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PubMed2026

Employing Metagenomics Capture targeted next-generation sequencing for the etiological diagnosis of bloodstream infections.

BACKGROUND: Bloodstream infections (BSIs) represent a significant public health concern. Metagenomic Capture targeted next-generation sequencing technology, as a newly emerging method for pathogen detection, has been applied in the etiological diagnosis of various infectious diseases and demonstrates good diagnostic efficacy. However, there is relatively limited research on the diagnostic value of this technology for the etiological diagnosis of BSIs. METHODS: A comprehensive retrospective analysis was performed on patients suspected of having BSIs who were admitted to the Affiliated Guangdong Second Provincial General Hospital of Jinan University in 2024. These patients underwent both blood culture analysis and Metagenomic Capture targeted next-generation sequencing technology for diagnostic testing, and a detailed comparison of the results was conducted. RESULTS: It was found that the Metagenomic Capture-targeted next-generation sequencing method has a shorter time to result [1.33 (1.18 - 1.69) vs 2.73 (1.89 - 3.84) days, p&#xa0;<&#xa0;0.001], more pathogenic microbial species detected, higher positive detection rate and higher sensitivity than blood culture. CONCLUSIONS: Metagenomic Capture targeted next-generation sequencing technology is a promising tool for pathogen identification in BSIs, offering substantial methodological advantages in terms of turnaround time, detection breadth, and sensitivity. These diagnostic performance characteristics support its potential utility in clinical microbiology practice.

Humans↗
PubMed2026

Discovering common and population-specific QTLs for leaf rust resistance in different Barley populations.

Multi-population GWAS lead to identification of common and population-specific QTLs for leaf rust resistance in barley. Genome-wide association studies (GWAS) are a powerful tool for detecting genetic markers associated with traits of interest. However, these studies are typically restricted to a single population, and transferability of identified marker effects across populations is challenged by population differences in linkage, allele frequencies, epistatic effects, and environmental context. When comparing GWAS results between populations, a lack of overlapping signals is often interpreted as a lack of common quantitative trait loci (QTLs), although such discrepancies may result from differences in statistical power to detect signals. In barley (Hordeum vulgare L.), where genetic leaf rust resistance is rapidly overcome by evolving pathogens, identification of cross-population robust and potentially transferable resistance loci is a key task. Here, we present a mixed model approach for multi-population GWAS that estimates correlated marker effects in multiple populations and use this to test for significant effects across and within populations. Applying this model to four barley breeding populations revealed both common and population-specific QTL effects for leaf rust resistance, including loci colocalizing with known Rph genes and novel regions with plausible candidate genes. Multi-population GWAS increased power, revealing signals not detected by GWAS within populations. We categorized the reported QTLs into three groups based on marker-associated allele effects: (1) consistent effect direction across populations, (2) differing effect direction across populations, and (3) present in a single population. The study highlights the transferability and limitations of leaf rust resistance QTLs across different barley populations and provides a general statistical framework to support robust marker-assisted selection across populations.

Quantitative Trait Loci↗
PubMed2026

[Microbiological Characterization of Exacerbations in Severe Asthma and Their Impact on Therapeutic Decision-Making].

INTRODUCTION: Severe asthma (SA) exacerbations impose a substantial healthcare burden. Microbiological characterization using molecular techniques may improve pathogen identification and contribute to a more individualized therapeutic approach. OBJECTIVE: To characterize the microbiological profile of exacerbations in patients with severe asthma and to analyze the prescription patterns for antibiotics (ATB) and systemic corticosteroids (SC). METHODS: This retrospective observational study was conducted in a Severe Asthma Unit. A total of 103 exacerbations were investigated using conventional microbiological methods and multiplex polymerase chain reaction (FilmArray&#x2122;) performed on respiratory samples. Bacterial findings were classified according to operational criteria compatible with infection or colonization based on genomic load and culture results. Associations between clinical, microbiological, and therapeutic variables were explored using univariate analyses. RESULTS: Microbiological detection was achieved in 78.6% of exacerbations. Viruses were identified in 59.2% of episodes, with rhinovirus representing the predominant pathogen (62.3% of viral detections). Bacteria were identified in 53.4% of exacerbations (H. influenzae 36,6%), frequently in association with viral coinfection. Bronchiectasis was associated with a higher probability of bacterial detection (OR 2.50; p&#xa0;=&#xa0;0.031). ATB and SC were prescribed in 61.2% and 44.6% of exacerbations, respectively, with frequent use of combination therapy. No significant differences in overall microbiological detection rates were observed according to biologic therapy status. Considerable microbiological variability was observed across recurrent exacerbations in the same patient. CONCLUSIONS: Microbiological findings were common during severe asthma exacerbations, with respiratory viruses, particularly rhinovirus, being the most frequently identified pathogens. Bronchiectasis was associated with higher rates of bacterial detection and ATB use. The marked variability observed between episodes supports the potential value of individualized microbiological assessment during exacerbations and warrants prospective studies aimed at optimizing therapeutic decision-making.

