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The World Health Organization characterized COVID-19 as a pandemic in March 2020, the second pandemic of the twenty-first century. Expanding virus populations, such as that of SARS-CoV-2, accumulate a number of narrowly shared polymorphisms, imposing a confounding effect on traditional clustering methods. In this context, approaches that reduce the complexity of the sequence space occupied by the SARS-CoV-2 population are necessary for robust clustering. Here, we propose subdividing the global SARS-CoV-2 population into six well-defined subtypes and 10 poorly represented genotypes named tentative subtypes by focusing on the widely shared polymorphisms in nonstructural ( nsp 3, nsp 4, nsp 6, nsp 12, nsp 13 and nsp 14) cistrons and structural ( spike and nucleocapsid ) and accessory ( ORF8 ) genes. The six subtypes and the additional genotypes showed amino acid replacements that might have phenotypic implications. Notably, three mutations (one of them in the Spike protein) were responsible for the geographical segregation of subtypes. We hypothesize that the virus subtypes detected in this study are records of the early stages of SARS-CoV-2 diversification that were randomly sampled to compose the virus populations around the world. The genetic structure determined for the SARS-CoV-2 population provides substantial guidelines for maximizing the effectiveness of trials for testing candidate vaccines or drugs.

Antibiotic resistance has become a major concern for human and animal health. As fluoroquinolones have been extensively used in human and veterinary medicine, there has also been the rapid emergence and spread of antimicrobial resistance around the world. Here, we analysed the microbiome of goat milk using samples from healthy goats and those diagnosed with persistent mastitis and treated using the antibiotic enrofloxacin with 16S rRNA amplicon sequencing. We selected a group of 11 goats and 22 samples of milk that did not respond clinically to enrofloxacin treatment. Milk samples were evaluated before and after treatment to verify changes of the microbiota; the three first lactating goats were selected from the healthy control group. The milk samples from the healthy control animals presented a larger abundance of different species of bacteria of the Staphylococcus genus, but a smaller number of different genera, which indicated a more specific niche of resident bacteria. The Firmicutes phylum was predominantly different between the studied groups. Samples from before-treatment animals had a higher number of new species than those from the control group, and after being treated again. These microbiota received new bacteria, increasing the differences in bacteria even more in relation to the control group. Genotypes such as Trueperella and Mannheimia , between other genera, had a high abundance in the samples from animals with persistent mastitis. The dysbiosis in this study, with marked evidence of a complex microbiota in activity in cases of the failure of antimicrobial treatment for persistent chronic mastitis, demonstrates a need to improve the accuracy of pathogen identification and increases concern regarding antibiotic treatments in milk production herds.

Bacterial communities in the mammalian reproductive system can be rich and diverse, differing in structure and quantity depending on location. In addition, its microbiome is associated with the state of health of this tract and reproductive success. This study evaluated the microbiome composition of the uterine body (UB) and uterine horn mucosa (UH) samples using 16S rRNA sequencing of samples extracted from cows in the Amazon region. It was observed that four main phyla were shared between the uterine sites: Actinobacteria , Bacteroidetes , Firmicutes , and Proteobacteria . Linear discriminant analysis effect size and heat tree analysis showed that members of Lachnospiraceae (NK3A20 group) and Oscillospiraceae were significantly more abundant in the UB than in UH. In addition, there are more unique genera in the UB than in the UH. A higher bacterial load in UB than in UH is expected because of the exposure to external factors of UB. However, comparing the site's communities through beta diversity did not generate well-defined clustering. Thus, it can be attributed to the closeness of the sites, which would make the niches similar ecologically and microbiologically. Therefore, this research provides knowledge to understand biomarkers in the prior reproduction period.

