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BackgroundProteus mirabilis is a conditionally pathogenic bacterium that is inherently resistant to polymyxin and tigecycline, largely due to antibiotic resistance genes (ARGs). These ARGs can be horizontally transferred to other bacteria, raising concerns about the Inc plasmid-mediated ARG transmission from Proteus mirabilis, which poses a serious public health threat. This study aims to investigate the presence of Inc plasmid types in pig-derived Proteus mirabilis in Kunming, Yunnan, China.MethodsFecal samples were collected from pig farms across six districts of Kunming (Luquan, Jinning, Yiliang, Anning, Songming, and Xundian) from 2022 to 2023. Proteus mirabilis isolates were identified using IDS and 16S rRNA gene sequencing. Then, positive strains underwent antimicrobial susceptibility testing and incompatibility plasmid typing. Multi-drug-resistant isolates with positive incompatibility plasmid genes were selected for whole-genome sequencing. Resistance and Inc group data were then isolated and compared with 126 complete genome sequences from public databases. Whole-genome multi-locus sequence typing, resistance group analysis, genomic island prediction, and plasmid structural gene analysis were performed.ResultsA total of 30 isolates were obtained from 230 samples, yielding a prevalence of 13.04%. All isolates exhibited multi-drug resistance, with 100% resistance to cotrimoxazole, erythromycin, penicillin G, chloramphenicol, ampicillin, and streptomycin. Among these, 15 isolates tested positive for the IncQ1α plasmid repC gene. The two most multi-drug-resistant and repC-positive strains, NO. 15 and 21, were sequenced to compare genomic features on Inc groups and ARGs with public data. Genome analysis revealed that the repC gene was primarily associated with IncQ1α, with structural genes from other F-type plasmids (TraV, TraU, TraN, TraL, TraK, TraI, TraH, TraG, TraF, TraE/GumN, and TraA) also present. Strain NO. 15 carried 33 ARGs, and strain NO. 21 carried 38 ARGs, conferring resistance to tetracyclines, fluoroquinolones, aminoglycosides, sulfonamides, peptides, chloramphenicol, cephalosporins, lincomycins, macrolides, and 2-aminopyrimidines.ConclusionThe repC gene is primarily associated with IncQ1α, with structural genes from other F-type plasmids. A comparison with 126 public genome datasets confirmed this association.

ABSTRACT Background Avian leukosis virus subgroup J (ALV‐J) primarily affects poultry, particularly chickens, leading to tumourigenesis and immunosuppression, which results in substantial economic losses. It is important to note that ALV‐J is commonly found in indigenous chicken breeds in China, and the virus's vertical transmission characteristics present a significant threat to the preservation of local chicken breeds. Objectives The study aimed to investigate the characteristics and effects of the recombinant ALV‐J strain LY2021J, with a focus on its genetic composition and its potential influence on virulence and pathogenicity. Methods LY2021J was isolated using DF‐1 cells and validated by enzyme‐linked immunosorbent assay (ELISA) and IFA. The proviral genome was amplified using segmented PCR and then spliced together using DNASTAR software. Genome‐wide genes, including gag, pol, gp85, and long terminal repeat (LTR), were compared. Recombination sites were analysed using RDP5 and SimPlot software. Pathogenicity was evaluated by monitoring symptoms and conducting examinations on SPF chickens. Results The outbreak of ALV‐J in China has caused significant economic losses in the poultry industry. Although largely controlled in white‐feather broilers and egg‐laying chickens, ALV‐J has spread to yellow‐feather broilers and local breeds. A strain, LY2021J, isolated from Hetian chickens, showed lower mortality despite severe dysplasia. Genetic analysis revealed high similarity between LY2021J and the Chinese strains JS14NT01 and NX0101, suggesting a shared origin. Recombination with strain ev‐1 and specific 3′ UTR deletions may explain LY2021J's reduced virulence. Continued monitoring and prevention strategies are essential to mitigate ALV‐J's impact.

