Wastewater can serve as a useful indicator of the presence of pathogens circulating in the human population, including zoonotic pathogens mainly adapted to rodents. Rodents are small mammals distributed worldwide and capable of inhabiting various ecosystems, including sewer systems. Enterocytozoon bieneusi is the main etiological agent of human microsporidiosis, a well-established zoonosis; however, little is known about the epidemiology of microsporidiosis in Scandinavia, except for two foodborne outbreaks reported in Sweden and Denmark, both of which were caused by genotype C. The aim of this study was to determine the presence and genetic diversity of E. bieneusi in wild rodent populations in Denmark and influent wastewater samples from wastewater treatment plants in Sweden. Samples were analysed using nested PCR targeting the ribosomal internal transcribed spacer (ITS) and flanking regions of E. bieneusi, followed by Sanger sequencing. Sampled species included Apodemus flavicollis, Apodemus sp., Apodemus sylvaticus, Micromys minutus, Microtus agrestis, Mus musculus, and Myodes glareolus, with an overall positivity rate of 25.0 % (95 % CI, 14.4-38.4) (14/56). Meanwhile, E. bieneusi was detected in 82.8 % (95 % CI, 64.2-94.2) (24/29) of the wastewater samples. Sequence analysis revealed the presence of two known (C, EBCMAP-032), and a novel genotype (DKE-1) in rodents, and eight established (C, CYG-4, D, EBCMAP-007, EBCMAP-031, EBCMAP-032, Type IV, WildBoar3) and four new genotypes (SweWW1-SweWW4) in Swedish wastewater. A relatively high frequency of genotype C was observed in this study, suggesting a zoonotic-and possibly rodent-adapted source of the previous foodborne outbreaks caused by this genotype in Sweden and Denmark.

Klebsiella pneumoniae (Kp) can cause infections in communities and hospitals. After a report of a first highly virulent strain, it has now become the important pathogens that threatens human health and can often infect patients in intensive care units (ICUs). Kp is invasive and causes damage to the liver, pancreas, blood, intestines, and even the central nervous system. Zebrafish is a model organism with many advantages in biomedicine, and it has been used as a host to evaluate the virulence of Kp. However, there are no reports using zebrafish as a host to study the pathological characteristics of Kp. In this study, three Kp strains (KP1053, KP1196, and KP1195) were isolated from two clinical patients. The genetic and drug-susceptibility properties of the strains were first studied, and then zebrafish was used as a host to evaluate their virulence and pathogenicity. The three clinical Kp strains led to a marked decrease in the zebrafish survival rate, heart rate, and swimming distance; they also impeded the development of the swim bladder and resulted in a notable increase in the number of inflammatory cells. The virulence of these three strains followed the sequence KP1196 > KP1053 > KP1195. The transcriptome analysis found that lung, liver, nerve, and other developmental processes were significantly enriched in differentially expressed genes (DEGs), indicating that Kp may affect organ pathology through these genes. Our research offers a valuable reference for comprehending the pathological mechanisms underlying Kp clinical isolates.

A molecular epidemiological study of Clostridioides difficile was performed in the border areas of Yunnan Province.

Bacillus cereus, a common spore-forming bacterium, is a major cause of foodborne illness worldwide. This study investigated its effects on mouse physiology and wellbeing-including body-weight trajectory, digestive/oxidative biochemistry, liver-based immune enzyme proxies, and the gut microbiota. Mice were given oral doses of B. cereus at concentrations ranging from 10 to 10 CFU/mL over seven days. Exposure resulted in acute physiological responses, including transient growth suppression, altered antioxidant enzyme activity (increased Total Antioxidant Capacity [T-AOC] and Superoxide Dismutase [SOD], decreased Lysozyme [LZM]), and reduced blood glucose and amylase levels, particularly at lower doses. These findings suggest immune disruption and metabolic imbalance. Gut microbiota analysis revealed marked compositional shifts, characterized by increased richness, a decreased Firmicutes/Bacteroidota ratio, enrichment of Akkermansia muciniphila, and a decline in beneficial genera such as Lactobacillus. Functional prediction indicated suppression of microbial pathways related to penicillin/cephalosporin biosynthesis. Collectively, these results indicate that short-term B. cereus exposure perturbs physiological status and the gut ecosystem, even at low doses, outlining potential subclinical risks of B. cereus contamination and implications for gut health and food safety.

