Strong Pathogenicity Research Articles

Genetic Characterization, Pathogenicity, and Epidemiology Analysis of Three Sub-Genotype Pigeon Newcastle Disease Virus Strains in China.

Pigeon Newcastle disease (ND) is a serious infectious illness caused by the pigeon Newcastle disease virus (NDV) or Paramyxovirus type 1 (PPMV-1). Genotype VI NDV is a primary factor in ND among Columbiformes (such as pigeons and doves). In a recent study, eight pigeon NDV strains were discovered in various provinces in China. These viruses exhibited mesogenic characteristics based on their MDT and ICPI values. The complete genome sequences of these eight strains showed a 90.40% to 99.19% identity match with reference strains of genotype VI, and a 77.86% to 80.45% identity match with the genotype II vaccine strain. Additionally, analysis of the F gene sequence revealed that these NDV strains were closely associated with sub-genotypes VI.2.2.2, VI.2.1.1.2.1, and VI.2.1.1.2.2. The amino acid sequence at the cleavage site of the F protein indicated virulent characteristics, with the sequences 112KRQKRF117 and 112RRQKRF117 observed. Pigeons infected with these sub-genotype strains had a low survival rate of only 20% to 30%, along with lesions in multiple tissues, highlighting the strong spread and high pathogenicity of these pigeon NDV strains. Molecular epidemiology data from the GenBank database revealed that sub-genotype VI.2.1.1.2.2 strains have been prevalent since 2011. In summary, the findings demonstrate that the prevalence of genotype VI NDV is due to strains from diverse sub-genotypes, with the sub-genotype VI.2.1.1.2.2 strain emerging as the current epidemic strain, highlighting the significance of monitoring pigeon NDV in China.

Challenges of mesenchymal stem cells in the clinical treatment of COVID-19.

The 2019 coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has brought an enormous public health burden to the global society. The duration of the epidemic, the number of infected people, and the widespread of the epidemic are extremely rare in modern society. In the initial stage of infection, people generally show fever, cough, and dyspnea, which can lead to pneumonia, acute respiratory syndrome, kidney failure, and even death in severe cases. The strong infectivity and pathogenicity of SARS-CoV-2 make it more urgent to find an effective treatment. Mesenchymal stem cells (MSCs) are a kind of pluripotent stem cells with the potential for self-renewal and multi-directional differentiation. They are widely used in clinical experiments because of their low immunogenicity and immunomodulatory function. Mesenchymal stem cell-derived exosomes (MSC-Exo) can play a physiological role similar to that of stem cells. Since the COVID-19 pandemic, a series of clinical trials based on MSC therapy have been carried out. The results show that MSCs are safe and can significantly improve patients' respiratory function and prognosis of COVID-19. Here, the effects of MSCs and MSC-Exo in the treatment of COVID-19 are reviewed, and the clinical challenges that may be faced in the future are clarified.

Comprehensive genome sequence analysis of Ralstonia solanacearum gd-2, a phylotype I sequevar 15 strain collected from a tobacco bacterial phytopathogen.

Plant bacterial wilt is an important worldwide disease caused by Ralstonia solanacearum which is a complex of species. In this study, we identified and sequenced the genome of R. solanacearum strain gd-2 isolated from tobacco. Strain gd-2 was identified as R. solanacearum species complex (RSSC) phylotype I sequevar 15 and exhibited strong pathogenicity to tobacco. The genome size of gd-2 was 5.93 Mb, including the chromosomes (3.83 Mb) and the megaplasmid (2.10 Mb). Gene prediction results showed that 3,434 and 1,640 genes were identified in the chromosomes and plasmids, respectively. Comparative genomic analysis showed that gd-2 exhibited high conservation with ten highly similar strain genomes and the differences between gd-2 and other genomes were mainly located at positions GI12-GI14. 72 type III effectors (T3Es) were identified and RipAZ2 was a T3E specific to gd-2 compared with other eight sequenced strain. Our study provides a new basis and evidence for studying the pathogenic mechanism of R. solanacearum.

