis levels. Conclusions The use of plant-derived peptones in a culture medium when using T7-lac hybrid promoter expression systems, such as Tabor-Studier, can lead to uncontrolled production of a recombinant protein. These conclusions also extend to other, lac operator-controlled promoters. In the case of proteins which are toxic to a recombinant host, this can result in mutations or deletions in the expression vector and/or cloned gene, the death of the host or highly decreased expression levels. This phenomenon is caused by the content of certain saccharides in plant peptones, some of which (galactosides) may act as T7-lac promoter inducer by interacting with a Lac repressor. Thus, when attempting to overexpress toxic proteins, it is recommended to either not use plant-derived media or to use them with caution and perform a pilot-scale evaluation of the derepression effect on a case-by-case basis.
Neeraja Punde, Jennifer Kooken, Dagmar Leary
et al.
Abstract Codon usage frequency influences protein structure and function. The frequency with which codons are used potentially impacts primary, secondary and tertiary protein structure. Poor expression, loss of function, insolubility, or truncation can result from species-specific differences in codon usage. “Codon harmonization” more closely aligns native codon usage frequencies with those of the expression host particularly within putative inter-domain segments where slower rates of translation may play a role in protein folding. Heterologous expression of Plasmodium falciparum genes in Escherichia coli has been a challenge due to their AT-rich codon bias and the highly repetitive DNA sequences. Here, codon harmonization was applied to the malarial antigen, CelTOS (Cell-traversal protein for ookinetes and sporozoites). CelTOS is a highly conserved P. falciparum protein involved in cellular traversal through mosquito and vertebrate host cells. It reversibly refolds after thermal denaturation making it a desirable malarial vaccine candidate. Protein expressed in E. coli from a codon harmonized sequence of P. falciparum CelTOS (CH-PfCelTOS) was compared with protein expressed from the native codon sequence (N-PfCelTOS) to assess the impact of codon usage on protein expression levels, solubility, yield, stability, structural integrity, recognition with CelTOS-specific mAbs and immunogenicity in mice. While the translated proteins were expected to be identical, the translated products produced from the codon-harmonized sequence differed in helical content and showed a smaller distribution of polypeptides in mass spectra indicating lower heterogeneity of the codon harmonized version and fewer amino acid misincorporations. Substitutions of hydrophobic-to-hydrophobic amino acid were observed more commonly than any other. CH-PfCelTOS induced significantly higher antibody levels compared with N-PfCelTOS; however, no significant differences in either IFN-γ or IL-4 cellular responses were detected between the two antigens.
Introduction: Patients with glioblastoma (GBM), one of the most aggressive forms of primary brain tumors, exhibit a wide range of neurologic signs, ranging from headaches to neurologic deficits and cognitive impairment, at first clinical presentation. While such variability is attributed to inter-individual differences in increased intracranial pressure, tumor infiltration, and vascular compromise, a direct association with disease stage, tumor size and location, edema, and necrotic cell death has yet to be established. The lack of specificity of neurologic symptoms often confounds the diagnosis of GBM. It also limits clinicians’ ability to elect treatment regimens that not only prolong survival but also promote symptom management and high quality of life.Methods: To decipher the heterogeneous presentation of neurologic symptoms in GBM, we investigated differences in the molecular makeup of tumors from patients with and without preoperative neurologic deficits. We used the Ivy GAP (Ivy Glioblastoma Atlas Project) database to integrate RNA sequencing data from histologically defined GBM tumor compartments and neurologic examination records for 41 patients. We investigated the association of neurologic deficits with various tumor and patient attributes. We then performed differential gene expression and co-expression network analysis to identify a transcriptional signature specific to neurologic deficits in GBM. Using functional enrichment analysis, we finally provided a comprehensive and detailed characterization of involved pathways and gene interactions.Results: An exploratory investigation of the association of tumor and patient variables with the early development of neurologic deficits in GBM revealed a lack of robust and consistent clinicopathologic prognostic factors. We detected significant differences in the expression of 728 genes (FDR-adjusted p-value ≤ 0.05 and relative fold-change ≥ 1.5), unique to the cellular tumor (CT) anatomical compartment, between neurologic deficit groups. Upregulated differentially expressed genes in CT were enriched for mesenchymal subtype-predictive genes. Applying a systems approach, we then identified co-expressed gene sets that correlated with neurological deficit manifestation (FDR-adjusted p-value < 0.1). Collectively, these findings uncovered significantly enriched immune activation, oxidative stress response, and cytokine-mediated proinflammatory processes.Conclusion: Our study posits that inflammatory processes, as well as a mesenchymal tumor subtype, are implicated in the pathophysiology of preoperative neurologic deficits in GBM.