Although the photon point cloud data acquired from ICESat-2/ATLAS can be efficiently employed in urban building height extraction, its universal applicability in undulating terrain scenarios is constrained, and there are noticeable issues of false positives and false negatives. This research establishes a terrain-adaptive methodological framework based on ICESat-2/ATLAS photon point cloud to extract high-precision, high-density building height data across varied urban topographical conditions. First, a terrain-adaptive elevation buffer is utilized to coarse denoise the photon point cloud, involving the removal of the majority of noise photons in the scene, thereby enhancing the efficiency of subsequent algorithms. Second, urban signal photons are extracted from the remaining original photons using the Adaptive Method Based on Single-Photon Spatial Distribution (SPSD-AM). This approach demonstrates high universality across various urban scenes, while simultaneously ensuring a stable accuracy of urban signal photon extraction. Subsequently, ground photons are extracted from the urban signal photons and fit the ground curve based on the Adaptive Method Based on Spatial Differences of Urban Signal Photons (USPSD-AM), which addresses the challenge of the potential mixing of ground and building photons in complex terrain scenarios. A precise ground curve is then employed to extract building photons from urban signal photons. In order to mitigate issues such as false positives and negatives, post-processing steps, including completion and denoising of building photons, are implemented. Finally, the acquired building photons and ground curve are adopted to extract accurate building height parameters. The precision verification results show that the extracted building heights are considerably consistent with the reference building heights. The mean RMSE and MAE are 0.273 m and 0.202 m for flat terrains and 1.168 m and 0.759 m for undulating terrains, respectively. The proposed method demonstrates superior applicability across diverse urban scenarios, providing a robust theoretical foundation for large-scale urban building height retrieval efforts.

IntroductionAvian leukosis, a viral disease affecting birds such as chickens, presents significant challenges in poultry farming due to tumor formation, decreased egg production, and increased mortality. Despite the absence of a commercial vaccine, avian leukosis virus (ALV) infections have been extensively documented, resulting in substantial economic losses in the poultry industry. This study aimed to develop alginate-chitosan composite microspheres loaded with ALV-J Gp85 protein (referred to as aCHP-gp85) as a potential vaccine candidate.MethodsSodium alginate and chitosan were utilized as encapsulating materials, with the ALV-J Gp85 protein serving as the active ingredient. The study involved 45 specific pathogen-free (SPF) chickens to evaluate the immunological effectiveness of aCHP-gp85 compared to a traditional Freund adjuvant-gp85 vaccine (Freund-gp85). Two rounds of vaccination were administered, and antibody levels, mRNA expression of immune markers, splenic lymphocyte proliferation, and immune response were assessed. An animal challenge experiment was conducted to evaluate the vaccine’s efficacy in reducing ALV-J virus presence and improving clinical conditions.ResultsThe results demonstrated that aCHP-gp85 induced a significant and sustained increase in antibody levels compared to Freund-gp85, with the elevated response lasting for 84 days. Furthermore, aCHP-gp85 significantly upregulated mRNA expression levels of key immune markers, notably TNF-α and IFN-γ. The application of ALV-J Gp85 protein within the aCHP-gp85 group led to a significant increase in splenic lymphocyte proliferation and immune response. In the animal challenge experiment, aCHP-gp85 effectively reduced ALV-J virus presence and improved clinical conditions compared to other groups, with no significant pathological changes observed.DiscussionThe findings suggest that aCHP-gp85 elicits a strong and prolonged immune response compared to Freund-gp85, indicating its potential as an innovative ALV-J vaccine candidate. These results provide valuable insights for addressing avian leukosis in the poultry industry, both academically and practically.

Global climate change and rapid urbanization have increased the frequency of flooding, making urban flood resilience a critical objective. This article introduces a methodology for assessing urban flood resilience, utilizing a social-ecological synthesis index that integrates geographical and temporal data with Geographic Information System (GIS). The study focuses on ten administrative subdistricts in Wuhua District, Kunming City, China, and selects 18 social-ecological indicators. These indicators, chosen from social and ecological perspectives, are weighted using the entropy weight method to determine their significance in the assessment system. By combining scores for each subdistrict, the study quantifies flood resilience and creates a spatial distribution map using ArcGIS. Key findings reveal that out of the ten administrative subdistricts, five in Wuhua District, particularly in the core urban area of Kunming, demonstrate strong overall flood resilience. Influenced by social-ecological indicators, there is significant spatial differentiation in flood resilience within Wuhua District, with a decreasing trend radiating from the city center to areas farther from the urban core. The research indicates that regions with well-established transportation infrastructure, a wide distribution of government institutions, improved water management facilities, and a substantial population with higher education levels contribute significantly to enhancing urban flood resilience. HIGHLIGHTS Analyzing urban flood resistance capacity from the perspective of resilience.; Considering the performance of both social and ecological dimensions in urban flood resilience.; Quantifying urban flood resilience through comprehensive index method.; Using geographic information technology to analyse the spatial characteristics of urban flood resilience.;