Metarhizium rileyi with broad-spectrum insecticidal ability confers resistance against phytopathogens and insect pests as a phytoendophyte.

Entomophagous fungi (EPF) not only directly kill insect pests, but also colonize plants and improve their resistance against pests. However, most previous research has focused on Beauveria bassiana and Metarhizium anisopliae, and there are few reports on whether other EPF can enhance resistance against pests via endogenous colonization. Herein, an EPF strain was isolated from diseased larvae of Spodoptera litura in a soybean field, and subjected to genome-wide sequencing at the chromosomal level. The pathogenicity of the isolate toward various pest insects was evaluated, and the ability to colonize plants and induce resistance against phytopathogens and insect pests was tested. The purified isolate was identified as M. rileyi and designated MrS1Gz1-1. Biological assays revealed its strong pathogenicity toward five insect pests belonging to Lepidoptera and Hemiptera. Furthermore, the strain inhibited the growth of soil-borne plant disease caused by Sclerotinia sclerotiorum in vitro. It colonized plants as an endophyte via soil application, thereby inducing plant resistance-related genes against phytopathogen infection, and it disrupted the feeding selectivity of S. litura larvae. M. rileyi MrS1Gz1-1 has potential as a broad-spectrum microbial control agent that can induce resistance against phytopathogens and insect pests feeding as an endotype. The complete genome provides a valuable resource for exploring host interactions. © 2024 Society of Chemical Industry.

Characterization of Fusarium species causing soybean root rot in Heilongjiang, China, and mechanism underlying the differences in sensitivity to DMI fungicides

Soybean root rot is a worldwide soil-borne disease threatening soybean production, causing large losses in soybean yield and quality. Fusarium species are the most detrimental pathogens of soybean root rot worldwide, causing large production losses. Fusarium root rot has been frequently reported in Heilongjiang Province of China, but the predominant Fusarium species and the sensitivity of these pathogens to different fungicides remain unclear. In this study, diseased soybean roots were collected from 14 regions of Heilongjiang province in 2021 and 2022. A total of 144 isolates of Fusarium spp. were isolated and identified as seven distinct species: F. scirpi, F. oxysporum, F. graminearum, F. clavum, F. acuminatum, F. avenaceum, and F. sporotrichioide. F. scirpi and F. oxysporum had high separation frequency and strong pathogenicity. The sensitivity of Fusarium spp. to five different fungicides was determined. Mefentrifluconazole and fludioxonil showed good inhibitory effects, and the sensitivity to pydiflumetofen and phenamacril varied between Fusarium species. In particular, the activity of DMI fungicide prothioconazole was lower than that of mefentrifluconazole. Molecular docking showed that mefentrifluconazole mainly bound to CYP51C, but prothioconazole mainly bound to CYP51B. Furthermore, the sensitivity to prothioconazole only significantly decreased in ΔFgCYP51B mutant, and the sensitivity to mefentrifluconazole changed in ΔFgCYP51C and ΔFgCYP51A mutants. The results demonstrated that the predominant Fusarium species causing soybean root rot in Heilongjiang province were F. scirpi and F. oxysporum and DMI fungicides had differences in binding cavity due to the diversity of CYP51 proteins in Fusarium.

Molecular warfare between pathogenic Fusarium oxysporum R1 and host Crocus sativus L. unraveled by dual transcriptomics.