Maria A. Prostova, Elena Smertina, Denis V. Bakhmutov
et al.
Replication of RNA viruses is generally markedly error-prone. Nevertheless, these viruses usually retain their identity under more or less constant conditions due to different mechanisms of mutation tolerance. However, there exists only limited information on quantitative aspects of the mutational tolerance of distinct viral functions. To address this problem, we used here as a model the interaction between a replicative <i>cis</i>-acting RNA element (<i>ori</i>L) of poliovirus and its ligand (viral protein 3CD). The mutational tolerance of a conserved tripeptide of 3CD, directly involved in this interaction, was investigated. Randomization of the relevant codons and reverse genetics were used to define the space of viability-compatible sequences. Surprisingly, at least 11 different amino acid substitutions in this tripeptide were not lethal. Several altered viruses exhibited wild-type-like phenotypes, whereas debilitated (but viable) genomes could increase their fitness by the acquisition of reversions or compensatory mutations. Together with our study on the tolerance of <i>ori</i>L (Prostova et al., 2015), the results demonstrate that at least 42 out of 51 possible nucleotide replacements within the two relevant genomic regions are viability-compatible. These results provide new insights into structural aspects of an important viral function as well as into the general problems of viral mutational robustness and evolution.
Graciela M. Dias, Araceli deSousa Pires, Vinicius S. Grilo
et al.
Abstract Burkholderia harbors versatile Gram‐negative species and is β‐Proteobacteria. Recently, it was proposed to split the genus in two main branches: one of animal and plant pathogens and another, Paraburkholderia, harboring environmental and plant‐beneficial species. Currently, Paraburkholderia comprises more than 70 species with ability to occupy very diverse environmental niches. Herein, we sequenced and analyzed the genome of Paraburkholderia kururiensis type strain KP23T, and compared to P. kururiensis M130, isolated in Brazil, and P. kururiensis susbp. thiooxydans, from Korea. This study focused on the gene content of the three genomes with special emphasis on their potential of plant‐association, biocontrol, and bioremediation. The comparative analyses revealed several genes related to plant benefits, including biosynthesis of IAA, ACC deaminase, multiple efflux pumps, dioxygenases, and degradation of aromatic compounds. Importantly, a range of genes for protein secretion systems (type III, IV, V, and VI) were characterized, potentially involved in P. kururiensis well documented ability to establish endophytic association with plants. These findings shed light onto bacteria‐plant interaction mechanisms at molecular level, adding novel information that supports their potential application in bioremediation, biofertilization, and biocontrol of plant pathogens. P. kururiensis emerges as a promising model to investigate adaptation mechanisms in different ecological niches.
Federica D’asta, Fenella Halstead, Paul Harrison
et al.
The infection of a wound is one of the major contributors to delays in healing and tissue regeneration. As multi-drug resistance to antibiotics is becoming a serious threat, research in this field has focused on finding new agents and strategies to fight infection and additionally to reduce healing times. The topical use of autologous Platelet Rich Plasma (PRP) as a biological accelerator of the healing process, has been safely used as a form of treatment for wounds since the 1990s. Although the presence or absence of leucocytes in PRP preparation was previously neglected, in the last decade more attention has been paid to their role and several studies have been conducted to explore both their immuno-metabolic effects and their antimicrobial properties. In this review, we aim to summarise the literature on the contribution of leucocytes included in PRP preparations in terms of their antimicrobial properties. This should help to inform clinical practice and additional research in this promising field.
Tomasz Bogiel, Aleksander Deptuła, Joanna Kwiecińska-Piróg
et al.
Pseudomonas aeruginosa rods are one of the most commonly isolated microorganisms from clinical specimens, usually responsible for nosocomial infections. Antibiotic-resistant P. aeruginosa strains may present reduced expression of virulence factors. This fact may be caused by appropriate genome management to adapt to changing conditions of the hospital environment. Virulence factors genes maybe replaced by those crucial to survive, like antimicrobial resistance genes. The aim of this study was to evaluate, using PCR, the occurrence of exoenzyme S-coding gene (exoS) in two distinct groups of P. aeruginosa strains: 83 multidrug-sensitive (MDS) and 65 multidrug-resistant (MDR) isolates. ExoS gene was noted in 72 (48.7%) of the examined strains: 44 (53.0%) MDS and 28 (43.1%) MDR. The observed differ­ences were not statistically significant (p = 0.1505). P. aeruginosa strains virulence is rather determined by the expression regulation of the possessed genes than the difference in genes frequency amongst strains with different antimicrobial susceptibility patterns.