In China, the incidence of syphilis varies across different regions, as do the frequencies of HLA haplotypes. The progression and stages of syphilis infection may be associated with HLA polymorphisms. This study employed an ecological study design, utilizing data from a nationwide survey on the distribution of HLA frequencies in the Chinese Bone Marrow Donor Program and the incidence of syphilis in China during the same period. Pearson and Spearman correlation analyses, adjusted for multiple testing using the Benjamini-Hochberg procedure, were performed to investigate the correlation between HLA polymorphism and the incidence of syphilis. The overall incidence of syphilis was significantly correlated with the frequencies of six specific HLA-A-C-B-DRB1-DQB1 haplotypes in China. Additionally, as many as 24 HLA-A-C-B-DRB1-DQB1 haplotypes were found to be correlated with the incidence of congenital syphilis. Nominal correlations were observed between several HLA haplotype frequencies and the incidences of secondary, tertiary, and latent syphilis prior to false discovery rate correction. These findings suggest that the frequencies of HLA haplotypes are correlated with the incidence of syphilis in China, particularly in congenital syphilis cases. Collectively, susceptibility to syphilis infection and disease progression appears to be closely linked to HLA polymorphisms.

Trypanosoma cruzi I (TcI) infects a broad range of mammalian and triatomine species across the Americas and displays broad genetic diversity. The transmission cycles of TcI remain poorly understood. We investigated whether TcI parasites from Didelphis albiventris opossums were linked to the TcI parasites found in domestic dogs, cats and peridomestic Triatoma sordida from the Argentinean Chaco or were linked to other T. cruzi genotypes in opossums. We analyzed the intergenic region of the spliced leader (SL-IR) of the mini-exon gene sequence from direct triatomine samples and culture isolates from those hosts captured in Pampa del Indio, Amamá, and Garupá municipalities. Of 56 sequences analyzed, 29 are original to this study and 27 were available at GenBank. Fifteen TcI genotypes were detected in Pampa del Indio, with at least three sub-groups circulating simultaneously. TcId was mainly linked to D. albiventris and T. sordida, suggesting a sylvatic/peridomestic transmission cycle. TcIa was found in a domestic dog and a cat at the same household, likely originated from an unidentified source. A third sub-group of TcI, closely related to sequences from Brazilian and Misiones (Argentina) opossums, was found in T. sordida. To our knowledge, this is the first report of TcI SL-IR sub-groups in T. sordida. Whether D. albiventris opossums are introducing sylvatic parasites to the peridomicile and T. sordida are getting the TcId-infection there or sylvatic T. sordida specimens are arriving to the peridomicile already infected deserves further research.

Interleukin-25 (IL-25) is a crucial cytokine in coordinating type 2 immunity against gut-dwelling helminths. IL-25 is produced by a variety of cells, including epithelial and immune cells, and primarily stimulates Th2-type immune responses characterized by the release of IL-13, IL-5, and IL-4, which play a vital role in eosinophilia induction, goblet cell hyperplasia, and IgE synthesis. This review critically examines IL-25's role in maintaining intestinal barrier integrity and modulating regulatory immune responses. This review addresses how IL-25 integrates signals from the epithelial interface, immune cells, and gut microbiota to calibrate appropriate host defense while preventing pathological inflammation. Furthermore, this paper presents recent evidence supporting IL-25's therapeutic potential, both as a potential adjuvant therapy to enhance parasite clearance and as a modulator of inflammatory conditions where type 2 immunity proves deficient.

The parasitic disease known as cystic echinococcosis (CE) is a significant zoonotic condition caused by Echinococcus granulosus sensu lato (s.l.). The current lack of safe and effective pharmacological treatments necessitates urgent efforts to identify and develop novel drug targets and therapeutic molecules. This study investigates the role of DNA repair protein 50 (Rad50) in Echinococcus granulosus sensu stricto (s.s.) and evaluates whether it serve as a viable target for CE. Three small interfering RNA (siRNA) fragments targeting EgRad50 were introduced into E. granulosus s.s. via electroporation, and qRT-PCR, Western blot, and immunofluorescence were performed to assess EgRad50 localization and expression. The survival rate of E. granulosus s.s. was evaluated through in vitro culture, DNA damage was assessed using a comet assay, and the impact of EgRad50 knockdown on DNA repair and ferroptosis was analyzed via Western blot. EgRad50 is expressed during the protoscolece (PSC) and metacestode (MTC) stages of E. granulosus s.s. and the knockdown of EgRad50 reduced the viability of E. granulosus s.s. PSCs in vitro. Moreover, inhibition of EgRad50 downregulates ATR phosphorylation levels and further activates ferroptosis, leading to the death of E. granulosus s.s. This investigation sheds light on the preliminary role of EgRad50 in DNA repair, highlighting its importance for parasite survival and suggesting it as a new potential drug target for CE therapy. The selective targeting of EgRad50 may facilitate a more effective resolution to the clinical challenges presented by CE.