Phenylpropanoid biosynthesis and plant-pathogen interaction pathways in saffron and cell wall degrading enzymes in Fusarium oxysporum R1 are key players involved in the interaction. Fusarium oxysporum causes corm rot in saffron (Crocus sativus L.), which is one of the most devastating fungal diseases impacting saffron yield globally. Though the corm rot agent and its symptoms are known widely, little is known about the defense mechanism of saffron in response to Fusarium oxysporum infection at molecular level. Therefore, the current study reports saffron-Fusarium oxysporum R1 (Fox R1) interaction at the molecular level using dual a transcriptomics approach. The results indicated the activation of various defense related pathways such as the mitogen activated protein kinase pathway (MAPK), plant-hormone signaling pathways, plant-pathogen interaction pathway, phenylpropanoid biosynthesis pathway and PR protein synthesis in the host during the interaction. The activation of pathways is involved in the hypersensitive response, production of various secondary metabolites, strengthening of the host cell wall, systemic acquired resistance etc. Concurrently, in the pathogen, 60 genes reported to be linked to pathogenicity and virulence has been identified during the invasion. The expression of genes encoding plant cell wall degrading enzymes, various transcription factors and effector proteins indicated the strong pathogenicity of Fusarium oxysporum R1. Based on the results obtained, the putative molecular mechanism of the saffron-Fox R1 interaction was identified. As saffron is a male sterile plant, and can only be improved by genetic manipulation, this work will serve as a foundation for identifying genes that can be used to create saffron varieties, resistant to Fusarium oxysporum infection.

First record of Aspergillus nomiae as a broad-spectrum entomopathogenic fungus that provides resistance against phytopathogens and insect pests by colonization of plants.

Aspergillus nomiae is known as a pathogenic fungus that infects humans and plants but has never been reported as an entomophagous fungus (EPF) that can provide other functions as an endotype. A strain of EPF was isolated and identified from diseased larvae of Spodoptera litura in a soybean field and designated AnS1Gzl-1. Pathogenicity of the strain toward various insect pests was evaluated, especially the ability to colonize plants and induce resistance against phytopathogens and insect pests. The isolated EPF strain AnS1Gzl-1 was identified as A. nomiae; it showed strong pathogenicity toward five insect pests belonging to Lepidoptera and Hemiptera. Furthermore, the strain inhibited the growth of Sclerotinia sclerotiorum in vitro, a causal agent of soil-borne plant disease. It colonized plants as an endophyte via root irrigation with a high colonization rate of 90%, thereby inducing plant resistance against phytopathogen infection, and disrupting the feeding selectivity of S. litura larvae. This is the first record of a natural infection of A. nomiae on insects. A. nomiae has the potential to be used as a dual biocontrol EPF because of its ability to not only kill a broad spectrum of insect pests directly but also induce resistance against phytopathogens via plant colonization.

The Novel 2.3.4.4b H5N6 Highly Pathogenic Avian Influenza Viruses Isolated From Wild Birds in 2023 Posing a Potential Risk to Human Health

The highly pathogenic avian influenza 2.3.4.4b H5 viruses have been a cause for concern recently, as they have been responsible for continuous outbreaks since 2021. In China, the H5N6 subtype has been predominantly circulating in domestic poultry but has rarely been detected in wild birds over the past 3 years. In December 2023, novel reassortant 2.3.4.4b H5N6 viruses were resurgent in wild birds and domestic ducks in Eastern Asia. The viruses were reassorted with those of currently prevalent 2.3.4.4b H5N1 viruses of wild bird origin worldwide, as well as the H5N6 viruses that caused human infections in 2022 and low pathogenic avian influenza viruses, such as the H9N2 virus, which also contributed internal gene to the novel H5N6 viruses. Based on the phylogenetic analyses, we inferred that this recombination process occurred in migratory breeding sites in early 2023. Given the rapid transmission and high mutation capacity of currently circulating H5N1 viruses, as well as the strong pathogenicity of H5N6 viruses to humans, the novel recombinant viruses may continue to evolve and pose new threats to human health. Therefore, continuous surveillance of H5N6 viruses in wild birds and domestic poultry should be strengthened.

Pest categorisation of Pratylenchus loosi.