The inappropriate use of antibiotics has led to the emergence of multidrug-resistant strains. Bacteriophages (phages) have gained renewed attention as promising alternatives or supplements to antibiotics. In this study, a lytic avian pathogenic Escherichia coli (APEC) phage designated as PEC9 was isolated and purified from chicken farm feces samples. The morphology, genomic information, optimal multiplicity of infection (MOI), one-step growth curve, thermal stability, pH stability, in vitro antibacterial ability and biofilm formation inhibition ability of the phage were determined. Subsequently, the therapeutic effects of the phages were investigated in the mice model. The results showed that PEC9 was a member of the siphovirus-like by electron microscopy observation. Biological characterization revealed that it could lyse two serotypes of E. coli, including O1 (9/20) and O2 (6/20). The optimal multiplicity of infection (MOI) of phage PEC9 was 0.1. Phage PEC9 had a latent period of 20 min and a burst period of 40 min, with an average burst size of 68 plaque-forming units (PFUs)/cell. It maintained good lytic activity at pH 3-11 and 4-50°C and could efficiently inhibit the bacterial planktonic cell growth and biofilm formation, and reduce bacterial counts within the biofilm, when the MOI was 0.01, 0.1, and 1, respectively. Whole-genome sequencing showed that PEC9 was a dsDNA virus with a genome of 44379 bp and GC content of 54.39%. The genome contains 56 putative ORFs and no toxin, virulence, or resistance-related genes were detected. Phylogenetic tree analysis showed that PEC9 is closely related to E. coli phages vB_EcoS_Zar3M, vB_EcoS_PTXU06, SECphi18, ZCEC10, and ZCEC11, but most of these phages exhibit different gene arrangement. The phage PEC9 could successfully protect mice against APEC infection, including improved survival rate, reduced bacterial loads, and organ lesions. To conclude, our results suggest that phage PEC9 may be a promising candidate that can be used as an alternative to antibiotics in the control of APEC infection.

Streptococcus suis (S. suis) is a zoonotic pathogen with multiple serotypes, and thus, multivalent vaccines generating cross-protection against S. suis infections are urgently needed to improve animal welfare and reduce antibiotic abuse. In this study, we established a systematic and comprehensive epitope prediction pipeline based on immunoinformatics. Ten candidate epitopes were ultimately selected for building the multi-epitope vaccine (MVSS) against S. suis infections. The ten epitopes of MVSS were all derived from highly conserved, immunogenic, and virulence-associated surface proteins in S. suis. In silico analyses revealed that MVSS was structurally stable and affixed with immune receptors, indicating that it would likely trigger strong immunological reactions in the host. Furthermore, mice models demonstrated that MVSS elicited high titer antibodies and diminished damages in S. suis serotype 2 and Chz infection, significantly reduced sequelae, induced cytokine transcription, and decreased organ bacterial burdens after triple vaccination. Meanwhile, anti-rMVSS serum inhibited five important S. suis serotypes in vitro, exerted beneficial protective effects against S. suis infections and significantly reduced histopathological damage in mice. Given the above, it is possible to develop MVSS as a universal subunit vaccine against multiple serotypes of S. suis infections.

Streptococcus pasteurianus is a zoonotic pathogen causing meningitis and bacteremia in animals and humans. A lack of accurate and convenient detection methods hinders preventing and controlling diseases caused by S. pasteurianus. Additionally, there is limited knowledge about its pathogenicity and antimicrobial resistance characteristics, as there are only three complete genome sequences available. In this study, we established a multiplex PCR assay for the detection of S. pasteurianus, which was applied to six fecal samples from cattle with diarrhea and 285 samples from healthy pigs. Out of the samples tested, 24 were positive, including 5 from pig tonsils, 18 from pig hilar lymph nodes, and 1 from cattle feces. Two strains were isolated from positive samples, and their complete genomes were sequenced. The two strains were non-virulent in mice and multidrug-resistant by the antimicrobial susceptibility test. We first found the presence of genes tet(O/W/32/O) and lsa(E) in S. pasteurianus, leading to resistance to lincosamides and tetracyclines. The convenient and specific multiplex PCR assay provides essential technical support for epidemiological research, and the complete genome sequence of two non-virulent strains contributes to understanding this zoonotic bacterium’s genomic characteristics and pathogenesis.

