Drug-resistant tuberculosis (DR-TB), resulting from newly emerging strains of Mycobacterium tuberculosis (Mtb), and the World Health Organisation (WHO) included it as a top-priority antimicrobial-resistant pathogen. Whole genome sequence analysis (WGS) of clinical Mtb isolates could correlate to their drug resistance phenotype and may also reflect their metabolome. In this report, clinical Mtb isolates (S1, S4, S5, S6, S7, S10) harvested from the sputum of tuberculosis patients were characterized using drug sensitive test (DST), electron microscope, WGS and untargeted Gas chromatography and mass spectrometry (GC-MS) based metabolomics analysis. The majority of these Mtb isolates showed similar size (length: 1.0-3.2μm; width: 0.32-0.52μm) to the H37Rv Mtb strain, whereas significant variations were observed in their growth kinetics, WGS and metabolome profiles. In-silico drug resistance prediction, from the WGS data (single-nucleotide polymorphisms (SNP) pattern) of these Mtb isolates, showed resistance to tuberculosis drugs and matched with DST results. Differences in the genes involved in stress response, pathogenicity, and drug efflux pumps were observed between isolates, but genes of the central carbon metabolic pathways and amino acid metabolism were conserved. GC-MS-based metabolite profiling of these clinical isolates identified 291 metabolites involved in various metabolic pathways, and a subset of these metabolites (glutamic acid, aspartic acid and serine) contributed to the drug resistance patterns. These clinical Mtb isolates could be useful as an alternate reagent for understanding host-pathogen interaction. The pipeline used for WGS analysis could be used to predict the drug resistance pattern of new Mtb isolates.

Saccharomyces cerevisiae is widely used in food and beverage production but faces stresses such as acidity during processing. In our previous studies, the S. cerevisiae mutant strain TAMC, which can tolerate an acidic environment of pH 2.3, was isolated via adaptive laboratory evolution; however, the genetic basis underlying the acid tolerance of this strain remained unclear. Herein, we aimed to elucidate the genetic basis of TAMC's acid tolerance via genome sequencing and functional analysis. The results revealed that a mutation (mROX1) in transcriptional regulator ROX1 was crucial for acid tolerance. Comparative transcriptome mining and reverse engineering revealed that the mROX1 mutation mediated cellular oxidation-reduction stress homeostasis maintenance by upregulating the expression of superoxide dismutase homologues and catalase, facilitating tolerance to acidity and detoxifying reactive oxygen species. This work uncovers a novel yeast intracellular homeostasis mechanism, providing a potential strategy for engineering novel acid-tolerant microbial cell chassis.

Vibrio harveyi is responsible for several shrimp diseases such as luminous vibriosis, hepatopancreas necrosis, red body, and black spot disease, which can cause substantial mortality in shrimp. Due to the increasing prevalence of antibiotic-resistant pathogenic infections, bacteriophage therapy is being considered as a potential alternative for disease treatment. In this study, a Vibrio-infecting bacteriophage VPMCC6 was isolated from an infected shrimp aquaculture pond. VPMCC6 bacteriophage had an icosahedral head (43.51 ± 1.07nm) and a short tail (14.60 ± 2.13nm). This bacteriophage produced 24 PFU/cell on its propagation strain V. harveyi S2A and could clearly lyse the host bacteria after 3h of bacteriophage addition. Whole genome sequence analysis confirmed that the bacteriophage VPMCC6 genome had no tRNA and no virulence or antibiotic resistance genes. Moreover, we evaluated the effectiveness of bacteriophage therapy in controlling vibriosis in Penaeus monodon. After vibriosis induction in P. monodon using 1 × 106 CFU/ mL of V. harveyi S2A in laboratory aquarium, the infected shrimp were treated with Vibrio-infecting bacteriophage VPMCC6 at MOI 1. Results showed that bacteriophage VPMCC6 significantly reduced the mortality of P. monodon (reduction of 54.76% compared to the infected group) and controlled V. harveyi infection in shrimp culture water. Histopathological analysis showed that the treatment group displayed less hepatopancreatic necrosis and reduced tissue damage. These findings suggest that bacteriophage VPMCC6 is a promising biocontrol agent against V. harveyi in P. monodon aquaculture.