Following the EFSA commodity risk assessment of Malus domestica plants imported from Türkiye into the EU, the EFSA Panel on Plant Health performed a pest categorisation of Pratylenchus loosi (Nematoda: Pratylenchidae) for the EU. Pratylenchus loosi belongs to the order Rhabditida, subfamily Pratylenchidae. This nematode is not known to be present in the EU. The species is not included in the EU Commission Implementing Regulation 2019/2072. The pest occurs primarily in tropical, subtropical and warm temperate areas. It is widely distributed in Asian countries, with tea plants (Camellia sinensis) as the main host. The pest was reported from more than 60 plant species, but reports from hosts other than C. sinensis, e.g. citrus (Citrus spp.) and banana (Musa spp.), are associated with high uncertainty due to doubtful pest identification. Morphological and molecular methods are available for the identification of the pest. Pathways of entry are host plants for planting except seeds, as well as soil attached to plants for planting, machinery or footwear. Soil import to the EU is prohibited from third countries. The climatic preferences of P. loosi are compatible with the microclimatic conditions occurring in the areas of the EU where tea is grown outside. The impact of the nematode is primarily known for Asian countries, where it is a devastating pathogen on tea plants, but there is a key uncertainty on impacts on hosts other than tea. Considering the strong pathogenicity of the pest, its establishment in tea producing areas would have negative consequences for tea producers. Therefore, the Panel concludes that P. loosi satisfies all the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Isolation and Pathogenicity Analysis of a G5P[23] Porcine Rotavirus Strain.

(1) Background: Group A rotaviruses (RVAs) are the primary cause of severe intestinal diseases in piglets. Porcine rotaviruses (PoRVs) are widely prevalent in Chinese farms, resulting in significant economic losses to the livestock industry. However, isolation of PoRVs is challenging, and their pathogenicity in piglets is not well understood. (2) Methods: We conducted clinical testing on a farm in Jiangsu Province, China, and isolated PoRV by continuously passaging on MA104 cells. Subsequently, the pathogenicity of the isolated strain in piglets was investigated. The piglets of the PoRV-infection group were orally inoculated with 1 mL of 1.0 × 106 TCID50 PoRV, whereas those of the mock-infection group were fed with an equivalent amount of DMEM. (3) Results: A G5P[23] genotype PoRV strain was successfully isolated from one of the positive samples and named RVA/Pig/China/JS/2023/G5P[23](JS). The genomic constellation of this strain was G5-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. Sequence analysis revealed that the genes VP3, VP7, NSP2, and NSP4 of the JS strain were closely related to human RVAs, whereas the remaining gene segments were closely related to porcine RVAs, indicating a reassortment between porcine and human strains. Furthermore, infection of 15-day-old piglets with the JS strain resulted in a diarrheal rate of 100% (8 of 8) and a mortality rate of 37.5% (3 of 8). (4) Conclusions: The isolated G5P[23] genotype rotavirus strain, which exhibited strong pathogenicity in piglets, may have resulted from recombination between porcine and human strains. It may serve as a potential candidate strain for developing vaccines, and its immunogenicity can be tested in future studies.

Epidemiological investigation of lower respiratory tract infections during influenza A (H1N1) pdm09 virus pandemic based on targeted next-generation sequencing.