The emergence of antibiotic-resistant pathogens is a significant global health concern that necessitates the development of new antimicrobial drugs. Due to its broad-spectrum action against bacteria, fungi, and viruses, human cathelicidin LL-37, an antimicrobial peptide (AMP), has emerged as a potential option.

Field studies on foot-and-mouth disease virus (FMDV) have historically concentrated on viral sequences obtained from clinical cases. However, FMDV often causes several forms of subclinical infections in ruminants, which are further complicated by heterologous FMDV coinfections and reinfections. The focus of this current study was genomic analysis of FMDV isolates obtained from domestic water buffalo (Bubalus bubalis) with no visible signs of disease - subclinical infections. Over a 12-month period, buffalo from dairy farms in Islamabad, Pakistan, were repeatedly sampled. We used full-genome next-generation sequencing to analyze FMDVs isolated from 68 oropharyngeal fluid (OPF) samples, representing 44 animals across 18 farms. The analysis revealed the circulation of three distinct serotypes - O, A, and Asia-1. Examination of persistent viruses showed variable within-host evolution, with 0-25 substitutions observed between sampling points. Notably, several animals were infected by recombinant viruses derived from antigenically distinct parental strains. This included at least five different recombinants recovered from one animal, as confirmed through plaque purification of OPF samples. In several instances, recombination events were determined to have occurred within the course of the study period. These results highlight the complexity of naturally occurring subclinical FMDV infections and emphasize the role of recombination in enhancing viral diversity in endemic regions.

Over the past decade, microbial genomics has been transformed by advances in sequencing technologies and bioinformatics, enabling the transition from targeted gene markers to complete genome assemblies and ecological scale metagenomic surveys. This review presents a comprehensive overview of the bioinformatics pipelines that structure this field, from sample preparation, PCR amplification, and next-generation sequencing (NGS) to read preprocessing, genome assembly, polishing, structural and functional annotation, and submission to public databases. We highlight the major tools that have become standards at each stage, including FastQC, SPAdes, Prokka, Bakta, CARD, GTDB-Tk, QIIME 2, and Kraken2, while also emphasizing recent innovations such as hybrid assemblers, ontology-driven annotation frameworks, and automated workflows (nf-core, Bactopia). Applications extend across microbiology, from antimicrobial resistance surveillance and phylogenetic classification to ecological studies, exemplified here by three case studies: termite gut microbiota profiling by 16S metabarcoding, the description of new Bartonella species from bats, and the genomic characterization of rare Salmonella enterica serovars from primates. Despite these advances, persistent challenges remain, including incomplete and biased reference databases, computational bottlenecks, and economic disparities in sequencing and storage capacities. In response, international initiatives increasingly promote open, interoperable, and reusable bioinformatics infrastructures. Conforming to the Findable, Accessible, Interoperable, Reusable (FAIR) principles and global frameworks such as Global Alliance for Genomics and Health (GA4GH), these efforts are driving greater standardization, transparency, and data sharing across the microbial genomics community. Future perspectives point toward the integration of artificial intelligence, long-read and telomere-to-telomere (T2T) sequencing, cloud-native infrastructures, and even quantum computing, paving the way for a predictive, reproducible, and globally inclusive microbial genomics.

This study aimed to characterize the epidemiological, clinical, and genomic features of norovirus GI.3[P13] outbreaks in Beijing from 2016 to 2019.

Echinococcus multilocularis is the causative agent of alveolar echinococcosis (AE). We explored the diversity of EmsB profiles of E. multilocularis from red foxes and humans in northern and northeastern Poland, with a particular focus on autochthonous Asian variants.