BackgroundIn recent years, Riemerella anatipestifer infection in chickens has markedly increased, resulting in substantial economic losses to the poultry industry. The present study was designed to assess the pathogenicity of R. anatipestifer in laying hens and to elucidate the molecular mechanisms underlying its altered virulence.MethodsRiemerella anatipestifer strains were isolated from laying hens presenting with oviduct obstruction and diminished egg production. Animal challenge experiments were conducted to evaluate the pathogenic potential of these hen-isolated strains. Genomic DNA sequences were subjected to comparative analysis to identify virulence genes differential between newly hen-derived and previous strains.ResultsThree serotypes, 1, 5, and 10, were identified using PCR and agglutination assays. Animal challenge experiments demonstrated that all three strains could induce oviduct obstruction in 30-, 60-, and 90-day-old hens. Genomic sequencing analysis revealed 18 mutated virulence genes associated with diverse virulence determinants, including type IV secretion systems (T4SSs), hemolysin, yersiniabactin (Ybt), lipooligosaccharide (LOS), lipopolysaccharide (LPS), BrkA, capsule biosynthesis, flagella, caseinolytic protease C (ClpC), FeoAB, and Vi antigens, all of which have been established as critical factors in bacterial pathogenicity.ConclusionThe findings of this study confirm an association between R. anatipestifer infection and reduced egg production in hens, and provide a foundation for elucidating the specific roles of virulence genes in the altered pathogenicity of R. anatipestifer in chickens.

Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home faecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomised into four groups defined by faecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted in and, of those, 88% returned a sample. Of those asked to provide a faecal sample via faecal occult blood test card (FOBT) and complete a short "day of sample" questionnaire (dosQ), 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home faecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.

Newcastle Disease (ND) remains a major threat to poultry production worldwide, particularly in regions where it is endemic, like Southern Asia. The disease is caused by virulent forms of avian paramyxovirus-1, commonly termed Newcastle Disease Virus (NDV), a highly contagious virus with significant genetic diversity and evolving pathogenicity. This study aimed to molecularly characterize NDV isolates obtained from chickens and pheasants during the 2020/21 ND outbreaks in Nepal, to understand their genetic makeup, phylogenetic relationships, and implications for control strategies. Necropsy samples, including trachea, liver, intestine, spleen, lungs, heart, and proventriculus were collected from ten birds. Isolates from five clinical samples were typed as NDV by hemagglutination and hemagglutination inhibition (HA/HI) assays and were subjected to whole genome sequencing (WGS). Full genomes of 15,192 nucleotides were recovered from each isolate. Fusion (F) gene sequence analysis revealed the presence of multi-basic cleavage site motif 112RRQKRF117 in all isolates, indicative of virulent strain and suggesting a potentially velogenic or mesogenic phenotype. Phylogenetic analyses consistently classified all isolates within genotype VII.2 of class II NDV. Further comparative analysis indicated a close genetic relationship between the Nepalese isolates and strains reported from India and Bangladesh, and BEAST analysis suggested Southern Asia as the likely source of introduction into Nepal. These viral genomes provide additional insight into contemporary NDV circulating in an area of endemicity.

Whole genome sequencing and phylogenetic analysis of the equine infectious anemia virus associated with 2017 Spain outbreaks.