Staphylococcus aureus is one of the main bacterial agents responsible for cases of mastitis in ruminants, playing an important role in the persistence and chronicity of diseases treated with antimicrobials. Using the multilocus sequence typing technique, network approaches and study of the population diversity of microorganisms, we performed analyzes of S . aureus (ES-GPM) isolated from goats with persistent mastitis (GPM). The most strains of ES-GPM were categorically different phylogenetically from the others and could be divided into two lineages: one with a majority belonging to ES-GPM and the other to varied strains. These two lineages were separated by 27 nuclear polymorphisms. The 43 strains comprised 22 clonal complexes (CCs), of which the ES-GPM strains were present in CC133, CC5 and a new complex formed by the sequence type 4966. The genetic diversity of some alleles showed be greater diversity and polymorphism than others, such as of the aroE and yqiL genes less than glpF gene. In addition, the sequences ES-GPM to the arc gene and glpF alleles showed the greatest number of mutations for ES-GPM in relation to non-ES-GPM. Therefore, this study identified genetic polymorphisms characteristic of S . aureus isolated from milk of goats diagnosed with persistent mastitis after the failed treatment with the antibiotic enrofloxacin. This study may help in the future to identify and discriminate this agent in cases of mastitis, and with that, the most appropriate antibiotic treatment can be performed in advance of the appearance of persistent mastitis caused by the agent, reducing the chances of premature culling and animal suffering.

The bacterium Actinobacillus pleuropneumoniae is the etiological agent of Contagious Porcine Pleuropneumonia, a disease responsible for economic losses in the swine industry worldwide. A. pleuropneumoniae is capable of producing proteinaceous exotoxins responsible for inducing hemorrhagic lesions, one of which is ApxI. Few studies have conducted an in-depth evaluation of polymorphisms of the nucleotides that make up the ApxI toxin gene. Here we analyze the polymorphisms of the apxIA gene region of A. pleuropneumoniae serovar 5 isolated from swine in different regions in Brazil and report the results of molecular sequencing and phylogenetic analysis. Analysis of the apxIA gene in 60 isolates revealed the presence of genetic diversity and variability. The polymorphisms in the nucleotide sequences determined the grouping of the Brazilian sequences and five more sequences from the GenBank database into 14 different haplotypes, which formed three main groups and revealed the presence of mutations in the nucleotide sequences. The estimation of selection pressures suggests the occurrence of genetic variations by positive selective pres- sure on A. pleuropneumoniae in large groups of animals in relatively small spaces. These conditions presumably favor the horizontal dissemination of apxIA gene mutations within bacterial populations with host reservoirs. As a result, the same serovar can demonstrate different antigenic capacities due to mutations in the apxIA gene. These alterations in sequences of the apxIA gene could occur in other areas of countries with intense swine production, which could lead to differences in the pathogenicity and immunogenicity of each serovar and have implications for the clinical status or diagnosis of A. pleuropneumoniae.

Animal embryos are vital tools in scientific research, providing insights into biological processes and disease mechanisms. This paper explores their historical and contemporary significance, highlighting the shift towards the refinement of in vitro systems as alternatives to animal experimentation. We have conducted a data review of the relevant literature on the use of embryos in research and synthesized the data to highlight the importance of this model for scientific progress and the ethical considerations and regulations surrounding embryo research, emphasizing the importance of minimizing animal suffering while promoting scientific progress through the principles of replacement, reduction, and refinement. Embryos from a wide range of species, including mammals, fish, birds, amphibians, and reptiles, play a crucial experimental role in enabling us to understand factors such as substance toxicity, embryonic development, metabolic pathways, physiological processes, etc., that contribute to the advancement of the biological sciences. To apply this model effectively, it is essential to match the research objectives with the most appropriate methodology, ensuring that the chosen approach is appropriate for the scope of the study.

Background Staphylococcus aureus is one of the main causative agents of mastitis in small ruminants. Antimicrobial use is the major treatment, but there are many flaws linked to resistance, tolerance or persistence. This study aimed to verify changes in resistance, virulence and clonal profiles of S. aureus isolated from persistent mastitis goat milk before and after enrofloxacin treatment. Results MIC increased to at least one antimicrobial in S. aureus isolates after enrofloxacin treatment compared to before. The most detected resistance genes before and after treatment were tetK , tetM , and blaZ , with more resistance genes detected after enrofloxacin treatment ( p  < 0.05). Occasional variations in efflux system gene detection were observed before and after treatment. Nine virulence genes ( hla , fnbA , fnbB , eta , etb , sea , sec , seh , and sej ) were detected at both times, and between these, the hla and eta genes were detected more in isolates after treatment. All isolates of S. aureus belonged to the same sequence type (ST) 133, except for two S. aureus isolates prior to enrofloxacin treatment which were classified as ST5 and the other as a new one, ST4966. Isolates of S. aureus 4, 8, and 100 from before and after treatment had identical pulse types, while others obtained from other animals before and after treatment were classified into distinct pulse types. Conclusion There were occasional changes in the studied profiles of S. aureus isolated before and after treatment of animals with enrofloxacin, which may have contributed to the permanence of bacteria in the mammary gland, even when using traditional treatment, resulting in persistent mastitis.