Co-infection has been a significant contributor to morbidity and mortality in previous influenza pandemics. However, the current influenza A (H1N1) pdm09 virus pandemic, as the first major outbreak following the SARS-CoV-2 pandemic, may differ epidemiologically. Further investigation is necessary to understand the specific features and impact of this influenza A pandemic. Study design: We conducted a retrospective cohort study at a Chinese hospital between January and April 2023, focusing on patients with lower respiratory tract infections. Pathogen detection employed targeted next-generation sequencing (tNGS) on bronchoalveolar lavage fluid (BALF) or sputum samples. This study enrolled 167 patients with lower respiratory tract infections, and the overall positivity rate detected through tNGS was around 80%. Among them, 40 patients had influenza A (H1N1) pdm09 virus infection, peaking in March. In these patients, 27.5% had sole infections, and 72.5% had co-infections, commonly with bacteria. The frequently detected pathogens were Aspergillus fumigatus, SARS-CoV-2, and Streptococcus pneumoniae. For non-influenza A virus-infected patients, the co-infection rate was 36.1%, with 42.3% having SARS-CoV-2. Patients with influenza A virus infection were younger, had more females and diabetes cases. Among them, those with sole infections were older, with less fever and asthma but more smoking history. Regarding prognosis, compared to sole influenza A virus infection, co-infected patients demonstrated higher 21-day recovery rates and a higher incidence of heart failure. However, they exhibited lower proportions of respiratory failure, acute kidney failure, septic shock, and hospital stays lasting more than 10 days. Interestingly, patients with non-influenza A virus infection had a significantly lower 21-day recovery rate. Correlation analysis indicated that the 21-day recovery rate was only associated with influenza A (H1N1) pdm09 virus. During the current pandemic, the influenza A (H1N1) pdm09 virus may have been influenced by the SARS-CoV-2 pandemic and did not exhibit a strong pathogenicity. In fact, patients infected with influenza A virus showed better prognoses compared to those infected with other pathogens. Additionally, tNGS demonstrated excellent detection performance in this study and showed great potential, prompting clinical physicians to consider its use as an auxiliary diagnostic tool.

CD4 memory has a hierarchical structure created by requirements for infection-derived signals at an effector checkpoint.

Our recent studies reveal that the persistence, location, and amount of both antigen and signals that induce pathogen recognition responses determine the number of CD4 memory cells, the subsets that develop, their location, and hence their protective efficacy. Non-replicating vaccines provide antigen that is short-lived and generate low levels of only some memory subsets that are mostly restricted to secondary lymphoid tissue. In contrast, exposure to long-lived replicating viruses and bacteria provides high levels of diverse antigens in sites of infection and induces strong pathogen recognition signals for extended periods of time, resulting in much higher levels of memory cells of diverse subsets in both lymphoid and nonlymphoid sites. These include memory subsets with highly potent functions such as T follicular helpers and cytotoxic CD4 effectors at sites of infection, where they can most effectively combat the pathogen early after re-infection. These effectors also do not develop without antigen and pathogen recognition signals at the effector stage, and both subsets must receive these signals in the tissue sites where they will become resident. We postulate that this leads to a hierarchical structure of memory, with the strongest memory induced only by replicating pathogens. This paradigm suggests a likely roadmap for markedly improving vaccine design.

Skin microbial dysbiosis is a characteristic of systemic drug-related intertriginous and flexural exanthema-like lesions induced by EGFR inhibitor

ObjectivesTo investigate the characteristics of the skin microbiome in severe afatinib-induced skin toxicity. MethodsBody site-matched skin surface samples were collected from the lesions on seven flexural sites of one lung cancer (Patient 1) with serious systemic drug-related intertriginous and flexural exanthema (SDRIFE)-like toxicity induced by EGFR-TKI and three healthy age/sex matched controls for whole metagenomics sequencing analysis. Lung cancer Patient 1 and Patient 2 were prescribed minocycline and followed up. ResultsIn SDRIFE-like toxicities induced by afatinib, lesion microbiota richness (ACE and Chao1 index: p < 0.001) and diversity (Shannon's and Simpson's diversity indices: p < 0.01) were reduced. Similarly, the beta diversity analysis (R = 1, p = 0.002 for ANOSIM) showed that the apparent difference in the microbiota composition was statistically significant. The microbial taxa composition in the patient showed an increased abundance of pathogenic bacteria and a decreased abundance of commensal bacteria. LEfSe analysis identified strong bacterial pathogenicity in the patient, while healthy controls exhibited enrichment in several pathways that are beneficial for skin commensal bacteria and skin physiology, including key amino acid metabolism, energy/lipid/glycan biosynthesis/metabolism, and cofactors/vitamins biosynthesis. Ultimately, the patients experienced significant improvement with minocycline. ConclusionMicrobial dysbiosis is a characteristic of severe SDRIFE-like toxicity induced by afatinib.