This study investigates the antibiotic resistance profiles, virulence factors and genomic characteristics, of Klebsiella pneumoniae isolates obtained from influent and effluent samples of a wastewater treatment plant. Data generated sheds light on the dissemination and persistence of antibiotic resistance in compartments in a wastewater treatment plant (WWTP). Given the increasing concern regarding the role of wastewater in the dissemination of antibiotic-resistant bacteria, this research focused on K. pneumoniae populations using culture-based and genomics approaches. The culture-based approach showed that antibiotic resistance to β-lactam antibiotics was corroborated by PCR detection of the genes. Whole Genome Sequencing (WGS) analysis revealed a diverse array of Antibiotic-Resistant Genes (ARGs), including those encoding extended-spectrum β-lactamases (ESBLs) and resistance to other clinically relevant ˙antibiotics. Plasmid analysis unveiled various replicon types indicative of horizontal gene transfer mechanisms. Moreover, the identification of virulence genes implicated in adhesion, biofilm formation, and iron acquisition underscores the pathogenic potential of K. pneumoniae isolates in wastewater. In addition, the genomics comparison between K. pneumoniae strains from the influent and effluent of the WWTPs ecosystem reveal that “core” genome is shared. However, unique genomic clusters in the environmental strains suggests niche-specific adaptations, shedding light on the genomic plasticity of K. pneumoniae in response to environmental cues. This may have implications for antibiotic resistance dissemination and ecological interactions within wastewater ecosystems. Data presented here highlights the urgent need for enhanced surveillance and management strategies to mitigate the spread of antibiotic resistance through wastewater treatment plants ecosystems.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-27081-y.

Bovine tuberculosis (bTB) has a certain incidence on farms in China, but little is known about its prevalence and the pathogenic Mycobacterium species. With the increasing application of whole-genome sequencing (WGS), it is now possible to investigate the genomic diversity, lineage distribution, and drug resistance profiles of M. bovis at high resolution. In this study, we sequenced 29 Mycobacterium tuberculosis complex (MTBC) isolates from two farms in China and incorporated genomic data from 79 publicly available M. bovis isolates from cattle farms in China for a comprehensive genomic analysis. The majority of the 106 M. bovis isolates (63.2%, 67/106) belong to lineage La1.4. The dataset was screened for isolates of two known clonal complexes, Eu1 and Eu3, corresponding to La1.8.1 and La1.2, respectively. In silico spoligotyping revealed nine previously identified profiles, and the most common spoligotype in this study is SB1903. All isolates have the H57D mutation in the pncA gene associated with pyrazinamide (PZA) resistance. 16.0% (17/106) of isolates have resistance mutations to first- or second-line drugs other than PZA, with one isolate classified as pre-XDR-TB. The distribution of cluster strains suggests the possibility of recent transmission and outbreak in the two farms. It is noted that two M. tuberculosis isolates from tissue samples had detectable drug resistance mutations. The results of this study provide the basis for in-depth analysis of genomic population characteristics and drug resistance of M. bovis in China. It should be noted that close contact between humans and cattle increases the risk of M. tuberculosis transmission from humans to cattle in rural areas or developing countries with low levels of human-animal separation.

Genome sequencing and comparative genome analysis of Clostridium perfringens of animal origin.

BackgroundUpper tract urothelial carcinoma (UTUC), including renal pelvic urothelial carcinoma and ureter urothelial carcinoma, accounts for 10% of urothelial carcinoma (UC). Poorer outcomes and different genetic characteristics of UTUC were reported compared to urothelial carcinoma of the bladder (UCB), which accounts for most cases of UC. Therefore, there is an urgent need for the development of molecular characterization and precision therapies tailored specifically for UTUC.MethodsTo elucidate the genetic landscape of UTUC, we included 4 UTUC samples in this study and also perform next-generation sequencing (NGS) of whole exome sequencing. After that, long-read sequencing (LRS) was employed to conduct Whole genome sequencing (WGS) analyses on tumor samples obtained from the four UTUC patients, utilizing the Pacific Biosciences (PacBio) REVIO platform.ResultsThe clinical phenotypes of four UTUC patients including tumor stage, location and response to treatment, etc. were collected. NGS of four patients yielded negative results. The WGS mapped the mutation landscape in the tumor tissues of four UTUC patients, and screened the sequencing results according to UTUC and solid tumor related genes. Seven pathogenic or likely pathogenic single nucleotide variant (SNV) were obtained. Among the detected structural variations (SVs), four patients shared multiple segments of SVs with close positions. The 12q24.31-p11.1 inversion was shared by four patients. In the detection of STR and DNA methylation, comparing the results of patients and normal controls, many different fragments were obtained. It shows that LRS has important advantages over NGS for accurate tumor detection and treatment.ConclusionThe analysis revealed multiple genetic variants potentially associated with UTUC carcinogenesis or development, and indicated advantages of TGS over next-generation sequencing (NGS) in cancer genetic variant detection, especially in SV and Short Tandem Repeats (STRs). This study may lay the groundwork for molecular classification and offer valuable insights into the development of precision therapies for UTUC.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12885-025-15254-x.