Biologic therapies.↗
PubMed2026

Characterisation of Carbapenem-Resistant Raoultella planticola and Structural Analysis of NDM Composite Plasmids.

OBJECTIVE: This study aimed to investigate the molecular characteristics, resistant plasmid structures and phylogeny of a carbapenem-resistant Raoultella planticola (CRRP) strain from a patient with pneumonia to inform antimicrobial resistance control strategies. METHODS: We performed strain identification using MALDI-TOF MS, the BD Phoenix 100 system and whole-genome sequencing (WGS). We assessed antimicrobial susceptibility and resistance gene transfer using PCR, conjugation and stability assays, plasmid structure using a bioinformatics tool and phylogeny using a core-genome phylogenetic tree. RESULTS: WGS confirmed the isolate as R. planticola (average nucleotide identity (ANI) > 98.9% with reference type strains), co-harbouring blaKPC-2 and blaNDM-1. It was resistant to 19 antimicrobial agents and susceptible to only polymyxin, amikacin and chloramphenicol. Resistance genes were present on two conjugative plasmids: pzwx_KPC (IncFIA) and pzwx_NDM (a novel repFIB/repHI5B hybrid assembled via non-homologous end joining). Both plasmids demonstrated efficient transfer and stable inheritance over 12 passages. pzwx_KPC was highly homologous to plasmids from Klebsiella pneumoniae. Phylogenetic analysis revealed the closest relationship with German R. planticola strains. CONCLUSION: CRRP carries highly transmissible and stable resistance plasmids. Strengthened monitoring in immunocompromised patients and improved environmental disinfection are recommended. The risk of misidentification by automated systems underscores the importance of WGS for accurate pathogen identification.

Carbapenem resistance↗
PubMed2026

DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.

SUMMARYDNA sequencing has revolutionized microbial surveillance in cystic fibrosis (CF), transforming pathogen identification from culture-dependent to total microbial community identification using molecular-based approaches. Techniques such as 16S rRNA gene sequencing have uncovered the complexity of the CF airway microbiome, while shotgun metagenomics, metatranscriptomics, and viromics now provide strain-level, functional, and viral insights beyond bacterial identification. Despite these advances, key technical and logistical challenges remain, including the processing of high-viscosity sputum samples, overwhelming host DNA contamination, managing large data sets, and the integration of complex bioinformatic outputs into clinical workflows. Emerging innovations such as host DNA depletion protocols, targeted enrichment panels, and adaptive sampling on Oxford Nanopore platforms are helping to overcome these barriers, improving microbial recovery and sequencing efficiency. As cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies are changing the lives of people with cystic fibrosis (pwCF), sequencing offers an unprecedented opportunity to track potential microbial adaptation in response. This review investigates current advances, limitations, and translational opportunities in DNA sequencing for CF airway microbiome surveillance, highlighting how these technologies can help reshape research and clinical microbiology in the post-modulator era.

Cystic Fibrosis↗
PubMed2024

Effect of Metagenomic Next-Generation Sequencing on Clinical Outcomes of Patients With Severe Community-Acquired Pneumonia in the ICU: A Multicenter, Randomized Controlled Trial.

BACKGROUND: Metagenomic next-generation sequencing (mNGS) was previously established as a method that can increase the pathogen identification rate in patients with severe community-acquired pneumonia (SCAP). RESEARCH QUESTION: What is the impact on clinical outcomes of mNGS of BAL fluid (BALF) in patients with SCAP in the ICU? STUDY DESIGN AND METHODS: A multicenter randomized controlled open-label clinical trial was conducted in 10 ICUs. Patients were randomized in a 1:1 ratio to undergo BALF assessment with conventional microbiological tests (CMTs) only (ie, the CMT group) or BALF assessment with both mNGS and CMTs (ie, the mNGS group). The primary outcome was the time to clinical improvement, defined as the time from randomization to either an improvement of two points on a six-category ordinal scale or discharge from the ICU, whichever occurred first. RESULTS: A total of 349 patients were randomized to treatment between January 1, 2021, and November 18, 2022; 170 were assigned to the CMT group and 179 to the mNGS group. In the intention-to-treat analysis, the time to clinical improvement was better in the mNGS group than in the CMT group (10&#xa0;days vs&#xa0;13&#xa0;days; difference, -2.0&#xa0;days; 95%&#xa0;CI, -3.0 to 0.0&#xa0;days). Similar results were obtained in the per-protocol analysis. The proportion of patients with clinical improvement within 14&#xa0;days was significantly higher in the mNGS group (62.0%) than in the CMT group (46.5%). There was no significant difference in other secondary outcomes. INTERPRETATION: We found that compared with the use of CMTs alone, mNGS combined with CMTs reduced the time to clinical improvement for patients with SCAP. CLINICAL TRIAL REGISTRATION: Chinese Clinical Trial Registry, ChiCTR; www.chictr.org.cn/index.html; ChiCTR2000037894.