Efficient Genome Editing in Most Staphylococcus aureus by Using the Restriction-Modification System Silent CRISPR-Cas9 Toolkit.

Staphylococcus aureus is a clinically important pathogen that threatens human health due to its strong pathogenicity and drug resistance, leading to meningitis, endocarditis, and skin and soft tissue infections. Genetic manipulation in S.aureus is a powerful approach for characterizing the molecular mechanisms of bacterial drug resistance, pathogenicity, and virulence. However, a strong restriction barrier presents a major obstacle to the extensive utilization of genetic manipulation tools in clinical isolates of S.aureus. Here, we constructed a restriction-modification (RM) system silent CRISPR-Cas9 toolkit that synonymously eliminated the type I RM targets of S.aureus from plasmids, downsized plasmids using minicircle technology, and combined with a plasmid artificial modification (PAM) method to circumvent the type II RM system. The RM-silent CRISPR-Cas9 toolkit enables a significant improvement in transformation (105-106 transformants per microgram plasmid in strains we tested) and high-success efficiency editing for gene deletion (knockout strain obtained in one-round electroporation) in a wide range of S.aureus species including clinical isolates of unknown genetic background. The RM-silent CRISPR-Cas9 toolkits could expedite the process of mutant construction in most S.aureus strains, and this approach could be applied to the design of other genetic toolkit plasmids for utilization in a wider range of S.aureus strains.

Unveiling the Molecular Mechanisms Behind the Devastating Impact of the ALK Protein on Pediatric Cancers: Insights into Deleterious SNPs through In Silico Predictions, Molecular Docking, and Dynamics Studies

Abstract Introduction Pediatric cancers present significant challenges in terms of diagnosis and treatment, and the anaplastic lymphoma kinase (ALK) protein has emerged as a crucial molecular target in these malignancies. ALK, a receptor tyrosine kinase, plays a vital role in normal cellular processes, but genetic alterations and aberrant activation of the ALK gene have been implicated in various pediatric cancer types. While genetic alterations have been well studied, the precise molecular mechanisms underlying the pathogenicity of the ALK protein in pediatric cancers remain poorly understood. Objective In this study, the primary objective is to uncover the molecular mechanisms associated with the effects of deleterious single-nucleotide polymorphisms (SNPs) on the structure and functionality of the ALK protein. Material and Methods Several known point mutations of the ALK protein were taken for the in silico predictions such as PolyPhen-2, SIFT, PANTHER, PredictSNP, etc., residue conservation analysis using Consurf server, molecular docking (AutoDock), and molecular dynamics simulation studies (GROMACS). Results The computation predictions found that the studied variants are deleterious in different tools. The residue conservation analysis reveals all the variants are located in highly conserved regions. The molecular docking study of wild-type and mutant structures with the crizotinib drug molecule found the variants were modulating the binding cavity and had a strong impact on the binding affinity. The binding energy of the wild-type is –5.896 kcal/mol, whereas the mutants have –9.988 kcal/mol. The specific amino acid Ala1200 of wild-type was found to interact with crizotinib, and Asp1203 residue was found to interact predominantly in the mutant structures. Conclusion The simulation study differentiates the variants in terms of structural stability and residue fluctuation. Among the studied variants, R1275Q, F1245V, and F1174L had strong deleterious effects, structural changes, and pathogenicity based on the in silico predictions. By elucidating the functional consequences of deleterious mutations within the ALK gene, this research may uncover novel therapeutic targets and personalized medicine approaches for the management of pediatric cancers. Ultimately, gaining insights into the molecular mechanisms of the ALK protein's role in driving response and resistance will contribute to improving patient outcomes and advancing our understanding of this complex disease.

Prevalence, drug resistance, molecular typing and comparative genomics analysis of MRSA strains from a tertiary A hospital in Shanxi Province, China.