CC5 MRSA isolates from goats and the farm environment are phylogenetically linked to isolates recovered from human clinical samples.

Mitochondrial genome sequencing and phylogenetic analysis of the freshwater snail Fukuia kurodai ooyagii (Pomatiopsidae)

Whole genome sequencing analysis reveals strong reproductive isolation between two hybridizing Rhododendron species in subgenus Tsutsusi

BackgroundThe importance of early prediction of Alzheimer's disease (AD) is emerging, and a genomic approach provides a promising path to this goal. One limitation is the high dimensionality of genomic data, which remains incompletely understood. Deep learning (DL) models hold potential for processing and interpreting such complex data. This study aimed to develop a novel DL model using a transformer architecture for predicting AD dementia based solely on whole genome sequencing (WGS) data.MethodWe analyzed 1,050 WGS data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and ADNI‐WGS‐2 with the Alzheimer's Disease Sequencing Project Follow‐Up Study (ADSP‐FUS1‐ADNI‐WGS‐2) (443 cognitively normal; 607 AD dementia). A 1,000,000 base pair segment of WGS data surrounding the APOE gene on chromosome 19 was utilized. Our DL model comprised three steps: (1) Window‐based step: calculation of attention scores using windowed WGS data. (2) Annotation‐enhanced step: analysis of attention scores across multiple layers of selected SNPs, incorporating annotated information to capture distant‐range influences, and generate global attention weights. (3) Prediction performance enhancement using graph convolutional network (GCN): a graph with key SNPs from the previous steps and their relationships was analyzed by GCN to enhance performance. The area under curves (AUCs) for AD dementia prediction from the window‐based step (local relationship patterns) and the entire model (integrating local and distant‐range relationships) were compared. Key SNPs relevant to ADD prediction were identified.ResultsThe window‐based step using 40bp‐sized windows yielded limited accuracy (AUC = 0.53), while the complete model showed significant improvement (AUC = 0.68). Among the top 25 SNPs identified via feature importance scores from the complete model, 9 were newly discovered compared to the SNPs from the window‐based step. Key SNPs included rs429358, rs120074114, rs120074111, and rs5122 located in APOE or APOC genes.ConclusionOur DL model enabled multi‐scale analysis of WGS data and improved AD dementia prediction accuracy using WGS data and identified different significant SNPs by integrating local and distant‐range relationships. This study investigated the potential of DL‐based models with transformer architecture in early prediction of AD and established a foundation for efficiently processing WGS data.