Forest canopy height is one of the critical parameters for carbon sink estimation. Although spaceborne lidar data can obtain relatively high precision canopy height on discrete light spots, to obtain continuous canopy height, the integration of optical remote sensing image data is required to achieve “from discrete to continuous” extrapolation based on different prediction models (parametric model and non-parametric model). This study focuses on the Shangri-La area and seeks to assess the practical applicability of two predictive models under complex mountainous conditions, using a combination of active and passive remote sensing data from ICESat-2 and Sentinel-2. The research aims to enhance our understanding of the effectiveness of these models in addressing the unique challenges presented by mountainous terrain, including rugged topography, variable vegetation cover, and extreme weather conditions. Through this work, we hope to contribute to the development of improved geospatial prediction algorithms for mountainous regions worldwide. The results show the following: (1) the fitting effect of the selected parametric model (empirical function regression) is poor in the area of Quercus acutissima and Pinus yunnanensis; (2) evaluation of the importance of each explanatory variable in the non-parametric model (random forest regression) shows that topographic and meteorological factors play a dominant role in canopy height inversion; (3) when random forest regression is applied to the inversion of canopy height, there is often a problem of error accumulation, which is of particular concern to the Quercus acutissima and Pinus yunnanensis; (4) the random forest regression with the optimal features has relatively higher precision by comparing the inversion accuracy of canopy height data of the empirical function regression, random forest regression with all features, and random forest regression with the optimal features in the study area, i.e., R2 (coefficient of determination) = 0.865 and RMSE (root mean square error) = 3.184 m. In contrast, the poor estimation results reflected by the empirical function regression, mainly resulting from the lack of consideration of topographic and meteorological factors, are not applicable to the inversion of canopy height under complex topographic conditions.

Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of bloodstream and other extraintestinal infections in human and animals. The greatest challenge encountered by ExPEC during an infection is posed by the host defense mechanisms, including lysozyme. ExPEC have developed diverse strategies to overcome this challenge. The aim of this study was to characterize the molecular mechanism of ExPEC resistance to lysozyme. For this, 15,000 transposon mutants of a lysozyme-resistant ExPEC strain NMEC38 were screened; 20 genes were identified as involved in ExPEC resistance to lysozyme—of which five were located in the gene cluster between galF and gnd, and were further confirmed to be involved in O-specific polysaccharide biosynthesis. The O-specific polysaccharide was able to inhibit the hydrolytic activity of lysozyme; it was also required by the complete lipopolysaccharide (LPS)-mediated protection of ExPEC against the bactericidal activity of lysozyme. The O-specific polysaccharide was further shown to be able to directly interact with lysozyme. Furthermore, LPS from ExPEC strains of different O serotypes was also able to inhibit the hydrolytic activity of lysozyme. Because of their cell surface localization and wide distribution in Gram-negative bacteria, O-specific polysaccharides appear to play a long-overlooked role in protecting bacteria against exogenous lysozyme.

Systemic infections by avian pathogenic Escherichia coli (APEC) are economically devastating to poultry industries worldwide. IbeR, located on genomic island GimA, was shown to serve as an RpoS-like regulator in rpoS gene mutation neonatal meningitis E. coli (NMEC) RS218. However, the role of IbeR in pathogenicity of APEC carrying active RpoS has not yet been investigated. We showed that the APEC IbeR could elicit antibodies in infected ducks, suggesting that IbeR might be involved in APEC pathogenicity. To investigate the function of IbeR in APEC pathogenesis, mutant and complementation strains were constructed and characterized. Inactivation of ibeR led to attenuated virulence and reduced invasion capacity towards DF-1 cells, brains and cerebrospinal fluid (CSF) in vitro and in vivo. Bactericidal assays demonstrated that the mutant strain had impaired resistance to environmental stress and specific pathogen-free (SPF) chicken serum. These virulence-related phenotypes were restored by genetic complementation. Quantitative real-time reverse transcription PCR revealed that IbeR controlled expression of stress-resistance genes and virulence genes, which might led to the associated virulence phenotype.

Streptococcus suis serotype 2 (SS2) is a zoonotic pathogen that can cause infections in pigs and humans. Bacterial surface proteins are often investigated as potential vaccine candidates and biomarkers of virulence. In this study, a novel method for identifying bacterial surface proteins is presented, which combines immunoproteomic and immunoserologic techniques. Critical to the success of this new method is an improved procedure for generating two-dimensional electrophoresis gel profiles of S. suis proteins. The S. suis surface proteins identified in this study include muramidase-released protein precursor (MRP) and an ABC transporter protein, while MRP is thought to be one of the main virulence factors in SS2 located on the bacterial surface. Herein, we demonstrate that the ABC transporter protein can bind to HEp-2 cells, which strongly suggests that this protein is located on the bacterial cell surface and may be involved in pathogenesis. An immunofluorescence assay confirmed that the ABC transporter is localized to the bacterial outer surface. This new method may prove to be a useful tool for identifying surface proteins, and aid in the development of new vaccine subunits and disease diagnostics.