Bovine viral diarrhea virus (BVDV) is a globally distributed and economically significant viral pathogen in the cattle industry. Despite ongoing circulation, molecular evolutionary and phylodynamic data on BVDV in the Republic of Korea (ROK) remain limited. This study aimed to investigate the prevalence and subtype of recent BVDVs circulating in the ROK and to analyze their phylodynamic patterns. A total of 5286 samples, including serum, blood, and diarrheic feces, were collected from Korean native cattle between 2021 and 2022. Of these, 29.9 % (1584/5286) tested positive for BVDV by real-time RT-PCR targeting the 5'UTR. BVDV was most frequently detected in serum (36.9 %), followed by feces (12.3 %) and blood (9.6 %). Sequencing analysis identified three subtypes: BVDV-1a (16.5 %), BVDV-1b (53.6 %), and BVDV-2a (29.9 %). The maximum clade credibility (MCC) tree based on the 5'UTR indicated that the most recent common ancestors of BVDV-1 and BVDV-2 in the ROK likely emerged around 1988 and 1995, respectively. The evolutionary rates of BVDV-1 and BVDV-2a were estimated at 3.99 × 10 and 4.0 × 10 substitutions/site/year, respectively, indicating rapid evolution compared with those in other countries. The MCC tree revealed an evolutionary order of BVDV-1a, -2a, and -1b. Phylogenetic analysis showed that recent BVDV-1b sequences exhibited greater genetic variation than those of other subtypes, suggesting accelerated and heterogeneous evolutionary dynamics. Bayesian skyline plot analysis demonstrated a marked increase in the viral population of BVDV-1 (especially BVDV-1b) around 2018, while BVDV-2a exhibited a more gradual expansion beginning around 2016. This was the first study to characterize the evolutionary dynamics of BVDVs in the ROK. These findings enhance understanding of the recent molecular epidemiology and evolutionary dynamics of BVDV in the ROK and underscore the need for continued molecular surveillance and control strategies.

Rat hepatitis E virus (ratHEV, Rocahepevirus ratti) is an emerging zoonotic pathogen which was recently identified in several human hepatitis patients. The virus has been demonstrated in its primary reservoir hosts, rats, in many countries of the world. However, little is known about the persistence and molecular evolution of ratHEV in a host population over time. Here, wild Norway rats (Rattus norvegicus) from Berlin, Germany, were screened for ratHEV, and virus strains and rats were genetically characterized. The ratHEV detection rate in 2023 (8.3 %, 11/131) was similar to that of 2009/2010 (11.5 %, 7/61). Generated virus genome sequences showed 89.3 % to 100 % nucleotide sequence similarity to each other. Phylogenetic analysis indicated clustering of the sequences from the rats and a human patient from Berlin, irrespective of year and separate from sequences from other parts of Germany. Strains from Berlin formed subclades according to sampling districts, and rivers were identified as possible barriers between subclades. Rat population genetics analysis indicated a stable rat population with a dominant genetic cluster containing most ratHEV-infected rats at both time-points, and the presence of closely related virus strains within a genetic subcluster. Analysis of all ratHEV strains identified variable amino acid positions in all four virus-encoded proteins. The results indicate long-term persistence of ratHEV in wild rat populations, which is mainly driven by local transmission of virus strains in small geographic areas. Environmental and rat surveillance for ratHEV, along with effective pest control, should be considered to reduce the risk of human infections in future.

The Anaerobutyricum genus, comprising Anaerobutyricum hallii and Anaerobutyricum soehngenii, is prevalent in the human gut microbiota and produces short-chain fatty acids (SCFAs) that influence host metabolism and inflammation. However, systematic genomic studies on this genus are limited. In this study, we conducted a comprehensive genomic analysis of 84 Anaerobutyricum genomes, based on the average nucleotide identity (ANI), average amino acid identity (AAI) and core genes phylogenetic tree analysis, we clustered the Anaerobutyricum genus to Anaerobutyricum spp., Anaerobutyricum hallii and Anaerobutyricum soehngenii. Specifically, Anaerobutyricum hallii and Anaerobutyricum soehngenii are specific to human hosts, possessing longer genomes and lower GC content. They contain more integrative and conjugative elements (ICEs), which genetically encoded dltA, mbtB and dhbE genes that responds for the biosynthesis of siderophore group nonribosomal peptides, which might contribute to its colonization. In addition, ICEs in Anaerobutyricum hallii and Anaerobutyricum soehngenii could also pose a risk for antibiotic resistance gene transfer. Our study advances the understanding the of Anaerobutyricum's and host adaptability, highlighting the importance of genomic analysis in refining taxonomic boundaries and assessing the safety of using these bacteria as probiotics.