As a core strategy for antibiotic replacement, probiotics have two advantages insofar as they enhance both animal productivity and pathogen suppression. In this study, we screened the intestines of antibiotic-naïve chickens for broad-spectrum antimicrobial lactic acid bacteria (LAB) with natural adaptability, based on the host–microbiota coevolution theory, and systematically evaluated their potential for development as poultry probiotics. We isolated a LAB strain, Lactiplantibacillus plantarum Y300, from traditional native free-range chickens, which showed strong inhibitory activity against avian pathogenic Salmonella, Escherichia coli, and Staphylococcus aureus. In vitro experiments indicated that the Lpb. plantarum strain Y300 had no hemolytic activity; excellent acid-producing ability;an outstanding tolerance to bile salts, low-pH environments, and simulated gastrointestinal fluids; a positive hydrophobic interaction with xylene, and good auto-aggregation characteristics. It also displayed a relatively high antioxidant capacity. Whole-genome sequencing revealed that the genome of Lpb. plantarum Y300 was approximately 3.05 mb, with a GC content of 44.74%. The main carbohydrate-active enzyme and bacteriocin genes were predicted in the Y300 genome, and no virulence genes or drug-resistance genes were detected. In summary, this study suggests that Lpb. plantarum Y300 has potential utility as a probiotic, and lays the theoretical foundation for the further development of microecological preparations of avian-sourced LAB.

Serratia species are opportunistic human pathogens found in diverse environmental habitats. Here, we report the first isolation of Serratia nevei from food samples in Nigeria. During a two-month epidemiological surveillance at a local food market in Dutsin-Ma, Katsina State, Nigeria, a total of 180 food samples were collected, and isolation and species identification were performed using chromogenic agar and MicroScan autoSCAN-4, respectively. Antimicrobial susceptibility and minimum inhibitory concentrations (MICs) were determined using the MicroScan autoSCAN-4 system. Strain F129B, recovered from a fresh, unprocessed beef sample, was initially identified as Klebsiella pneumoniae by chromogenic agar and MicroScan autoSCAN-4, and subsequently as Serratia marcescens by MALDI-TOF MS. Only Whole Genome Sequencing (WGS) and bioinformatics analyses confirmed its identity as S. nevei. The strain was then selected for further characterization by Whole Genome Sequencing (WGS) and bioinformatics analyses to confirm its identity. The strain was phenotypically resistant to amoxicillin/clavulanic acid and colistin, with elevated MICs for aztreonam (4 mg/L) and cefuroxime (16 mg/L). In silico analyses of its genome confirmed the isolate as S. nevei, harboring genes conferring resistance to β-lactams (blaSTR-2), aminoglycosides (aac (6′)-Ic), fosfomycin (fosA), streptomycin (satA), and tetracycline (tet (41)). Its virulence repertoire comprises genes associated with adhesion (yidE, yidR, yidQ), colicin tolerance (creA and creD), and heavy metal resistance (czcD, chrBACF operon). These findings underscore the need for genomic characterization for accurate species identification within the Serratia genus. Our findings revealed the emergence of S. nevei in the food supply chain and highlighted its potential for zoonotic transmission. Robust surveillance of the local food supply chain is urgently needed in north-western Nigeria.

Human brucellosis is a re-emerging disease in Yunnan, China, that poses serious threats to public health. However, the species/biovars, geographic distribution, and genetic diversity profile of circulating strains remain unclear. In this study, bacteriology procedures, AMOS-PCR, agglutination tests with anti-A and anti-M monospecific sera, and multiple-locus variable-number tandem-repeat analysis (MLVA) genotyping approaches were applied to investigate the genetic diversity profile of the strains. A total of 514 B. melitensis strains were isolated and identified from 2017 to 2023, of which 498 were in biovar (bv.) 3 and 16 were in bv. 1; the strains were distributed in 12 cities/prefectures and 67 counties. These data show that human B. melitensis infection has become a serious public health challenge. Moreover, 514 strains were sorted into three MLVA-11 clusters (I-III): those strains harboring 15 MLVA-11 genotypes, those strains belonging to the Eastern Mediterranean lineage, and those strains exhibiting high genetic diversity. MLVA-16 was used to divide 514 strains into eight (a-h) clades that contained 208 MLVA-16 genotypes (GTs), of which 96 shared GTs comprising 402 strains, with a cluster rate of 78.21%, suggesting that the disease was potentially dominated by a cluster epidemic; however, further genome sequence analysis is necessary to uncover the epidemic pattern of the disease. The remaining 112 GTs were unique (single strain), suggesting they were linked to sporadic cases rather than a cluster epidemic. A nationwide MLVA-16 comparison showed that 81 genotypes were shared by strains from the present study and strains from 29 other provinces, implying that strains from the nationally recognized B. melitensis genotypes were continuously spread. However, further genome-based analysis is necessary to identify the transmission chain and source of infection. Another MLVA-16 comparison with global datasets showed that the strains in this study had genotypes that were completely identical to strains from Asia (Afghanistan, Kazakhstan, Mongolia, Syria, Turkey, Saudi Arabia, Vietnam, Iraq and India) and Europe (Portugal, Spain, and Greece), indicating that these strains belonged to internationally recognized lineages. Further genome analysis is needed to identify the phylogenetic relationships of these strains. The present study describes a comprehensive scenario involving bio-typing and genetic diversity characteristics of B. melitensis strains, which can provide vital clues to tailor surveillance and control measures for human brucellosis.