Anaplasmosis remains a significant threat to livestock production in tropical regions, particularly in the Amazon basin, where ecological complexity and limited veterinary infrastructure challenge effective disease management. This review focuses on Anaplasma marginale and Anaplasma phagocytophilum , the primary species associated with bovine and granulocytic anaplasmosis, respectively. We examine the current state of diagnostic tools, highlighting the limited accessibility of molecular techniques in rural settings and the emerging but underutilized potential of technologies. Persistent infection and antigenic variation are explored as major obstacles for disease eradication and vaccine development. Although live attenuated and inactivated vaccines are in use for A. marginale , none provide sterilizing immunity, and no commercial vaccines exist for A. phagocytophilum . The review evaluates recent advances in recombinant antigens, chimeric constructs, and genetically attenuated strains, as well as future directions involving multiepitope design, novel adjuvants, and next-generation vaccine platforms. Additionally, we assess the role of tick control in disease prevention and emphasize the importance of integrated strategies in regions like the Amazon. Together, these findings underscore the need for context-specific solutions that address the ecological and epidemiological complexity of anaplasmosis in the Amazon basin.

An environmental enrichment protocol is essential for testing experimental models because it upholds animal welfare, aligns with ethical principles in animal experimentation, and reduces the number of animals needed. Calomys callosus , a South American rodent from the Cricetidae family, is bred in rodent animal facilities for its ease of handling, longevity, prolificacy, and effectively mimicking diseases like Toxoplasmosis, Leishmaniasis, Chagas, and Schistosomiasis. There are no reports on environmental enrichments for this species or their impact on reproductive parameters. This study aimed to analyze the influence of the Environmental Enrichment Program (EEP) on the reproductive and zootechnical performance of C. callosus kept in the Rodents Animal Facilities Complex of Universidade Federal de Uberlândia (UFU). Two experimental groups were established: with environmental enrichment EE+ and without environmental enrichment EE−. The materials used in the experimental design were changed weekly and alternated between dietary, occupational, physical/cognitive, and non-enrichment items. After the inclusion of the EEP, an improvement in the reproductive indices of C. callosus was identified in the EE+ group. These improvements included increased female precocity, a decreased interbirth interval, and a higher number of pairs producing more offspring. The postpartum zootechnical indices were also better, such as the number of animals born alive, improved weaning rates, and a reduced average number of deaths from birth to weaning. After the inclusion of the EEP, the general health status of C. callosus improved, reducing cases of non-infectious lumbar alopecia. Therefore, EEP allows C. callosus to express natural reproductive behaviors and improves parental care.

Chronic kidney disease (CKD) is a global public health problem, and the absence of reliable and accurate diagnostic and monitoring tools contributes to delayed treatment, impacting patients' quality of life and increasing treatment costs in public health. Proteomics using saliva is a key strategy for identifying potential disease biomarkers. We analyzed the untargeted proteomic profiles of saliva samples from 20 individuals with end-stage kidney disease (ESKD) (  = 10) and healthy individuals (  = 10) using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify potential biomarkers for CKD. A volcano plot was generated using a -value of ≤0.05 and a fold change (FC) ≥ 2.0. Multivariate analysis was performed to generate the orthogonal partial least squares discriminant analysis (OPLS-DA) model and the variable importance in projection (VIP) scores. The accuracy of candidate biomarker proteins was evaluated using receiver operating characteristic (ROC) curves. In total, 431 proteins were identified in the salivary proteomic profile, and 3 proteins were significantly different between the groups: apoptosis inhibitor 5 (API5), phosphoinositide phospholipase C (PI-PLC), and small G protein signaling modulator 2 (Sgsm2). These proteins showed good accuracy based on the ROC curve and a VIP score of >2.0. During pathway enrichment, PI-PLC participates in the synthesis of IP3 and IP4 in the cytosol. Gene ontology (GO) analysis revealed data on molecular functions, biological processes, cellular components, and protein classes. We can conclude that the salivary API5, PI-PLC, and Sgsm2 can be potential biomarker candidates for CKD detection. These proteins may participate in pathways related to renal fibrosis and other associated diseases, such as mineral and bone disorders.