Carbapenem resistance in non-baumannii Acinetobacter has been increasingly reported worldwide. This study investigated the genetic basis of carbapenem resistance in Acinetobacter pittii isolate KBN12P06770 carrying bla and bla using whole-genome sequencing. Two carbapenemase genes were located on the chromosome. Two copies of bla located on Tn2006 were identified. Additional chromosomally encoded antimicrobial resistance genes, including bla and ant(3")-IIc, as well as efflux pump genes (adeIJK, adeFGH, abeM, and abaQ), were identified, with the exception of plasmid-borne ant(2")-Ia. qPCR analysis revealed that the bla was more highly expressed than bla. Notably, bla featured the Ser225Pro substitution, first characterized in this study, which may enhance β-lactamase activity based on structural modeling. Furthermore, multilocus sequence typing (MLST) assigned KBN12P06770 to ST1611 within clonal complex 63 (CC63), with close clustering to ST2737 indicating recent divergence. The comprehensive genomic analysis of A. pittii isolate KBN12P06770 highlights the complex genetic architecture underlying carbapenem resistance.

Rotavirus A (RVA), belonging to the species Rotavirus alphagastroenteritidis, is among the most frequently diagnosed viral causes of gastroenteritis. The inclusion of RVA vaccines in the primary childhood immunisation schedules of multiple countries has led to significant reductions in yearly-reported cases. Nevertheless, such interventions may exert selective pressures that could result in the emergence of novel vaccine escape variants. RVA classification has traditionally focused on two of eleven gene segments encoding the capsid proteins, VP4 and VP7, which limits evolutionary assessments of genomic diversity and reassortments involving the other segments. A viral metagenomics approach (NetoVIR) was employed to investigate the genomic diversity of RVA in Ireland. The analysis focused on clinical samples (n = 140) collected from patients between 2015 and 2021. Besides the Wa-like or DS-1-like genotype constellations, 4/140 genomes (3 %) were identified as reassortant, with an NSP2 genotype 1 in a DS-1-like constellation. Also, we confirmed the circulation of OP354-like P[8] strains in six G9P[8] samples. Notably, these strains show dissimilarity in the antigenic epitopes of the VP4 protein compared to the Rotarix vaccine. Furthermore, we detected strains with an equine-like G3 (EQL-G3) VP7 gene within a DS-1-like constellation (n = 5/140, 4 %) and the unusual combination of G1P[8] with a DS-1-like constellation in 6/22 (27 %) of the G1P[8] samsples. Our study supports using a viral metagenomic approach for RVA genetic characterisation to determine pathogen diversity and reassortments. The public health implications of the identified reassortant RVA strains, requires investigations for any potential impacts on vaccine efficacies.

Group A fluoroquinolones (FLQs) are essential for treating multidrug-resistant tuberculosis (MDR-TB). Mutations in gyrA and gyrB cause FLQ resistance, but their patterns vary by region. This study evaluated FLQ-associated mutations in the gyrA and gyrB genes by analyzing minimum inhibitory concentrations (MICs) using 7H9 broth microdilution (BMD) and Löwenstein-Jensen phenotypic drug susceptibility test (L-J pDST).

Erwinia amylovora, the causative agent of fire blight in Rosaceae plants like apple and pear, is a major agricultural pathogen responsible for significant economic losses. This gram-negative phytopathogen has the potential to acquire antibiotic resistance and virulence genes, a situation that becomes more severe and restricts treatment options. Using an in silico approach, we analyzed 268 E. amylovora genomes and identified seven high-quality temperate prophages, all classified under Caudoviricetes, with average genome sizes of 44.2 kbp and 51 % GC content. These prophages exhibited unique genomic features, including tRNA genes (Ph-Ea644), anti-defense systems like ardc (Ph-Ea6-96), and regulatory/lysis genes (Ph-EaFC01). Comparative genomics and phylogenetic analyses grouped them into five clades, with Ph-Ea4-96, Ph-Ea3-97, and Ph-Ea2-97 being genetically identical. Functional annotation revealed streptomycin resistance genes and a CAZyme (GH23) in Ph-Ea7-3, virulence factors (e.g., alginate biosynthesis proteins), and six auxiliary metabolic genes (AMGs) linked to metabolic adaptation. Additionally, Ph-Ea644 encoded a cell wall-binding receptor protein. The prophages also carried defense systems (Gabija, CBASS) and 31 anti-CRISPR proteins (ACRs), suggesting evasion of host immunity. CRISPR-Cas analysis indicated fewer arrays and spacers in prophage-containing strains, underscoring CRISPR's role in lysogeny resistance. These findings highlight the genomic plasticity of E. amylovora prophages, their interactions with bacterial defenses, and their potential influence on pathogen evolution. This study enhances understanding of temperate phages in agricultural pathogens and underscores challenges in phage-based biocontrol strategies.