Staphylococcus aureus (S. aureus) is an important zoonotic pathogen that causes a high incidence rate and mortality worldwide. This study investigated the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) strains in a tertiary A hospital in Shanxi Province, China, in order to determine the major epidemic clones as well as their antibiotic resistance and virulence characteristics. A total of 212 S. aureus strains were collected in this hospital, and were subjected to antimicrobial susceptibility testing, detection of virulence genes, resistance genes, and efflux pump genes. Among them, 38 MRSA strains were further subjected to detection of biofilm genes, assessment of biofilm formation ability, MLST, spa typing, SCCmec typing, and phylogenetic analysis. The majority of S. aureus strains came from the neonatology department, with secretions and purulent fluid being the main source of samples. The strains showed high resistance to penicillin (98.11%), erythromycin (64.62%) and clindamycin (59.91%), while being sensitive to vancomycin and linezolid. The detection rates of efflux pump genes and resistance genes were high, and there was a significant correlation between resistance gene types and phenotypes, with mecA showing a close correlation with oxacillin. The detection rates of virulence genes and the toxin gene profiles of MSSA and MRSA strains showed significant differences. And the detection rate of biofilm genes in MRSA strains was relatively high, with 13.16% of MRSA strains showing strong biofilm formation ability. The most common epidemic clone of MRSA was ST59-SCCmecIV-t437, followed by ST59-SCCmecV-t437. The former had a higher detection rate of resistance genes and a stronger biofilm formation ability, while the latter had a higher positive rate for pvl gene and stronger pathogenicity, making it more likely to cause systemic infections. Phylogenetic analysis showed that all MRSA strains in this study clustered into three major branches, with distinct differences in antibiotic resistance and virulence characteristics among the branches. ST59-MRSA strains from different species showed consistency and inter-species transmission, but there were differences among ST59-MRSA strains from different geographical locations. In general, most MSSA and MRSA strains exhibited multidrug resistance and carried multiple resistance genes, virulence genes, and biofilm formation genes, warranting further research to elucidate the mechanisms of drug resistance and pathogenesis.

Isolation and Characterization of a Novel Recombinant Classical Pseudorabies Virus in the Context of the Variant Strains Pandemic in China.

Pseudorabies virus (PRV) variants were discovered in immunized pigs in Northern China and have become the dominant strains since 2011, which caused huge economic losses. In this study, a classical PRV strain was successfully isolated in a PRV gE positive swine farm. The complete genome sequence was obtained using a high-throughput sequencing method and the virus was named JS-2020. The nucleotide homology analysis and phylogenetic tree based on complete genome sequences or gC gene showed that the JS-2020 strain was relatively close to the classical Ea strain in genotype II clade. However, a large number of amino acid variations occurred in the JS-2020 strain compared with the Ea strain, including multiple immunogenic and virulence-related genes. In particular, the gE protein of JS-2020 was similar to earlier Chinese PRV strains without Aspartate insertion. However, the amino acid variations analysis based on major immunogenic and virulence-related genes showed that the JS-2020 strain was not only homologous with earlier PRV strains, but also with strains isolated in recent years. Moreover, the JS-2020 strain was identified as a recombinant between the GXGG-2016 and HLJ-2013 strains. The pathogenicity analysis proved that the PRV JS-2020 strain has typical neurogenic infections and a strong pathogenicity in mice. Together, a novel recombinant classical strain was isolated and characterized in the context of the PRV variant pandemic in China. This study provided some valuable information for the study of the evolution of PRV in China.