Humans↗
PubMed2026

Genomic characteristics and tracing analysis of an acute gastroenteritis outbreak associated with rotavirus C in a boarding high school.

BACKGROUND: Rotaviruses are major pathogens of childhood acute gastroenteritis, dominated by rotavirus A (RVA). Outbreaks caused by human rotavirus C (RVC) are rarely reported, and relevant genomic data remain scarce. This genomic investigation of an RVC outbreak improves our understanding of viral diversity and transmission dynamics. METHODS: We performed epidemiological surveys, nucleic acid testing and whole-genome sequencing (WGS) on specimens from a 2025 RVC-associated gastroenteritis outbreak at a Chinese boarding high school. Sequence alignment, phylogenetic and molecular tracing analyses were conducted to explore RVC evolution via point mutation, segment reassortment and genomic recombination. RESULTS: This typical point-source campus outbreak was linked to an indoor student gathering matching the incubation period of RVC. Thirteen RVC FX strains were recovered from 11 rectal swabs and two vomitus samples. Their viral protein (VP) 4 and VP7 sequences shared high homology with Russian reference strains, carrying distinct amino acid variations. No segment reassortment or recombination was detected in VP4/VP7 genes. CONCLUSIONS: Dense, closed campus settings facilitate RVC clustered transmission. Limitations included absent screening of asymptomatic canteen staff. Rapid nucleic acid testing enabled timely pathogen identification for outbreak control. Greater attention should be paid to the public health risk of RVC. These whole-genome sequencing data enrich resources for studying RVC evolution and vaccine development.

Acute gastroenteritis outbreak↗
PubMed2026

Artificial intelligence in molecular diagnostics for pandemic preparedness.

INTRODUCTION: Molecular diagnostics focusing on the detection and analysis of nucleic acids are indispensable tools for early pathogen identification, transmission monitoring, and genomic surveillance during pandemics. Recent technological advances have broadened the diagnostic landscape, incorporating PCR-based methods, isothermal amplification, high-CRISPR-based amplification detection, and sequencing. Despite their diagnostic potential, widespread implementation remains limited by high validation costs, time and logistical constraints, the need for specialized professional knowledge, and a lack of adaptability in resource-limited settings. Artificial intelligence (AI) is increasingly recognized as a promising but challenging approach, offering tools that streamline assay development, automate data interpretation, and optimize real-time diagnostic performance. AREAS COVERED: This review introduces recently published AI tools with potential to enhance the in-silico design validation process of oligonucleotides for molecular assays. These cover tools for initial assay design and optimization to validation and continuous assay updates. The limitations, including concerns regarding data accuracy, the lack of transparency in data processing ('black box' models), and unresolved licensing and regulatory issues, are highlighted for each tool and as expert opinion. EXPERT OPINION: Collectively, these challenges currently confine most AI-based approaches to research settings and prevent their routine implementation in clinical molecular diagnostics. Their widespread adoption depends on addressing remaining technical, regulatory, and practical challenges.

Humans↗
PubMed2026

Potential of plasma metagenomic next-generation sequencing to guide antibiotic therapy in acute necrotizing pancreatitis with early fever: a prospective multicenter cohort study.

BACKGROUND: Indiscriminate antibiotic use remains common in febrile patients with acute necrotizing pancreatitis (ANP), particularly during the early phase. Metagenomic next&#x2011;generation sequencing (mNGS) has shown diagnostic utility for infected pancreatic necrosis (IPN) and may offer a means to guide antimicrobial therapy. We aimed to explore whether mNGS could potentially improve the appropriateness of antibiotic use in ANP patients presenting with early fever. METHODS: This prospective multicenter cohort study was conducted at five hospitals in China, enrolling ANP patients who developed fever within two weeks of symptom onset. Antibiotic susceptibility was defined per local microbiology laboratory reports. The hypothetical impact of mNGS on reducing inappropriate antibiotic use was evaluated through a retrospective simulation using predefined criteria from the BGI China antimicrobial drug usage card, as mNGS results were not disclosed to the treating teams during the actual clinical course. RESULTS: Between May 2023 and December 2024, 125 ANP patients with early fever were enrolled. Antibiotics were administered to 91.2% (114/125) of patients, whereas only 23.2% (29/125)were eventually confirmed to have IPN, and the rate of appropriate antibiotic use was 14.5% (17/117) based on conventional culture. In our simulated model, if therapy had been guided by plasma mNGS results, the estimated rate of appropriate antibiotic use could have increased to 71.8%. CONCLUSIONS: Plasma mNGS facilitates rapid pathogen identification and shows potential for improving antibiotic appropriateness in ANP patients with early fever.