The adoption of whole genome sequencing (WGS) in clinical oncology is challenged by low data quality and increased artifacts in standard-of-care formalin-fixed paraffin-embedded (FFPE) samples. Analysis of 56 fresh frozen (FF) and FFPE matched pairs demonstrates that FFPE processing results in a median 20-fold enrichment in artifactual calls across mutation classes and impairs detection of clinically relevant biomarkers such as homologous recombination deficiency (HRD). We demonstrate that implementation of consensus calling reduces artifactual structural variant (SV) calls by 98% but is not sufficient in mitigating artifactual calls for single nucleotide variants (SNVs) and indels as compared to FF data. We develop FFPErase, a machine learning framework that filters SNV/indel artifacts and delivers clinical grade variant reporting allowing accurate quantification of clinically relevant biomarkers. Comparison of FFPErase WGS calls to clinical reporting by FDA-approved panel tests demonstrates 99% sensitivity and enables reporting of 24% more clinically relevant findings.

Two Gram-stain-negative, facultatively anaerobic, non-motile and rod-shaped bacterial strains, designated 2201CG32-9T and 2304DJ12-6T, were isolated from marine sponges collected in the Republic of Korea. Both strains exhibited catalase and oxidase activities but tested negative for nitrate reduction and indole production. Strain 2201CG32-9T showed optimal growth at 30 °C and pH 7.0-8.0 in the presence of 3% (w/v) NaCl, whereas strain 2304DJ12-6T grew optimally at 25 °C, pH 8.0 and 3% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene and phylogenomic analysis of genome sequences indicated that strains 2201CG32-9T and 2304DJ12-6T represented novel species within the genus Microbulbifer. Based on whole-genome phylogenomic analysis, the two strains were most closely related to Microbulbifer okhotskensis OS29T and Microbulbifer variabilis ATCC 700307T, respectively. The average nucleotide identity values of these strains were found to be <75.9%, and their digital DNA-DNA hybridization values were <22.5%. The DNA G+C contents of strains 2201CG32-9T and 2304DJ12-6T were 56.5 and 53.5 mol%, respectively. In both strains, ubiquinone-8 was identified as the predominant respiratory quinone, and the major cellular fatty acids (>5.0%) were C16:0, iso-C11:0 3-OH, iso-C15:0, iso-C17:0, summed feature 8 and summed feature 9. As for polar lipids, both strains comprised phosphatidylglycerol, phosphatidylethanolamine and phosphoglycolipid as common major polar lipids. Strains 2201CG32-9T and 2304DJ12-6T are classified as two novel species of the genus Microbulbifer based on a polyphasic taxonomic approach, for which the names Microbulbifer discodermiae sp. nov. (2201CG32-9T=KACC 23829T=JCM 37223T) and Microbulbifer jejuensis sp. nov. (2304DJ12-6T=KACC 23832T=MCCC 1K09533T) are proposed, respectively.