Identification of SARS-CoV-2 m6A modification sites correlate with viral pathogenicity

It has recently been found that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) m6A modifications can affect viral replication and function. However, no studies to date have shown a correlation between SARS-CoV-2 m6A modifications and viral pathogenicity. In this study, we analyzed m6A modification in 2,190,667 SARS-CoV-2 genomic RNAs. m6A modifications of SARS-CoV-2 from different lineages, causing mild or severe COVID-19 and showing breakthrough for different vaccines were analyzed to explore correlations with viral pathogenicity. The results suggested that the presence of more m6A modifications in the SARS-CoV-2 N region (positive strand) correlates with weaker pathogenicity. In addition, we identified three m6A modification sites correlating with weak pathogenicity (924 in ORF1ab, 15,659 in ORF1ab, 28,288 in N, 28,633 in N and 29,385 in N, 29,707 in 3′UTR) and one with strong pathogenicity (74 in 5′UTR). These results provide new information for understanding the prevalence of SARS-CoV-2 and controlling the virus.

Soft rot of postharvest pepper: bacterial pathogen, pathogenicity and its biological control using Lactobacillus farciminis LJLAB1.

Soft rot is the most important bacterial disease of postharvest pepper during storage and transportation. The main objectives of this study were to investigate the bacterial pathogen species causing pepper soft rot and seek for an antagonistic bacterium to control this disease. Pathogens Pectobacterium carotovorum, Enterobacter sp., Klebsiella sp., Pseudomonas sp. and Bacillus sp. were verified to be the causes of soft rot which were isolated from rotten peppers. Among them, P. carotovorum had the highest prevalence, including P. carotovorum subsp. carotovorum (Pcc) and P. carotovorum subsp. brasilisesis (Pcb). The result of pathogenicity analysis showed that Pcb Jm2 had strong pathogenicity at 25 °C even at a cell concentration of 103 CFU mL-1 . Its pathogenicity decreased at 4 °C. Multiple pathogenic factors were identified in the draft genome of Pcb Jm2, including cellulase, pectinase, pectin methylesterase, pectinesterase, pectin lyase, polygalacturonase and so forth. Further, the disease control ability of Lactobacillus farciminis LJLAB1 was investigated. The cell-free supernatant (CFS) and crude bacteriocin of L. farciminis LJLAB1 had good antibacterial activities to Pcb Jm2 in vitro, but CFS exhibited a better disease control effect in vivo. CFS treatment prevented the damage of pepper epidermal structure caused by Pcb Jm2, and 99.26% of pathogen cells on pepper were killed by it. Moreover, CFS treatment delayed firmness decrease, soluble solid content loss, weight loss, yellowing and malonaldehyde accumulation of pepper during storage after pathogen infection. L. farciminis LJLAB1 can be an effective biological control agent to control pepper soft rot caused by Pcb. © 2023 Society of Chemical Industry.

Isolation and Identification of Aeromonas hydrophila from Pangasius bocourti with Bacterial Septicemia and Drug Screening for Treatment

The pathogenic bacterium Aeromonas hydrophila was isolated and identified from Pangasius bocourti with bacterial septicemia in an aquaculture farm in Lingao County, Hainan Province, China. The feasibility of rapid selection of preventative and therapeutic drugs was investigated via antimicrobial susceptibility and re-infection tests. A dominant bacterial strain was isolated from P. bocourti and designated as FXZ01. Morphological analysis and Gram staining showed that the phenotypic characteristics of the strain were consistent with those of Aeromonas. The results of 16S rRNA sequencing revealed that FXZ01 was 97.3% similar to Aeromonas hydrophila. Additionally, the re-infection test validated the strong pathogenicity of FXZ01 to P. bocourti, as the symptoms were similar to those of the natural disease. Therefore, the bacterium was identified as A. hydrophila. The sensitivity of FXZ01 to 10 antibiotics was determined via the Kirby–Bauer test. The results showed that FXZ01 was highly sensitive to 8 antibiotics, namely, amikacin, cefazolin, ciprofloxacin, norfloxacin, erythromycin, chloramphenicol, gentamicin, and sulfamethoxazole, but was resistant to penicillin and ampicillin. The findings of this study provide useful information for further study of the prevention and treatment of bacterial diseases in P. bocourti.