Adult↗
PubMed1976

[Identification of conditionally pathogenic enterobacteria in laboratory practice in the diagnosis of acute intestinal diseases].

Identification of 361 cultures isolated from patients suffering from various acute intestinal diseasesand from persons who had sustained them, as well as from contacts and persons examined prophylactically with the use of various biochemical tests showed that ty their taxonomic properties the cultures were referred to conditionally-pathogenic representatives of Enterobacteriaceae of the corresponding genera:Citrobacter, Hafnia, Klebsiella, Proteus, Providencia. Serological typing of the strains of bacteria of the Citrobacter pointed to the most frequent circulation of the strains of the serological groups 04, 01, 03, 013, 05, 022, 08; among these groups 04, encountered among all the categories under study, prevailed. At the current stage of identification of conditionally pathogenic enterobacteria in practical laboratories it is of expedience to use in the diagnosis of intestinal diseases the serological typing along with a complex from several additional biochemical tests.

Citrobacter↗
PubMed1975

A simple carbohydrate fermentation test for identification of the pathogenic Neisseria.

The carbohydrate fermentation test in cystine-Trypticase agar-tubed medium was compared with the Minitek system with carbohydrate-impregnated paper disks in Müeller-Hinton broth for identification of Neisseria gonorrhoeae and N. meningitidis. There was 100% agreement between the methods for confirmation of N. meningitidis. The paper disk method confirmed 98% of the N. gonorrhoeae isolates; the cystine-Trypticase agar method confirmed 96%. Reactions with the paper disk method could be read in 4 h.

Bacteriological Techniques↗
PubMed2024

An integrated in-silico approach for drug target identification in human pathogen Shigella dysenteriae.

Shigella dysenteriae, is a Gram-negative bacterium that emerged as the second most significant cause of bacillary dysentery. Antibiotic treatment is vital in lowering Shigella infection rates, yet the growing global resistance to broad-spectrum antibiotics poses a significant challenge. The persistent multidrug resistance of S. dysenteriae complicates its management and control. Hence, there is an urgent requirement to discover novel therapeutic targets and potent medications to prevent and treat this disease. Therefore, the integration of bioinformatics methods such as subtractive and comparative analysis provides a pathway to compute the pan-genome of S. dysenteriae. In our study, we analysed a dataset comprising 27 whole genomes. The S. dysenteriae strain SD197 was used as the reference for determining the core genome. Initially, our focus was directed towards the identification of the proteome of the core genome. Moreover, several filters were applied to the core genome, including assessments for non-host homology, protein essentiality, and virulence, in order to prioritize potential drug targets. Among these targets were Integration host factor subunit alpha and Tyrosine recombinase XerC. Furthermore, four drug-like compounds showing potential inhibitory effects against both target proteins were identified. Subsequently, molecular docking analysis was conducted involving these targets and the compounds. This initial study provides the list of novel targets against S. dysenteriae. Conclusively, future in vitro investigations could validate our in-silico findings and uncover potential therapeutic drugs for combating bacillary dysentery infection.

Shigella dysenteriae↗
PubMed1978

The use of fluorescein-labelled lectins in the detection and identification of fungi pathogenic for man: a preliminary study.

Fluorescein-labelled lectins of known specificities for different sugars were used in an attempt to identify fungi in paraffin sections of surgical and post-mortem material. Aspergillus fumigatus, Blastomyces dermatitidis, Candida albicans, Cryptococcus neoformans, Paracoccidioides brasiliensis and Rhizopus oryzae have been studied with five fluorescein-labelled lectins and with basis of differences in their reactions with these stains. The results accord well with what is known of the chemistry of the organisms and the method offers promise to practising histopathologists.

Aspergillus fumigatus↗
PubMed1977

[Pseudomonas putida: identification, antibiotic sensitivity and pathogenicity (author's transl)].

This work studies 51 strains of Pseudomonas putida, isolated from clinical specimens (17) and hospital environment (34). Identification is performed by study of 41 physiologica and biochemical characters and 78 nutritional characters. According to the two biotypes A and B, described by Stanier, Palleroni and Doudoroff, these 51 strains can be grouped as follows: 48 have typical characters of biotype A, widely predominant, 3 can be distinguished from biotype A only by their auxanogram and included in biotype B. Antibiogram pattern of P. putida shows two salient features: resistant to carbenicillin and sensitivity to kanamycin. Among 17 human isolates, only 4 have likely pathogenic significance. By intraperitoneal challenge in mice, one half of strains is avirulent, other strains have a very low virulence (LD50: from 2,2 to 5 X 10(8) viable cells). There is no relationship between experimental virulence and bacterial sources.

Animals↗